Author: "Martin P McHugh" - Searchworks@Jio Institute Digital Library Search Results

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1. Development of an amplicon-based sequencing approach in response to the global emergence of mpox.

Author: Nicholas F G Chen, Chrispin Chaguza, Luc Gagne, Matthew Doucette, Sandra Smole, Erika Buzby, Joshua Hall, Stephanie Ash, Rachel Harrington, Seana Cofsky, Selina Clancy, Curtis J Kapsak, Joel Sevinsky, Kevin Libuit, Daniel J Park, Peera Hemarajata, Jacob M Garrigues, Nicole M Green, Sean Sierra-Patev, Kristin Carpenter-Azevedo, Richard C Huard, Claire Pearson, Kutluhan Incekara, Christina Nishimura, Jian Ping Huang, Emily Gagnon, Ethan Reever, Jafar Razeq, Anthony Muyombwe, Vítor Borges, Rita Ferreira, Daniel Sobral, Silvia Duarte, Daniela Santos, Luís Vieira, João Paulo Gomes, Carly Aquino, Isabella M Savino, Karinda Felton, Moneeb Bajwa, Nyjil Hayward, Holly Miller, Allison Naumann, Ria Allman, Neel Greer, Amary Fall, Heba H Mostafa, Martin P McHugh, Daniel M Maloney, Rebecca Dewar, Juliet Kenicer, Abby Parker, Katharine Mathers, Jonathan Wild, Seb Cotton, Kate E Templeton, George Churchwell, Philip A Lee, Maria Pedrosa, Brenna McGruder, Sarah Schmedes, Matthew R Plumb, Xiong Wang, Regina Bones Barcellos, Fernanda M S Godinho, Richard Steiner Salvato, Aimee Ceniseros, Mallery I Breban, Nathan D Grubaugh, Glen R Gallagher, and Chantal B F Vogels
Subjects: Biology (General), QH301-705.5
Abstract: The 2022 multicountry mpox outbreak concurrent with the ongoing Coronavirus Disease 2019 (COVID-19) pandemic further highlighted the need for genomic surveillance and rapid pathogen whole-genome sequencing. While metagenomic sequencing approaches have been used to sequence many of the early mpox infections, these methods are resource intensive and require samples with high viral DNA concentrations. Given the atypical clinical presentation of cases associated with the outbreak and uncertainty regarding viral load across both the course of infection and anatomical body sites, there was an urgent need for a more sensitive and broadly applicable sequencing approach. Highly multiplexed amplicon-based sequencing (PrimalSeq) was initially developed for sequencing of Zika virus, and later adapted as the main sequencing approach for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Here, we used PrimalScheme to develop a primer scheme for human monkeypox virus that can be used with many sequencing and bioinformatics pipelines implemented in public health laboratories during the COVID-19 pandemic. We sequenced clinical specimens that tested presumptively positive for human monkeypox virus with amplicon-based and metagenomic sequencing approaches. We found notably higher genome coverage across the virus genome, with minimal amplicon drop-outs, in using the amplicon-based sequencing approach, particularly in higher PCR cycle threshold (Ct) (lower DNA titer) samples. Further testing demonstrated that Ct value correlated with the number of sequencing reads and influenced the percent genome coverage. To maximize genome coverage when resources are limited, we recommend selecting samples with a PCR Ct below 31 Ct and generating 1 million sequencing reads per sample. To support national and international public health genomic surveillance efforts, we sent out primer pool aliquots to 10 laboratories across the United States, United Kingdom, Brazil, and Portugal. These public health laboratories successfully implemented the human monkeypox virus primer scheme in various amplicon sequencing workflows and with different sample types across a range of Ct values. Thus, we show that amplicon-based sequencing can provide a rapidly deployable, cost-effective, and flexible approach to pathogen whole-genome sequencing in response to newly emerging pathogens. Importantly, through the implementation of our primer scheme into existing SARS-CoV-2 workflows and across a range of sample types and sequencing platforms, we further demonstrate the potential of this approach for rapid outbreak response.
Published: 2023
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2. Genomics-informed outbreak investigations of SARS-CoV-2 using civet.

Author: Áine O'Toole, Verity Hill, Ben Jackson, Rebecca Dewar, Nikita Sahadeo, Rachel Colquhoun, Stefan Rooke, J T McCrone, Kate Duggan, Martin P McHugh, Samuel M Nicholls, Radoslaw Poplawski, COVID-19 Genomics UK (COG-UK) Consortium, COVID-19 Impact Project (Trinidad & Tobago Group), David Aanensen, Matt Holden, Tom Connor, Nick Loman, Ian Goodfellow, Christine V F Carrington, Kate Templeton, and Andrew Rambaut
Subjects: Public aspects of medicine, RA1-1270
Abstract: The scale of data produced during the SARS-CoV-2 pandemic has been unprecedented, with more than 13 million sequences shared publicly at the time of writing. This wealth of sequence data provides important context for interpreting local outbreaks. However, placing sequences of interest into national and international context is difficult given the size of the global dataset. Often outbreak investigations and genomic surveillance efforts require running similar analyses again and again on the latest dataset and producing reports. We developed civet (cluster investigation and virus epidemiology tool) to aid these routine analyses and facilitate virus outbreak investigation and surveillance. Civet can place sequences of interest in the local context of background diversity, resolving the query into different 'catchments' and presenting the phylogenetic results alongside metadata in an interactive, distributable report. Civet can be used on a fine scale for clinical outbreak investigation, for local surveillance and cluster discovery, and to routinely summarise the virus diversity circulating on a national level. Civet reports have helped researchers and public health bodies feedback genomic information in the appropriate context within a timeframe that is useful for public health.
Published: 2022
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3. Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study

Author: Mark S Graham, PhD, Carole H Sudre, PhD, Anna May, MA, Michela Antonelli, PhD, Benjamin Murray, MSc, Thomas Varsavsky, MSc, Kerstin Kläser, MSc, Liane S Canas, PhD, Erika Molteni, PhD, Marc Modat, PhD, David A Drew, PhD, Long H Nguyen, MD, Lorenzo Polidori, MSc, Somesh Selvachandran, MSc, Christina Hu, MA, Joan Capdevila, PhD, Alexander Hammers, ProfPhD, Andrew T Chan, ProfMD, Jonathan Wolf, MA, Tim D Spector, ProfPhD, Claire J Steves, PhD, Sebastien Ourselin, ProfPhD, Cherian Koshy, Amy Ash, Emma Wise, Nathan Moore, Matilde Mori, Nick Cortes, Jessica Lynch, Stephen Kidd, Derek J Fairley, Tanya Curran, James P McKenna, Helen Adams, Christophe Fraser, Tanya Golubchik, David Bonsall, Mohammed O Hassan-Ibrahim, Cassandra S Malone, Benjamin J Cogger, Michelle Wantoch, Nicola Reynolds, Ben Warne, Joshua Maksimovic, Karla Spellman, Kathryn McCluggage, Michaela John, Robert Beer, Safiah Afifi, Sian Morgan, Angela Marchbank, Anna Price, Christine Kitchen, Huw Gulliver, Ian Merrick, Joel Southgate, Martyn Guest, Robert Munn, Trudy Workman, Thomas R Connor, William Fuller, Catherine Bresner, Luke B Snell, Amita Patel, Themoula Charalampous, Gaia Nebbia, Rahul Batra, Jonathan Edgeworth, Samuel C Robson, Angela H Beckett, David M Aanensen, Anthony P Underwood, Corin A Yeats, Khalil Abudahab, Ben EW Taylor, Mirko Menegazzo, Gemma Clark, Wendy Smith, Manjinder Khakh, Vicki M Fleming, Michelle M Lister, Hannah C Howson-Wells, Louise Berry, Tim Boswell, Amelia Joseph, Iona Willingham, Carl Jones, Christopher Holmes, Paul Bird, Thomas Helmer, Karlie Fallon, Julian Tang, Veena Raviprakash, Sharon Campbell, Nicola Sheriff, Victoria Blakey, Lesley-Anne Williams, Matthew W Loose, Nadine Holmes, Christopher Moore, Matthew Carlile, Victoria Wright, Fei Sang, Johnny Debebe, Francesc Coll, Adrian W Signell, Gilberto Betancor, Harry D Wilson, Sahar Eldirdiri, Anita Kenyon, Thomas Davis, Oliver G Pybus, Louis du Plessis, Alex E Zarebski, Jayna Raghwani, Moritz UG Kraemer, Sarah Francois, Stephen W Attwood, Tetyana I Vasylyeva, Marina Escalera Zamudio, Bernardo Gutierrez, M. Estee Torok, William L Hamilton, Ian G Goodfellow, Grant Hall, Aminu S Jahun, Yasmin Chaudhry, Myra Hosmillo, Malte L Pinckert, Iliana Georgana, Samuel Moses, Hannah Lowe, Luke Bedford, Jonathan Moore, Susanne Stonehouse, Chloe L Fisher, Ali R Awan, John BoYes, Judith Breuer, Kathryn Ann Harris, Julianne Rose Brown, Divya Shah, Laura Atkinson, Jack CD Lee, Nathaniel Storey, Flavia Flaviani, Adela Alcolea-Medina, Rebecca Williams, Gabrielle Vernet, Michael R Chapman, Lisa J Levett, Judith Heaney, Wendy Chatterton, Monika Pusok, Li Xu-McCrae, Darren L Smith, Matthew Bashton, Gregory R Young, Alison Holmes, Paul Anthony Randell, Alison Cox, Pinglawathee Madona, Frances Bolt, James Price, Siddharth Mookerjee, Manon Ragonnet-Cronin, Fabricia F. Nascimento, David Jorgensen, Igor Siveroni, Rob Johnson, Olivia Boyd, Lily Geidelberg, Erik M Volz, Aileen Rowan, Graham P Taylor, Katherine L Smollett, Nicholas J Loman, Joshua Quick, Claire McMurray, Joanne Stockton, Sam Nicholls, Will Rowe, Radoslaw Poplawski, Alan McNally, Rocio T Martinez Nunez, Jenifer Mason, Trevor I Robinson, Elaine O'Toole, Joanne Watts, Cassie Breen, Angela Cowell, Graciela Sluga, Nicholas W Machin, Shazaad S Y Ahmad, Ryan P George, Fenella Halstead, Venkat Sivaprakasam, Wendy Hogsden, Chris J Illingworth, Chris Jackson, Emma C Thomson, James G Shepherd, Patawee Asamaphan, Marc O Niebel, Kathy K Li, Rajiv N Shah, Natasha G Jesudason, Lily Tong, Alice Broos, Daniel Mair, Jenna Nichols, Stephen N Carmichael, Kyriaki Nomikou, Elihu Aranday-Cortes, Natasha Johnson, Igor Starinskij, Ana da Silva Filipe, David L Robertson, Richard J Orton, Joseph Hughes, Sreenu Vattipally, Joshua B Singer, Seema Nickbakhsh, Antony D Hale, Louissa R Macfarlane-Smith, Katherine L Harper, Holli Carden, Yusri Taha, Brendan AI Payne, Shirelle Burton-Fanning, Sheila Waugh, Jennifer Collins, Gary Eltringham, Steven Rushton, Sarah O'Brien, Amanda Bradley, Alasdair Maclean, Guy Mollett, Rachel Blacow, Kate E Templeton, Martin P McHugh, Rebecca Dewar, Elizabeth Wastenge, Samir Dervisevic, Rachael Stanley, Emma J Meader, Lindsay Coupland, Louise Smith, Clive Graham, Edward Barton, Debra Padgett, Garren Scott, Emma Swindells, Jane Greenaway, Andrew Nelson, Clare M McCann, Wen C Yew, Monique Andersson, Timothy Peto, Anita Justice, David Eyre, Derrick Crook, Tim J Sloan, Nichola Duckworth, Sarah Walsh, Anoop J Chauhan, Sharon Glaysher, Kelly Bicknell, Sarah Wyllie, Scott Elliott, Allyson Lloyd, Robert Impey, Nick Levene, Lynn Monaghan, Declan T Bradley, Tim Wyatt, Elias Allara, Clare Pearson, Husam Osman, Andrew Bosworth, Esther Robinson, Peter Muir, Ian B Vipond, Richard Hopes, Hannah M Pymont, Stephanie Hutchings, Martin D Curran, Surendra Parmar, Angie Lackenby, Tamyo Mbisa, Steven Platt, Shahjahan Miah, David Bibby, Carmen Manso, Jonathan Hubb, Meera Chand, Gavin Dabrera, Mary Ramsay, Daniel Bradshaw, Alicia Thornton, Richard Myers, Ulf Schaefer, Natalie Groves, Eileen Gallagher, David Lee, David Williams, Nicholas Ellaby, Ian Harrison, Hassan Hartman, Nikos Manesis, Vineet Patel, Chloe Bishop, Vicki Chalker, Juan Ledesma, Katherine A Twohig, Matthew T.G. Holden, Sharif Shaaban, Alec Birchley, Alexander Adams, Alisha Davies, Amy Gaskin, Amy Plimmer, Bree Gatica-Wilcox, Caoimhe McKerr, Catherine Moore, Chris Williams, David Heyburn, Elen De Lacy, Ember Hilvers, Fatima Downing, Giri Shankar, Hannah Jones, Hibo Asad, Jason Coombes, Joanne Watkins, Johnathan M Evans, Laia Fina, Laura Gifford, Lauren Gilbert, Lee Graham, Malorie Perry, Mari Morgan, Matthew Bull, Michelle Cronin, Nicole Pacchiarini, Noel Craine, Rachel Jones, Robin Howe, Sally Corden, Sara Rey, Sara Kumziene-SummerhaYes, Sarah Taylor, Simon Cottrell, Sophie Jones, Sue Edwards, Justin O'Grady, Andrew J Page, Alison E Mather, David J Baker, Steven Rudder, Alp Aydin, Gemma L Kay, Alexander J Trotter, Nabil-Fareed Alikhan, Leonardo de Oliveira Martins, Thanh Le-Viet, Lizzie Meadows, Anna Casey, Liz Ratcliffe, David A Simpson, Zoltan Molnar, Thomas Thompson, Erwan Acheson, Jane AH Masoli, Bridget A Knight, Sian Ellard, Cressida Auckland, Christopher R Jones, Tabitha W Mahungu, Dianne Irish-Tavares, Tanzina Haque, Jennifer Hart, Eric Witele, Melisa Louise Fenton, Ashok Dadrah, Amanda Symmonds, Tranprit Saluja, Yann Bourgeois, Garry P Scarlett, Katie F Loveson, Salman Goudarzi, Christopher Fearn, Kate Cook, Hannah Dent, Hannah Paul, David G Partridge, Mohammad Raza, Cariad Evans, Kate Johnson, Steven Liggett, Paul Baker, Stephen Bonner, Sarah Essex, Ronan A Lyons, Kordo Saeed, Adhyana I.K Mahanama, Buddhini Samaraweera, Siona Silveira, Emanuela Pelosi, Eleri Wilson-Davies, Rachel J Williams, Mark Kristiansen, Sunando Roy, Charlotte A Williams, Marius Cotic, Nadua Bayzid, Adam P Westhorpe, John A Hartley, Riaz Jannoo, Helen L Lowe, Angeliki Karamani, Leah Ensell, Jacqui A Prieto, Sarah Jeremiah, Dimitris Grammatopoulos, Sarojini Pandey, Lisa Berry, Katie Jones, Alex Richter, Andrew Beggs, Angus Best, Benita Percival, Jeremy Mirza, Oliver Megram, Megan Mayhew, Liam Crawford, Fiona Ashcroft, Emma Moles-Garcia, Nicola Cumley, Colin P Smith, Giselda Bucca, Andrew R Hesketh, Beth Blane, Sophia T Girgis, Danielle Leek, Sushmita Sridhar, Sally Forrest, Claire Cormie, Harmeet K Gill, Joana Dias, Ellen E Higginson, Mailis Maes, Jamie Young, Leanne M Kermack, Ravi Kumar Gupta, Catherine Ludden, Sharon J Peacock, Sophie Palmer, Carol M Churcher, Nazreen F Hadjirin, Alessandro M Carabelli, Ellena Brooks, Kim S Smith, Katerina Galai, Georgina M McManus, Chris Ruis, Rose K Davidson, Andrew Rambaut, Thomas Williams, Carlos E Balcazar, Michael D Gallagher, Áine O'Toole, Stefan Rooke, Verity Hill, Kathleen A Williamson, Thomas D Stanton, Stephen L Michell, Claire M Bewshea, Ben Temperton, Michelle L Michelsen, Joanna Warwick-Dugdale, Robin Manley, Audrey Farbos, James W Harrison, Christine M Sambles, David J Studholme, Aaron R Jeffries, Alistair C Darby, Julian A Hiscox, Steve Paterson, Miren Iturriza-Gomara, Kathryn A Jackson, Anita O Lucaci, Edith E Vamos, Margaret Hughes, Lucille Rainbow, Richard Eccles, Charlotte Nelson, Mark Whitehead, Lance Turtle, Sam T Haldenby, Richard Gregory, Matthew Gemmell, Claudia Wierzbicki, Hermione J Webster, Thushan I de Silva, Nikki Smith, Adrienn Angyal, Benjamin B Lindsey, Danielle C Groves, Luke R Green, Dennis Wang, Timothy M Freeman, Matthew D Parker, Alexander J Keeley, Paul J Parsons, Rachel M Tucker, Rebecca Brown, Matthew Wyles, Max Whiteley, Peijun Zhang, Marta Gallis, Stavroula F Louka, Chrystala Constantinidou, Meera Unnikrishnan, Sascha Ott, Jeffrey K.J. Cheng, Hannah E. Bridgewater, Lucy R. Frost, Grace Taylor-Joyce, Richard Stark, Laura Baxter, Mohammad T. Alam, Paul E Brown, Dinesh Aggarwal, Alberto C Cerda, Tammy V Merrill, Rebekah E Wilson, Patrick C McClure, Joseph G Chappell, Theocharis Tsoleridis, Jonathan Ball, David Buck, John A Todd, Angie Green, Amy Trebes, George MacIntyre-Cockett, Mariateresa de Cesare, Alex Alderton, Roberto Amato, Cristina V Ariani, Mathew A Beale, Charlotte Beaver, Katherine L Bellis, Emma Betteridge, James Bonfield, John Danesh, Matthew J Dorman, Eleanor Drury, Ben W Farr, Luke Foulser, Sonia Goncalves, Scott Goodwin, Marina Gourtovaia, Ewan M Harrison, David K Jackson, Dorota Jamrozy, Ian Johnston, Leanne Kane, Sally Kay, Jon-Paul Keatley, Dominic Kwiatkowski, Cordelia F Langford, Mara Lawniczak, Laura Letchford, Rich Livett, Stephanie Lo, Inigo Martincorena, Samantha McGuigan, Rachel Nelson, Steve Palmer, Naomi R Park, Minal Patel, Liam Prestwood, Christoph Puethe, Michael A Quail, Shavanthi Rajatileka, Carol Scott, Lesley Shirley, John Sillitoe, Michael H Spencer Chapman, Scott AJ Thurston, Gerry Tonkin-Hill, Danni Weldon, Diana Rajan, Iraad F Bronner, Louise Aigrain, Nicholas M Redshaw, Stefanie V Lensing, Robert Davies, Andrew Whitwham, Jennifier Liddle, Kevin Lewis, Jaime M Tovar-Corona, Steven Leonard, Jillian Durham, Andrew R Bassett, Shane McCarthy, Robin J Moll, Keith James, Karen Oliver, Alex Makunin, Jeff Barrett, and Rory N Gunson
Subjects: Public aspects of medicine, RA1-1270
Abstract: Summary: Background: The SARS-CoV-2 variant B.1.1.7 was first identified in December, 2020, in England. We aimed to investigate whether increases in the proportion of infections with this variant are associated with differences in symptoms or disease course, reinfection rates, or transmissibility. Methods: We did an ecological study to examine the association between the regional proportion of infections with the SARS-CoV-2 B.1.1.7 variant and reported symptoms, disease course, rates of reinfection, and transmissibility. Data on types and duration of symptoms were obtained from longitudinal reports from users of the COVID Symptom Study app who reported a positive test for COVID-19 between Sept 28 and Dec 27, 2020 (during which the prevalence of B.1.1.7 increased most notably in parts of the UK). From this dataset, we also estimated the frequency of possible reinfection, defined as the presence of two reported positive tests separated by more than 90 days with a period of reporting no symptoms for more than 7 days before the second positive test. The proportion of SARS-CoV-2 infections with the B.1.1.7 variant across the UK was estimated with use of genomic data from the COVID-19 Genomics UK Consortium and data from Public Health England on spike-gene target failure (a non-specific indicator of the B.1.1.7 variant) in community cases in England. We used linear regression to examine the association between reported symptoms and proportion of B.1.1.7. We assessed the Spearman correlation between the proportion of B.1.1.7 cases and number of reinfections over time, and between the number of positive tests and reinfections. We estimated incidence for B.1.1.7 and previous variants, and compared the effective reproduction number, Rt, for the two incidence estimates. Findings: From Sept 28 to Dec 27, 2020, positive COVID-19 tests were reported by 36 920 COVID Symptom Study app users whose region was known and who reported as healthy on app sign-up. We found no changes in reported symptoms or disease duration associated with B.1.1.7. For the same period, possible reinfections were identified in 249 (0·7% [95% CI 0·6–0·8]) of 36 509 app users who reported a positive swab test before Oct 1, 2020, but there was no evidence that the frequency of reinfections was higher for the B.1.1.7 variant than for pre-existing variants. Reinfection occurrences were more positively correlated with the overall regional rise in cases (Spearman correlation 0·56–0·69 for South East, London, and East of England) than with the regional increase in the proportion of infections with the B.1.1.7 variant (Spearman correlation 0·38–0·56 in the same regions), suggesting B.1.1.7 does not substantially alter the risk of reinfection. We found a multiplicative increase in the Rt of B.1.1.7 by a factor of 1·35 (95% CI 1·02–1·69) relative to pre-existing variants. However, Rt fell below 1 during regional and national lockdowns, even in regions with high proportions of infections with the B.1.1.7 variant. Interpretation: The lack of change in symptoms identified in this study indicates that existing testing and surveillance infrastructure do not need to change specifically for the B.1.1.7 variant. In addition, given that there was no apparent increase in the reinfection rate, vaccines are likely to remain effective against the B.1.1.7 variant. Funding: Zoe Global, Department of Health (UK), Wellcome Trust, Engineering and Physical Sciences Research Council (UK), National Institute for Health Research (UK), Medical Research Council (UK), Alzheimer's Society.
Published: 2021
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4. Discordance between semi-quantitative nucleic acid detection of bacteria and quantitative bacteriology in sputum from patients with pneumonia

Author: Naomi J. Gadsby, James J. Dunn, Coreen L. Johnson, Taylor McQuillan, Martin P. McHugh, Kate E. Templeton, Maria C. Rodriguez-Barradas, and Daniel M. Musher
Subjects: Microbiology (medical), Infectious Diseases
Published: 2023
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5. Analysis of the ARTIC V4 and V4.1 SARS-CoV-2 primers and their impact on the detection of Omicron BA.1 and BA.2 lineage-defining mutations

Author: Fatima R. Ulhuq, Madhuri Barge, Kerry Falconer, Jonathan Wild, Goncalo Fernandes, Abbie Gallagher, Suzie McGinley, Ahmad Sugadol, Muhammad Tariq, Daniel Maloney, Juliet Kenicer, Rebecca Dewar, Kate Templeton, Martin P. McHugh, University of St Andrews. Infection and Global Health Division, and University of St Andrews. School of Medicine
Subjects: MCC, QR355, SARS-CoV-2, COVID-19, DAS, General Medicine, NIS, omicron, genome sequencing, Whole genome sequencing, BA.1, nanopore, BA.2, QR355 Virology
Abstract: The ARTIC protocol uses a multiplexed PCR approach with two primer pools tiling the entire SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) genome. Primer pool updates are necessary for accurate amplicon sequencing of evolving SARS-CoV-2 variants with novel mutations. The suitability of the ARTIC V4 and updated V4.1 primer scheme was assessed using whole genome sequencing of Omicron from clinical samples using Oxford Nanopore Technology. Analysis of Omicron BA.1 genomes revealed that 93.22 % of clinical samples generated improved genome coverage at 50× read depth with V4.1 primers when compared to V4 primers. Additionally, the V4.1 primers improved coverage of BA.1 across amplicons 76 and 88, which resulted in the detection of the variant-defining mutations G22898A, A26530G and C26577G. The Omicron BA.2 sub-variant (VUI-22JAN-01) replaced BA.1 as the dominant variant by March 2022, and analysis of 168 clinical samples showed reduced coverage across amplicons 15 and 75. Upon further interrogation of primer binding sites, a mutation at C4321T [present in 163/168 (97 %) of samples] was identified as a possible cause of complete dropout of amplicon 15. Furthermore, two mutations were identified within the primer binding regions for amplicon 75: A22786C (present in 90 % of samples) and C22792T (present in 12.5 % of samples). Together, these mutations may result in reduced coverage of amplicon 75, and further primer updates would allow the identification of the two BA.2-defining mutations present in amplicon 75: A22688G and T22679C. This work highlights the need for ongoing surveillance of primer matches as circulating variants evolve and change. Publisher PDF
Published: 2023
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6. Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes

Author: S. Cotton, M.P. McHugh, R. Dewar, J.G. Haas, K. Templeton, Samuel C. Robson, Thomas R. Connor, Nicholas J. Loman, Tanya Golubchik, Rocio T. Martinez Nunez, David Bonsall, Andrew Rambaut, Luke B. Snell, Rich Livett, Catherine Ludden, Sally Corden, Eleni Nastouli, Gaia Nebbia, Ian Johnston, Jacqui A. Prieto, Kordo Saeed, David K. Jackson, Catherine Houlihan, Dan Frampton, William L. Hamilton, Adam A. Witney, Giselda Bucca, Cassie F. Pope, Catherine Moore, Emma C. Thomson, Teresa Cutino-Moguel, Ewan M. Harrison, Colin P. Smith, Fiona Rogan, Shaun M. Beckwith, Abigail Murray, Dawn Singleton, Kirstine Eastick, Liz A. Sheridan, Paul Randell, Leigh M. Jackson, Cristina V. Ariani, Sónia Gonçalves, Derek J. Fairley, Matthew W. Loose, Joanne Watkins, Samuel Moses, Sam Nicholls, Matthew Bull, Roberto Amato, Darren L. Smith, David M. Aanensen, Jeffrey C. Barrett, Beatrix Kele, Dinesh Aggarwal, James G. Shepherd, Martin D. Curran, Surendra Parmar, Matthew D. Parker, Catryn Williams, Sharon Glaysher, Anthony P. Underwood, Matthew Bashton, Nicole Pacchiarini, Katie F. Loveson, Matthew Byott, Alessandro M. Carabelli, Kate E. Templeton, Sharon J. Peacock, Thushan I. de Silva, Dennis Wang, Cordelia F. Langford, John Sillitoe, Rory N. Gunson, Simon Cottrell, Justin O’Grady, Dominic Kwiatkowski, Patrick J. Lillie, Nicholas Cortes, Nathan Moore, Claire Thomas, Phillipa J. Burns, Tabitha W. Mahungu, Steven Liggett, Angela H. Beckett, Matthew TG. Holden, Lisa J. Levett, Husam Osman, Mohammed O. Hassan-Ibrahim, David A. Simpson, Meera Chand, Ravi K. Gupta, Alistair C. Darby, Steve Paterson, Oliver G. Pybus, Erik M. Volz, Daniela de Angelis, David L. Robertson, Andrew J. Page, Inigo Martincorena, Louise Aigrain, Andrew R. Bassett, Nick Wong, Yusri Taha, Michelle J. Erkiert, Michael H. Spencer Chapman, Rebecca Dewar, Martin P. McHugh, Siddharth Mookerjee, Stephen Aplin, Matthew Harvey, Thea Sass, Helen Umpleby, Helen Wheeler, James P. McKenna, Ben Warne, Joshua F. Taylor, Yasmin Chaudhry, Rhys Izuagbe, Aminu S. Jahun, Gregory R. Young, Claire McMurray, Clare M. McCann, Andrew Nelson, Scott Elliott, Hannah Lowe, Anna Price, Matthew R. Crown, Sara Rey, Sunando Roy, Ben Temperton, Sharif Shaaban, Andrew R. Hesketh, Kenneth G. Laing, Irene M. Monahan, Judith Heaney, Emanuela Pelosi, Siona Silviera, Eleri Wilson-Davies, Helen Fryer, Helen Adams, Louis du Plessis, Rob Johnson, William T. Harvey, Joseph Hughes, Richard J. Orton, Lewis G. Spurgin, Yann Bourgeois, Chris Ruis, Áine O'Toole, Marina Gourtovaia, Theo Sanderson, Christophe Fraser, Jonathan Edgeworth, Judith Breuer, Stephen L. Michell, John A. Todd, Michaela John, David Buck, Kavitha Gajee, Gemma L. Kay, David Heyburn, Themoula Charalampous, Adela Alcolea-Medina, Katie Kitchman, Alan McNal, David T. Pritch, Samir Dervisevic, Peter Muir, Esther Robinson, Barry B. Vipond, Newara A. Ramadan, Christopher Jeanes, Danni Weldon, Jana Catalan, Neil Jones, Ana da Silva Filipe, Chris Williams, Marc Fuchs, Julia Miskelly, Aaron R. Jeffries, Karen Oliver, Naomi R. Park, Amy Ash, Cherian Koshy, Magdalena Barrow, Sarah L. Buchan, Anna Mantzouratou, Gemma Clark, Christopher W. Holmes, Sharon Campbell, Thomas Davis, Ngee Keong Tan, Julianne R. Brown, Kathryn A. Harris, Stephen P. Kidd, Paul R. Grant, Li Xu-McCrae, Alison Cox, Pinglawathee Madona, Marcus Pond, Paul A. Randell, Karen T. Withell, Cheryl Williams, Clive Graham, Rebecca Denton-Smith, Emma Swindells, Robyn Turnbull, Tim J. Sloan, Andrew Bosworth, Stephanie Hutchings, Hannah M. Pymont, Anna Casey, Liz Ratcliffe, Christopher R. Jones, Bridget A. Knight, Tanzina Haque, Jennifer Hart, Dianne Irish-Tavares, Eric Witele, Craig Mower, Louisa K. Watson DipHE, Jennifer Collins, Gary Eltringham, Dorian Crudgington, Ben Macklin, Miren Iturriza-Gomara, Anita O. Lucaci, Patrick C. McClure, Matthew Carlile, Nadine Holmes, Christopher Moore, Nathaniel Storey, Stefan Rooke, Gonzalo Yebra, Noel Craine, Malorie Perry, Nabil-Fareed Alikhan, Stephen Bridgett, Kate F. Cook, Christopher Fearn, Salman Goudarzi, Ronan A. Lyons, Thomas Williams, Sam T. Haldenby, Jillian Durham, Steven Leonard, Robert M. Davies, Rahul Batra, Beth Blane, Moira J. Spyer, Perminder Smith, Mehmet Yavus, Rachel J. Williams, Adhyana IK. Mahanama, Buddhini Samaraweera, Sophia T. Girgis, Samantha E. Hansford, Angie Green, Charlotte Beaver, Katherine L. Bellis, Matthew J. Dorman, Sally Kay, Liam Prestwood, Shavanthi Rajatileka, Joshua Quick, Radoslaw Poplawski, Nicola Reynolds, Andrew Mack, Arthur Morriss, Thomas Whalley, Bindi Patel, Iliana Georgana, Myra Hosmillo, Malte L. Pinckert, Joanne Stockton, John H. Henderson, Amy Hollis, William Stanley, Wen C. Yew, Richard Myers, Alicia Thornton, Alexander Adams, Tara Annett, Hibo Asad, Alec Birchley, Jason Coombes, Johnathan M. Evans, Laia Fina, Bree Gatica-Wilcox, Lauren Gilbert, Lee Graham, Jessica Hey, Ember Hilvers, Sophie Jones, Hannah Jones, Sara Kumziene-Summerhayes, Caoimhe McKerr, Jessica Powell, Georgia Pugh, Sarah Taylor, Alexander J. Trotter, Charlotte A. Williams, Leanne M. Kermack, Benjamin H. Foulkes, Marta Gallis, Hailey R. Hornsby, Stavroula F. Louka, Manoj Pohare, Paige Wolverson, Peijun Zhang, George MacIntyre-Cockett, Amy Trebes, Robin J. Moll, Lynne Ferguson, Emily J. Goldstein, Alasdair Maclean, Rachael Tomb, Igor Starinskij, Laura Thomson, Joel Southgate, Moritz UG. Kraemer, Jayna Raghwani, Alex E. Zarebski, Olivia Boyd, Lily Geidelberg, Chris J. Illingworth, Chris Jackson, David Pascall, Sreenu Vattipally, Timothy M. Freeman, Sharon N. Hsu, Benjamin B. Lindsey, Keith James, Kevin Lewis, Gerry Tonkin-Hill, Jaime M. Tovar-Corona, MacGregor Cox, Khalil Abudahab, Mirko Menegazzo, Ben EW. Taylor, Corin A. Yeats, Afrida Mukaddas, Derek W. Wright, Leonardo de Oliveira Martins, Rachel Colquhoun, Verity Hill, Ben Jackson, J.T. McCrone, Nathan Medd, Emily Scher, Jon-Paul Keatley, Tanya Curran, Sian Morgan, Patrick Maxwell, Ken Smith, Sahar Eldirdiri, Anita Kenyon, Alison H. Holmes, James R. Price, Tim Wyatt, Alison E. Mather, Timofey Skvortsov, John A. Hartley, Martyn Guest, Christine Kitchen, Ian Merrick, Robert Munn, Beatrice Bertolusso, Jessica Lynch, Gabrielle Vernet, Stuart Kirk, Elizabeth Wastnedge, Rachael Stanley, Giles Idle, Declan T. Bradley, Nicholas F. Killough, Jennifer Poyner, Matilde Mori, Owen Jones, Victoria Wright, Ellena Brooks, Carol M. Churcher, Laia Delgado Callico, Mireille Fragakis, Katerina Galai, Andrew Jermy, Sarah Judges, Anna Markov, Georgina M. McManus, Kim S. Smith, Peter MD. Thomas-McEwen, Elaine Westwick, Stephen W. Attwood, Frances Bolt, Alisha Davies, Elen De Lacy, Fatima Downing, Sue Edwards, Lizzie Meadows, Sarah Jeremiah, Nikki Smith, Luke Foulser, Amita Patel, Louise Berry, Tim Boswell, Vicki M. Fleming, Hannah C. Howson-Wells, Amelia Joseph, Manjinder Khakh, Michelle M. Lister, Paul W. Bird, Karlie Fallon, Thomas Helmer, Claire L. McMurray, Mina Odedra, Jessica Shaw, Julian W. Tang, Nicholas J. Willford, Victoria Blakey, Veena Raviprakash, Nicola Sheriff, Lesley-Anne Williams, Theresa Feltwell, Luke Bedford, James S. Cargill, Warwick Hughes, Jonathan Moore, Susanne Stonehouse, Laura Atkinson, Jack CD. Lee, Divya Shah, Natasha Ohemeng-Kumi, John Ramble, Jasveen Sehmi, Rebecca Williams, Wendy Chatterton, Monika Pusok, William Everson, Anibolina Castigador, Emily Macnaughton, Kate El Bouzidi, Temi Lampejo, Malur Sudhanva, Cassie Breen, Graciela Sluga, Shazaad SY. Ahmad, Ryan P. George, Nicholas W. Machin, Debbie Binns, Victoria James, Rachel Blacow, Lindsay Coupland, Louise Smith, Edward Barton, Debra Padgett, Garren Scott, Aidan Cross, Mariyam Mirfenderesky, Jane Greenaway, Kevin Cole, Phillip Clarke, Nichola Duckworth, Sarah Walsh, Kelly Bicknell, Robert Impey, Sarah Wyllie, Richard Hopes, Chloe Bishop, Vicki Chalker, Ian Harrison, Laura Gifford, Zoltan Molnar, Cressida Auckland, Cariad Evans, Kate Johnson, David G. Partridge, Mohammad Raza, Paul Baker, Stephen Bonner, Sarah Essex, Leanne J. Murray, Andrew I. Lawton, Shirelle Burton-Fanning, Brendan AI. Payne, Sheila Waugh, Andrea N. Gomes, Maimuna Kimuli, Darren R. Murray, Paula Ashfield, Donald Dobie, Fiona Ashford, Angus Best, Liam Crawford, Nicola Cumley, Megan Mayhew, Oliver Megram, Jeremy Mirza, Emma Moles-Garcia, Benita Percival, Megan Driscoll, Leah Ensell, Helen L. Lowe, Laurentiu Maftei, Matteo Mondani, Nicola J. Chaloner, Benjamin J. Cogger, Lisa J. Easton, Hannah Huckson, Jonathan Lewis, Sarah Lowdon, Cassandra S. Malone, Florence Munemo, Manasa Mutingwende, Roberto Nicodemi, Olga Podplomyk FD, Thomas Somassa, Andrew Beggs, Alex Richter, Claire Cormie, Joana Dias, Sally Forrest, Ellen E. Higginson, Mailis Maes, Jamie Young, Rose K. Davidson, Kathryn A. Jackson, Alexander J. Keeley, Jonathan Ball, Timothy Byaruhanga, Joseph G. Chappell, Jayasree Dey, Jack D. Hill, Emily J. Park, Arezou Fanaie, Rachel A. Hilson, Geraldine Yaze, Stephanie Lo, Safiah Afifi, Robert Beer, Joshua Maksimovic, Kathryn McCluggage, Karla Spellman, Catherine Bresner, William Fuller, Angela Marchbank, Trudy Workma, Ekaterina Shelest, Johnny Debebe, Fei Sang, Sarah Francois, Bernardo Gutierrez, Tetyana I. Vasylyeva, Flavia Flaviani, Manon Ragonnet-Cronin, Katherine L. Smollett, Alice Broos, Daniel Mair, Jenna Nichols, Kyriaki Nomikou, Lily Tong, Ioulia Tsatsani, Sarah O'Brien, Steven Rushton, Roy Sanderson, Jon Perkins, Seb Cotton, Abbie Gallagher, Elias Allara, Clare Pearson, David Bibby, Gavin Dabrer, Nicholas Ellaby, Eileen Gallagher, Jonathan Hubb, Angie Lackenby, David Lee, Nikos Manesis, Tamyo Mbisa, Steven Platt, Katherine A. Twohig, Mari Morgan, Alp Aydin, David J. Baker, Ebenezer Foster-Nyarko, Sophie J. Prosolek, Steven Rudder, Chris Baxter, Sílvia F. Carvalho, Deborah Lavin, Arun Mariappan, Clara Radulescu, Aditi Singh, Miao Tang, Helen Morcrette, Nadua Bayzid, Marius Cotic, Carlos E. Balcazar, Michael D. Gallagher, Daniel Maloney, Thomas D. Stanton, Kathleen A. Williamson, Robin Manley, Michelle L. Michelsen, Christine M. Sambles, David J. Studholme, Joanna Warwick-Dugdale, Richard Eccles, Matthew Gemmell, Richard Gregory, Margaret Hughes, Charlotte Nelson, Lucille Rainbow, Edith E. Vamos, Hermione J. Webster, Mark Whitehead, Claudia Wierzbicki, Adrienn Angyal, Luke R. Green, Max Whiteley, Emma Betteridge, Iraad F. Bronner, Ben W. Farr, Scott Goodwin, Stefanie V. Lensing, Shane A. McCarthy, Michael A. Quail, Diana Rajan, Nicholas M. Redshaw, Carol Scott, Lesley Shirley, Scott AJ. Thurston, Will Rowe, Amy Gaskin, Thanh Le-Viet, James Bonfield, Jennifier Liddle, Andrew Whitwham, University of St Andrews. School of Medicine, University of St Andrews. Infection and Global Health Division, and Apollo - University of Cambridge Repository
Subjects: Microbiology (medical), MCC, Introduction, SARS-CoV-2, NDAS, COVID-19, Care homes, General Medicine, NIS, Patient Discharge, Hospitals, Hospitalization, Infectious Diseases, SDG 3 - Good Health and Well-being, RA0421, RA0421 Public health. Hygiene. Preventive Medicine, Humans, Hospital discharge
Abstract: COG-UK is supported by funding from the MRC part of UK Research & Innovation, the National Institute of Health Research (Grant code MC_PC_19027), and Genome Research Limited, operating as the Welcome Sanger Institute. Background The first epidemic wave of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Scotland resulted in high case numbers and mortality in care homes. In Lothian, over one-third of care homes reported an outbreak, while there was limited testing of hospital patients discharged to care homes. Aim To investigate patients discharged from hospitals as a source of SARS-CoV-2 introduction into care homes during the first epidemic wave. Methods A clinical review was performed for all patients discharges from hospitals to care homes from 1st March 2020 to 31st May 2020. Episodes were ruled out based on coronavirus disease 2019 (COVID-19) test history, clinical assessment at discharge, whole-genome sequencing (WGS) data and an infectious period of 14 days. Clinical samples were processed for WGS, and consensus genomes generated were used for analysis using Cluster Investigation and Virus Epidemiological Tool software. Patient timelines were obtained using electronic hospital records. Findings In total, 787 patients discharged from hospitals to care homes were identified. Of these, 776 (99%) were ruled out for subsequent introduction of SARS-CoV-2 into care homes. However, for 10 episodes, the results were inconclusive as there was low genomic diversity in consensus genomes or no sequencing data were available. Only one discharge episode had a genomic, time and location link to positive cases during hospital admission, leading to 10 positive cases in their care home. Conclusion The majority of patients discharged from hospitals were ruled out for introduction of SARS-CoV-2 into care homes, highlighting the importance of screening all new admissions when faced with a novel emerging virus and no available vaccine. Publisher PDF
Published: 2023

7. Multi-site validation of an amplicon-based sequencing approach for human monkeypox virus

Author: Nicholas F G, Chen, Chrispin, Chaguza, Luc, Gagne, Matthew, Doucette, Sandra, Smole, Erika, Buzby, Joshua, Hall, Stephanie, Ash, Rachel, Harrington, Seana, Cofsky, Selina, Clancy, Curtis J, Kapsak, Joel, Sevinsky, Kevin, Libuit, Daniel J, Park, Peera, Hemarajata, Jacob M, Garrigues, Nicole M, Green, Sean, Sierra-Patev, Kristin, Carpenter-Azevedo, Richard C, Huard, Claire, Pearson, Kutluhan, Incekara, Christina, Nishimura, Jian Ping, Huang, Emily, Gagnon, Ethan, Reever, Jafar, Razeq, Anthony, Muyombwe, Vítor, Borges, Rita, Ferreira, Daniel, Sobral, Silvia, Duarte, Daniela, Santos, Luís, Vieira, João Paulo, Gomes, Carly, Aquino, Isabella M, Savino, Karinda, Felton, Moneeb, Bajwa, Nyjil, Hayward, Holly, Miller, Allison, Naumann, Ria, Allman, Neel, Greer, Amary, Fall, Heba H, Mostafa, Martin P, McHugh, Daniel M, Maloney, Rebecca, Dewar, Juliet, Kenicer, Abby, Parker, Katharine, Mathers, Jonathan, Wild, Seb, Cotton, Kate E, Templeton, George, Churchwell, Philip A, Lee, Maria, Pedrosa, Brenna, McGruder, Sarah, Schmedes, Matthew R, Plumb, Xiong, Wang, Regina Bones, Barcellos, Fernanda M S, Godinho, Richard Steiner, Salvato, Aimee, Ceniseros, Mallery I, Breban, Nathan D, Grubaugh, Glen R, Gallagher, and Chantal B F, Vogels
Abstract: The 2022 multi-country monkeypox outbreak concurrent with the ongoing COVID-19 pandemic has further highlighted the need for genomic surveillance and pathogen whole genome sequencing. While metagenomic sequencing approaches have been used to sequence many of the early human monkeypox virus infections, these methods are resource intensive and require samples with high viral DNA concentrations. Given the atypical clinical presentation of cases associated with the current outbreak and uncertainty regarding viral load across both the course of infection and anatomical body sites, there is an urgent need for a more sensitive and broadly applicable sequencing approach. Amplicon-based sequencing (PrimalSeq) was initially developed for sequencing of Zika virus, and later adapted as the main sequencing approach for SARS-CoV-2. Here, we used PrimalScheme to develop a primer scheme for human monkeypox virus that can be used with many sequencing and bioinformatics pipelines implemented during the COVID-19 pandemic. We sequenced clinical samples that tested presumptive positive for monkeypox virus with amplicon-based and metagenomic sequencing approaches. Upon comparison, we found notably higher genome coverage across the virus genome, particularly in higher PCR cycle threshold (lower DNA titer) samples, with minimal amplicon drop-outs, in using the amplicon-based sequencing approach. By sending out primer pool aliquots to laboratories across the United States and internationally, we validated the primer scheme in 12 public health laboratories with their established Illumina or Oxford Nanopore Technologies sequencing workflows and with different sample types across a range of Ct values. Our findings suggest that amplicon-based sequencing increases the success rate across a wider range of viral DNA concentrations, with the PCR Ct value threshold at which laboratories were able to achieve 80% genome coverage at 10X ranging between Ct 25-33. Therefore, it increases the number of samples where near-complete genomes can be generated and it provides a cost-effective and widely applicable alternative to metagenomics for continued human monkeypox virus genomic surveillance. Importantly, we show that the human monkeypox virus primer scheme can be used with currently implemented amplicon-based SARS-CoV-2 sequencing workflows, with minimal change to the protocol.
Published: 2022

8. Development of an amplicon-based sequencing approach in response to the global emergence of human monkeypox virus

Author: Nicholas F.G. Chen, Chrispin Chaguza, Luc Gagne, Matthew Doucette, Sandra Smole, Erika Buzby, Joshua Hall, Stephanie Ash, Rachel Harrington, Seana Cofsky, Selina Clancy, Curtis J. Kapsak, Joel Sevinsky, Kevin Libuit, Daniel J. Park, Peera Hemarajata, Jacob M. Garrigues, Nicole M. Green, Sean Sierra-Patev, Kristin Carpenter-Azevedo, Richard C. Huard, Claire Pearson, Kutluhan Incekara, Christina Nishimura, Jian Ping Huang, Emily Gagnon, Ethan Reever, Jafar Razeq, Anthony Muyombwe, Vítor Borges, Rita Ferreira, Daniel Sobral, Silvia Duarte, Daniela Santos, Luís Vieira, João Paulo Gomes, Carly Aquino, Isabella M. Savino, Karinda Felton, Moneeb Bajwa, Nyjil Hayward, Holly Miller, Allison Naumann, Ria Allman, Neel Greer, Amary Fall, Heba H. Mostafa, Martin P. McHugh, Daniel M. Maloney, Rebecca Dewar, Juliet Kenicer, Abby Parker, Katharine Mathers, Jonathan Wild, Seb Cotton, Kate E. Templeton, George Churchwell, Philip A. Lee, Maria Pedrosa, Brenna McGruder, Sarah Schmedes, Matthew R. Plumb, Xiong Wang, Regina Bones Barcellos, Fernanda M.S. Godinho, Richard Steiner Salvato, Aimee Ceniseros, Mallery I. Breban, Nathan D. Grubaugh, Glen R. Gallagher, and Chantal B.F. Vogels
Abstract: The 2022 multi-country monkeypox (mpox) outbreak concurrent with the ongoing COVID-19 pandemic has further highlighted the need for genomic surveillance and rapid pathogen whole genome sequencing. While metagenomic sequencing approaches have been used to sequence many of the early mpox infections, these methods are resource intensive and require samples with high viral DNA concentrations. Given the atypical clinical presentation of cases associated with the outbreak and uncertainty regarding viral load across both the course of infection and anatomical body sites, there was an urgent need for a more sensitive and broadly applicable sequencing approach. Highly multiplexed amplicon-based sequencing (PrimalSeq) was initially developed for sequencing of Zika virus, and later adapted as the main sequencing approach for SARS-CoV-2. Here, we used PrimalScheme to develop a primer scheme for human monkeypox virus that can be used with many sequencing and bioinformatics pipelines implemented in public health laboratories during the COVID-19 pandemic. We sequenced clinical samples that tested presumptive positive for human monkeypox virus with amplicon-based and metagenomic sequencing approaches. We found notably higher genome coverage across the virus genome, with minimal amplicon drop-outs, in using the amplicon-based sequencing approach, particularly in higher PCR cycle threshold (lower DNA titer) samples. Further testing demonstrated that Ct value correlated with the number of sequencing reads and influenced the percent genome coverage. To maximize genome coverage when resources are limited, we recommend selecting samples with a PCR cycle threshold below 31 Ct and generating 1 million sequencing reads per sample. To support national and international public health genomic surveillance efforts, we sent out primer pool aliquots to 10 laboratories across the United States, United Kingdom, Brazil, and Portugal. These public health laboratories successfully implemented the human monkeypox virus primer scheme in various amplicon sequencing workflows and with different sample types across a range of Ct values. Thus, we show that amplicon based sequencing can provide a rapidly deployable, cost-effective, and flexible approach to pathogen whole genome sequencing in response to newly emerging pathogens. Importantly, through the implementation of our primer scheme into existing SARS-CoV-2 workflows and across a range of sample types and sequencing platforms, we further demonstrate the potential of this approach for rapid outbreak response.
Published: 2022
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9. Consideration of within-patient diversity highlights transmission pathways and antimicrobial resistance gene variability in vancomycin resistantEnterococcus faecium

Author: Martin P McHugh, Kerry A Pettigrew, Surabhi Taori, Thomas J Evans, Alistair Leanord, Stephen H Gillespie, Kate E Templeton, and Matthew TG Holden
Abstract: SynopsisBackgroundWhole genome sequencing (WGS) is increasingly applied to healthcare-associated vancomycin-resistantEnterococcus faecium(VREfm) outbreaks. Within-patient diversity could complicate transmission resolution if single colonies are sequenced from identified cases.ObjectivesDetermine the impact of within-patient diversity on transmission resolution of VREfmMethodsFourteen colonies were collected from VREfm positive rectal screens, single colonies were collected from clinical samples, and Illumina WGS performed. Two isolates were selected for Oxford Nanopore sequencing and hybrid genome assembly to generate lineage-specific reference genomes. Mapping to closely related references was used to identify genetic variations and closely related genomes. A transmission network was inferred for the entire genome set using Phyloscanner.ResultsIn total, 229 isolates from 11 patients were sequenced. Carriage of 2-3 sequence types was detected in 27% of patients. Presence of antimicrobial resistance genes and plasmids was variable within genomes from the same patient and sequence type. We identified two dominant sequence types (ST80 and ST1424), with two putative transmission clusters of two patients within ST80, and a single cluster of six patients within ST1424. We found transmission resolution was impaired using fewer than 14 colonies.ConclusionsPatients can carry multiple sequence types of VREfm, and even within related lineages the presence of mobile genetic elements and antimicrobial resistance genes can vary. VREfm within-patient diversity should be considered to ensure accurate resolution of transmission networks.
Published: 2022
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10. Bacterial and fungal communities in tracheal aspirates of intubated COVID-19 patients: a pilot study

Author: Alicia, Ruiz-Rodriguez, Paula, Lusarreta-Parga, Wouter A A, de Steenhuijsen Piters, Lilian, Koppensteiner, Carlos E, Balcazar-Lopez, Robyn, Campbell, Rebecca, Dewar, Martin P, McHugh, David, Dockrell, Kate E, Templeton, and Debby, Bogaert
Subjects: Multidisciplinary, Bacteria, Coinfection, COVID-19, Humans, Pilot Projects, Mycobiome
Abstract: Co-infections with bacterial or fungal pathogens could be associated with severity and outcome of disease in COVID-19 patients. We, therefore, used a 16S and ITS-based sequencing approach to assess the biomass and composition of the bacterial and fungal communities in endotracheal aspirates of intubated COVID-19 patients. Our method combines information on bacterial and fungal biomass with community profiling, anticipating the likelihood of a co-infection is higher with (1) a high bacterial and/or fungal biomass combined with (2) predominance of potentially pathogenic microorganisms. We tested our methods on 42 samples from 30 patients. We observed a clear association between microbial outgrowth (high biomass) and predominance of individual microbial species. Outgrowth of pathogens was in line with the selective pressure of antibiotics received by the patient. We conclude that our approach may help to monitor the presence and predominance of pathogens and therefore the likelihood of co-infections in ventilated patients, which ultimately, may help to guide treatment.
Published: 2022
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11. Rapid molecular testing for Staphylococcus aureus bacteraemia improves clinical management

Author: Fiona M. MacKenzie, Benjamin J. Parcell, Kate Templeton, and Martin P McHugh
Subjects: 0301 basic medicine, Microbiology (medical), medicine.medical_specialty, Diagnostic methods, medicine.diagnostic_test, business.industry, 030106 microbiology, Staphylococcus aureus bacteraemia, General Medicine, Antimicrobial, medicine.disease_cause, Microbiology, Patient management, 03 medical and health sciences, 0302 clinical medicine, Staphylococcus aureus, Internal medicine, Medicine, Antimicrobial stewardship, Blood culture, 030212 general & internal medicine, Coagulase, business
Abstract: Introduction. Staphylococcus aureus bacteraemia (SAB) causes significant morbidity and mortality. Standard diagnostic methods require 24–48 h to provide results, during which time management is guideline-based and may be suboptimal. Aim. Evaluate the impact of rapid molecular detection of S. aureus in positive blood culture bottle fluid on patient management. Methodology. Samples were tested prospectively at two clinical centres. Positive blood cultures with Gram-positive cocci in clusters on microscopy were tested with the Xpert MRSA/SA blood culture assay (Cepheid), as well as standard culture-based identification and antimicrobial sensitivity tests. Results were passed to clinical microbiologists in real time and used for patient management. Results. Of 264 blood cultures tested (184 and 80 from each centre), S. aureus was grown from 39 (14.8 %) with one identified as methicillin-resistant S. aureus ; all Xpert results agreed with culture results. Median turnaround time from culture flagging positive to result reporting for Xpert was 1.7 h, compared to 25.7 h for species identification by culture. Xpert results allowed early changes to management in 40 (16.8 %) patients, with Xpert positive patients starting specific therapy for SAB and Xpert negative patients stopping or avoiding empiric antimicrobials for SAB. Conclusion. Rapid and accurate detection of S. aureus with the Xpert MRSA/SA BC assay in positive blood culture bottles allowed earlier targeted patient management. Negative Xpert results are suggestive of coagulase negative staphylococci, allowing de-escalation of antimicrobial therapy if clinically appropriate.
Published: 2020
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12. Presence of

Author: Martin P, McHugh, Benjamin J, Parcell, Kerry A, Pettigrew, Geoff, Toner, Elham, Khatamzas, Noha, El Sakka, Anne Marie, Karcher, Joanna, Walker, Robert, Weir, Danièle, Meunier, Katie L, Hopkins, Neil, Woodford, Kate E, Templeton, Stephen H, Gillespie, and Matthew T G, Holden
Subjects: Drug Resistance, Bacterial, Enterococcus faecium, Enterococcus faecalis, Linezolid, Animals, Microbial Sensitivity Tests, Gram-Positive Bacterial Infections, Anti-Bacterial Agents, Multilocus Sequence Typing, Plasmids
Abstract: Transferable linezolid resistance due to
Published: 2022

13. Presence of optrA-mediated linezolid resistance in multiple lineages and plasmids of Enterococcus faecalis revealed by long read sequencing

Author: Martin P. McHugh, Benjamin J. Parcell, Kerry A. Pettigrew, Geoff Toner, Elham Khatamzas, Noha el Sakka, Anne Marie Karcher, Joanna Walker, Robert Weir, Danièle Meunier, Katie L. Hopkins, Neil Woodford, Kate E. Templeton, Stephen H. Gillespie, Matthew T. G. Holden, Erasmus School of Social and Behavioural Sciences, The Wellcome Trust, University of St Andrews. School of Medicine, University of St Andrews. Infection and Global Health Division, University of St Andrews. Sir James Mackenzie Institute for Early Diagnosis, University of St Andrews. Centre for Biophotonics, University of St Andrews. Biomedical Sciences Research Complex, University of St Andrews. Global Health Implementation Group, University of St Andrews. Gillespie Group, and University of St Andrews. St Andrews Bioinformatics Unit
Subjects: MCC, RM, optrA, Linezolid, QR Microbiology, 3rd-DAS, biochemical phenomena, metabolism, and nutrition, Antimicrobial resistance, Microbiology, Plasmid, RM Therapeutics. Pharmacology, QR, Tn6993, Enterococcus faecalis
Abstract: Transferable linezolid resistance due to optrA, poxtA, cfr and cfr-like genes is increasingly detected in enterococci associated with animals and humans globally. We aimed to characterize the genetic environment of optrA in linezolid-resistant Enterococcus faecalis isolates from Scotland. Six linezolid-resistant E. faecalis isolated from urogenital samples were confirmed to carry the optrA gene by PCR. Short read (Illumina) sequencing showed the isolates were genetically distinct (>13900 core SNPs) and belonged to different MLST sequence types. Plasmid contents were examined using hybrid assembly of short and long read (Oxford Nanopore MinION) sequencing technologies. The optrA gene was located on distinct plasmids in each isolate, suggesting that transfer of a single plasmid did not contribute to optrA dissemination in this collection. pTM6294-2, BX5936-1 and pWE0438-1 were similar to optrA-positive plasmids from China and Japan, while the remaining three plasmids had limited similarity to other published examples. We identified the novel Tn6993 transposon in pWE0254-1 carrying linezolid (optrA), macrolide (ermB) and spectinomycin [ANT(9)-Ia] resistance genes. OptrA amino acid sequences differed by 0–20 residues. We report multiple variants of optrA on distinct plasmids in diverse strains of E. faecalis . It is important to identify the selection pressures driving the emergence and maintenance of resistance against linezolid to retain the clinical utility of this antibiotic.
Published: 2022

14. Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study

Author: Harry D Wilson, Elaine O'Toole, Andrew Bassett, Moritz U. G. Kraemer, Beth Blane, Scott Goodwin, Giri Shankar, Joseph Hughes, Lucy R. Frost, Alicia Thornton, Scott Elliott, Tammy V Merrill, Sheila Waugh, Alexander Adams, Peter Muir, Graciela Sluga, Rebecca Williams, Hannah Dent, Christophe Fraser, Shavanthi Rajatileka, John C. Hartley, Luke B Snell, Benjamin J Cogger, Lance Turtle, Alex Makunin, John A. Todd, Victoria Wright, Daniela De Angelis, James McKenna, Dinesh Aggarwal, Jonathan K. Ball, Jillian Durham, Garren Scott, Thushan I de Silva, Veena Raviprakash, Hannah M Pymont, Jason Coombes, Anita Lucaci, Luke R. Green, Leigh M Jackson, Hermione J. Webster, Louis du Plessis, David A. Jackson, Minal Patel, Áine O'Toole, Ravi Gupta, Marc Niebel, Garry Scarlett, Rajiv Shah, Guy Mollett, Kathy Li, Rory Gunson, Matthew Bashton, Carl Jones, Sara Kumziene-Summerhayes, Zoltan Molnar, Siona Silveira, Malte L Pinckert, Catherine Ludden, Angeliki Karamani, Leanne Kane, Brendan A I Payne, Alan McNally, Clare M. McCann, Holli Carden, Mohammad Raza, Alison E. Mather, Kate B. Cook, Amy Gaskin, David J. Williams, Shaun R. Seaman, Christopher I. Jones, Gilberto Betancor, Matthew T. G. Holden, Jennifier Liddle, Meera Unnikrishnan, Angie Green, Ben Taylor, Kelly Bicknell, Alexander J. Trotter, Emma Meader, Leanne M Kermack, Nathaniel Storey, Michelle Cronin, Sally Forrest, Sarah Jeremiah, Asad Zaidi, M Morgan, Alasdair MacLean, Thomas R. Connor, Johnathan M Evans, Rachael Stanley, Ryan P George, Nadine Holmes, Richard H. Myers, Christine Sambles, Bernardo Gutierrez, Jeffrey K. J. Cheng, Tim Wyatt, Natasha Jesudason, Lindsay Coupland, Monika Pusok, Manon Ragonnet-Cronin, Jenifer Mason, Joshua Maksimovic, Russell Hope, Alison Holmes, David Simpson, Radoslaw Poplawski, Amelia Joseph, Erwan Acheson, James Bonfield, Mara K. N. Lawniczak, Sascha Ott, Lesley-Anne Williams, Jessica Lynch, Graham P. Taylor, Anita Kenyon, Elizabeth Wastenge, Megan Mayhew, Adhyana I K Mahanama, Stavroula F Louka, Chloe Bishop, Esther Robinson, Darren Smith, Anne M. Presanis, Matthew Carlile, Thomas D Stanton, Dennis Wang, Katerina Galai, Adam P Westhorpe, Flavia Flaviani, Michelle Wantoch, Max Whiteley, Yann Bourgeois, Matthew Gemmell, Mary Ramsay, A Lloyd, Simon Thelwall, Hannah C. Howson-Wells, Joseph G. Chappell, Steve Paterson, Gary Eltringham, Robert Impey, Siddharth Mookerjee, Steven Platt, Emma Swindells, Laura Letchford, Alex Alderton, Lee Graham, Safiah Afifi, David C. Lee, Cassie Breen, Melisa Louise Fenton, Benita Percival, Adrian W Signell, Tanya Golubchik, Ian B Vipond, Eleri Wilson-Davies, Angie Lackenby, Laura Atkinson, Sarojini Pandey, Nazreen F. Hadjirin, Michael A Chapman, Huw Gulliver, Joana Dias, Grant Hall, Antony D Hale, Hassan Hartman, Alp Aydin, Louise Smith, Ashok Dadrah, Johnny Debebe, Sarah Walsh, Stephanie W. Lo, Andrew Bosworth, Bridget Knight, Hannah E Bridgewater, Nadua Bayzid, Gemma L. Kay, Richard Gregory, Sally Kay, Ellena Brooks, Andre Charlett, Georgina M McManus, Riaz Jannoo, Victoria Blakey, Carol Scott, Rachel Nelson, Liz Ratcliffe, Gerry Tonkin-Hill, Verity Hill, Joanne D. Stockton, Danielle Leek, Steven Leonard, Stephanie Hutchings, Jonathan D. Moore, Kathryn Ann Harris, Sophie Jones, Venkat Sivaprakasam, Amy Plimmer, Tanzina Haque, Katherine L. Bellis, Khalil Abudahab, Dianne Irish-Tavares, Gaia Nebbia, Kathryn A Jackson, Stephen W Attwood, Daniel Mair, Sreenu Vattipally, Susanne Stonehouse, Ian Merrick, Lucille Rainbow, Mathew A. Beale, Angela Helen Beckett, Ember Hilvers, Thomas Helmer, Jenna Nichols, Giselda Bucca, Salman Goudarzi, Christopher Ruis, Surendra Parmar, Angela Cowell, Alberto C Cerda, Divya K. Shah, Judith Heaney, E. Thomson, Kyriaki Nomikou, Nicole Pacchiarini, Katherine L Harper, Fatima Downing, M. Estée Török, Michelle L Michelsen, Aaron R. Jeffries, Jennifer Collins, Christopher Williams, Katie F. Loveson, Steven Rudder, Theocharis Tsoleridis, Robert Davies, David Robertson, Katherine Smollett, Kathryn McCluggage, Liam Crawford, Inigo Martincorena, Charlotte Beaver, Oliver Megram, Karla Spellman, Sam Haldenby, Emma Betteridge, William D. Fuller, Will P. M. Rowe, Cherian Koshy, Tim E. A. Peto, Alison Cox, Natasha Johnson, Tanya Curran, Sharif Shaaban, Tamyo Mbisa, Cordelia Langford, Eric Witele, Andrew J. Page, Christoph Puethe, Nicola Reynolds, Paul W Bird, Louise Aigrain, Ronan Lyons, Amy Trebes, Sally Corden, Steven Rushton, Jack Cd Lee, Jane Greenaway, Hibo Asad, Amanda Bradley, Mohammed O Hassan-Ibrahim, Shane McCarthy, Fei Sang, Matthew Loose, Hannah Jones, Keith D. James, Chloe L Fisher, Chrystala Constantinidou, Alex G. Richter, Jane A. H. Masoli, Michael Gallagher, Vicki M. Fleming, Anna Price, Amy Ash, Michaela John, Alex Zarebski, Fenella D. Halstead, John Danesh, Christine Kitchen, Aminu S Jahun, Mark Whitehead, Julianne R Brown, Catherine Bresner, Marius Cotic, Stefanie V Lensing, Nick Levene, Louissa R Macfarlane-Smith, Wendy Hogsden, Cressida Auckland, Eleanor Drury, Richard Eccles, Jennifer Hart, Seema Nickbakhsh, Alisha Davies, David M. Aanensen, Shirelle Burton-Fanning, Ben Farr, Buddhini Samaraweera, Sarah Wyllie, Hannah Lowe, Richard J. Orton, Martin D. Curran, Carol Churcher, Karen Oliver, Elihu Aranday-Cortes, Wen Yew, Thanh Le-Viet, Matthew Parker, Katherine A Twohig, Shahjahan Miah, Samuel M. Nicholls, G MacIntyre-Cockett, Tranprit Saluja, Charlotte Nelson, Vicki Chalker, Roberto Amato, Ellen Higginson, Timothy M. Freeman, Christopher W Holmes, Yasmin Chaudhry, Elias Allara, Alec Birchley, Iraad Bronner, Emma Moles-Garcia, Angus I. Best, Anna L. Casey, Audrey Farbos, Nicholas W Machin, David W Eyre, Tim Boswell, Charlotte A Williams, Elen De Lacy, Matthew J. Bull, Matilde Mori, Carmen F. Manso, Peijun Zhang, Sahar Eldirdiri, Dimitris Grammatopoulos, Corin Yeats, Claudia Wierzbicki, David G Partridge, Kordo Saeed, Nichola Duckworth, David J. Studholme, Harmeet K Gill, Juan Ledesma, Thomas R. A. Davis, Sushmita Sridhar, Clive Graham, Husam Osman, Julian A. Hiscox, Helen Adams, Christopher Fearn, Fabrícia F. Nascimento, Ulf Schaefer, James W. Harrison, Andrew J. Nelson, Joshua Quick, Mohammad Tauqeer Alam, Liam Prestwood, Nikos Manesis, Julian Tang, Justin O'Grady, Sophia T Girgis, Louise Berry, Gemma Clark, Marina Escalera Zamudio, Karlie Fallon, Tim J Sloan, Joanne Watkins, Clare Pearson, Andrew D Beggs, Rachel Williams, Luke Bedford, Trevor Robinson, Nicholas M Redshaw, Richard Hopes, Mirko Menegazzo, Katherine Twohig, Gabrielle Vernet, Steven Liggett, Mariateresa de Cesare, Derrick W. Crook, Dominic P. Kwiatkowski, Mark Kristiansen, Miren Iturriza-Gomara, Christopher I. Moore, Claire Cormie, Olivia Boyd, Nikki Smith, Noel Craine, Kathleen A. Williamson, John Boyes, Sian Ellard, Cristina V. Ariani, Wendy Chatterton, David Bonsall, Kevin Lewis, David Jorgensen, Ian Harrison, Christopher Jackson, Martin P McHugh, Danni Weldon, Michael A. Quail, Amita Patel, Lily Geidelberg, Myra Hosmillo, Judith Breuer, Cariad Evans, Edward Barton, Trudy Workman, Derek Fairley, Vineet Patel, Daniel Bradshaw, Robin Manley, Scott Aj Thurston, John Sillitoe, Monique Andersson, Sharon J. Peacock, Jamie Lopez-Bernal, Thomas Thompson, Nabil-Fareed Alikhan, Ben Temperton, Paul Baker, Robin J Moll, Laura Gifford, Nicholas J. Loman, Jayna Raghwani, Jacqui Prieto, Andrew Hesketh, Oliver G. Pybus, Adela Alcolea-Medina, David Buck, Gregory R Young, Alistair C. Darby, Sónia Gonçalves, Aileen G. Rowan, Tabitha Mahungu, Nicholas Ellaby, Jon-Paul Keatley, Lily Tong, Robert Beer, Martyn Guest, Lisa J Levett, Ali R Awan, Iliana Georgana, Paul E Brown, Li Xu-McCrae, Stephen P. Kidd, Sara Rey, Shazaad Ahmad, Danielle C. Groves, Tetyana I. Vasylyeva, David F. Bibby, Nathan Moore, Fiona Ashcroft, Igor Starinskij, Hannah Paul, Claire McMurray, Michael Spencer Chapman, Carlos Balcazar, Joanna Warwick-Dugdale, Pinglawathee Madona, Edith Vamos, Lesley Shirley, Kate Templeton, Luke Foulser, Igor Siveroni, Ewan M. Harrison, Sian Morgan, Diana Rajan, S Taylor, Laia Fina, Naomi Park, Sarah J. O'Brien, Alessandro M Carabelli, Angela Marchbank, Sunando Roy, Leonardo de Oliveira Martins, Steve Palmer, Jonathan Hubb, Alexander J Keeley, Francesc Coll, Malorie Perry, Paul J. Parsons, Anthony Underwood, Patawee Asamaphan, William L Hamilton, Tommy Nyberg, Sophie Palmer, Amanda Symmonds, Anoop Chauhan, Robert Johnson, Christopher J. R. Illingworth, James Shepherd, Wendy Smith, Rich Livett, Rachel Blacow, Margaret Hughes, Jeremy Mirza, Joanne Watts, Jonathan D. Edgeworth, Sarah François, Sue Edwards, Adrienn Angyal, Thomas N. Williams, Marta Gallis, Lauren Gilbert, Paul Randell, Kate Johnson, Eileen Gallagher, Nick Cortes, Yusri Taha, Leah Ensell, Emanuela Pelosi, Stefan Rooke, Michelle Lister, Ana da Silva Filipe, Cassandra S Malone, Themoula Charalampous, Benjamin B Lindsey, Natalie Groves, Colin Smith, Ross J Harris, Rebekah E Wilson, Stephen Bonner, Richard Stark, Sharon Campbell, Nicola Sheriff, Helen L Lowe, Rachel Jones, Ben Warne, Rose K Davidson, Declan Bradley, Ian Johnston, Jeffrey C. Barrett, Joshua B Singer, Shirin Aliabadi, Andrew Whitwham, Patrick McClure, Samuel Robson, Sharon Glaysher, Robert J. Munn, Emma L. Wise, Laura Baxter, Kim S Smith, Catherine Moore, Bree Gatica-Wilcox, Alice Broos, Sarah Essex, David Baker, Manjinder Khakh, Dorota Jamrozy, Rachel Tucker, Ian Goodfellow, S.E. Moses, Nicola Cumley, Robin Howe, Meera Chand, James I. Price, Marina Gourtovaia, Debra Padgett, Jaime Tovar-Corona, Stephen L. Michell, Matthew J. Dorman, Lizzie Meadows, David Heyburn, Iona Willingham, Rocio Martinez Nunez, Grace Taylor-Joyce, Claire M Bewshea, Anita Justice, Simon Cottrell, Rebecca C H Brown, Jamie Young, Gavin Dabrera, Matthew Wyles, Stephen Carmichael, Lisa Berry, Frances Bolt, Andrew Rambaut, Samir Dervisevic, Erik M. Volz, Rahul Batra, Caoimhe McKerr, Samantha McGuigan, Katie Jones, Mailis Maes, Rebecca Dewar, Mary Sinnathamby, Joel Southgate, and Lynn Monaghan
Subjects: medicine.medical_specialty, business.industry, Proportional hazards model, Public health, Hazard ratio, Attendance, C500, Vaccination, Infectious Diseases, Relative risk, Internal medicine, Cohort, medicine, business, Cohort study
Abstract: Background: \ud The SARS-CoV-2 delta (B.1.617.2) variant was first detected in England in March, 2021. It has since rapidly become the predominant lineage, owing to high transmissibility. It is suspected that the delta variant is associated with more severe disease than the previously dominant alpha (B.1.1.7) variant. We aimed to characterise the severity of the delta variant compared with the alpha variant by determining the relative risk of hospital attendance outcomes.\ud \ud Methods: \ud This cohort study was done among all patients with COVID-19 in England between March 29 and May 23, 2021, who were identified as being infected with either the alpha or delta SARS-CoV-2 variant through whole-genome sequencing. Individual-level data on these patients were linked to routine health-care datasets on vaccination, emergency care attendance, hospital admission, and mortality (data from Public Health England's Second Generation Surveillance System and COVID-19-associated deaths dataset; the National Immunisation Management System; and NHS Digital Secondary Uses Services and Emergency Care Data Set). The risk for hospital admission and emergency care attendance were compared between patients with sequencing-confirmed delta and alpha variants for the whole cohort and by vaccination status subgroups. Stratified Cox regression was used to adjust for age, sex, ethnicity, deprivation, recent international travel, area of residence, calendar week, and vaccination status.\ud \ud Findings: \ud Individual-level data on 43 338 COVID-19-positive patients (8682 with the delta variant, 34 656 with the alpha variant; median age 31 years [IQR 17–43]) were included in our analysis. 196 (2·3%) patients with the delta variant versus 764 (2·2%) patients with the alpha variant were admitted to hospital within 14 days after the specimen was taken (adjusted hazard ratio [HR] 2·26 [95% CI 1·32–3·89]). 498 (5·7%) patients with the delta variant versus 1448 (4·2%) patients with the alpha variant were admitted to hospital or attended emergency care within 14 days (adjusted HR 1·45 [1·08–1·95]). Most patients were unvaccinated (32 078 [74·0%] across both groups). The HRs for vaccinated patients with the delta variant versus the alpha variant (adjusted HR for hospital admission 1·94 [95% CI 0·47–8·05] and for hospital admission or emergency care attendance 1·58 [0·69–3·61]) were similar to the HRs for unvaccinated patients (2·32 [1·29–4·16] and 1·43 [1·04–1·97]; p=0·82 for both) but the precision for the vaccinated subgroup was low.\ud \ud Interpretation: \ud This large national study found a higher hospital admission or emergency care attendance risk for patients with COVID-19 infected with the delta variant compared with the alpha variant. Results suggest that outbreaks of the delta variant in unvaccinated populations might lead to a greater burden on health-care services than the alpha variant.\ud \ud Funding: \ud Medical Research Council; UK Research and Innovation; Department of Health and Social Care; and National Institute for Health Research.
Published: 2022

15. Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant

Author: Mohammad Raza, Alison E. Mather, Gilberto Betancor, Ian Merrick, Ben Taylor, Mathew A. Beale, Helen Ward, Samir Dervisevic, Michelle Cronin, Aaron R. Jeffries, Louise Smith, Steven Rudder, Mara K. N. Lawniczak, Sascha Ott, Ashok Dadrah, Luke Bedford, Gabrielle Vernet, Erik M. Volz, Rahul Batra, Johnny Debebe, Caoimhe McKerr, Samantha McGuigan, Oliver Megram, Katie Jones, Mailis Maes, Rebecca Dewar, Emma Swindells, Robert E. Johnson, Myra Hosmillo, Wen C Yew, Vineet Patel, Scott Aj Thurston, Matthew Bashton, Luke B Snell, Lynn Monaghan, David Buck, Gregory R Young, Garren Scott, Louis du Plessis, Sara Kumziene-Summerhayes, David M. Aanensen, Carl Jones, Nadine Holmes, Bernardo Gutierrez, Elizabeth Wastenge, Stavroula F Louka, Dennis Wang, Richard I. Gregory, M. Estée Török, Alistair C. Darby, Ulf Schaefer, Marc Niebel, David Robertson, E. Thomson, Carol Churcher, Patrick C McClure, Scott Elliott, Sarah Jeremiah, Katerina Galai, Matthew W. Loose, Megan Mayhew, Adhyana I K Mahanama, Angeliki Karamani, Naomi R Park, David J. Williams, Lance Turtle, Lucy R. Frost, Alicia Thornton, Jennifier Liddle, M Morgan, Tim Wyatt, Paul W Bird, Chloe Bishop, Esther Robinson, Alasdair MacLean, Inigo Martincorena, Bridget A. Knight, Emma Meader, Thomas R. Connor, Hermione J. Webster, Peter Muir, Sarah Walsh, Stephanie W. Lo, Andrew Bosworth, Hannah E Bridgewater, David Simpson, Radoslaw Poplawski, Angus I. Best, David Baker, Laura Letchford, Cassie Breen, Yann Bourgeois, Matthew Gemmell, Nikki Smith, Alison Holmes, Iliana Georgana, Christophe Fraser, Natasha Jesudason, Johnathan M Evans, Rachael Stanley, Lesley-Anne Williams, Jessica Lynch, Hannah Lowe, Eleri Wilson-Davies, Paul A. Baker, Alex Makunin, James Bonfield, Helen Adams, Christopher Fearn, Peter J. Diggle, Harry D Wilson, Carmen F. Manso, Nichola Duckworth, D Haw, Anna L. Casey, Audrey Farbos, Sam Haldenby, Vicki Chalker, Roberto Amato, Elen De Lacy, Ben Farr, Eric Witele, Buddhini Samaraweera, G MacIntyre-Cockett, Husam Osman, Jane Greenaway, Justin O'Grady, Sally Forrest, Andrew Nelson, Monika Pusok, A Lloyd, Edward Barton, James W. Harrison, Sophie Palmer, Amanda Symmonds, James Shepherd, Nazreen F. Hadjirin, Stephen L. Michell, Mohammed O Hassan-Ibrahim, Fiona Ashcroft, Daniel Mair, Richard H. Myers, Dianne Irish-Tavares, Hannah C. Howson-Wells, Jacqui Prieto, Christine Sambles, Andrew Hesketh, Alp Aydin, Sónia Gonçalves, Tabitha Mahungu, Tanzina Haque, Nicholas Ellaby, Karen Oliver, Hannah Paul, Joanne Watts, Claire McMurray, Lisa J Levett, Darren Smith, Simon Cottrell, Joanna Warwick-Dugdale, Pinglawathee Madona, Matthew J. Dorman, Lizzie Meadows, Ali R Awan, Leanne M Kermack, Jennifer Hart, Angie Lackenby, Carol Scott, Michael Spencer Chapman, Lucille Rainbow, Kyriaki Nomikou, Julianne R Brown, Juan Ledesma, Adam P Westhorpe, Giri Shankar, Karlie Fallon, Tim J Sloan, Joanne Watkins, Robert Impey, Sue Edwards, Rebecca C H Brown, Robin J Moll, Karla Spellman, Laura Gifford, Jamie Young, Adrienn Angyal, Graham Phillip Taylor, Robin Manley, Gavin Dabrera, Michelle Wantoch, Rachel Williams, David Heyburn, Mirko Menegazzo, Derrick W. Crook, Gaia Nebbia, Rachel Nelson, Elaine O'Toole, Luke Foulser, Katherine L Harper, Fatima Downing, Hassan Hartman, Nathan Moore, Gemma L. Kay, Matthew Wyles, Thanh Le-Viet, Edith Vamos, John Sillitoe, Lesley Shirley, Nicholas J. Loman, Iona Willingham, Elihu Aranday-Cortes, Ian B Vipond, Jeremy Mirza, Alberto C Cerda, Michelle L Michelsen, Steven Riley, Alison Cox, Igor Siveroni, Nadua Bayzid, Shavanthi Rajatileka, Giselda Bucca, Benjamin J Cogger, Tim Boswell, Matthew J. Bull, Stephen Carmichael, Lisa Berry, Frances Bolt, Kylie E. C. Ainslie, Martyn Guest, Sarojini Pandey, Katherine L. Bellis, Shane A. McCarthy, Christopher Ruis, Fei Sang, David Bonsall, Danni Weldon, Alex Alderton, Lee Graham, Amy Trebes, Sally Corden, Adrian W Signell, Tanya Golubchik, Huw Gulliver, Rocio Martinez Nunez, Dinesh Aggarwal, Tanya Curran, Jonathan K. Ball, Sharif Shaaban, Paul Randell, Jillian Durham, Alec Birchley, Matilde Mori, Joana Dias, Katherine A Twohig, Grant Hall, Antony D Hale, Alan McNally, Jonathan D. Edgeworth, Safiah Afifi, Andrew Rambaut, Katherine Smollett, David N. Lee, Tamyo Mbisa, Shahjahan Miah, Steven Rushton, Grace Taylor-Joyce, Hannah M Pymont, Chloe L Fisher, Cordelia Langford, Alex G. Richter, Jane A. H. Masoli, Michael Gallagher, Vicki M. Fleming, Kathleen A. Williamson, Anna Price, Holli Carden, Khalil Abudahab, Joanne D. Stockton, Meera Unnikrishnan, Jennifer Collins, Emma Moles-Garcia, Michaela John, Christine Kitchen, Tranprit Saluja, Ian Harrison, Lily Tong, Thomas G. Thompson, Thomas Helmer, Amita Patel, Siona Silveira, Deborah Ashby, Claire M Bewshea, Anita Justice, Brendan A I Payne, Alexander J. Trotter, Nikos Manesis, Katie F. Loveson, Cristina V. Ariani, Wendy Chatterton, Robert J. Munn, Julian A. Hiscox, Robert Beer, Judith Breuer, Caroline E. Walters, Liam Crawford, Ara Darzi, Will P. M. Rowe, Cariad Evans, Matthew Parker, Tammy V Merrill, Louise Aigrain, Joshua Quick, Leigh M Jackson, Samuel M. Nicholls, Jonathan W. Moore, John A Hartley, Graham P. Taylor, Cherian Koshy, Shirelle Burton-Fanning, Sheila Waugh, Catherine Moore, Danielle C. Groves, Peijun Zhang, Sahar Eldirdiri, Derek Fairley, Tim E. A. Peto, Jack Cd Lee, Sharon Glaysher, Liam Prestwood, Hannah Dent, Anita Kenyon, Stephen P. Kidd, Nick Levene, Igor Starinskij, Joseph G. Chappell, Steve Paterson, Gary Eltringham, Laia Fina, Angela Marchbank, Daniel Bradshaw, Marina Escalera Zamudio, Scott Goodwin, Andrew D Beggs, Seema Nickbakhsh, Trevor Robinson, Christina Atchison, David K. Jackson, Kathy Li, Rory Gunson, Sunando Roy, Graham S Cooke, Steven Liggett, Yasmin Chaudhry, Anoop Chauhan, Ben Temperton, Mariateresa de Cesare, Paul E Brown, Li Xu-McCrae, Martin P McHugh, Catherine Ludden, Wendy Smith, Danielle Leek, Divya K. Shah, Judith Heaney, Dominic P. Kwiatkowski, Kate M. Johnson, Robin Howe, Malorie Perry, Tetyana I. Vasylyeva, David F. Bibby, Haowei Wang, Steve Palmer, Nicholas W Machin, Charlotte A Williams, Bree Gatica-Wilcox, Angie Green, John A. Todd, Paul Elliott, Noel Craine, Jeffrey K. J. Cheng, Kate Templeton, Jonathan Hubb, Joshua Maksimovic, Christl A. Donnelly, Monique Andersson, Christopher Holmes, Dimitris Grammatopoulos, Christopher B. Williams, David G Partridge, Aminu S Jahun, Alexander Adams, Marius Cotic, Sarah Essex, Christopher J. Moore, Trudy Workman, Nicola Sheriff, Helen L Lowe, Ewan M. Harrison, Dorota Jamrozy, Rachel Jones, Ellen Higginson, Erwan Acheson, Christopher R. Jones, Oliver G. Pybus, Francesc Coll, Sian Morgan, Paul J. Parsons, Patawee Asamaphan, Veena Raviprakash, Andrew R. Bassett, Declan Bradley, Laura Atkinson, Anthony Underwood, Graciela Sluga, Sally Kay, Ellena Brooks, Oliver Eales, Andrew Whitwham, Surendra Parmar, Angela Cowell, Nicole Pacchiarini, Theocharis Tsoleridis, Jason Coombes, Robert Davies, Flavia Flaviani, Benita Percival, Jenna Nichols, Natasha M. Johnson, Salman Goudarzi, Hibo Asad, Amanda Bradley, Hannah Jones, Chrystala Constantinidou, Georgina M McManus, Minal Patel, Steven Leonard, Rebecca Williams Bmbs, Andrew J. Page, Christoph Puethe, Nicola Reynolds, Amy Ash, John Danesh, Corin Yeats, Claudia Wierzbicki, Kordo Saeed, John Boyes, Michael A. Quail, Sharon J. Peacock, Nabil-Fareed Alikhan, Jon-Paul Keatley, Claudio Fronterre, Garry Scarlett, James McKenna, Thushan I de Silva, Malte L Pinckert, Kate B. Cook, Amy Gaskin, Rajiv Shah, Matthew T. G. Holden, Sophie J Prosolek, Nathaniel Storey, Ryan P George, Lindsay Coupland, Jenifer Mason, Matthew Carlile, Thomas D Stanton, Guy Mollett, Siddharth Mookerjee, Mary Ramsay, Steven Platt, Stephen W Attwood, Susanne Stonehouse, Sophie Jones, Venkat Sivaprakasam, Amy Plimmer, Mark Whitehead, Catherine Bresner, Stefanie V Lensing, Louissa R Macfarlane-Smith, Colin P. Smith, Wendy Hogsden, Charlotte Nelson, Ian Johnston, Jeffrey C. Barrett, Joshua B Singer, Samuel Robson, Zoltán Molnár, Emma L. Wise, Sian Ellard, Kim S Smith, Alice Broos, Manjinder Khakh, Kathryn A Jackson, Claire Cormie, Rachel Tucker, Ian Goodfellow, S.E. Moses, Nicola Cumley, Meera Chand, Debra Padgett, Cassandra S Malone, James V. Price, Themoula Charalampous, Ronan A Lyons, Natalie Groves, Stefan Rooke, Rebekah E Wilson, Stephen Bonner, Richard Stark, Sharon Campbell, Michelle Lister, Carlos Balcazar, Ana da Silva Filipe, Ben Warne, Thomas N. Williams, Marta Gallis, Lauren Gilbert, Rose K Davidson, Angela Helen Beckett, Ember Hilvers, Kathryn McCluggage, Eileen Gallagher, Charlotte Beaver, Nick Cortes, Alisha Davies, Yusri Taha, Leah Ensell, Emanuela Pelosi, Elias Allara, Cressida Auckland, Eleanor Drury, Richard Eccles, Adela Alcolea-Medina, William L Hamilton, Rich Livett, Rachel Blacow, Margaret Hughes, Sarah François, Melisa Louise Fenton, Liz Ratcliffe, Verity Hill, Stephanie Hutchings, Kathryn Ann Harris, Emma Betteridge, William D. Fuller, Sophia T Girgis, Louise Berry, Gemma Clark, Nicholas M Redshaw, Richard Hopes, Leonardo de Oliveira Martins, Alexander J Keeley, Beth Blane, Wendy S. Barclay, Victoria Wright, Anita Lucaci, Luke R. Green, Fenella D. Halstead, Sarah Wyllie, Iraad F. Bronner, Áine O'Toole, Ravi Gupta, Leanne Kane, Clare M. McCann, Michael R Chapman, David W Eyre, Kelly Bicknell, Aileen G. Rowan, Sara Rey, Shazaad Ahmad, Diana Rajan, S Taylor, Sarah J. O'Brien, Alessandro M Carabelli, Amelia Joseph, Max Whiteley, Riaz Jannoo, Victoria Blakey, Martin D. Curran, David J. Studholme, Harmeet K Gill, Thomas R. A. Davis, Sushmita Sridhar, Clive Graham, Julian Tang, Clare Pearson, Mark Kristiansen, Miren Iturriza-Gomara, National Institute for Health Research, and UK Research and Innovation
Subjects: Delta, Adult, Male, 2019-20 coronavirus outbreak, COVID-19 Vaccines, Vaccination Coverage, Coronavirus disease 2019 (COVID-19), Adolescent, General Science & Technology, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Vaccine Efficacy, Biology, Young Adult, Exponential growth, Ethnicity, Prevalence, Humans, Child, Aged, Family Characteristics, Multidisciplinary, High prevalence, COVID-19 Genomics UK (COG-UK) Consortium11‡, SARS-CoV-2, Age Factors, COVID-19, Middle Aged, Virology, Hospitalization, England, Socioeconomic Factors, COVID-19 Nucleic Acid Testing, Child, Preschool, Female, Self Report
Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections were rising during early summer 2021 in many countries as a result of the Delta variant. We assessed reverse transcription polymerase chain reaction swab positivity in the Real-time Assessment of Community Transmission–1 (REACT-1) study in England. During June and July 2021, we observed sustained exponential growth with an average doubling time of 25 days, driven by complete replacement of the Alpha variant by Delta and by high prevalence at younger, less-vaccinated ages. Prevalence among unvaccinated people [1.21% (95% credible interval 1.03%, 1.41%)] was three times that among double-vaccinated people [0.40% (95% credible interval 0.34%, 0.48%)]. However, after adjusting for age and other variables, vaccine effectiveness for double-vaccinated people was estimated at between ~50% and ~60% during this period in England. Increased social mixing in the presence of Delta had the potential to generate sustained growth in infections, even at high levels of vaccination.
Published: 2021

16. The impact of viral mutations on recognition by SARS-CoV-2 specific T cells

Author: Thushan I. de Silva, Guihai Liu, Benjamin B. Lindsey, Danning Dong, Shona C. Moore, Nienyun Sharon Hsu, Dhruv Shah, Dannielle Wellington, Alexander J. Mentzer, Adrienn Angyal, Rebecca Brown, Matthew D. Parker, Zixi Ying, Xuan Yao, Lance Turtle, Susanna Dunachie, Mala K. Maini, Graham Ogg, Julian C. Knight, Yanchun Peng, Sarah L. Rowland-Jones, Tao Dong, David M. Aanensen, Khalil Abudahab, Helen Adams, Alexander Adams, Safiah Afifi, Dinesh Aggarwal, Shazaad S.Y. Ahmad, Louise Aigrain, Adela Alcolea-Medina, Nabil-Fareed Alikhan, Elias Allara, Roberto Amato, Tara Annett, Stephen Aplin, Cristina V. Ariani, Hibo Asad, Amy Ash, Paula Ashfield, Fiona Ashford, Laura Atkinson, Stephen W. Attwood, Cressida Auckland, Alp Aydin, David J. Baker, Paul Baker, Carlos E. Balcazar, Jonathan Ball, Jeffrey C. Barrett, Magdalena Barrow, Edward Barton, Matthew Bashton, Andrew R. Bassett, Rahul Batra, Chris Baxter, Nadua Bayzid, Charlotte Beaver, Angela H. Beckett, Shaun M. Beckwith, Luke Bedford, Robert Beer, Andrew Beggs, Katherine L. Bellis, Louise Berry, Beatrice Bertolusso, Angus Best, Emma Betteridge, David Bibby, Kelly Bicknell, Debbie Binns, Alec Birchley, Paul W. Bird, Chloe Bishop, Rachel Blacow, Victoria Blakey, Beth Blane, Frances Bolt, James Bonfield, Stephen Bonner, David Bonsall, Tim Boswell, Andrew Bosworth, Yann Bourgeois, Olivia Boyd, Declan T. Bradley, Cassie Breen, Catherine Bresner, Judith Breuer, Stephen Bridgett, Iraad F. Bronner, Ellena Brooks, Alice Broos, Julianne R. Brown, Giselda Bucca, Sarah L. Buchan, David Buck, Matthew Bull, Phillipa J. Burns, Shirelle Burton-Fanning, Timothy Byaruhanga, Matthew Byott, Sharon Campbell, Alessandro M. Carabelli, James S. Cargill, Matthew Carlile, Silvia F. Carvalho, Anna Casey, Anibolina Castigador, Jana Catalan, Vicki Chalker, Nicola J. Chaloner, Meera Chand, Joseph G. Chappell, Themoula Charalampous, Wendy Chatterton, Yasmin Chaudhry, Carol M. Churcher, Gemma Clark, Phillip Clarke, Benjamin J. Cogger, Kevin Cole, Jennifer Collins, Rachel Colquhoun, Thomas R. Connor, Kate F. Cook, Jason Coombes, Sally Corden, Claire Cormie, Nicholas Cortes, Marius Cotic, Seb Cotton, Simon Cottrell, Lindsay Coupland, MacGregor Cox, Alison Cox, Noel Craine, Liam Crawford, Aidan Cross, Matthew R. Crown, Dorian Crudgington, Nicola Cumley, Tanya Curran, Martin D. Curran, Ana da Silva Filipe, Gavin Dabrera, Alistair C. Darby, Rose K. Davidson, Alisha Davies, Robert M. Davies, Thomas Davis, Daniela de Angelis, Elen De Lacy, Leonardo de Oliveira Martins, Johnny Debebe, Rebecca Denton-Smith, Samir Dervisevic, Rebecca Dewar, Jayasree Dey, Joana Dias, Donald Dobie, Matthew J. Dorman, Fatima Downing, Megan Driscoll, Louis du Plessis, Nichola Duckworth, Jillian Durham, Kirstine Eastick, Lisa J. Easton, Richard Eccles, Jonathan Edgeworth, Sue Edwards, Kate El Bouzidi, Sahar Eldirdiri, Nicholas Ellaby, Scott Elliott, Gary Eltringham, Leah Ensell, Michelle J. Erkiert, Marina Escalera Zamudio, Sarah Essex, Johnathan M. Evans, Cariad Evans, William Everson, Derek J. Fairley, Karlie Fallon, Arezou Fanaie, Ben W. Farr, Christopher Fearn, Theresa Feltwell, Lynne Ferguson, Laia Fina, Flavia Flaviani, Vicki M. Fleming, Sally Forrest, Ebenezer Foster-Nyarko, Benjamin H. Foulkes, Luke Foulser, Mireille Fragakis, Dan Frampton, Sarah Francois, Christophe Fraser, Timothy M. Freeman, Helen Fryer, Marc Fuchs, William Fuller, Kavitha Gajee, Katerina Galai, Abbie Gallagher, Eileen Gallagher, Michael D. Gallagher, Marta Gallis, Amy Gaskin, Bree Gatica-Wilcox, Lily Geidelberg, Matthew Gemmell, Iliana Georgana, Ryan P. George, Laura Gifford, Lauren Gilbert, Sophia T. Girgis, Sharon Glaysher, Emily J. Goldstein, Tanya Golubchik, Andrea N. Gomes, Sónia Gonçalves, Ian G. Goodfellow, Scott Goodwin, Salman Goudarzi, Marina Gourtovaia, Clive Graham, Lee Graham, Paul R. Grant, Luke R. Green, Angie Green, Jane Greenaway, Richard Gregory, Martyn Guest, Rory N. Gunson, Ravi K. Gupta, Bernardo Gutierrez, Sam T. Haldenby, William L. Hamilton, Samantha E. Hansford, Tanzina Haque, Kathryn A. Harris, Ian Harrison, Ewan M. Harrison, Jennifer Hart, John A. Hartley, William T. Harvey, Matthew Harvey, Mohammed O. Hassan-Ibrahim, Judith Heaney, Thomas Helmer, John H. Henderson, Andrew R. Hesketh, Jessica Hey, David Heyburn, Ellen E. Higginson, Verity Hill, Jack D. Hill, Rachel A. Hilson, Ember Hilvers, Matthew T.G. Holden, Amy Hollis, Christopher W. Holmes, Nadine Holmes, Alison H. Holmes, Richard Hopes, Hailey R. Hornsby, Myra Hosmillo, Catherine Houlihan, Hannah C. Howson-Wells, Jonathan Hubb, Hannah Huckson, Warwick Hughes, Joseph Hughes, Margaret Hughes, Stephanie Hutchings, Giles Idle, Chris J. Illingworth, Robert Impey, Dianne Irish-Tavares, Miren Iturriza-Gomara, Rhys Izuagbe, Chris Jackson, Ben Jackson, Leigh M. Jackson, Kathryn A. Jackson, David K. Jackson, Aminu S. Jahun, Victoria James, Keith James, Christopher Jeanes, Aaron R. Jeffries, Sarah Jeremiah, Andrew Jermy, Michaela John, Rob Johnson, Kate Johnson, Ian Johnston, Owen Jones, Sophie Jones, Hannah Jones, Christopher R. Jones, Neil Jones, Amelia Joseph, Sarah Judges, Gemma L. Kay, Sally Kay, Jon-Paul Keatley, Alexander J. Keeley, Anita Kenyon, Leanne M. Kermack, Manjinder Khakh, Stephen P. Kidd, Maimuna Kimuli, Stuart Kirk, Christine Kitchen, Katie Kitchman, Bridget A. Knight, Cherian Koshy, Moritz U.G. Kraemer, Sara Kumziene-Summerhayes, Dominic Kwiatkowski, Angie Lackenby, Kenneth G. Laing, Temi Lampejo, Cordelia F. Langford, Deborah Lavin, Andrew I. Lawton, Jack Lee, David Lee, Stefanie V. Lensing, Steven Leonard, Lisa J. Levett, Thanh Le-Viet, Jonathan Lewis, Kevin Lewis, Jennifier Liddle, Steven Liggett, Patrick J. Lillie, Michelle M. Lister, Rich Livett, Stephanie Lo, Nicholas J. Loman, Matthew W. Loose, Stavroula F. Louka, Katie F. Loveson, Sarah Lowdon, Hannah Lowe, Helen L. Lowe, Anita O. Lucaci, Catherine Ludden, Jessica Lynch, Ronan A. Lyons, Katrina Lythgoe, Nicholas W. Machin, George MacIntyre-Cockett, Andrew Mack, Ben Macklin, Alasdair Maclean, Emily Macnaughton, Pinglawathee Madona, Mailis Maes, Laurentiu Maftei, Adhyana I.K. Mahanama, Tabitha W. Mahungu, Daniel Mair, Joshua Maksimovic, Cassandra S. Malone, Daniel Maloney, Nikos Manesis, Robin Manley, Anna Mantzouratou, Angela Marchbank, Arun Mariappan, Inigo Martincorena, Rocio T. Martinez Nunez, Alison E. Mather, Patrick Maxwell, Megan Mayhew, Tamyo Mbisa, Clare M. McCann, Shane A. McCarthy, Kathryn McCluggage, Patrick C. McClure, J.T. McCrone, Martin P. McHugh, James P. McKenna, Caoimhe McKerr, Georgina M. McManus, Claire L. McMurray, Claire McMurray, Alan McNally, Lizzie Meadows, Nathan Medd, Oliver Megram, Mirko Menegazzo, Ian Merrick, Stephen L. Michell, Michelle L. Michelsen, Mariyam Mirfenderesky, Jeremy Mirza, Julia Miskelly, Emma Moles-Garcia, Robin J. Moll, Zoltan Molnar, Irene M. Monahan, Matteo Mondani, Siddharth Mookerjee, Christopher Moore, Jonathan Moore, Nathan Moore, Catherine Moore, Helen Morcrette, Sian Morgan, Mari Morgan, Matilde Mori, Arthur Morriss, Samuel Moses, Craig Mower, Peter Muir, Afrida Mukaddas, Florence Munemo, Robert Munn, Abigail Murray, Leanne J. Murray, Darren R. Murray, Manasa Mutingwende, Richard Myers, Eleni Nastouli, Gaia Nebbia, Andrew Nelson, Charlotte Nelson, Sam Nicholls, Jenna Nichols, Roberto Nicodemi, Kyriaki Nomikou, Justin O’Grady, Sarah O'Brien, Mina Odedra, Natasha Ohemeng-Kumi, Karen Oliver, Richard J. Orton, Husam Osman, null xeine O'Toole, Nicole Pacchiarini, Debra Padgett, Andrew J. Page, Emily J. Park, Naomi R. Park, Surendra Parmar, David G. Partridge, David Pascall, Amita Patel, Bindi Patel, Steve Paterson, Brendan A.I. Payne, Sharon J. Peacock, Clare Pearson, Emanuela Pelosi, Benita Percival, Jon Perkins, Malorie Perry, Malte L. Pinckert, Steven Platt, Olga Podplomyk, Manoj Pohare, Marcus Pond, Cassie F. Pope, Radoslaw Poplawski, Jessica Powell, Jennifer Poyner, Liam Prestwood, Anna Price, James R. Price, Jacqui A. Prieto, David T. Pritchard, Sophie J. Prosolek, Georgia Pugh, Monika Pusok, Oliver G. Pybus, Hannah M. Pymont, Michael A. Quail, Joshua Quick, Clara Radulescu, Jayna Raghwani, Manon Ragonnet-Cronin, Lucille Rainbow, Diana Rajan, Shavanthi Rajatileka, Newara A. Ramadan, Andrew Rambaut, John Ramble, Paul A. Randell, Paul Randell, Liz Ratcliffe, Veena Raviprakash, Mohammad Raza, Nicholas M. Redshaw, Sara Rey, Nicola Reynolds, Alex Richter, David L. Robertson, Esther Robinson, Samuel C. Robson, Fiona Rogan, Stefan Rooke, Will Rowe, Sunando Roy, Steven Rudder, Chris Ruis, Steven Rushton, Felicity Ryan, Kordo Saeed, Buddhini Samaraweera, Christine M. Sambles, Roy Sanderson, Theo Sanderson, Fei Sang, Thea Sass, Emily Scher, Garren Scott, Carol Scott, Jasveen Sehmi, Sharif Shaaban, Divya Shah, Jessica Shaw, Ekaterina Shelest, James G. Shepherd, Liz A. Sheridan, Nicola Sheriff, Lesley Shirley, John Sillitoe, Siona Silviera, David A. Simpson, Aditi Singh, Dawn Singleton, Timofey Skvortsov, Tim J. Sloan, Graciela Sluga, Ken Smith, Kim S. Smith, Perminder Smith, Darren L. Smith, Louise Smith, Colin P. Smith, Nikki Smith, Katherine L. Smollett, Luke B. Snell, Thomas Somassa, Joel Southgate, Karla Spellman, Michael H. Spencer Chapman, Lewis G. Spurgin, Moira J. Spyer, Rachael Stanley, William Stanley, Thomas D. Stanton, Igor Starinskij, Joanne Stockton, Susanne Stonehouse, Nathaniel Storey, David J. Studholme, Malur Sudhanva, Emma Swindells, Yusri Taha, Ngee Keong Tan, Julian W. Tang, Miao Tang, Ben E.W. Taylor, Joshua F. Taylor, Sarah Taylor, Ben Temperton, Kate E. Templeton, Claire Thomas, Laura Thomson, Emma C. Thomson, Alicia Thornton, Scott A.J. Thurston, John A. Todd, Rachael Tomb, Lily Tong, Gerry Tonkin-Hill, M. Estee Torok, Jaime M. Tovar-Corona, Amy Trebes, Alexander J. Trotter, Ioulia Tsatsani, Robyn Turnbull, Katherine A. Twohig, Helen Umpleby, Anthony P. Underwood, Edith E. Vamos, Tetyana I. Vasylyeva, Sreenu Vattipally, Gabrielle Vernet, Barry B. Vipond, Erik M. Volz, Sarah Walsh, Dennis Wang, Ben Warne, Joanna Warwick-Dugdale, Elizabeth Wastnedge, Joanne Watkins, Louisa K. Watson, Sheila Waugh, Hermione J. Webster, Danni Weldon, Elaine Westwick, Thomas Whalley, Helen Wheeler, Mark Whitehead, Max Whiteley, Andrew Whitwham, Claudia Wierzbicki, Nicholas J. Willford, Lesley-Anne Williams, Rebecca Williams, Cheryl Williams, Chris Williams, Charlotte A. Williams, Rachel J. Williams, Thomas Williams, Catryn Williams, Kathleen A. Williamson, Eleri Wilson-Davies, Eric Witele, Karen T. Withell, Adam A. Witney, Paige Wolverson, Nick Wong, Trudy Workman, Victoria Wright, Derek W. Wright, Tim Wyatt, Sarah Wyllie, Li Xu-McCrae, Mehmet Yavus, Geraldine Yaze, Corin A. Yeats, Gonzalo Yebra, Wen C. Yew, Gregory R. Young, Jamie Young, Alex E. Zarebski, Peijun Zhang, J. Kenneth Baillie, Malcolm G. Semple, Peter J.M. Openshaw, Gail Carson, Beatrice Alex, Petros Andrikopoulos, Benjamin Bach, Wendy S. Barclay, Debby Bogaert, Kanta Chechi, Graham S. Cooke, Annemarie B. Docherty, Gonçalo dos Santos Correia, Marc-Emmanuel Dumas, Jake Dunning, Tom Fletcher, Christopher A. Green, William Greenhalf, Julian L. Griffin, Rishi K. Gupta, Ewen M. Harrison, Julian A. Hiscox, Antonia Ying Wai Ho, Peter W. Horby, Samreen Ijaz, Saye Khoo, Paul Klenerman, Andrew Law, Matthew R. Lewis, Sonia Liggi, Wei Shen Lim, Lynn Maslen, Laura Merson, Alison M. Meynert, Mahdad Noursadeghi, Michael Olanipekun, Anthonia Osagie, Massimo Palmarini, Carlo Palmieri, William A. Paxton, Georgios Pollakis, Nicholas Price, Clark D. Russell, Vanessa Sancho-Shimizu, Caroline J. Sands, Janet T. Scott, Louise Sigfrid, Tom Solomon, Shiranee Sriskandan, David Stuart, Charlotte Summers, Olivia V. Swann, Zoltan Takats, Panteleimon Takis, Richard S. Tedder, A.A. Roger Thompson, Ryan S. Thwaites, Maria Zambon, Hayley Hardwick, Chloe Donohue, Fiona Griffiths, Wilna Oosthuyzen, Cara Donegan, Rebecca G. Spencer, Jo Dalton, Michelle Girvan, Egle Saviciute, Stephanie Roberts, Janet Harrison, Laura Marsh, Marie Connor, Sophie Halpin, Clare Jackson, Carrol Gamble, Daniel Plotkin, James Lee, Gary Leeming, Murray Wham, Sara Clohisey, Ross Hendry, James Scott-Brown, Victoria Shaw, Sarah E. McDonald, Seán Keating, Katie A. Ahmed, Jane A. Armstrong, Milton Ashworth, Innocent G. Asiimwe, Siddharth Bakshi, Samantha L. Barlow, Laura Booth, Benjamin Brennan, Katie Bullock, Benjamin W.A. Catterall, Jordan J. Clark, Emily A. Clarke, Sarah Cole, Louise Cooper, Helen Cox, Christopher Davis, Oslem Dincarslan, Chris Dunn, Philip Dyer, Angela Elliott, Anthony Evans, Lorna Finch, Lewis W.S. Fisher, Terry Foster, Isabel Garcia-Dorival, Philip Gunning, Catherine Hartley, Rebecca L. Jensen, Christopher B. Jones, Trevor R. Jones, Shadia Khandaker, Katharine King, Robyn T. Kiy, Chrysa Koukorava, Annette Lake, Suzannah Lant, Diane Latawiec, Lara Lavelle-Langham, Daniella Lefteri, Lauren Lett, Lucia A. Livoti, Maria Mancini, Sarah McDonald, Laurence McEvoy, John McLauchlan, Soeren Metelmann, Nahida S. Miah, Joanna Middleton, Joyce Mitchell, Ellen G. Murphy, Rebekah Penrice-Randal, Jack Pilgrim, Tessa Prince, Will Reynolds, P. Matthew Ridley, Debby Sales, Victoria E. Shaw, Rebecca K. Shears, Benjamin Small, Krishanthi S. Subramaniam, Agnieska Szemiel, Aislynn Taggart, Jolanta Tanianis-Hughes, Jordan Thomas, Erwan Trochu, Libby van Tonder, Eve Wilcock, J. Eunice Zhang, Lisa Flaherty, Nicole Maziere, Emily Cass, Alejandra Doce Carracedo, Nicola Carlucci, Anthony Holmes, Hannah Massey, Lee Murphy, Nicola Wrobel, Sarah McCafferty, Kirstie Morrice, Alan MacLean, Kayode Adeniji, Daniel Agranoff, Ken Agwuh, Dhiraj Ail, Erin L. Aldera, Ana Alegria, Sam Allen, Brian Angus, Abdul Ashish, Dougal Atkinson, Shahedal Bari, Gavin Barlow, Stella Barnass, Nicholas Barrett, Christopher Bassford, Sneha Basude, David Baxter, Michael Beadsworth, Jolanta Bernatoniene, John Berridge, Colin Berry, Nicola Best, Pieter Bothma, David Chadwick, Robin Brittain-Long, Naomi Bulteel, Tom Burden, Andrew Burtenshaw, Vikki Caruth, Duncan Chambler, Nigel Chee, Jenny Child, Srikanth Chukkambotla, Tom Clark, Paul Collini, Catherine Cosgrove, Jason Cupitt, Maria-Teresa Cutino-Moguel, Paul Dark, Chris Dawson, Phil Donnison, Sam Douthwaite, Andrew Drummond, Ingrid DuRand, Ahilanadan Dushianthan, Tristan Dyer, Chi Eziefula, Chrisopher Fegan, Adam Finn, Duncan Fullerton, Sanjeev Garg, Atul Garg, Effrossyni Gkrania-Klotsas, Jo Godden, Arthur Goldsmith, Elaine Hardy, Stuart Hartshorn, Daniel Harvey, Peter Havalda, Daniel B. Hawcutt, Maria Hobrok, Luke Hodgson, Anil Hormis, Michael Jacobs, Susan Jain, Paul Jennings, Agilan Kaliappan, Vidya Kasipandian, Stephen Kegg, Michael Kelsey, Jason Kendall, Caroline Kerrison, Ian Kerslake, Oliver Koch, Gouri Koduri, George Koshy, Shondipon Laha, Steven Laird, Susan Larkin, Tamas Leiner, Patrick Lillie, James Limb, Vanessa Linnett, Jeff Little, Mark Lyttle, Michael MacMahon, Emily MacNaughton, Ravish Mankregod, Huw Masson, Elijah Matovu, Katherine McCullough, Ruth McEwen, Manjula Meda, Gary Mills, Jane Minton, Kavya Mohandas, Quen Mok, James Moon, Elinoor Moore, Patrick Morgan, Craig Morris, Katherine Mortimore, Mbiye Mpenge, Rohinton Mulla, Michael Murphy, Megan Nagel, Thapas Nagarajan, Mark Nelson, Lillian Norris, Matthew K. O'Shea, Igor Otahal, Marlies Ostermann, Mark Pais, Selva Panchatsharam, Danai Papakonstantinou, Hassan Paraiso, Brij Patel, Natalie Pattison, Justin Pepperell, Mark Peters, Mandeep Phull, Stefania Pintus, Jagtur Singh Pooni, Tim Planche, Frank Post, David Price, Rachel Prout, Nikolas Rae, Henrik Reschreiter, Tim Reynolds, Neil Richardson, Mark Roberts, Devender Roberts, Alistair Rose, Guy Rousseau, Bobby Ruge, Brendan Ryan, Taranprit Saluja, Matthias L. Schmid, Aarti Shah, Prad Shanmuga, Anil Sharma, Anna Shawcross, Jeremy Sizer, Manu Shankar-Hari, Richard Smith, Catherine Snelson, Nick Spittle, Nikki Staines, Tom Stambach, Richard Stewart, Pradeep Subudhi, Tamas Szakmany, Kate Tatham, Jo Thomas, Chris Thompson, Robert Thompson, Ascanio Tridente, Darell Tupper-Carey, Mary Twagira, Nick Vallotton, Rama Vancheeswaran, Lisa Vincent-Smith, Shico Visuvanathan, Alan Vuylsteke, Sam Waddy, Rachel Wake, Andrew Walden, Ingeborg Welters, Tony Whitehouse, Paul Whittaker, Ashley Whittington, Padmasayee Papineni, Meme Wijesinghe, Martin Williams, Lawrence Wilson, Stephen Winchester, Martin Wiselka, Adam Wolverson, Daniel G. Wootton, Andrew Workman, Bryan Yates, Peter Young, UK Research and Innovation, Division of Computational and Systems Medicine, Imperial College London, London, SW7 2AZ, UK, Imperial College London - National Heart and Lung Institute, Centre National de la Recherche Scientifique (CNRS), and Apollo - University of Cambridge Repository
Subjects: Molecular biology, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Science, Immunology, Biology, Epitope, Article, A900, 03 medical and health sciences, 0302 clinical medicine, Data sequences, Immune system, COVID-19 Genomics UK (COG-UK) Consortium, Virology, Cytotoxic T cell, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Immune response, Receptor, ISARIC4C Investigators, 030304 developmental biology, 0303 health sciences, Multidisciplinary, C100, A300, C900, 3. Good health, Phylogenetics, 030220 oncology & carcinogenesis, Humoral immunity, [SDV.IMM]Life Sciences [q-bio]/Immunology, CD8
Abstract: We identify amino acid variants within dominant SARS-CoV-2 T-cell epitopes by interrogating global sequence data. Several variants within nucleocapsid and ORF3a epitopes have arisen independently in multiple lineages and result in loss of recognition by epitope-specific T-cells assessed by IFN-γ and cytotoxic killing assays. Complete loss of T-cell responsiveness was seen due to Q213K in the A*01:01-restricted CD8+ ORF3a epitope FTSDYYQLY207-215, due to P13L, P13S and P13T in the B*27:05-restricted CD8+ nucleocapsid epitope QRNAPRITF9-17, and due to T362I and P365S in the A*03:01/A*11:01-restricted CD8+ nucleocapsid epitope KTFPPTEPK361-369. CD8+ T-cell lines unable to recognise variant epitopes have diverse T-cell receptor repertoires. These data demonstrate the potential for T-cell evasion and highlight the need for ongoing surveillance for variants capable of escaping T-cell as well as humoral immunity., Graphical Abstract
Published: 2021
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17. Defining the analytical and clinical sensitivity of the ARTIC method for the detection of SARS-CoV-2

Author: Nabil-Fareed Alikhan, Alistair C. Darby, Samuel M. Nicholls, Nicholas J. Loman, Samir Dervisevic, Andrew J. Page, Matthew Bashton, Martin P McHugh, Stefan Rooke, Gemma L. Kay, Alexander J. Trotter, Matthew Loose, Joshua Quick, Justin O'Grady, and Samuel Robson
Subjects: Protocol (science), Computer science, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Diagnostic test, Computational biology, Sensitivity (control systems), Amplicon, Genome, DNA sequencing, Virus detection
Abstract: The SARS-CoV-2 ARTIC amplicon protocol is the most widely used genome sequencing method for SARS-CoV-2, accounting for over 43% of publicly-available genome sequences. The protocol utilises 98 primers to amplify ∼400bp fragments of the SARS-CoV-2 genome covering all 30,000 bases. Understanding the analytical performance metrics of this protocol will improve how the data is used and interpreted. Different concentrations of SARS-CoV-2 control material were used to establish the limit of detection (LoD) of the ARTIC protocol. Results demonstrated the LoD was a minimum of 25-50 virus particles per mL. The sensitivity of ARTIC was comparable to the published sensitivities of commercial diagnostics assays and could therefore be used to confirm diagnostic testing results. A set of over 3,600 clinical samples from three UK regions were then evaluated to compare the protocols performance to clinical diagnostic assays (Roche Lightcycler 480 II, AusDiagnostics, Roche Cobas, Hologic Panther, Corman RdRp, Roche Flow, ABI QuantStudio 5, Seegene Nimbus, Qiagen Rotorgene, Abbott M2000, Thermo TaqPath, Xpert). We developed a Python tool, RonaLDO, to perform this validation (available under the GNU GPL3 open-source licence fromhttps://github.com/quadram-institute-bioscience/ronaldo). Positives detected by diagnostic platforms were generally supported by sequencing data; platforms that used RT-qPCR were the best predictors of whether the sample would subsequently sequence successfully. To maximise success of sample sequencing for phylogenetic analysis, samples with Ct
Published: 2021
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18. The SARS-CoV-2 Alpha variant is associated with increased clinical severity of COVID-19 in Scotland: a genomics-based retrospective cohort analysis

Author: Alasdair Campbell, David Robertson, Samantha Lycett, John Haughney, Ruth Forrester, James Shepherd, Martin P McHugh, David J Pascall, Sharif Shabaan, Ben Parcell, Katherine Smollett, Rachel M Blacow, Rory Gunson, Guy Mollett, Ludmila Fjodorova, Emily Goldstein, Ana Da Silva Filipe, Noha El Sakka, Naomi Bulteel, Matthew T. G. Holden, Eddie A. James, Chris Davis, Patrick Honour, Joseph Hughes, Sarah Clifford, Tim Lewis, Yusuke Onishi, and Robyn Campbell
Subjects: medicine.medical_specialty, Lineage (genetic), business.industry, Transmission (medicine), Internal medicine, Severity of illness, Medicine, Alpha (ethology), Clinical severity, Odds ratio, Disease, business, Viral load
Abstract: Background The B.1.1.7 (Alpha) SARS-CoV-2 variant of concern was associated with increased transmission relative to other variants present at the time of its emergence and several studies have shown an association between the B.1.1.7 lineage infection and increased 28-day mortality. However, to date none have addressed the impact of infection on severity of illness or the need for oxygen or ventilation. Methods In this prospective clinical cohort sub-study of the COG-UK consortium, 1475 samples from hospitalised and community cases collected between the 1st November 2020 and 30th January 2021 were collected. These samples were sequenced in local laboratories and analysed for the presence of B.1.1.7-defining mutations. We prospectively matched sequence data to clinical outcomes as the lineage became dominant in Scotland and modelled the association between B.1.1.7 infection and severe disease using a 4-point scale of maximum severity by 28 days: 1. no support, 2. oxygen, 3. ventilation and 4. death. Additionally, we calculated an estimate of the growth rate of B.1.1.7-associated infections following introduction into Scotland using phylogenetic data. Results B.1.1.7 was responsible for a third wave of SARS-CoV-2 in Scotland, and rapidly replaced the previously dominant second wave lineage B.1.177) due to a significantly higher transmission rate (∼5 fold). Of 1475 patients, 364 were infected with B.1.1.7, 1030 with B.1.177 and 81 with other lineages. Our cumulative generalised linear mixed model analyses found evidence (cumulative odds ratio: 1.40, 95% CI: 1.02, 1.93) of a positive association between increased clinical severity and lineage (B.1.1.7 versus non-B.1.1.7). Viral load was higher in B.1.1.7 samples than in non-B.1.1.7 samples as measured by cycle threshold (Ct) value (mean Ct change: -2.46, 95% CI: -4.22, -0.70). Conclusions The B.1.1.7 lineage was associated with more severe clinical disease in Scottish patients than co-circulating lineages. Funding COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) and Genome Research Limited, operating as the Wellcome Sanger Institute. Funding was also provided by UKRI through the JUNIPER consortium (grant number MR/V038613/1). Sequencing and bioinformatics support was funded by the Medical Research Council (MRC) core award (MC UU 1201412).
Published: 2021
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19. Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7

Author: Bo Meng, Steven A. Kemp, Guido Papa, Rawlings Datir, Isabella A.T.M. Ferreira, Sara Marelli, William T. Harvey, Spyros Lytras, Ahmed Mohamed, Giulia Gallo, Nazia Thakur, Dami A. Collier, Petra Mlcochova, Lidia M. Duncan, Alessandro M. Carabelli, Julia C. Kenyon, Andrew M. Lever, Anna De Marco, Christian Saliba, Katja Culap, Elisabetta Cameroni, Nicholas J. Matheson, Luca Piccoli, Davide Corti, Leo C. James, David L. Robertson, Dalan Bailey, Ravindra K. Gupta, Samuel C. Robson, Nicholas J. Loman, Thomas R. Connor, Tanya Golubchik, Rocio T. Martinez Nunez, Catherine Ludden, Sally Corden, Ian Johnston, David Bonsall, Colin P. Smith, Ali R. Awan, Giselda Bucca, M. Estee Torok, Kordo Saeed, Jacqui A. Prieto, David K. Jackson, William L. Hamilton, Luke B. Snell, Catherine Moore, Ewan M. Harrison, Sonia Goncalves, Derek J. Fairley, Matthew W. Loose, Joanne Watkins, Rich Livett, Samuel Moses, Roberto Amato, Sam Nicholls, Matthew Bull, Darren L. Smith, Jeff Barrett, David M. Aanensen, Martin D. Curran, Surendra Parmar, Dinesh Aggarwal, James G. Shepherd, Matthew D. Parker, Sharon Glaysher, Matthew Bashton, Anthony P. Underwood, Nicole Pacchiarini, Katie F. Loveson, Kate E. Templeton, Cordelia F. Langford, John Sillitoe, Thushan I. de Silva, Dennis Wang, Dominic Kwiatkowski, Andrew Rambaut, Justin O’Grady, Simon Cottrell, Matthew T.G. Holden, Emma C. Thomson, Husam Osman, Monique Andersson, Anoop J. Chauhan, Mohammed O. Hassan-Ibrahim, Mara Lawniczak, Alex Alderton, Meera Chand, Chrystala Constantinidou, Meera Unnikrishnan, Alistair C. Darby, Julian A. Hiscox, Steve Paterson, Inigo Martincorena, Erik M. Volz, Andrew J. Page, Oliver G. Pybus, Andrew R. Bassett, Cristina V. Ariani, Michael H. Spencer Chapman, Kathy K. Li, Rajiv N. Shah, Natasha G. Jesudason, Yusri Taha, Martin P. McHugh, Rebecca Dewar, Aminu S. Jahun, Claire McMurray, Sarojini Pandey, James P. McKenna, Andrew Nelson, Gregory R. Young, Clare M. McCann, Scott Elliott, Hannah Lowe, Ben Temperton, Sunando Roy, Anna Price, Sara Rey, Matthew Wyles, Stefan Rooke, Sharif Shaaban, Mariateresa de Cesare, Laura Letchford, Siona Silveira, Emanuela Pelosi, Eleri Wilson-Davies, Myra Hosmillo, Áine O’Toole, Andrew R. Hesketh, Richard Stark, Louis du Plessis, Chris Ruis, Helen Adams, Yann Bourgeois, Stephen L. Michell, Dimitris Grammatopoulos, Jonathan Edgeworth, Judith Breuer, John A. Todd, Christophe Fraser, David Buck, Michaela John, Gemma L. Kay, Steve Palmer, Sharon J. Peacock, David Heyburn, Danni Weldon, Esther Robinson, Alan McNally, Peter Muir, Ian B. Vipond, John Boyes, Venkat Sivaprakasam, Tranprit Salluja, Samir Dervisevic, Emma J. Meader, Naomi R. Park, Karen Oliver, Aaron R. Jeffries, Sascha Ott, Ana da Silva Filipe, David A. Simpson, Chris Williams, Jane A.H. Masoli, Bridget A. Knight, Christopher R. Jones, Cherian Koshy, Amy Ash, Anna Casey, Andrew Bosworth, Liz Ratcliffe, Li Xu-McCrae, Hannah M. Pymont, Stephanie Hutchings, Lisa Berry, Katie Jones, Fenella Halstead, Thomas Davis, Christopher Holmes, Miren Iturriza-Gomara, Anita O. Lucaci, Paul Anthony Randell, Alison Cox, Pinglawathee Madona, Kathryn Ann Harris, Julianne Rose Brown, Tabitha W. Mahungu, Dianne Irish-Tavares, Tanzina Haque, Jennifer Hart, Eric Witele, Melisa Louise Fenton, Steven Liggett, Clive Graham, Emma Swindells, Jennifer Collins, Gary Eltringham, Sharon Campbell, Patrick C. McClure, Gemma Clark, Tim J. Sloan, Carl Jones, Jessica Lynch, Ben Warne, Steven Leonard, Jillian Durham, Thomas Williams, Sam T. Haldenby, Nathaniel Storey, Nabil-Fareed Alikhan, Nadine Holmes, Christopher Moore, Matthew Carlile, Malorie Perry, Noel Craine, Ronan A. Lyons, Angela H. Beckett, Salman Goudarzi, Christopher Fearn, Kate Cook, Hannah Dent, Hannah Paul, Robert Davies, Beth Blane, Sophia T. Girgis, Mathew A. Beale, Katherine L. Bellis, Matthew J. Dorman, Eleanor Drury, Leanne Kane, Sally Kay, Samantha McGuigan, Rachel Nelson, Liam Prestwood, Shavanthi Rajatileka, Rahul Batra, Rachel J. Williams, Mark Kristiansen, Angie Green, Anita Justice, Adhyana I.K. Mahanama, Buddhini Samaraweera, Nazreen F. Hadjirin, Joshua Quick, Radoslaw Poplawski, Leanne M. Kermack, Nicola Reynolds, Grant Hall, Yasmin Chaudhry, Malte L. Pinckert, Iliana Georgana, Robin J. Moll, Alicia Thornton, Richard Myers, Joanne Stockton, Charlotte A. Williams, Wen C. Yew, Alexander J. Trotter, Amy Trebes, George MacIntyre-Cockett, Alec Birchley, Alexander Adams, Amy Plimmer, Bree Gatica-Wilcox, Caoimhe McKerr, Ember Hilvers, Hannah Jones, Hibo Asad, Jason Coombes, Johnathan M. Evans, Laia Fina, Lauren Gilbert, Lee Graham, Michelle Cronin, Sara Kumziene-Summerhayes, Sarah Taylor, Sophie Jones, Danielle C. Groves, Peijun Zhang, Marta Gallis, Stavroula F. Louka, Igor Starinskij, Chris Jackson, Marina Gourtovaia, Gerry Tonkin-Hill, Kevin Lewis, Jaime M. Tovar-Corona, Keith James, Laura Baxter, Mohammad T. Alam, Richard J. Orton, Joseph Hughes, Sreenu Vattipally, Manon Ragonnet-Cronin, Fabricia F. Nascimento, David Jorgensen, Olivia Boyd, Lily Geidelberg, Alex E. Zarebski, Jayna Raghwani, Moritz U.G. Kraemer, Joel Southgate, Benjamin B. Lindsey, Timothy M. Freeman, Jon-Paul Keatley, Joshua B. Singer, Leonardo de Oliveira Martins, Corin A. Yeats, Khalil Abudahab, Ben E.W. Taylor, Mirko Menegazzo, John Danesh, Wendy Hogsden, Sahar Eldirdiri, Anita Kenyon, Jenifer Mason, Trevor I. Robinson, Alison Holmes, James Price, John A. Hartley, Tanya Curran, Alison E. Mather, Giri Shankar, Rachel Jones, Robin Howe, Sian Morgan, Elizabeth Wastenge, Michael R. Chapman, Siddharth Mookerjee, Rachael Stanley, Wendy Smith, Timothy Peto, David Eyre, Derrick Crook, Gabrielle Vernet, Christine Kitchen, Huw Gulliver, Ian Merrick, Martyn Guest, Robert Munn, Declan T. Bradley, Tim Wyatt, Charlotte Beaver, Luke Foulser, Sophie Palmer, Carol M. Churcher, Ellena Brooks, Kim S. Smith, Katerina Galai, Georgina M. McManus, Frances Bolt, Francesc Coll, Lizzie Meadows, Stephen W. Attwood, Alisha Davies, Elen De Lacy, Fatima Downing, Sue Edwards, Garry P. Scarlett, Sarah Jeremiah, Nikki Smith, Danielle Leek, Sushmita Sridhar, Sally Forrest, Claire Cormie, Harmeet K. Gill, Joana Dias, Ellen E. Higginson, Mailis Maes, Jamie Young, Michelle Wantoch, Dorota Jamrozy, Stephanie Lo, Minal Patel, Verity Hill, Claire M. Bewshea, Sian Ellard, Cressida Auckland, Ian Harrison, Chloe Bishop, Vicki Chalker, Alex Richter, Andrew Beggs, Angus Best, Benita Percival, Jeremy Mirza, Oliver Megram, Megan Mayhew, Liam Crawford, Fiona Ashcroft, Emma Moles-Garcia, Nicola Cumley, Richard Hopes, Patawee Asamaphan, Marc O. Niebel, Rory N. Gunson, Amanda Bradley, Alasdair Maclean, Guy Mollett, Rachel Blacow, Paul Bird, Thomas Helmer, Karlie Fallon, Julian Tang, Antony D. Hale, Louissa R. Macfarlane-Smith, Katherine L. Harper, Holli Carden, Nicholas W. Machin, Kathryn A. Jackson, Shazaad S.Y. Ahmad, Ryan P. George, Lance Turtle, Elaine O’Toole, Joanne Watts, Cassie Breen, Angela Cowell, Adela Alcolea-Medina, Themoula Charalampous, Amita Patel, Lisa J. Levett, Judith Heaney, Aileen Rowan, Graham P. Taylor, Divya Shah, Laura Atkinson, Jack C.D. Lee, Adam P. Westhorpe, Riaz Jannoo, Helen L. Lowe, Angeliki Karamani, Leah Ensell, Wendy Chatterton, Monika Pusok, Ashok Dadrah, Amanda Symmonds, Graciela Sluga, Zoltan Molnar, Paul Baker, Stephen Bonner, Sarah Essex, Edward Barton, Debra Padgett, Garren Scott, Jane Greenaway, Brendan A.I. Payne, Shirelle Burton-Fanning, Sheila Waugh, Veena Raviprakash, Nicola Sheriff, Victoria Blakey, Lesley-Anne Williams, Jonathan Moore, Susanne Stonehouse, Louise Smith, Rose K. Davidson, Luke Bedford, Lindsay Coupland, Victoria Wright, Joseph G. Chappell, Theocharis Tsoleridis, Jonathan Ball, Manjinder Khakh, Vicki M. Fleming, Michelle M. Lister, Hannah C. Howson-Wells, Louise Berry, Tim Boswell, Amelia Joseph, Iona Willingham, Nichola Duckworth, Sarah Walsh, Emma Wise, Nathan Moore, Matilde Mori, Nick Cortes, Stephen Kidd, Rebecca Williams, Laura Gifford, Kelly Bicknell, Sarah Wyllie, Allyson Lloyd, Robert Impey, Cassandra S. Malone, Benjamin J. Cogger, Nick Levene, Lynn Monaghan, Alexander J. Keeley, David G. Partridge, Mohammad Raza, Cariad Evans, Kate Johnson, Emma Betteridge, Ben W. Farr, Scott Goodwin, Michael A. Quail, Carol Scott, Lesley Shirley, Scott A.J. Thurston, Diana Rajan, Iraad F. Bronner, Louise Aigrain, Nicholas M. Redshaw, Stefanie V. Lensing, Shane McCarthy, Alex Makunin, Carlos E. Balcazar, Michael D. Gallagher, Kathleen A. Williamson, Thomas D. Stanton, Michelle L. Michelsen, Joanna Warwick-Dugdale, Robin Manley, Audrey Farbos, James W. Harrison, Christine M. Sambles, David J. Studholme, Angie Lackenby, Tamyo Mbisa, Steven Platt, Shahjahan Miah, David Bibby, Carmen Manso, Jonathan Hubb, Gavin Dabrera, Mary Ramsay, Daniel Bradshaw, Ulf Schaefer, Natalie Groves, Eileen Gallagher, David Lee, David Williams, Nicholas Ellaby, Hassan Hartman, Nikos Manesis, Vineet Patel, Juan Ledesma, Katherine A. Twohig, Elias Allara, Clare Pearson, Jeffrey K.J. Cheng, Hannah E. Bridgewater, Lucy R. Frost, Grace Taylor-Joyce, Paul E. Brown, Lily Tong, Alice Broos, Daniel Mair, Jenna Nichols, Stephen N. Carmichael, Katherine L. Smollett, Kyriaki Nomikou, Elihu Aranday-Cortes, Natasha Johnson, Seema Nickbakhsh, Edith E. Vamos, Margaret Hughes, Lucille Rainbow, Richard Eccles, Charlotte Nelson, Mark Whitehead, Richard Gregory, Matthew Gemmell, Claudia Wierzbicki, Hermione J. Webster, Chloe L. Fisher, Adrian W. Signell, Gilberto Betancor, Harry D. Wilson, Gaia Nebbia, Flavia Flaviani, Alberto C. Cerda, Tammy V. Merrill, Rebekah E. Wilson, Marius Cotic, Nadua Bayzid, Thomas Thompson, Erwan Acheson, Steven Rushton, Sarah O’Brien, David J. Baker, Steven Rudder, Alp Aydin, Fei Sang, Johnny Debebe, Sarah Francois, Tetyana I. Vasylyeva, Marina Escalera Zamudio, Bernardo Gutierrez, Angela Marchbank, Joshua Maksimovic, Karla Spellman, Kathryn McCluggage, Mari Morgan, Robert Beer, Safiah Afifi, Trudy Workman, William Fuller, Catherine Bresner, Adrienn Angyal, Luke R. Green, Paul J. Parsons, Rachel M. Tucker, Rebecca Brown, Max Whiteley, James Bonfield, Christoph Puethe, Andrew Whitwham, Jennifier Liddle, Will Rowe, Igor Siveroni, Thanh Le-Viet, Amy Gaskin, Rob Johnson, Irina Abnizova, Mozam Ali, Laura Allen, Ralph Anderson, Cristina Ariani, Siobhan Austin-Guest, Sendu Bala, Jeffrey Barrett, Andrew Bassett, Kristina Battleday, James Beal, Mathew Beale, Sam Bellany, Tristram Bellerby, Katie Bellis, Duncan Berger, Matt Berriman, Paul Bevan, Simon Binley, Jason Bishop, Kirsty Blackburn, Nick Boughton, Sam Bowker, Timothy Brendler-Spaeth, Iraad Bronner, Tanya Brooklyn, Sarah Kay Buddenborg, Robert Bush, Catarina Caetano, Alex Cagan, Nicola Carter, Joanna Cartwright, Tiago Carvalho Monteiro, Liz Chapman, Tracey-Jane Chillingworth, Peter Clapham, Richard Clark, Adrian Clarke, Catriona Clarke, Daryl Cole, Elizabeth Cook, Maria Coppola, Linda Cornell, Clare Cornwell, Craig Corton, Abby Crackett, Alison Cranage, Harriet Craven, Sarah Craw, Mark Crawford, Tim Cutts, Monika Dabrowska, Matt Davies, Joseph Dawson, Callum Day, Aiden Densem, Thomas Dibling, Cat Dockree, David Dodd, Sunil Dogga, Matthew Dorman, Gordon Dougan, Martin Dougherty, Alexander Dove, Lucy Drummond, Monika Dudek, Laura Durrant, Elizabeth Easthope, Sabine Eckert, Pete Ellis, Ben Farr, Michael Fenton, Marcella Ferrero, Neil Flack, Howerd Fordham, Grace Forsythe, Matt Francis, Audrey Fraser, Adam Freeman, Anastasia Galvin, Maria Garcia-Casado, Alex Gedny, Sophia Girgis, James Glover, Oliver Gould, Andy Gray, Emma Gray, Coline Griffiths, Yong Gu, Florence Guerin, Will Hamilton, Hannah Hanks, Ewan Harrison, Alexandria Harrott, Edward Harry, Julia Harvison, Paul Heath, Anastasia Hernandez-Koutoucheva, Rhiannon Hobbs, Dave Holland, Sarah Holmes, Gary Hornett, Nicholas Hough, Liz Huckle, Lena Hughes-Hallet, Adam Hunter, Stephen Inglis, Sameena Iqbal, Adam Jackson, David Jackson, Carlos Jimenez Verdejo, Matthew Jones, Kalyan Kallepally, Keely Kay, Jon Keatley, Alan Keith, Alison King, Lucy Kitchin, Matt Kleanthous, Martina Klimekova, Petra Korlevic, Ksenia Krasheninnkova, Greg Lane, Cordelia Langford, Adam Laverack, Katharine Law, Stefanie Lensing, Amanah Lewis-Wade, Jennifer Liddle, Quan Lin, Sarah Lindsay, Sally Linsdell, Rhona Long, Jamie Lovell, Jon Lovell, James Mack, Mark Maddison, Aleksei Makunin, Irfan Mamun, Jenny Mansfield, Neil Marriott, Matt Martin, Matthew Mayho, Jo McClintock, Sandra McHugh, Liz MapcMinn, Carl Meadows, Emily Mobley, Robin Moll, Maria Morra, Leanne Morrow, Kathryn Murie, Sian Nash, Claire Nathwani, Plamena Naydenova, Alexandra Neaverson, Ed Nerou, Jon Nicholson, Tabea Nimz, Guillaume G. Noell, Sarah O’Meara, Valeriu Ohan, Charles Olney, Doug Ormond, Agnes Oszlanczi, Yoke Fei Pang, Barbora Pardubska, Naomi Park, Aaron Parmar, Gaurang Patel, Maggie Payne, Sharon Peacock, Arabella Petersen, Deborah Plowman, Tom Preston, Michael Quail, Richard Rance, Suzannah Rawlings, Nicholas Redshaw, Joe Reynolds, Mark Reynolds, Simon Rice, Matt Richardson, Connor Roberts, Katrina Robinson, Melanie Robinson, David Robinson, Hazel Rogers, Eduardo Martin Rojo, Daljit Roopra, Mark Rose, Luke Rudd, Ramin Sadri, Nicholas Salmon, David Saul, Frank Schwach, Phil Seekings, Alison Simms, Matt Sinnott, Shanthi Sivadasan, Bart Siwek, Dale Sizer, Kenneth Skeldon, Jason Skelton, Joanna Slater-Tunstill, Lisa Sloper, Nathalie Smerdon, Chris Smith, Christen Smith, James Smith, Katie Smith, Michelle Smith, Sean Smith, Tina Smith, Leighton Sneade, Carmen Diaz Soria, Catarina Sousa, Emily Souster, Andrew Sparkes, Michael Spencer-Chapman, Janet Squares, Robert Stanley, Claire Steed, Tim Stickland, Ian Still, Mike Stratton, Michelle Strickland, Allen Swann, Agnieszka Swiatkowska, Neil Sycamore, Emma Swift, Edward Symons, Suzanne Szluha, Emma Taluy, Nunu Tao, Katy Taylor, Sam Taylor, Stacey Thompson, Mark Thompson, Mark Thomson, Nicholas Thomson, Scott Thurston, Dee Toombs, Benjamin Topping, Jaime Tovar-Corona, Daniel Ungureanu, James Uphill, Jana Urbanova, Philip Jansen Van, Valerie Vancollie, Paul Voak, Danielle Walker, Matthew Walker, Matt Waller, Gary Ward, Charlie Weatherhogg, Niki Webb, Alan Wells, Eloise Wells, Luke Westwood, Theo Whipp, Thomas Whiteley, Georgia Whitton, Sara Widaa, Mia Williams, Mark Wilson, Sean Wright, and Apollo - University of Cambridge Repository
Subjects: 0301 basic medicine, Resistance, MC UU 1201412, Plasma protein binding, Antibodies, Viral, medicine.disease_cause, MR/R024758/1, 0302 clinical medicine, Recurrence, Chlorocebus aethiops, deletion, Biology (General), Receptor, Phylogeny, Infectivity, Mutation, biology, infectivity, MC_UU_12014/12, C500, C700, UKRI, MRC, Antibody Escape, Spike Glycoprotein, Coronavirus, antibody escape, Antibody, Protein Binding, QH301-705.5, Sars-cov-2, Alpha (ethology), Article, General Biochemistry, Genetics and Molecular Biology, Virus, Cell Line, resistance, Deletion, 03 medical and health sciences, spike mutation, medicine, Alpha Variant, Animals, Humans, neutralizing antibodies, B.1.1.7, Vero Cells, Pandemics, Immune Evasion, SARS-CoV-2, Biochemistry, Genetics and Molecular Biology(all), COVID-19, MR/P008801/1, Antibodies, Neutralizing, Virology, body regions, HEK293 Cells, 030104 developmental biology, Alpha variant, Spike Mutation, biology.protein, Vero cell, Neutralizing Antibodies, 030217 neurology & neurosurgery
Abstract: We report severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike ΔH69/V70 in multiple independent lineages, often occurring after acquisition of receptor binding motif replacements such as N439K and Y453F, known to increase binding affinity to the ACE2 receptor and confer antibody escape. In vitro, we show that, although ΔH69/V70 itself is not an antibody evasion mechanism, it increases infectivity associated with enhanced incorporation of cleaved spike into virions. ΔH69/V70 is able to partially rescue infectivity of spike proteins that have acquired N439K and Y453F escape mutations by increased spike incorporation. In addition, replacement of the H69 and V70 residues in the Alpha variant B.1.1.7 spike (where ΔH69/V70 occurs naturally) impairs spike incorporation and entry efficiency of the B.1.1.7 spike pseudotyped virus. Alpha variant B.1.1.7 spike mediates faster kinetics of cell-cell fusion than wild-type Wuhan-1 D614G, dependent on ΔH69/V70. Therefore, as ΔH69/V70 compensates for immune escape mutations that impair infectivity, continued surveillance for deletions with functional effects is warranted., Graphical abstract, Meng et al. report that the SARS-CoV-2 spike ΔH69/V70 has arisen multiple times. The deletion increases entry efficiency associated with increased cleaved spike in virions and can compensate for loss of infectivity. The B.1.1.7 spike requires ΔH69/V70 for efficient cell entry and cell-cell fusion activity.
Published: 2021
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20. Epidemic waves of COVID-19 in Scotland: a genomic perspective on the impact of the introduction and relaxation of lockdown on SARS-CoV-2

Author: Rachel M. Colquhoun, David Robertson, Stephen Carmichael, Gianluigi Rossi, Tom Stanton, Andrew Rambaut, James Shepherd, Stefan Rooke, Ana da Silva Filipe, Amy Shepherd, Alasdair MacLean, Elihu Aranday-Cortes, Carlos E Balcazar-Lopez, Verity Hill, Igor Starinskij, Lu Lu, Katherine Smollett, Kathy Li, Michael Gallagher, Kathleen A. Williamson, John T. McCrone, Rory Gunson, Ben Jackson, Thomas C Williams, Rebecca Dewar, Kirstyn Brunker, Rhys Inward, Sharif Shaaban, Martin P McHugh, Kate Templeton, Seb Cotton, Mark E. J. Woolhouse, Daniel Balaz, Alice Broos, Sarah E. McDonald, Rajiv Shah, Jenna Nichols, Lily Tong, Thomas Doherty, Rowland R. Kao, Áine O'Toole, Natasha Johnson, Patawee Asamaphan, Yasmin A Parr, Vattipally B. Sreenu, E. Thomson, Marc Niebel, Natasha Jesudason, Daniel Mair, Kyriaki Nomikou, Emily Scher, Matthew T. G. Holden, Samantha Lycett, and Joseph Hughes
Subjects: medicine.medical_specialty, education.field_of_study, Coronavirus disease 2019 (COVID-19), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Public health, Population, National health service, Quarter (United States coin), Geography, Epidemiology, medicine, Health board, education, Demography
Abstract: The second SARS virus, SARS-CoV-2, emerged in December 2019, and within a month was globally distributed. It was first introduced into Scotland in February 2020 associated with returning travellers and visitors. By March it was circulating in communities across the UK, and to control COVID-19 cases, and prevent overwhelming of the National Health Service (NHS), a ‘lockdown’ was introduced on 23rd March 2020 with a restriction of people’s movements. To augment the public health efforts a large-scale genome epidemiology effort (as part of the COVID-19 Genomics UK (COG-UK) consortium) resulted in the sequencing of over 5000 SARS-CoV-2 genomes by 18th August 2020 from Scottish cases, about a quarter of the estimated number of cases at that time. Here we quantify the geographical origins of the first wave introductions into Scotland from abroad and other UK regions, the spread of these SARS-CoV-2 lineages to different regions within Scotland (defined at the level of NHS Health Board) and the effect of lockdown on virus ‘success’. We estimate that approximately 300 introductions seeded lineages in Scotland, with around 25% of these lineages composed of more than five viruses, but by June circulating lineages were reduced to low levels, in line with low numbers of recorded positive cases. Lockdown was, thus, associated with a dramatic reduction in infection numbers and the extinguishing of most virus lineages. Unfortunately since the summer cases have been rising in Scotland in a second wave, with >1000 people testing positive on a daily basis, and hospitalisation of COVID-19 cases on the rise again. Examining the available Scottish genome data from the second wave, and comparing it to the first wave, we find that while some UK lineages have persisted through the summer, the majority of lineages responsible for the second wave are new introductions from outside of Scotland and many from outside of the UK. This indicates that, while lockdown in Scotland is directly linked with the first wave case numbers being brought under control, travel-associated imports (mostly from Europe or other parts of the UK) following the easing of lockdown are responsible for seeding the current epidemic population. This demonstrates that the impact of stringent public health measures can be compromised if following this, movements from regions of high to low prevalence are not minimised.
Published: 2021
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21. Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity

Author: Erik Volz, Verity Hill, John T. McCrone, Anna Price, David Jorgensen, Áine O’Toole, Joel Southgate, Robert Johnson, Ben Jackson, Fabricia F. Nascimento, Sara M. Rey, Samuel M. Nicholls, Rachel M. Colquhoun, Ana da Silva Filipe, James Shepherd, David J. Pascall, Rajiv Shah, Natasha Jesudason, Kathy Li, Ruth Jarrett, Nicole Pacchiarini, Matthew Bull, Lily Geidelberg, Igor Siveroni, Ian Goodfellow, Nicholas J. Loman, Oliver G. Pybus, David L. Robertson, Emma C. Thomson, Andrew Rambaut, Thomas R. Connor, Cherian Koshy, Emma Wise, Nick Cortes, Jessica Lynch, Stephen Kidd, Matilde Mori, Derek J. Fairley, Tanya Curran, James P. McKenna, Helen Adams, Christophe Fraser, Tanya Golubchik, David Bonsall, Catrin Moore, Sarah L. Caddy, Fahad A. Khokhar, Michelle Wantoch, Nicola Reynolds, Ben Warne, Joshua Maksimovic, Karla Spellman, Kathryn McCluggage, Michaela John, Robert Beer, Safiah Afifi, Sian Morgan, Angela Marchbank, Christine Kitchen, Huw Gulliver, Ian Merrick, Martyn Guest, Robert Munn, Trudy Workman, William Fuller, Catherine Bresner, Luke B. Snell, Themoula Charalampous, Gaia Nebbia, Rahul Batra, Jonathan Edgeworth, Samuel C. Robson, Angela Beckett, Katie F. Loveson, David M. Aanensen, Anthony P. Underwood, Corin A. Yeats, Khalil Abudahab, Ben E.W. Taylor, Mirko Menegazzo, Gemma Clark, Wendy Smith, Manjinder Khakh, Vicki M. Fleming, Michelle M. Lister, Hannah C. Howson-Wells, Louise Berry, Tim Boswell, Amelia Joseph, Iona Willingham, Paul Bird, Thomas Helmer, Karlie Fallon, Christopher Holmes, Julian Tang, Veena Raviprakash, Sharon Campbell, Nicola Sheriff, Matthew W. Loose, Nadine Holmes, Christopher Moore, Matthew Carlile, Victoria Wright, Fei Sang, Johnny Debebe, Francesc Coll, Adrian W. Signell, Gilberto Betancor, Harry D. Wilson, Theresa Feltwell, Charlotte J. Houldcroft, Sahar Eldirdiri, Anita Kenyon, Thomas Davis, Oliver Pybus, Louis du Plessis, Alex Zarebski, Jayna Raghwani, Moritz Kraemer, Sarah Francois, Stephen Attwood, Tetyana Vasylyeva, M. Estee Torok, William L. Hamilton, Ian G. Goodfellow, Grant Hall, Aminu S. Jahun, Yasmin Chaudhry, Myra Hosmillo, Malte L. Pinckert, Iliana Georgana, Anna Yakovleva, Luke W. Meredith, Samuel Moses, Hannah Lowe, Felicity Ryan, Chloe L. Fisher, Ali R. Awan, John Boyes, Judith Breuer, Kathryn Ann Harris, Julianne Rose Brown, Divya Shah, Laura Atkinson, Jack C.D. Lee, Adela Alcolea-Medina, Nathan Moore, Nicholas Cortes, Rebecca Williams, Michael R. Chapman, Lisa J. Levett, Judith Heaney, Darren L. Smith, Matthew Bashton, Gregory R. Young, John Allan, Joshua Loh, Paul A. Randell, Alison Cox, Pinglawathee Madona, Alison Holmes, Frances Bolt, James Price, Siddharth Mookerjee, Aileen Rowan, Graham P. Taylor, Manon Ragonnet-Cronin, Rob Johnson, Olivia Boyd, Erik M. Volz, Kirstyn Brunker, Katherine L. Smollett, Joshua Quick, Claire McMurray, Joanne Stockton, Sam Nicholls, Will Rowe, Radoslaw Poplawski, Rocio T. Martinez-Nunez, Jenifer Mason, Trevor I. Robinson, Elaine O'Toole, Joanne Watts, Cassie Breen, Angela Cowell, Catherine Ludden, Graciela Sluga, Nicholas W. Machin, Shazaad S.Y. Ahmad, Ryan P. George, Fenella Halstead, Venkat Sivaprakasam, James G. Shepherd, Patawee Asamaphan, Marc O. Niebel, Kathy K. Li, Rajiv N. Shah, Natasha G. Jesudason, Yasmin A. Parr, Lily Tong, Alice Broos, Daniel Mair, Jenna Nichols, Stephen N. Carmichael, Kyriaki Nomikou, Elihu Aranday-Cortes, Natasha Johnson, Igor Starinskij, Richard J. Orton, Joseph Hughes, Sreenu Vattipally, Joshua B. Singer, Antony D. Hale, Louissa R. Macfarlane-Smith, Katherine L. Harper, Yusri Taha, Brendan A.I. Payne, Shirelle Burton-Fanning, Sheila Waugh, Jennifer Collins, Gary Eltringham, Kate E. Templeton, Martin P. McHugh, Rebecca Dewar, Elizabeth Wastenge, Samir Dervisevic, Rachael Stanley, Reenesh Prakash, Claire Stuart, Ngozi Elumogo, Dheeraj K. Sethi, Emma J. Meader, Lindsay J. Coupland, Will Potter, Clive Graham, Edward Barton, Debra Padgett, Garren Scott, Emma Swindells, Jane Greenaway, Andrew Nelson, Wen C. Yew, Paola C. Resende Silva, Monique Andersson, Robert Shaw, Timothy Peto, Anita Justice, David Eyre, Derrick Crooke, Sarah Hoosdally, Tim J. Sloan, Nichola Duckworth, Sarah Walsh, Anoop J. Chauhan, Sharon Glaysher, Kelly Bicknell, Sarah Wyllie, Ethan Butcher, Scott Elliott, Allyson Lloyd, Robert Impey, Nick Levene, Lynn Monaghan, Declan T. Bradley, Elias Allara, Clare Pearson, Peter Muir, Ian B. Vipond, Richard Hopes, Hannah M. Pymont, Stephanie Hutchings, Martin D. Curran, Surendra Parmar, Angie Lackenby, Tamyo Mbisa, Steven Platt, Shahjahan Miah, David Bibby, Carmen Manso, Jonathan Hubb, Meera Chand, Gavin Dabrera, Mary Ramsay, Daniel Bradshaw, Alicia Thornton, Richard Myers, Ulf Schaefer, Natalie Groves, Eileen Gallagher, David Lee, David Williams, Nicholas Ellaby, Ian Harrison, Hassan Hartman, Nikos Manesis, Vineet Patel, Chloe Bishop, Vicki Chalker, Husam Osman, Andrew Bosworth, Esther Robinson, Matthew T.G. Holden, Sharif Shaaban, Alec Birchley, Alexander Adams, Alisha Davies, Amy Gaskin, Amy Plimmer, Bree Gatica-Wilcox, Caoimhe McKerr, Catherine Moore, Chris Williams, David Heyburn, Elen De Lacy, Ember Hilvers, Fatima Downing, Giri Shankar, Hannah Jones, Hibo Asad, Jason Coombes, Joanne Watkins, Johnathan M. Evans, Laia Fina, Laura Gifford, Lauren Gilbert, Lee Graham, Malorie Perry, Mari Morgan, Michelle Cronin, Noel Craine, Rachel Jones, Robin Howe, Sally Corden, Sara Rey, Sara Kumziene-Summerhayes, Sarah Taylor, Simon Cottrell, Sophie Jones, Sue Edwards, Justin O’Grady, Andrew J. Page, John Wain, Mark A. Webber, Alison E. Mather, David J. Baker, Steven Rudder, Muhammad Yasir, Nicholas M. Thomson, Alp Aydin, Ana P. Tedim, Gemma L. Kay, Alexander J. Trotter, Rachel A.J. Gilroy, Nabil-Fareed Alikhan, Leonardo de Oliveira Martins, Thanh Le-Viet, Lizzie Meadows, Anastasia Kolyva, Maria Diaz, Andrew Bell, Ana Victoria Gutierrez, Ian G. Charles, Evelien M. Adriaenssens, Robert A. Kingsley, Anna Casey, David A. Simpson, Zoltan Molnar, Thomas Thompson, Erwan Acheson, Jane A.H. Masoli, Bridget A. Knight, Andrew Hattersley, Sian Ellard, Cressida Auckland, Tabitha W. Mahungu, Dianne Irish-Tavares, Tanzina Haque, Yann Bourgeois, Garry P. Scarlett, David G. Partridge, Mohammad Raza, Cariad Evans, Kate Johnson, Steven Liggett, Paul Baker, Sarah Essex, Ronan A. Lyons, Laura G. Caller, Sergi Castellano, Rachel J. Williams, Mark Kristiansen, Sunando Roy, Charlotte A. Williams, Patricia L. Dyal, Helena J. Tutill, Yasmin N. Panchbhaya, Leysa M. Forrest, Paola Niola, Jacqueline Findlay, Tony T. Brooks, Artemis Gavriil, Lamia Mestek-Boukhibar, Sam Weeks, Sarojini Pandey, Lisa Berry, Katie Jones, Alex Richter, Andrew Beggs, Colin P. Smith, Giselda Bucca, Andrew R. Hesketh, Ewan M. Harrison, Sharon J. Peacock, Sophie Palmer, Carol M. Churcher, Katherine L. Bellis, Sophia T. Girgis, Plamena Naydenova, Beth Blane, Sushmita Sridhar, Chris Ruis, Sally Forrest, Claire Cormie, Harmeet K. Gill, Joana Dias, Ellen E. Higginson, Mailis Maes, Jamie Young, Leanne M. Kermack, Nazreen F. Hadjirin, Dinesh Aggarwal, Luke Griffith, Tracey Swingler, Rose K. Davidson, Thomas Williams, Carlos E. Balcazar, Michael D. Gallagher, Áine O'Toole, Stefan Rooke, Rachel Colquhoun, Jordan Ashworth, J.T. McCrone, Emily Scher, Xiaoyu Yu, Kathleen A. Williamson, Thomas D. Stanton, Stephen L. Michell, Claire M. Bewshea, Ben Temperton, Michelle L. Michelsen, Joanna Warwick-Dugdale, Robin Manley, Audrey Farbos, James W. Harrison, Christine M. Sambles, David J. Studholme, Aaron R. Jeffries, Alistair C. Darby, Julian A. Hiscox, Steve Paterson, Miren Iturriza-Gomara, Kathryn A. Jackson, Anita O. Lucaci, Edith E. Vamos, Margaret Hughes, Lucille Rainbow, Richard Eccles, Charlotte Nelson, Mark Whitehead, Lance Turtle, Sam T. Haldenby, Richard Gregory, Matthew Gemmell, Dominic Kwiatkowski, Thushan I. de Silva, Nikki Smith, Adrienn Angyal, Benjamin B. Lindsey, Danielle C. Groves, Luke R. Green, Dennis Wang, Timothy M. Freeman, Matthew D. Parker, Alexander J. Keeley, Paul J. Parsons, Rachel M. Tucker, Rebecca Brown, Matthew Wyles, Chrystala Constantinidou, Meera Unnikrishnan, Sascha Ott, Jeffrey K.J. Cheng, Hannah E. Bridgewater, Lucy R. Frost, Grace Taylor-Joyce, Richard Stark, Laura Baxter, Mohammad T. Alam, Paul E. Brown, Patrick C. McClure, Joseph G. Chappell, Theocharis Tsoleridis, Jonathan Ball, Dimitris Grammatopoulos, David Buck, John A. Todd, Angie Green, Amy Trebes, George MacIntyre-Cockett, Mariateresa de Cesare, Cordelia Langford, Alex Alderton, Roberto Amato, Sonia Goncalves, David K. Jackson, Ian Johnston, John Sillitoe, Steve Palmer, Mara Lawniczak, Matt Berriman, John Danesh, Rich Livett, Lesley Shirley, Ben Farr, Mike Quail, Scott Thurston, Naomi Park, Emma Betteridge, Danni Weldon, Scott Goodwin, Rachel Nelson, Charlotte Beaver, Laura Letchford, David A. Jackson, Luke Foulser, Liz McMinn, Liam Prestwood, Sally Kay, Leanne Kane, Matthew J. Dorman, Inigo Martincorena, Christoph Puethe, Jon-Paul Keatley, Gerry Tonkin-Hill, Christen Smith, Dorota Jamrozy, Mathew A. Beale, Minal Patel, Cristina Ariani, Michael Spencer-Chapman, Eleanor Drury, Stephanie Lo, Shavanthi Rajatileka, Carol Scott, Keith James, Sarah K. Buddenborg, Duncan J. Berger, Gaurang Patel, Maria V. Garcia-Casado, Thomas Dibling, Samantha McGuigan, Hazel A. Rogers, Adam D. Hunter, Emily Souster, Alexandra S. Neaverson, Medical Research Council (MRC), Pascall, David [0000-0002-7543-0860], and Apollo - University of Cambridge Repository
Subjects: Genome, Genetic analysis, 0302 clinical medicine, Clade, 11 Medical and Health Sciences, Genetics, 0303 health sciences, education.field_of_study, Phylogenetic tree, Virulence, C500, COG-UK Consortium, C700, Transmissibility (vibration), 3. Good health, founder effect, Spike Glycoprotein, Coronavirus, epidemiology, Viral load, Population, Glycine, B100, Genomics, Genome, Viral, Biology, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, evolution, Humans, education, 030304 developmental biology, Aspartic Acid, Whole Genome Sequencing, Biochemistry, Genetics and Molecular Biology(all), SARS-CoV-2, COVID-19, spike, The COVID-19 Genomics UK Consortium, A300, 06 Biological Sciences, United Kingdom, Amino Acid Substitution, Evolutionary biology, Mutation, Biological dispersal, 030217 neurology & neurosurgery, Founder effect, Developmental Biology
Abstract: Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant., Graphical Abstract, Highlights • Increasing frequency of SARS-CoV-2 D614G is consistent with a selective advantage • Phylodynamic analyses do not show significantly different growth of D614G clusters • There is no association of D614G replacement with greater severity of infection • The D614G replacement is associated with higher viral loads and younger patient age, Analysis of the spread and frequency of SARS-CoV-2 D614G in the United Kingdom suggests a selective advantage for this strain that is associated with higher viral loads in younger patients but not higher COVID-19 clinical severity or mortality.
Published: 2021
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22. Genomic epidemiology of SARS-CoV-2 spread in Scotland highlights the role of European travel in COVID-19 emergence

Author: Kathy Li, Rory Gunson, Antonia Ho, David Robertson, Elihu Aranday-Cortes, Daniel Mair, Katherine Smollett, Igor Starinskij, Kyriaki Nomikou, Natasha Johnson, Sarah E. McDonald, Vattipally B. Sreenu, Sharif Shaaban, Patawee Asamaphan, E. Thomson, Jenna Nichols, Carlos Balcazar, Joseph Hughes, Marc Niebel, Michael Gallagher, Kirstyn Brunker, Elizabeth Wastnedge, E. Carol McWilliam Leitch, Martin P McHugh, Massimo Palmarini, Natasha Jesudason, Kate Templeton, Áine O'Toole, Lily Tong, Matthew T. G. Holden, Joshua B Singer, Rajiv Shah, James Shepherd, Yasmin A Parr, Thomas C Williams, Richard J. Orton, Stephen Carmichael, Andrew Rambaut, Alasdair MacLean, Rebecca Dewar, Stefan Rooke, and Ana da Silva Filipe
Subjects: medicine.medical_specialty, Coronavirus disease 2019 (COVID-19), European travel, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Outbreak, law.invention, Geography, Infectious disease (medical specialty), law, Quarantine, Epidemiology, medicine, Contact tracing, Demography
Abstract: SARS-CoV-2, the causative agent of COVID-19, emerged in Wuhan, China in December 2019 and spread rapidly throughout the world. Understanding the introductions of this new coronavirus in different settings may assist control efforts and the establishment of frameworks to support rapid response in future infectious disease outbreaks.We investigated the first four weeks of emergence of the SARS-CoV-2 virus in Scotland after the first case reported on the 1st March 2020. We obtained full genome sequences from 452 individuals with a laboratory-confirmed diagnosis of COVID-19, representing 20% of all cases until 1st April 2020 (n=2310). This permitted a genomic epidemiology approach to study the introductions and spread of the SARS-2 virus in Scotland.From combined phylogenetic and epidemiological analysis, we estimated at least 113 introductions of SARS-CoV-2 into Scotland during this period. Clusters containing multiple sequences suggestive of onward transmission occurred in 48/86 (56%). 42/86 (51%) clusters had no known international travel history indicating undetected introductions.The majority of viral sequences were most closely related to those circulating in other European countries, including Italy, Austria and Spain. Travel-associated introductions of SARS-CoV-2 into Scotland predated travel restrictions in the UK and other European countries. The first local transmission occurred three days after the first case. A shift from travel-associated to sustained community transmission was apparent after only 11 days. Undetected introductions occurred prior to the first known case of COVID-19. Earlier travel restrictions and quarantine measures might have resulted in fewer introductions into Scotland, thereby reducing the number of cases and the subsequent burden on health services. The high number of introductions and transmission rates were likely to have impacted on national contact tracing efforts. Our results also demonstrate that local real-time genomic epidemiology can be used to monitor transmission clusters and facilitate control efforts to restrict the spread of COVID-19.FundingMRC (MC UU 1201412), UKRI/Wellcome (COG-UK), Wellcome Trust Collaborator Award (206298/Z/17/Z – ARTIC Network; TCW Wellcome Trust Award 204802/Z/16/ZResearch in contextEvidence before this studyCoronavirus disease-2019 (COVID-19) was first diagnosed in Scotland on the 1st of March 2020 following the emergence of the causative severe acute respiratory system coronavirus 2 (SARS-CoV-2) virus in China in December 2019. During the first month of the outbreak in Scotland, 2310 positive cases of COVID-19 were detected, associated with 1832 hospital admissions, 207 intensive care admissions and 126 deaths. The number of introductions into Scotland and the source of those introductions was not known prior to this study.Added value of this studyUsing a combined phylogenetic and epidemiological approach following real-time next generation sequencing of 452 SARS-CoV-2 samples, it was estimated that the virus was introduced to Scotland on at least 113 occasions, mostly from other European countries, including Italy, Austria and Spain. Localised outbreaks occurred in the community across multiple Scottish health boards, within healthcare facilities and an international conference and community transmission was established rapidly, before local and international lockdown measures were introduced.
Published: 2020

23. Multicenter evaluation of QIAstat-Dx respiratory panel V2 for detection of viral and bacterial respiratory pathogens

Author: Marga Toonen, Stefan A. Boers, Cas J. A. Peters, Martin P McHugh, Willem J. G. Melchers, Eric C. J. Claas, Kate Templeton, University of St Andrews. School of Medicine, and University of St Andrews. Infection and Global Health Division
Subjects: Microbiology (medical), respiratory pathogen panel, respiratory tract infections, Respiratory tract infections, Respiratory pathogen panel, molecular diagnostics, Molecular diagnostics, Humans, Infection control, Medicine, syndromic testing, Multiplex, Respiratory system, QIAstat-Dx, Retrospective Studies, QR355, Cycle threshold, Women's cancers Radboud Institute for Molecular Life Sciences [Radboudumc 17], Bacteria, Syndromic testing, Diagnostic Tests, Routine, business.industry, Respiratory Pathogen Panel, ePlex, DAS, Bacteriology, Respiratory pathogens, Molecular Diagnostic Techniques, RB Pathology, Immunology, RB, business, QR355 Virology
Abstract: QIAstat-Dx Respiratory Panel V2 (RP) is a novel molecular-method-based syndromic test for the simultaneous and rapid (∼70-min) detection of 18 viral and 3 bacterial pathogens causing respiratory infections. This report describes the first multicenter retrospective comparison of the performance of the QIAstat-Dx RP assay to the established ePlex Respiratory Pathogen Panel (RPP) assay, for which we used 287 respiratory samples from patients suspected with respiratory infections. The QIAstat-Dx RP assay detected 312 (92%) of the 338 respiratory targets that were detected by the ePlex RPP assay., QIAstat-Dx Respiratory Panel V2 (RP) is a novel molecular-method-based syndromic test for the simultaneous and rapid (∼70-min) detection of 18 viral and 3 bacterial pathogens causing respiratory infections. This report describes the first multicenter retrospective comparison of the performance of the QIAstat-Dx RP assay to the established ePlex Respiratory Pathogen Panel (RPP) assay, for which we used 287 respiratory samples from patients suspected with respiratory infections. The QIAstat-Dx RP assay detected 312 (92%) of the 338 respiratory targets that were detected by the ePlex RPP assay. Most of the discrepant results have been observed in the low-pathogen-load samples. In addition, the QIAstat-Dx RP assay detected 19 additional targets in 19 respiratory samples that were not detected by the ePlex RPP assay. Nine of these discordant targets were considered to represent true positives after discrepancy testing by a third method. The main advantage of the QIAstat-Dx system compared to other syndromic testing systems, including the ePlex RPP assay, is the ability to generate cycle threshold (CT) values, which could help with the interpretation of results. Taking the data together, this study showed good performance of the QIAstat-Dx RP assay in comparison to the ePlex RPP assay for the detection of respiratory pathogens. The QIAstat-Dx RP assay offers a new, rapid, and accurate sample-to-answer multiplex panel for the detection of the most common viral and bacterial respiratory pathogens and therefore has the potential to direct appropriate therapy and infection control precautions.
Published: 2020

24. Rapid molecular testing for

Author: Martin P, McHugh, Benjamin J, Parcell, Fiona M, MacKenzie, Kate E, Templeton, and Scottish Microbiology And Virology Network Smvn Molecular Diagnostics Evaluation Group
Subjects: Staphylococcus aureus, Blood, Blood Culture, Humans, Bacteremia, Prospective Studies, Staphylococcal Infections
Published: 2020

25. Evaluation of Staphylococcus aureus eradication therapy in orthopaedic surgery

Author: Steff Lewis, Kate Templeton, Timothy S. Walsh, Peter J. Gwynne, S.T.J. Tsang, A. H. R. W. Simpson, Martin P McHugh, Daniel Guerendiain, I. F. Laurenson, and Julia Boyd
Subjects: Male, Microbiology (medical), Staphylococcus aureus, medicine.medical_specialty, Joint replacement, medicine.medical_treatment, Population, Mupirocin, Context (language use), Nose, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Throat, Preoperative Care, medicine, Humans, Surgical Wound Infection, 030212 general & internal medicine, education, Aged, 030222 orthopedics, education.field_of_study, business.industry, General Medicine, Middle Aged, Staphylococcal Infections, United Kingdom, Anti-Bacterial Agents, Surgery, Anterior nares, Regimen, Orthopedics, medicine.anatomical_structure, chemistry, Elective Surgical Procedures, Carrier State, Orthopedic surgery, Pharynx, Female, Nasal Cavity, business
Abstract: Purpose. Despite WHO recommendations there is currently no national screening and eradication policy for the detection of methicillin-sensitive Staphylococcus aureus (MSSA) in the UK prior to elective orthopaedic surgery. This study aimed to evaluate the effectiveness of current standard methicillin-resistant S. aureus (MRSA) eradication therapies in the context of S. aureus (both MRSA and MSSA) decolonisation in an elective orthopaedic population. Methodology. A total of 100 patients awaiting joint replacement surgery who were positive for S. aureus on PCR nasal screening underwent the current standard MRSA pre-operative decolonisation regimen for five days. Prior to commencement of the eradication therapy swabs of the anterior nares, throat, and perineum were taken for culture. Further culture swabs were taken at 48-96 hours following treatment, at hospital admission for surgery, and at hospital discharge. Following completion of treatment patients were asked to provide feedback on their experience using Likert rating scales. The primary outcome of this study was S. aureus clearance 48-96 hours following eradication treatment. Results/Key Findings. Clearance of S. aureus 48-96 hours following treatment was 94% anterior nares, 66% throat, and 88% groin. Mean completion with nasal mupirocin was 98%. There was no statistically significant recolonisation effect between the end of the eradication treatment period and the day of surgery (p>0.05) at a median time of 10 days. Conclusion. Current MRSA decolonisation regimens are well-tolerated and effective for MSSA decolonisation for the anterior nares and groin. The decolonisation effect is preserved for at least 10 days following treatment.
Published: 2018
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26. Multicenter Evaluation of the Cepheid Xpert Hepatitis C Virus Viral Load Assay

Author: Kate Templeton, Martin P McHugh, M. Hallin, Alan H.B. Wu, Stéphane Chevaliez, and Jean-Michel Pawlotsky
Subjects: Microbiology (medical), Genotype, Response to therapy, Hepatitis C virus, Hepacivirus, medicine.disease_cause, Mean difference, 03 medical and health sciences, 0302 clinical medicine, Virology, External quality assessment, medicine, Humans, 030212 general & internal medicine, biology, Plasma samples, business.industry, Liter, Viral Load, biology.organism_classification, Hepatitis C, Immunology, RNA, Viral, 030211 gastroenterology & hepatology, business, Viral load
Abstract: Viral load monitoring for hepatitis C virus (HCV) is necessary to diagnose infection and monitor response to therapy, but the tests involved are currently confined to specialist institutions. There is a need for a fast, accurate assay with limited operator input to enhance the access to viral load monitoring. We evaluated the quantification of HCV RNA in serum and plasma by the Cepheid Xpert HCV Viral Load assay in comparison to the Abbott RealTi m e HCV assay. Serum and plasma samples were gathered from HCV-infected individuals at four international sites. These were tested with the Xpert HCV Viral Load assay, and results were compared to quantification by the Abbott RealTi m e HCV assay. An external quality assessment panel of eight samples was also tested. In total, 614 samples were analyzed in the study, and the qualitative results agreed on the two platforms for 588 (95.8%) samples. Further analysis of 396 samples quantified by both tests showed strong correlation (correlation coefficient r = 0.99) across the quantifiable range, with Bland-Altman plot data showing a mean difference (±1.96 standard deviation) of 0.03 ± 0.44 log 10 IU/ml. In the external quality assessment panel, the Xpert HCV Viral Load assay results (quantified in log 10 IU per milliliter) were within 1 standard deviation of the target value for all but one sample, which was also similarly misquantified by the Abbott RealTime HCV assay. The Xpert HCV Viral Load assay performs well compared to a market-leading HCV viral load test and should be considered for instances where rapid near-to-patient testing is required.
Published: 2017
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27. Emergence of optrA-mediated linezolid resistance in multiple lineages and plasmids of Enterococcus faecalis revealed by long read sequencing

Author: Elham Khatamzas, Kate Templeton, Benjamin J. Parcell, Robert Weir, Geoff Toner, Martin P McHugh, Katie L. Hopkins, Kerry A. Pettigrew, Anne Marie Karcher, Neil Woodford, Matthew T. G. Holden, Danièle Meunier, Joanna Walker, and Stephen H. Gillespie
Subjects: Genetics, Transposable element, 0303 health sciences, education.field_of_study, 030306 microbiology, Strain (biology), Population, Biology, biology.organism_classification, Genome, Enterococcus faecalis, 3. Good health, 03 medical and health sciences, Plasmid, Gene cassette, education, Gene, 030304 developmental biology
Abstract: ObjectivesTo characterise the genetic environment of optrA in linezolid-resistant Enterococcus faecalis isolates from Scotland.MethodsLinezolid-resistant E. faecalis were identified in three Scottish Health Boards and confirmed to carry the optrA gene at the national reference laboratory. WGS was performed with short read (Illumina MiSeq) and long read (Oxford Nanopore MinION) technologies to generate complete genome assemblies. Illumina reads for 94 E. faecalis bloodstream isolates were used to place the optrA-positive isolates in a larger UK phylogeny.ResultsSix optrA-positive linezolid-resistant E. faecalis were isolated from urogenital samples in three Scottish Health Boards (2014-2017). No epidemiological links were identified between the patients, four were community-based, and only one had recent linezolid exposure. Reference-based mapping confirmed the isolates were genetically distinct (>13,900 core SNPs). optrA was located on a plasmid in each isolate and these plasmids showed limited nucleotide similarity. There was variable presence of transposable elements surrounding optrA, (including IS1216, IS3, and Tn3) and not always as a recognisable gene cassette. OptrA amino acid sequences were also divergent, resulting in four protein variants differing in 1-20 residues. One isolate belonged to ST16 and clustered with three other isolates in the UK collection (76-182 SNPs), otherwise the optrA-positive isolates were genetically distinct from the bloodstream isolates (>6,000 SNPs).ConclusionsWe report multiple variants of the linezolid resistance gene optrA in diverse E. faecalis strain and plasmid backgrounds, suggesting multiple introductions of the gene into the E. faecalis population and selection driving recent emergence.
Published: 2020
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28. Board-Level BIST.

Author: J. Braden, K. Brough, J. Evans, Martin P. McHugh, and G. Young
Published: 1996
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29. Comparison of Unyvero P55 Pneumonia Cartridge, in-house PCR and culture for the identification of respiratory pathogens and antibiotic resistance in bronchoalveolar lavage fluids in the critical care setting

Author: Martin P McHugh, Callum Forbes, Laura MacKenzie, Naomi J. Gadsby, David M Griffith, Kate Templeton, and Stephen K D Hamilton
Subjects: 0301 basic medicine, Microbiology (medical), Adult, Male, medicine.medical_specialty, Microbiological culture, medicine.drug_class, 030106 microbiology, Antibiotics, Sensitivity and Specificity, Microbiology, law.invention, 03 medical and health sciences, 0302 clinical medicine, Medical microbiology, Antibiotic resistance, law, Medicine, Infection control, Humans, 030212 general & internal medicine, Aged, Retrospective Studies, Bacteriological Techniques, medicine.diagnostic_test, Bacteria, business.industry, Diagnostic Tests, Routine, Drug Resistance, Microbial, General Medicine, Pneumonia, Middle Aged, medicine.disease, Intensive care unit, Anti-Bacterial Agents, Intensive Care Units, Infectious Diseases, Bronchoalveolar lavage, Female, business, Bronchoalveolar Lavage Fluid, Multiplex Polymerase Chain Reaction
Abstract: Faster respiratory pathogen detection and antibiotic resistance identification are important in critical care due to the severity of illness, significant prior antibiotic exposure and infection control implications. Our objective was to compare the performance of the commercial Unyvero P55 Pneumonia Cartridge (Curetis AG) with routine bacterial culture methods and in-house bacterial multiplex real-time PCR assays. Seventy-four bronchoalveolar lavage specimens from patients admitted to a Scottish intensive care unit (ICU) over a 33-month period were tested prospectively by routine culture and viral PCR and retrospectively by Unyvero P55 and in-house bacterial PCR. Sensitivity/specificity was 56.9%/58.5% and 63.2%/54.8% for the Unyvero P55 and in-house bacterial PCR panels respectively; sensitivity for in-panel targets was 63.5 and 83.7% respectively. Additional organisms were detected by Unyvero P55 and in-house bacterial PCR panels in 16.2% specimens. Antibiotics were changed on the basis of routine test results in 48.3% cases; of these, true-positive or true-negative results would have been obtained earlier by Unyvero P55 or in-house bacterial PCR panel in 15 (53.6%) and 17 (60.7%) cases respectively. However, a false-negative molecular test result may have been acted upon in six (21.4%) cases with either assay. Sensitivity/specificity of Unyvero P55 antibiotic resistance detection was 18.8%/94.9% respectively. Molecular testing identified a number of respiratory pathogens in this patient cohort that were not grown in culture, but resistance detection was not a reliable tool for faster antibiotic modification. In their current set-up, molecular tests may only have benefit as additional tests in the ICU pneumonia setting.
Published: 2018
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30. Comprehensive Molecular Testing for Respiratory Pathogens in Community-Acquired Pneumonia

Author: Clark D Russell, Andrew Conway Morris, Ian F. Laurenson, Adam T. Hill, Martin P McHugh, Naomi J. Gadsby, Kate Templeton, Harriet Mark, Conway Morris, Andrew [0000-0002-3211-3216], Apollo - University of Cambridge Repository, and University of St Andrews. School of Medicine
Subjects: 0301 basic medicine, Male, community-acquired pneumonia, medicine.disease_cause, Polymerase Chain Reaction, Haemophilus influenzae, 0302 clinical medicine, Community-acquired pneumonia, 030212 general & internal medicine, Viral, Pathogen, Middle Aged, Viral Load, Antimicrobial, Anti-Bacterial Agents, Community-Acquired Infections, Infectious Diseases, PCR, Streptococcus pneumoniae, Molecular Diagnostic Techniques, RB Pathology, Female, medicine.symptom, Pneumonia (non-human), Viral load, QR355 Virology, viral, Microbiology (medical), 030106 microbiology, Pneumonia, Viral, Microbial Sensitivity Tests, Molecular testing, Microbiology, 03 medical and health sciences, medicine, Pneumonia, Bacterial, Humans, Aged, Retrospective Studies, QR355, molecular testing, business.industry, bacterial load, DAS, medicine.disease, Sputum, business, RB, Bacterial load
Abstract: Funding: This work was supported by the Chief Scientist Office (grant number ETM/250). Background. The frequent lack of a microbiological diagnosis in community-acquired pneumonia (CAP) impairs pathogen-directed antimicrobial therapy. This study assessed the use of comprehensive multibacterial, multiviral molecular testing, including quantification, in adults hospitalized with CAP. Methods. Clinical and laboratory data were collected for 323 adults with radiologically-confirmed CAP admitted to 2 UK tertiary care hospitals. Sputum (96%) or endotracheal aspirate (4%) specimens were cultured as per routine practice and also tested with fast multiplex real-time polymerase-chain reaction (PCR) assays for 26 respiratory bacteria and viruses. Bacterial loads were also calculated for 8 bacterial pathogens. Appropriate pathogen-directed therapy was retrospectively assessed using national guidelines adapted for local antimicrobial susceptibility patterns. Results. Comprehensive molecular testing of single lower respiratory tract (LRT) specimens achieved pathogen detection in 87% of CAP patients compared with 39% with culture-based methods. Haemophilus influenzae and Streptococcus pneumoniae were the main agents detected, along with a wide variety of typical and atypical pathogens. Viruses were present in 30% of cases; 82% of these were codetections with bacteria. Most (85%) patients had received antimicrobials in the 72 hours before admission. Of these, 78% had a bacterial pathogen detected by PCR but only 32% were culture-positive (P < .0001). Molecular testing had the potential to enable de-escalation in number and/or spectrum of antimicrobials in 77% of patients. Conclusions. Comprehensive molecular testing significantly improves pathogen detection in CAP, particularly in antimicrobial-exposed patients, and requires only a single LRT specimen. It also has the potential to enable early de-escalation from broad-spectrum empirical antimicrobials to pathogen-directed therapy. Publisher PDF
Published: 2016
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31. Reduced turnaround time and improved diagnosis of invasive serogroup B Neisseria meningitidis and Streptococcus pneumoniae infections using a lyophilized quadruplex quantitative PCR

Author: Malcolm Guiver, Steve J. Gray, Edward B. Kaczmarski, and Martin P McHugh
Subjects: Microbiology (medical), Pneumolysin, Neisseria meningitidis serogroup B, Neisseria meningitidis, General Medicine, Meningitis, Meningococcal, Neisseria meningitidis, Serogroup B, Biology, Real-Time Polymerase Chain Reaction, medicine.disease_cause, medicine.disease, Microbiology, Virology, Pneumococcal Infections, Group B, Streptococcus pneumoniae Infections, Streptococcus pneumoniae, Real-time polymerase chain reaction, Bacterial Proteins, medicine, Humans, Meningitis
Abstract: Since 1996 the Meningococcal Reference Unit (MRU) in Manchester has provided a national service for PCR confirmation of meningococcal and pneumococcal disease. Neisseria meningitidis serogroup B is predominant in the UK, accounting for >60 % of cases. In response to this, the MRU has developed a quadruplex quantitative PCR that detects N. meningitidis capsule transporter (ctrA), serogroup B sialyltransferase (siaD B ), Streptococcus pneumoniae pneumolysin (ply) and an internal control. The assay was prepared in a ready-to-use lyophilized format by Applied Biosystems. Laboratory validation showed excellent performance in a specificity panel of 52 isolates and improved detection in comparison with the routine assay. Testing of 244 patient samples showed sensitivity of 93 % [95 % confidence interval (CI): 88–98 %] for the ctrA assay, 95 % (95 % CI: 91–100 %) for the siaD B assay and 100 % (95 % CI: 95–100 %) for the ply assay. Specificity was 100 % (95 % CI: 98–100 %) for both meningococcal targets and 95 % (95 % CI: 92–98 %) for ply. The quadruplex also retained high performance in mixed samples and had acceptable reproducibility. After introduction of the quadruplex into routine use the turnaround time for N. meningitidis group B PCR confirmation reduced from 37 to 29 h and the internal control has proved useful for detecting inhibitory samples. The quadruplex assay provides rapid group B confirmation of meningococcal positive samples, enabling timely public health interventions for the most common disease-causing meningococcal serogroup in the UK.
Published: 2015
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32. Detection of Norovirus by BD MAX™, Xpert

Author: Martin P, McHugh, Daniel, Guerendiain, Alison, Hardie, Juliet, Kenicer, Laura, MacKenzie, and Kate E, Templeton
Subjects: Aged, 80 and over, Male, Vomiting, Norovirus, Middle Aged, Sensitivity and Specificity, Gastroenteritis, Feces, Molecular Diagnostic Techniques, Humans, Female, Reagent Kits, Diagnostic, Multiplex Polymerase Chain Reaction, Aged
Abstract: Norovirus is a leading cause of infectious gastroenteritis, characterized by outbreaks of diarrhoea and vomiting in closed settings. Nucleic acid amplification tests allow rapid and sensitive laboratory diagnosis of norovirus, with a number of commercial platforms now available.Evaluate the performance of the Becton Dickinson BD-MAX™System, Cepheid Xpert® Norovirus Assay, and Luminex xTAG® Gastrointestinal Pathogen Panel (GPP) for norovirus detection in stool. Assess the performance of the Xpert® Norovirus Assay and BD-MAX™ in vomit samples.163 diarrhoeal stool samples were tested on four diagnostic systems (laboratory-defined real time RT-PCR (assigned as gold standard), BD MAX™, Xpert® Norovirus Assay, and xTAG® GPP). A further 70 vomit samples were tested on the Xpert and BD MAX platforms.In stool, sensitivity and specificity of the BD-MAX™ was 96.8% and 100%, for Xpert® Norovirus Assay was 91.9% and 100%, and for xTAG® GPP was 79.0% and 87.1%. In vomit samples positive and negative percent agreement was 95.6% and 92.0%, between the BD-MAX™ and Xpert® Norovirus.The BD-MAX™ System with user defined settings and the Xpert® Norovirus Assay showed acceptable sensitivity and specificity for detection of norovirus from stool and vomit. The xTAG GPP assay was less reliable for norovirus detection but can detect a number of other clinically useful enteropathogens. Clinical laboratories must consider skill mix, budget, and sample throughput to determine the best fit for their service.
Published: 2018

33. Underestimation of Staphylococcus aureus (MRSA and MSSA) carriage associated with standard culturing techniques : One third of carriers missed

Author: Daniel Guerendiain, Timothy S. Walsh, Peter J. Gwynne, Martin P McHugh, I. F. Laurenson, Shao-Ting Jerry Tsang, A. H. R. W. Simpson, Julia Boyd, Kate Templeton, University of St Andrews. School of Medicine, and University of St Andrews. Infection and Global Health Division
Subjects: 0301 basic medicine, medicine.medical_specialty, Staphylococcus aureus, Joint arthroplasty, 030106 microbiology, NDAS, medicine.disease_cause, 03 medical and health sciences, Periprosthetic Joint Infection, Internal medicine, Surgical site, Periprosthetic joint infection, Medicine, Orthopedics and Sports Medicine, Staphylococcus Aureus, business.industry, RD Surgery, Surgical Site Infection, Increased risk, Carriage, Nasal Swab, Population study, Surgery, business, Infection, Staphylococcus, Surgical site infection, RD
Abstract: Objectives Nasal carriers of Staphylococcus (S.) aureus (MRSA and MSSA) have an increased risk for healthcare-associated infections. There are currently limited national screening policies for the detection of S. aureus despite the World Health Organization’s recommendations. This study aimed to evaluate the diagnostic performance of molecular and culture techniques in S. aureus screening, determine the cause of any discrepancy between the diagnostic techniques, and model the potential effect of different diagnostic techniques on S. aureus detection in orthopaedic patients. Methods Paired nasal swabs for polymerase chain reaction (PCR) assay and culture of S. aureus were collected from a study population of 273 orthopaedic outpatients due to undergo joint arthroplasty surgery. Results The prevalence of MSSA nasal colonization was found to be between 22.4% to 35.6%. The current standard direct culturing methods for detecting S. aureus significantly underestimated the prevalence (p = 0.005), failing to identify its presence in approximately one-third of patients undergoing joint arthroplasty surgery. Conclusion Modelling these results to national surveillance data, it was estimated that approximately 5000 to 8000 S. aureus surgical site infections could be prevented, and approximately $140 million to $950 million (approximately £110 million to £760 million) saved in treatment costs annually in the United States and United Kingdom combined, by using alternative diagnostic methods to direct culture in preoperative S. aureus screening and eradication programmes. Cite this article: S. T. J. Tsang, M. P. McHugh, D. Guerendiain, P. J. Gwynne, J. Boyd, A. H. R. W. Simpson, T. S. Walsh, I. F. Laurenson, K. E. Templeton. Underestimation of Staphylococcus aureus (MRSA and MSSA) carriage associated with standard culturing techniques: One third of carriers missed. Bone Joint Res 2018;7:79–84. DOI: 10.1302/2046-3758.71.BJR-2017-0175.R1.
Published: 2018
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34. 来自 AD 患者的金黄色葡萄球菌的局部抗生素耐药性

Author: M. T. G. Holden, Julian Parkhill, Katarina Oravcova, Kerry A. Pettigrew, Martin P McHugh, Maeve A. McAleer, Alan D. Irvine, Désirée Bennett, O.M. Fleury, Charlotte M. Proby, Robert S. Dawe, Catriona P. Harkins, and Joan A. Geoghegan
Subjects: Dermatology
Published: 2018
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35. Topical antimicrobial resistance in S. aureus from patients with AD

Author: Julian Parkhill, Katarina Oravcova, M. T. G. Holden, Joan A. Geoghegan, Kerry A. Pettigrew, Martin P McHugh, Maeve A. McAleer, O.M. Fleury, Robert S. Dawe, Alan D. Irvine, Charlotte M. Proby, Désirée Bennett, and Catriona P. Harkins
Subjects: Antibiotic resistance, business.industry, Medicine, Dermatology, business, Microbiology
Published: 2018
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36. Stacked Search For Gravitational Waves From The 2006 Sgr 1900+14 Storm

Author: Antonio Lucianetti, J. Ulmen, P. G. Murray, Keisuke Goda, J. H. Hough, N. A. Robertson, S. Kandhasamy, Jolien D. E. Creighton, D. Ugolini, Douglas R. Cook, Erik Katsavounidis, S. Caride, Michele Zanolin, And J. Zweizig, D. Hammer, F. Seifert, Lindy Blackburn, K. Holt, V. Sandberg, M. Lormand, Giuseppe Castaldi, M. J. Lubinski, Kirk McKenzie, Jonah Kanner, J. C. Dumas, Albert Lazzarini, Tom Fricke, G. McIntyre, John G. Dwyer, Rajesh Kumar, Vladimir B. Braginsky, S. Mrka, G. D. Hammond, K. Kokeyama, N. Fotopoulos, D. J. Hosken, J. G. Rollins, Leo C. Stein, B. Lantz, V. V. Frolov, V. Parameshwaraiah, H. Vahlbruch, K. Riles, C. Veltkamp, H. Overmier, D. Barker, A. Bullington, Rahul Biswas, D. S. Rabeling, K. Haughian, E. Espinoza, M. Weinert, L. Bogue, D. Sellers, V. Kondrashov, R. DeSalvo, S. R. P. Mohapatra, Peter Kalmus, S. Roddy, Supriyo Sinha, B. Moe, Alberto Vecchio, B. Sorazu, A. Thüring, R. L. Ward, L. Prokhorov, Kazuhiro Hayama, K. Mors, B. Behnke, John D. Scott, R. A. Mercer, M. A. Arain, A. C. Melissinos, T. Morioka, Ravi Kumar Kopparapu, A. M. Cruise, Simon Chelkowski, M. Guenther, Gregory M. Harry, H. Lin, R. M. S. Schofield, K. A. Hodge, Roberto Conte, Evan Ochsner, Chad Forrest, Vuk Mandic, J. A. Giaime, D. F. Menéndez, E. E. Doomes, Stanislav Babak, Duncan A. Brown, D. Talukder, C. Pankow, I. W. Harry, M. Lei, C. Aulbert, A. M. Sintes, P. Aufmuth, L. Sancho De La Jordana, Matthew P. Edgar, A. J. Weinstein, T. Z. Summerscales, I. Gholami, W. Wu, Matthew Benacquista, Scott Koranda, L. Matone, A. F. Brooks, E. Chalkley, R. L. Savage, P. Armor, Kevin M. Ryan, Benjamin J. Owen, T. Isogai, Lee Samuel Finn, Tyson Littenberg, R. M. Culter, J. Dueck, Jesper Munch, Cheng Li, N. D. Smith, Jordan Camp, S. Wen, G. S. Allen, H. Yamamoto, P. J. Sutton, C. C. Wipf, Patrick Brady, K. V. Tokmakov, Badri Krishnan, Benno Willke, H. Rehbein, I. W. Martin, P. Shawhan, Virginio Sannibale, J. Betzwieser, A. Franzen, David E. McClelland, Seiji Kawamura, C. Torres, F. Y. Khalili, A. Sibley, C. M. Mow-Lowry, K. Flasch, M. V. Van Der Sluys, Shantanu Desai, P. Charlton, Kip S. Thorne, T. Chalermsongsak, John S. Markowitz, A. Grant, S. B. Anderson, Ruslan Vaulin, David B. Tanner, Chunnong Zhao, David H. Shoemaker, Reinhard Prix, A. Effler, Elizabeth Harstad, V. Raymond, J. H. Romie, Martin Hewitson, Junwei Cao, L. Cunningham, P. Ehrens, F. J. Raab, C. N. Colacino, L. Zhang, T. Reed, Z. Frei, C. Echols, K. Mailand, Rana X. Adhikari, A. Stroeer, Peter Fritschel, P. Lu, O. Burmeister, Gareth Jones, I. Wilmut, I. A. Bilenko, V. Dergachev, B. Machenschalk, M. Sung, Karel E. Urbanek, D. O. Bridges, Maurizio Longo, Walter Winkler, N. A. Lockerbie, A. Ivanov, David J. Ottaway, Osamu Miyakawa, David H. Reitze, E. Hirose, J. E. Brau, Matthew Evans, R. Mittleman, B. F. Whiting, S. H. Huttner, Roman Schnabel, D. Muhammad, A. Stochino, V. P. Mitrofanov, M. C. Araya, Nelson Christensen, F. Donovan, A. S. Markosyan, A. A. van Veggel, Andrew Melatos, Harald Lück, A. Cumming, S. Foley, Efim A. Khazanov, Moritz Mehmet, Kenneth A. Strain, M. Pedraza, G. P. Newton, M. Fyffe, L. Cardenas, Gabriela Gonzalez, Maria Alessandra Papa, H. Mukhopadhyay, B. Johnson, M. Bastarrika, H. Radkins, K. Wette, J. S. Kissel, Timothy Evans, S. Saraf, S. P. Vyachanin, B. Schulz, J. M. Hallam, S. C. McGuire, D. J. A. McKechan, A. Dietz, D. Kasprzyk, B. O'Reilly, S. Klimenko, H. Müller-Ebhardt, D. Sigg, C. Van Den Broeck, C. T. Y. Chung, Michael E Zucker, Roger Jones, Boris Hage, T. Etzel, R. Taylor, P. T. Baker, B. Hughey, S. Giampanis, Ilya Mandel, A. C. Searle, P. Sarin, I. Leonor, John K. Cannizzo, D. Hoyland, P. Savov, Alessandra Buonanno, David Coward, Christian Röver, Hansheng Lei, S. W. Ballmer, Michael Landry, H. R. Williams, R. Gustafson, Yi Pan, T. P. Bodiya, C. M. Reed, James Whelan, P. Ajith, I. Duke, A. L. Stuver, David Jones, G. Moreno, Jon M. Miller, J. Slutsky, Imre Bartos, D. Hoak, Richard A. Matzner, G. Billingsley, V. Quetschke, M. S. Meyer, Bangalore Suryanarayana Sathyaprakash, E. Black, Michael L. Gorodetsky, Marco Cavaglia, E. J. Daw, K. D. Giardina, J. Minelli, C. Barker, Helena Armandula, H. J. Pletsch, Kipp Cannon, G. Traylor, Thomas Corbitt, R. J. S. Greenhalgh, Gavin Davies, R. S. Ottens, J. R. Smith, T. Nash, Sanichiro Yoshida, J. O'Dell, Ke-Xun Sun, K. Kawabe, Rainer Weiss, C. Gray, S. M. Aston, R. W. P. Drever, E. Myers, A. W. Heptonstall, Peter R. Saulson, B. Sears, Mark A. Satterthwaite, Graham Woan, D. B. Kozak, S. Penn, A. Nishizawa, G. H. Ogin, N. Rainer, C. Vorvick, Pamela J. Russell, Yoichi Aso, B. Rivera, Pablo Barriga, A. M. Gretarsson, W. W. Johnson, M. V. Plissi, M. Mageswaran, Kentaro Somiya, M. Ito, L. Wallace, Vicky Kalogera, Robert L. Byer, Stuart Reid, H. Fehrmann, L. Tang, M. Brinkmann, Andreas Freise, Vincenzo Pierro, Matthew Pitkin, Kenji Numata, David Blair, S. E. Strigin, Robert Stone, R. Frey, C. Messenger, C. Robinson, Laura Cadonati, S. Goler, Stefan Hild, Benjamin William Allen, P. T. Beyersdorf, Hartmut Grote, Malcolm B. Gray, M. A. Barton, G. Mendell, R. Wooley, P. J. King, B. Shapiro, J. K. Blackburn, Yaohui Fan, Bernard F. Schutz, Li Ju, Karsten Danzmann, Yasushi Mino, Carlos Cepeda, Robert J. McCarthy, Linqing Wen, P. Raffai, D.B. DeBra, A. G. Wiseman, M. R. Smith, A. S. Sengupta, J. Hanson, Susan M. Scott, Guido Mueller, Teviet Creighton, Slawomir Gras, Nick Leindecker, O. Punken, M. Frei, Sheila Rowan, Neil J. Cornish, Maik Frede, A. Weidner, Ping Koy Lam, Marco Aurelio Diaz, Chad Hanna, D. C. Coyne, C. Wilkinson, Shuichi Sato, P. E. Lindquist, Martin P McHugh, B. J. J. Slagmolen, Fabio Postiglione, P. Kwee, D. Lodhia, K. A. Thorne, A. J. Stein, Fumiko Kawazoe, Riccardo Bassiri, F. Matichard, P. Schwinberg, J. R. Taylor, J. N. Marx, C. I. Torrie, J. Thacker, A. Perreca, E. Maros, P. J. Veitch, D. R. Ingram, Phil Willems, A. Brummit, Soma Mukherjee, Guenakh Mitselmakher, A. M. Sergeev, V. Boschi, Joseph D. Romano, H. Zur Mühlen, W. G. Anderson, Drew Keppel, Zewu Yan, J. H. Clayton, Vincenzo Galdi, Sarah Caudill, Lisa M. Goggin, R. Gouaty, B. Daudert, B. P. Abbott, E. K. Gustafson, R. Bork, Innocenzo M. Pinto, F. Grimaldi, Z. Mrka, D. E. Clark, Thomas Cokelaer, Kasem Mossavi, S. Vass, Jian Zhang, W. Kells, Lucía Santamaría, Soumya D. Mohanty, Maria Ilaria Del Principe, G. P. Szokoly, S. Grunewald, N. Zotov, K. Mason, Sanjeev Dhurandhar, R. M. Martin, S. L. Danilishin, K. L. Dooley, M. Scanlan, Xavier Siemens, Lisa Barsotti, J. Garofoli, Yi Chen, Jan Harms, Lutz Winkelmann, Evan Goetz, Paul Roberts, S. Meshkov, John Veitch, M. MacInnis, R. S. Amin, A. E. Villar, Nergis Mavalvala, Jerome Degallaix, J. Heefner, R. Grosso, John A. Clark, S. J. Waldman, J. Myers, Shourov Chatterji, D. Fazi, Suvadeep Bose, Michele Vallisneri, Ik Siong Heng, S. Steplewski, Emma L. Robinson, S. P. Tarabrin, John Nelson, I. Yakushin, S. E. Whitcomb, S. Sakata, Rubab Khan, Miquel Trias, A. Mullavey, Richard O'Shaughnessy, B. Barr, P. Patel, Malik Rakhmanov, J. Worden, L. Williams, A. Rüdiger, R. Riesen, Roland Schilling, Y. Faltas, Richard J. Abbott, Alexander Khalaidovski, B. Bland, G. Brunet, Z. Raics, and Stephen Fairhurst
Subjects: Physics, High Energy Astrophysical Phenomena (astro-ph.HE), Gravitational wave, gamma rays: bursts, Astrophysics::High Energy Astrophysical Phenomena, MAGNETIZED NEUTRON-STARS, Gamma ray, Soft gamma repeater, Astronomy, FOS: Physical sciences, Astronomy and Astrophysics, Astrophysics, pulsars: individual (SGR 1900+14), LIGO, Neutron star, Stars, stars: neutron, SOFT GAMMA-REPEATERS, Pulsar, gravitational waves, Space and Planetary Science, Astrophysics - High Energy Astrophysical Phenomena, Gamma-ray burst, QC
Abstract: We present the results of a LIGO search for short-duration gravitational waves (GWs) associated with the 2006 March 29 SGR 1900+14 storm. A new search method is used, "stacking'' the GW data around the times of individual soft-gamma bursts in the storm to enhance sensitivity for models in which multiple bursts are accompanied by GW emission. We assume that variation in the time difference between burst electromagnetic emission and potential burst GW emission is small relative to the GW signal duration, and we time-align GW excess power time-frequency tilings containing individual burst triggers to their corresponding electromagnetic emissions. We use two GW emission models in our search: a fluence-weighted model and a flat (unweighted) model for the most electromagnetically energetic bursts. We find no evidence of GWs associated with either model. Model-dependent GW strain, isotropic GW emission energy E_GW, and \gamma = E_GW / E_EM upper limits are estimated using a variety of assumed waveforms. The stacking method allows us to set the most stringent model-dependent limits on transient GW strain published to date. We find E_GW upper limit estimates (at a nominal distance of 10 kpc) of between 2x10^45 erg and 6x10^50 erg depending on waveform type. These limits are an order of magnitude lower than upper limits published previously for this storm and overlap with the range of electromagnetic energies emitted in SGR giant flares., Comment: 7 pages, 3 figures
Published: 2009
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37. The Brans-Dicke Theory and Its Experimental Tests

Author: Martin P. McHugh
Subjects: Physics, Gravitational wave, General relativity, Solar neutrino, Subject (philosophy), 01 natural sciences, Binary pulsar, 010305 fluids & plasmas, symbols.namesake, Theoretical physics, Extension (metaphysics), 0103 physical sciences, Brans–Dicke theory, symbols, Einstein, 010306 general physics
Abstract: Carl Brans submitted his doctoral dissertation to the Princeton committee in May of 1961. By November, the Brans-Dicke theory was disseminated widely with the publication of a 10-page paper in Physical Review. An extension of Einstein’s general relativity, it generated great interest and was the subject of enormous effort to test its implications experimentally. We examine the history and impact of the experimental tests of this theory.
Published: 2016
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38. Search for gravitational-wave bursts in LIGO data from the fourth science run

Author: Pamela J. Russell, Roger K. Route, K. A. Thorne, J. Betzwieser, D. Ugolini, Stefan Hild, D. B. Kozak, David Jones, C. Vorvick, F. Ya. Khalili, Atsushi J. Nishizawa, Erika D'Ambrosio, Peter R. Saulson, V. Kondrashov, Roman Schnabel, R. Abbott, R. DeSalvo, J. E. Brau, Subhasish Mitra, H. Bantilan, Nicolás Yunes, M. A. Barton, Vincenzo Matta, Benno Willke, J. Clark, Pankaj Sarin, D. Meyers, L. Ruet, S. Gossler, D.B. DeBra, P. J. Sutton, K. Y. Franzen, A. L. Stuver, T. Demma, A. M. Rogan, Giuseppe Castaldi, P. Schwinberg, I. Gholami, Albrecht Rüdiger, Alessandra Buonanno, J. A. Sidles, E. E. Doomes, Fabio Postiglione, Martin P McHugh, B. J. J. Slagmolen, C. Messenger, S. Saraf, P. J. Veitch, J. Bogenstahl, L. Ribichini, Roberto Conte, E. Maros, P. Shawhan, W. G. Anderson, E. Innerhofer, Walter Winkler, Harald Lück, P. Charlton, L. Sancho De La Jordana, I. Wilmut, S. C. McGuire, Michael E Zucker, Massimo Tinto, A. Di Credico, L. Matone, R. L. Ward, Laura Cadonati, J. S. Kissel, B. P. Abbott, C. Aulbert, Ping Koy Lam, Shantanu Desai, Kip S. Thorne, Keisuke Goda, I. A. Bilenko, V. Dergachev, David J. Ottaway, Roger Jones, V. Leonhardt, J. C. Dumas, E. Chin, K. Rawlins, M. Guenther, M. Degree, A. Moylan, J. H. Romie, A. Sibley, S. Vass, Albert Lazzarini, K. Bayer, Erik Katsavounidis, Susan M. Scott, Teviet Creighton, M. J. Lubinski, D. Jackrel, Chad Hanna, F. J. Raab, B. Bland, K. Kawabe, Marco Aurelio Diaz, S. M. Aston, W. Kells, M. R. Smith, S. Wen, D. Busby, X. Siemens, V. P. Mitrofanov, John G. Dwyer, R. Gustafson, B. Rivera, Pablo Barriga, Daniel C. Woods, Vladimir B. Braginsky, H. Vahlbruch, K. Riles, M. A. Arain, T. Etzel, M. Mageswaran, S. Giampanis, John Worden, Boris Hage, S. H. Huttner, Gregory M. Harry, M. C. Araya, M. Lei, E. Espinoza, M. Weinert, David H. Shoemaker, C. Torres, A. Rodriguez, C. Barker, Andreas Freise, Vincenzo Pierro, K. Kokeyama, P. G. Murray, Holger J. Pletsch, C. Wilkinson, C. Zhao, Alicia M. Sintes, M. Ramsunder, E. Hirose, Juri Agresti, A. Dietz, Badri Krishnan, E. Chalkey, Matthew Pitkin, M. Varvella, R. Wooley, J. Heefner, R. Grosso, Stephen Fairhurst, J. Zweizig, Antony C. Searle, R. P. Croce, D. J. Hosken, C. M. Mow-Lowry, J. G. Rollins, Yousuke Itoh, Marco G. Tarallo, I. W. Martin, B. Johnson, J. H. Hough, D. Kasprzyk, Frank Seifert, D. Hoyland, Virginio Sannibale, David E. McClelland, M. Samidi, T. Hayler, Peter Fritschel, J. Dickson, C. I. Torrie, Jan Harms, A. S. Sengupta, A. J. Weinstein, W. Wu, P. T. Beyersdorf, V. Boschi, K. C. Cannon, J. Slutsky, C. Van Den Broeck, Kris Ryan, D. Webber, J. Greenhalgh, S. Wise, I. Yakushin, Helge Müller-Ebhardt, Michele Vallisneri, S. E. Whitcomb, S. Grunewald, K. Mailand, Maurizio Longo, Krzysztof Belczynski, Douglas R. Cook, R. Mittleman, Ravi Kumar Kopparapu, Soumya D. Mohanty, Rana X. Adhikari, C. Gray, M. Ito, A. M. Cruise, Ik Siong Heng, R.L. Coldwell, Evan Goetz, Gareth Jones, Nelson Christensen, N. Zotov, P. Cochrane, Emma L. Robinson, V. Quetschke, Bangalore Suryanarayana Sathyaprakash, E. Black, Martin M. Fejer, J. R. Smith, R. Bork, G. Traylor, Kentaro Somiya, Michele Zanolin, P. Kwee, A. Grant, B. Machenschalk, C. A. Cantley, K. Mason, Eric Howell, T. Nash, Michael Landry, Sanjeev Dhurandhar, Kenji Numata, L. Zhang, J. Zhang, Vuk Mandic, Thomas Corbitt, S. Sakata, Miquel Trias, Richard O'Shaughnessy, B. Barr, P. Patel, Malik Rakhmanov, S. B. Anderson, Kenneth G. Libbrecht, C. Robinson, Benjamin William Allen, S. Ray-Majumder, Karsten Danzmann, Kirk McKenzie, S. Meshkov, L. Williams, R. L. Savage, H. Ward, Peter King, A. Heptonstall, R. Riesen, Slawomir Gras, Roland Schilling, Stefano Marano, G. Billingsley, C. N. Colacino, M. Malec, H. Rehbein, K. Watts, Oliver Burmeister, Vincenzo Galdi, Francesco Chiadini, D. M. Whitbeck, D. R. Ingram, Phil Willems, Morag M. Casey, M. Heurs, Yi Chen, N. Fotopoulos, R. Rahkola, A. Franzen, A. E. Villar, Alberto Vecchio, Graham Woan, David B. Tanner, D. M. Strom, A. C. Melissinos, V. V. Frolov, Robert L. Byer, V. Parameshwaraiah, Nergis Mavalvala, Stuart Reid, Jerome Degallaix, H. Yamamoto, John Veitch, R. J. Dupuis, Jong H. Chow, B. C. Barish, David Crooks, T. T. Fricke, Lisa M. Goggin, D. Chin, Supriyo Sinha, Stanislav Babak, Bernard F. Schutz, Li Ju, Sascha Schediwy, M. MacInnis, R. S. Amin, A. Cumming, Eugeniy E. Mikhailov, J. Hanson, Duncan A. Brown, Guido Mueller, A. M. Gretarsson, M. Sung, E. Messaritaki, G. Mendell, Sheila Rowan, A. Brooks, P. Ehrens, H. zur Mühlen, N. A. Lockerbie, B. Lantz, Carlos Cepeda, Robert J. McCarthy, J. A. Giaime, K. Wette, Timothy Evans, Karel E. Urbanek, Gianpietro Cagnoli, D. Sigg, S. W. Ballmer, R. M. S. Schofield, G. Moreno, M. Fyffe, Gabriela Gonzalez, Benjamin J. Owen, Shuichi Sato, P. Savov, James Whelan, P. Ajith, M. Pedraza, J. Myers, E. Myers, Christopher Wipf, K. V. Tokmakov, Shourov Chatterji, D. Fazi, S. J. Waldman, Suvadeep Bose, Martin Hewitson, Junwei Cao, Maria Alessandra Papa, Malcolm B. Gray, Joseph D. Romano, Jared Markowitz, Vincenzo Fiumara, Fumiko Kawazoe, Kasem Mossavi, Kent Blackburn, J. Thacker, Soma Mukherjee, Drew Keppel, Zewu Yan, R. Taylor, N. A. Robertson, G. Diederichs, Helena Armandula, Andre Thüring, Ke-Xun Sun, D. Hammer, Michael C. B. Ashley, Peter Kalmus, Carlo Ungarelli, Jason S. Pelc, I. Leonor, John K. Cannizzo, K. D. Giardina, J. W C McNabb, Jordan Camp, T. Meier, J. Dalrymple, G. Newton, B. Lee, Matthew Evans, L. Cardenas, M. V. Plissi, Hartmut Grote, S. Klimenko, D. Barker, P. E. Lindquist, Peter Aufmuth, M. Lormand, S. Roddy, B. Bhawal, J. N. Marx, A. Bullington, Rahul Biswas, Lee Samuel Finn, L. Bogue, Sean T. McWilliams, J. Garofoli, Shuhei Yoshida, B. F. Whiting, H. Overmier, L. Wallace, R. Frey, D. Sellers, Simon Chelkowski, A. G. Wiseman, D. C. Coyne, D. Hoak, Patrick Brady, T. Z. Summerscales, Hirotaka Takahashi, Gavin Davies, B. Sears, Guenakh Mitselmakher, Vicky Kalogera, A. Bunkowski, Jonathan C. Leiner, S. Márka, V. Re, Yaohui Fan, Kenneth A. Strain, A. Weidner, Innocenzo M. Pinto, Thomas Cokelaer, Rainer Weiss, R. W. P. Drever, Seiji Kawamura, Reinhard Prix, Elizabeth Harstad, W. W. Johnson, Osamu Miyakawa, David H. Reitze, B. O'Reilly, N. Rainer, David Blair, Yi Pan, Jolien D. E. Creighton, Lindy Blackburn, Chunglee Kim, V. Sandberg, D. S. Rabeling, R. A. Mercer, Jesper Munch, A. Ivanov, H. Radkins, Damien Mudge, S. P. Vyachanin, M. Brinkmann, W. Tyler, David Coward, S. Penn, LSC Collaboration, The, Castaldi, G., Galdi, V., Pierro, V., and Pinto, I. M.
Subjects: Physics, Physics and Astronomy (miscellaneous), Gravitational wave, Monte Carlo method, FOS: Physical sciences, Astrophysics, General Relativity and Quantum Cosmology (gr-qc), LIGO, General Relativity and Quantum Cosmology, Black hole, QC350, Amplitude, Binary black hole, NAUTILUS, EXPLORER, Waveform, Noise (radio), QC
Abstract: The fourth science run of the LIGO and GEO 600 gravitational-wave detectors, carried out in early 2005, collected data with significantly lower noise than previous science runs. We report on a search for short-duration gravitational-wave bursts with arbitrary waveform in the 64-1600 Hz frequency range appearing in all three LIGO interferometers. Signal consistency tests, data quality cuts, and auxiliary-channel vetoes are applied to reduce the rate of spurious triggers. No gravitational-wave signals are detected in 15.5 days of live observation time; we set a frequentist upper limit of 0.15 per day (at 90% confidence level) on the rate of bursts with large enough amplitudes to be detected reliably. The amplitude sensitivity of the search, characterized using Monte Carlo simulations, is several times better than that of previous searches. We also provide rough estimates of the distances at which representative supernova and binary black hole merger signals could be detected with 50% efficiency by this analysis., Comment: Corrected amplitude sensitivities (7% change on average); 30 pages, submitted to Classical and Quantum Gravity
Published: 2007
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39. Stochastic background search correlating ALLEGRO with LIGO engineering data

Author: Albert Lazzarini, Martin P McHugh, James Whelan, E. J. Daw, and Ik Siong Heng
Subjects: Physics, Physics and Astronomy (miscellaneous), 010308 nuclear & particles physics, Gravitational wave, Frequency band, Bar (music), Detector, Astrophysics::Instrumentation and Methods for Astrophysics, FOS: Physical sciences, General Relativity and Quantum Cosmology (gr-qc), Astrophysics, 01 natural sciences, General Relativity and Quantum Cosmology, LIGO, Interferometry, 0103 physical sciences, Astronomical interferometer, 010306 general physics, Environmental noise
Abstract: We describe the role of correlation measurements between the LIGO interferometer in Livingston, LA, and the ALLEGRO resonant bar detector in Baton Rouge, LA, in searches for a stochastic background of gravitational waves. Such measurements provide a valuable complement to correlations between interferometers at the two LIGO sites, since they are sensitive in a different, higher, frequency band. Additionally, the variable orientation of the ALLEGRO detector provides a means to distinguish gravitational wave correlations from correlated environmental noise. We describe the analysis underway to set a limit on the strength of a stochastic background at frequencies near 900 Hz using ALLEGRO data and data from LIGO's E7 Engineering Run., 8 pages, 2 encapsulated PostScript figures, uses IOP class files, submitted to the proceedings of the 7th Gravitational Wave Data Analysis Workshop (which will be published in Classical and Quantum Gravity)
Published: 2003
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40. Allegro: noise performance and the ongoing search for gravitational waves

Author: W. W. Johnson, E. J. Daw, Ik Siong Heng, W. O. Hamilton, J. A. Giaime, and Martin P McHugh
Subjects: Gravitation, Physics, Physics and Astronomy (miscellaneous), Physics::Instrumentation and Detectors, Gravitational wave, Acoustics, Detector, Astrophysics, Impulse (physics), Noise level, Electronic equipment, Particle detector, LIGO
Abstract: The noise performance of Allegro since 1993 is summarized. We show that the noise level of Allegro is, in general, stationary. Non-Gaussian impulse excitations persist despite efforts to isolate the detector from environmental disturbances. Some excitations are caused by seismic activity and flux jumps in the SQUID. Algorithms to identify and automatically veto these events are presented. Also, the contribution of Allegro to collaborations with other resonant-mass detectors via the International Gravitational Event Collaboration and with LIGO is reviewed.
Published: 2002
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41. Progress on stochastic background search codes for LIGO

Author: Warren G. Anderson, James Whelan, Martha Casquette, Joseph D. Romano, Alberto Vecchio, M. C. Díaz, Rosa M. Trejo, Ik Siong Heng, C. Torres, and Martin P McHugh
Subjects: Physics, Physics and Astronomy (miscellaneous), 010308 nuclear & particles physics, Gravitational wave, business.industry, Detector, Astrophysics::Instrumentation and Methods for Astrophysics, FOS: Physical sciences, Astronomy, General Relativity and Quantum Cosmology (gr-qc), 01 natural sciences, General Relativity and Quantum Cosmology, LIGO, Interferometry, Software, 0103 physical sciences, Astronomical interferometer, business, 010303 astronomy & astrophysics
Abstract: One of the types of signals for which the LIGO interferometric gravitational wave detectors will search is a stochastic background of gravitational radiation. We review the technique of searching for a background using the optimally-filtered cross-correlation statistic, and describe the state of plans to perform such cross-correlations between the two LIGO interferometers as well as between LIGO and other gravitational-wave detectors, in particular the preparation of software to perform such data analysis., Comment: 7 pages, 1 encapsulated PostScript figure, uses IOP class files, submitted to the proceedings of the 4th Amaldi meeting (which will be published in Classical and Quantum Gravity)
Published: 2002
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42. THE ALLEGRO GRAVITATIONAL WAVE DETECTOR

Author: Warren W. Johnson, W. O. Hamilton, G. Santostasi, Z. A. Allen, and Martin P McHugh
Subjects: Physics, Gravitational-wave observatory, Optics, Space and Planetary Science, Continuous operation, Duty cycle, business.industry, Astronomy and Astrophysics, Astrophysics, Noise level, business, Mathematical Physics
Abstract: The ALLEGRO gravitational wave detector has been in nearly continuous operation for the past four years with a duty cycle of over 90%. The data is continuously filtered for bursts and has a noise level near 12 mK , or 8×10-22 strain/Hz. An initial data exchange under the IGEC has been completed.
Published: 2000
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43. Cutoff frequencies and noise power law model of spectral density: adaptation of the multivariance method for irregularly spaced timing data using the lowest-mode estimator approach

Author: Martin P McHugh, G. Zalamansky, Francois Vernotte, and E. Lantz
Subjects: Noise power, Acoustics and Ultrasonics, Spectral density estimation, Estimator, Spectral density, Noise, Phase noise, Statistics, Cutoff, Sensitivity (control systems), Electrical and Electronic Engineering, Instrumentation, Algorithm, Mathematics
Abstract: The concept of structure functions, which is an extension of the variance approach, is useful to determine the variance (the structure function) which is optimized for a type of noise and for an order of drift. The multivariance method was developed to use different variances over the same signal. It is then possible to select a set of variances in which each variance is optimized to the determination of one parameter (of one noise level, drift, or cutoff frequency). Recently, we adapted this method to irregularly spaced timing data. In this connection, we replaced the structure functions by another method of spectral density estimation: the lowest-mode estimator, introduced by J.E. Deeter and P.E. Boynton (1982, 1984) for the analysis of pulsar timing data. Different lowest-mode estimators can be constructed according to two priorities: the order of drifts that must be removed and the type of noise for which the sensitivity must be maximum. Thus, a multivariance system is developed using a set of different estimators. The details of this method are described, and the results for different signals are discussed in this paper.
Published: 1996
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44. Reply to Zelyas and Robinson

Author: Adam T. Hill, Harriet Mark, Martin P McHugh, Naomi J. Gadsby, Ian F. Laurenson, Kate Templeton, Clark D Russell, and Andrew Conway Morris
Subjects: 0301 basic medicine, Microbiology (medical), 03 medical and health sciences, 0302 clinical medicine, Infectious Diseases, business.industry, 030106 microbiology, Medicine, Library science, 030212 general & internal medicine, business
Published: 2016
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45. IGEC2: A 17-month search for gravitational wave bursts in 2005-2007

Author: L. Taffarello, M. Bassan, G. Cavallari, J. Hanson, A. Rocchi, L. Baggio, Stefano Longo, Antonello Ortolan, R. Terenzi, W. O. Hamilton, G. Giordano, S. Frasca, A. Mion, L. Conti, J. P. Zendri, F.J. Ronga, G. Modestino, Andrea Carlo Marini, Damon Nettles, G. A. Prodi, Riccardo Sturani, Stefano Foffa, Martin P McHugh, G. Pizzella, Michele Maggiore, Arturo Moleti, Francesco Salemi, M. Visco, S. D'Antonio, Giovanni Vittorio Pallottino, P. Miller, Michele Bonaldi, G. Vedovato, M. Bignotto, E. Coccia, W. W. Johnson, J. Weaver, M. Drago, Pierluigi Fortini, P. Bonifazi, M. Di Paolo Emilio, Renato Mezzena, Francesco Marin, P. Zhang, N. Liguori, V. Re, Stefano Vitale, Y. Minenkov, Paolo Falferi, Andrea Vinante, Massimo Cerdonio, S. Poggi, P. Astone, V. Fafone, Laboratoire Atmosphères, Milieux, Observations Spatiales (LATMOS), and Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: coincidenze, Nuclear and High Energy Physics, Gravitational wave detectors and experiments, Onde Gravitazionali, FOS: Physical sciences, Astrophysics, ddc:500.2, General Relativity and Quantum Cosmology (gr-qc), Particle detector, General Relativity and Quantum Cosmology, Observatory, Coincident, Gravitational radiation magnetic fields and other observations, fondo, Relativity and gravitation, Physics, AURIGA, General Relativity and Cosmology, Gravitational wave, 95.85.Sz, Settore FIS/01 - Fisica Sperimentale, Astronomy, rivelatori, 04.80.Nn, LIGO, Amplitude, Duty cycle, [SDU]Sciences of the Universe [physics], Onde Gravitazionali, rivelatori, coincidenze, fondo, 95.30.Sf
Abstract: We present here the results of a 515 days long run of the IGEC2 observatory, consisting of the four resonant mass detectors ALLEGRO, AURIGA, EXPLORER and NAUTILUS. The reported results are related to the fourfold observation time from Nov. 6 2005 until Apr. 14 2007, when Allegro ceased its operation. This period overlapped with the first long term observations performed by the LIGO interferometric detectors. The IGEC observations aim at the identification of gravitational wave candidates with high confidence, keeping the false alarm rate at the level of 1 per century, and high duty cycle, namely 57% with all four sites and 94% with at least three sites in simultaneous observation. The network data analysis is based on time coincidence searches over at least three detectors: the four 3-fold searches and the 4-fold one are combined in a logical OR. We exchanged data with the usual blind procedure, by applying a unique confidential time offset to the events in each set of data. The accidental background was investigated by performing sets of 10^8 coincidence analyses per each detector configuration on off-source data, obtained by shifting the time series of each detector. The thresholds of the five searches were tuned so as to control the overall false alarm rate to 1/century. When the confidential time shifts was disclosed, no gravitational wave candidate was found in the on-source data. As an additional output of this search, we make available to other observatories the list of triple coincidence found below search thresholds, corresponding to a false alarm rate of 1/month., Comment: 10 pages, 8 figures Accepted for publication on Phys. Rev. D
Published: 2010
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46. First LIGO search for gravitational wave bursts from cosmic (super)strings

Author: I. Leonor, John K. Cannizzo, D. Hoak, Michael L. Gorodetsky, T. Morioka, Ravi Kumar Kopparapu, Soumya D. Mohanty, N. Zotov, K. Mason, I. Duke, A. L. Stuver, E. J. Daw, M. V. Plissi, Hartmut Grote, S. Penn, A. M. Cruise, K. D. Giardina, Pamela J. Russell, Sanjeev Dhurandhar, Neil J. Cornish, P. E. Lindquist, Shantanu Desai, Kip S. Thorne, T. Chalermsongsak, R. M. Martin, Stefan Hild, Peter Aufmuth, Vuk Mandic, T. Reed, J. N. Marx, Yoichi Aso, A. Stochino, V. P. Mitrofanov, Yasushi Mino, J. H. Clayton, C. M. Reed, M. Scanlan, Yi Chen, M. S. Meyer, J. A. Giaime, Boris Hage, Peter Fritschel, D. Muhammad, L. Wallace, R. Frey, Rainer Weiss, R. W. P. Drever, P. J. King, D. F. Menéndez, F. Robinet, S. Márka, A. Stroeer, Kenneth A. Strain, B. O'Reilly, Yi Pan, C. T. Y. Chung, W. W. Johnson, A. G. Wiseman, Alexander Khalaidovski, D. S. Rabeling, John D. Scott, A. C. Searle, Michael E Zucker, J. Dueck, C. Aulbert, R. L. Ward, P. J. Sutton, David Blair, D. C. Coyne, R. A. Mercer, H. J. Pletsch, G. Traylor, Thomas Corbitt, Benno Willke, D. B. Kozak, C. Vorvick, B. Bland, G. Brunet, Matthew P. Edgar, J. Betzwieser, R. M. Culter, Jesper Munch, Malcolm B. Gray, Rana X. Adhikari, P. Raffai, Gareth Jones, N. A. Robertson, B. Machenschalk, G. Mendell, J. H. Romie, L. Cunningham, F. J. Raab, S. Saraf, Laura Cadonati, F. Donovan, Z. Frei, Antonio Lucianetti, J. Ulmen, Alessandra Buonanno, D. Ugolini, Z. Raics, H. Lin, Kipp Cannon, Karel E. Urbanek, D. O. Bridges, S. Kandhasamy, H. Fehrmann, L. Tang, Maik Frede, A. Weidner, P. Schwinberg, G. P. Newton, M. Fyffe, Walter Winkler, C. Messenger, Gabriela Gonzalez, J. M. Hallam, B. Shapiro, N. Fotopoulos, C. Veltkamp, A. S. Markosyan, Harald Lück, H. Mukhopadhyay, D. Hammer, F. Seifert, Kevin M. Ryan, Susan M. Scott, Teviet Creighton, Keisuke Goda, M. Lormand, K. Flasch, S. R. P. Mohapatra, Peter Kalmus, S. H. Huttner, H. Overmier, Kirk McKenzie, Stephen Fairhurst, R. S. Ottens, Chad Hanna, X. Siemens, C. Wilkinson, A. Ivanov, C. Robinson, Benjamin William Allen, Karsten Danzmann, Slawomir Gras, Ping Koy Lam, D. Sellers, H. Radkins, R. Gustafson, A. Bullington, Rahul Biswas, L. Bogue, S. P. Vyachanin, M. Brinkmann, Marco Aurelio Diaz, Simon Chelkowski, M. Guenther, S. C. McGuire, D. J. A. McKechan, S. Sakata, S. Giampanis, Ilya Mandel, Rubab Khan, Miquel Trias, D. Barker, David Coward, Erik Katsavounidis, Andrew Melatos, B. Schulz, H. Zur Mühlen, W. G. Anderson, M. J. Lubinski, E. Chalkley, P. Shawhan, Alberto Vecchio, A. Mullavey, L. Prokhorov, G. S. Allen, S. E. Strigin, Nick Leindecker, John G. Dwyer, Christian Röver, Jordan Camp, T. Etzel, J. Slutsky, Imre Bartos, A. Dietz, B. Hughey, P. Charlton, A. Franzen, B. Sorazu, Richard O'Shaughnessy, B. Barr, P. Patel, Malik Rakhmanov, I. A. Bilenko, J. Worden, L. Williams, A. Rüdiger, S. Roddy, M. Bastarrika, B. P. Abbott, E. K. Gustafson, D. E. Clark, V. Quetschke, M. A. Barton, V. Dergachev, C. Echols, H. Rehbein, J. Zweizig, Bangalore Suryanarayana Sathyaprakash, E. Black, J. R. Smith, R. Bork, Patrick Brady, Rajesh Kumar, Vladimir B. Braginsky, H. Vahlbruch, K. Riles, A. Thüring, C. I. Torrie, David J. Ottaway, K. Mailand, E. Espinoza, A. C. Melissinos, M. Weinert, Maurizio Longo, Jonah Kanner, R. Riesen, S. Vass, Jian Zhang, W. Kells, T. Nash, Lucía Santamaría, S. B. Anderson, J. C. Dumas, Chad Forrest, Roland Schilling, D.B. DeBra, Richard A. Matzner, Ruslan Vaulin, David B. Tanner, G. H. Ogin, J. R. Taylor, A. M. Sintes, B. Moe, Fumiko Kawazoe, D. R. Ingram, Phil Willems, A. Brummit, R. Mittleman, T. Z. Summerscales, Jolien D. E. Creighton, Albert Lazzarini, K. Mors, R. J. S. Greenhalgh, Gavin Davies, Nelson Christensen, Tom Fricke, Matthew Evans, L. Cardenas, J. Thacker, Lee Samuel Finn, R. Taylor, Y. Faltas, Soma Mukherjee, Drew Keppel, Zewu Yan, M. Sung, C. Barker, Roman Schnabel, S. Caride, Lindy Blackburn, M. Ito, K. Holt, V. Sandberg, A. F. Brooks, S. Klimenko, Tyson Littenberg, B. Sears, Atsushi J. Nishizawa, J. E. Brau, V. V. Frolov, A. A. van Veggel, Efim A. Khazanov, Moritz Mehmet, B. Behnke, M. Pedraza, Samuel J. Waldman, Vicky Kalogera, K. Kokeyama, A. E. Villar, Fabio Postiglione, T. P. Bodiya, Maria Alessandra Papa, M. R. Smith, Badri Krishnan, V. Parameshwaraiah, Sarah Caudill, Lisa M. Goggin, P. Kwee, A. S. Sengupta, Pankaj Sarin, A. Perreca, K. A. Thorne, H. R. Williams, Guenakh Mitselmakher, Supriyo Sinha, G. P. Szokoly, I. Yakushin, Stanislav Babak, Robert Stone, R. Gouaty, B. Daudert, S. E. Whitcomb, Roberto Conte, Scott Koranda, P. Baker, D. J. Hosken, Duncan A. Brown, K. A. Hodge, C. M. Mow-Lowry, F. Matichard, Nergis Mavalvala, M. C. Araya, P. Ehrens, L. Matone, A. M. Sergeev, Hansheng Lei, Giuseppe Castaldi, S. Grunewald, Helena Armandula, J. G. Rollins, P. J. Veitch, Mark A. Satterthwaite, Yaohui Fan, A. Sibley, Jerome Degallaix, David Jones, Evan Ochsner, A. J. Weinstein, J. O'Dell, Ke-Xun Sun, N. Rainer, Leo C. Stein, I. Gholami, W. Wu, P. T. Beyersdorf, M. V. van der Sluys, Cheng Li, Marco Cavaglia, Martin P McHugh, B. J. J. Slagmolen, M. Landry, J. Heefner, R. Grosso, R. L. Savage, P. Armor, K. Haughian, T. Isogai, B. F. Whiting, John A. Clark, Innocenzo M. Pinto, Riccardo Bassiri, A. Grant, F. Grimaldi, Carlos Cepeda, Robert J. McCarthy, A. W. Heptonstall, Peter R. Saulson, L. Zhang, C. Torres, Maria Ilaria Del Principe, Seiji Kawamura, Kazuhiro Hayama, F. Y. Khalili, E. Maros, Thomas Cokelaer, D. Talukder, G. McIntyre, Reinhard Prix, A. Effler, Elizabeth Harstad, Linqing Wen, C. Pankow, I. W. Harry, Shuichi Sato, R. Abbott, H. Yamamoto, D. Lodhia, Osamu Miyakawa, S. Wen, C. N. Colacino, N. D. Smith, C. Van Den Broeck, K. Wette, Timothy Evans, V. Boschi, Joseph D. Romano, Jared Markowitz, David H. Reitze, S. Foley, Kasem Mossavi, Chunnong Zhao, Michele Vallisneri, J. Myers, Ik Siong Heng, David H. Shoemaker, S. Steplewski, Shourov Chatterji, D. Fazi, Suvadeep Bose, Emma L. Robinson, P. Lu, O. Burmeister, Z. Márka, S. P. Tarabrin, John Nelson, S. Goßler, D. Sigg, M. A. Arain, B. Johnson, D. Kasprzyk, Gregory M. Harry, V. Kondrashov, M. Lei, V. Raymond, R. DeSalvo, N. A. Lockerbie, C. Gray, S. W. Ballmer, E. E. Doomes, E. Myers, Kentaro Somiya, Kenji Numata, L. Sancho De La Jordana, D. Hoyland, G. Moreno, P. Savov, James Whelan, P. Ajith, I. W. Martin, P. G. Murray, Virginio Sannibale, David E. McClelland, J. H. Hough, Douglas R. Cook, Michele Zanolin, G. D. Hammond, Andreas Freise, Vincenzo Pierro, Matthew Pitkin, R. Wooley, O. Punken, M. Frei, Lutz Winkelmann, John Veitch, M. MacInnis, R. S. Amin, I. Wilmut, J. S. Kissel, Roger Jones, K. Kawabe, S. M. Aston, B. Rivera, Pablo Barriga, M. Mageswaran, J. Garofoli, Jan Harms, Evan Goetz, Paul Roberts, S. Meshkov, Vincenzo Galdi, S. L. Danilishin, K. L. Dooley, Lisa Barsotti, A. Cumming, J. Minelli, A. M. Gretarsson, J. K. Blackburn, Sheila Rowan, Sanichiro Yoshida, Graham Woan, Robert L. Byer, Stuart Reid, Bernard F. Schutz, Li Ju, J. Hanson, Guido Mueller, A. J. Stein, B. Lantz, R. M. S. Schofield, Matthew Benacquista, Benjamin J. Owen, Christopher Wipf, K. V. Tokmakov, Martin Hewitson, Junwei Cao, E. Hirose, H. Müller-Ebhardt, Jon M. Miller, G. Billingsley, LSC Collaboration, The, Castaldi, G., Galdi, V., Pierro, V., Pinto, I. M., Principe, M., The LIGO Scientific Collaboration, Laboratoire de l'Accélérateur Linéaire (LAL), and Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université Paris-Sud - Paris 11 (UP11)
Subjects: Nuclear and High Energy Physics, Cosmology and Nongalactic Astrophysics (astro-ph.CO), Gravitational-wave observatory, Physics and Astronomy (miscellaneous), [SDU.ASTR.CO]Sciences of the Universe [physics]/Astrophysics [astro-ph]/Cosmology and Extra-Galactic Astrophysics [astro-ph.CO], Astrophysics::High Energy Astrophysical Phenomena, FOS: Physical sciences, Astrophysics, 01 natural sciences, String (physics), [PHYS.ASTR.CO]Physics [physics]/Astrophysics [astro-ph]/Cosmology and Extra-Galactic Astrophysics [astro-ph.CO], Gravitation, General Relativity and Quantum Cosmology, 0103 physical sciences, 010306 general physics, QC, Nuclear and High Energy Physic, QB, Physics, COSMIC cancer database, 010308 nuclear & particles physics, Gravitational wave, Superstring theory, LIGO, Cosmic string, [PHYS.GRQC]Physics [physics]/General Relativity and Quantum Cosmology [gr-qc], Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract: We report on a matched-filter search for gravitational wave bursts from cosmic string cusps using LIGO data from the fourth science run (S4) which took place in February and March 2005. No gravitational waves were detected in 14.9 days of data from times when all three LIGO detectors were operating. We interpret the result in terms of a frequentist upper limit on the rate of gravitational wave bursts and use the limits on the rate to constrain the parameter space (string tension, reconnection probability, and loop sizes) of cosmic string models., Comment: 11 pages, 3 figures. Replaced with version submitted to PRD
Published: 2009
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47. Search for gravitational waves from low mass compact binary coalescence in 186 days of LIGO's fifth science run

Author: K. Mailand, Maurizio Longo, R. Mittleman, Nelson Christensen, Hansheng Lei, Alberto Vecchio, L. Prokhorov, P. Ehrens, N. D. Smith, K. Wette, Timothy Evans, Sanichiro Yoshida, Graham Woan, Robert L. Byer, Stuart Reid, H. Yamamoto, V. Raymond, R. L. Ward, P. J. Sutton, J. H. Romie, L. Cunningham, D. Sigg, S. W. Ballmer, G. Moreno, B. Hughey, F. J. Raab, S. Saraf, C. Messenger, N. A. Lockerbie, Ping Koy Lam, R. Gustafson, Roman Schnabel, J. E. Brau, A. A. van Veggel, Efim A. Khazanov, Moritz Mehmet, Carlos Cepeda, Robert J. McCarthy, Linqing Wen, Ke Sun, Bernard F. Schutz, Li Ju, D. Hoyland, C. I. Torrie, G. McIntyre, Shuichi Sato, S. H. Huttner, H. R. Williams, J. Hanson, P. Savov, S. E. Strigin, M. A. Arain, Gregory M. Harry, James Whelan, S. Penn, M. Lei, I. W. Martin, D. R. Ingram, Virginio Sannibale, David E. McClelland, Andrew Melatos, B. Schulz, D. Lodhia, A. Dietz, I. Leonor, John K. Cannizzo, Pamela J. Russell, Nick Leindecker, J. Zweizig, M. Bastarrika, Phil Willems, A. Brummit, Guido Mueller, P. Ajith, I. Duke, C. Barker, A. L. Stuver, V. Boschi, Joseph D. Romano, Jared Markowitz, E. J. Daw, Vincenzo Galdi, C. D. Capano, Stefan Hild, A. J. Stein, J. R. Taylor, K. D. Giardina, M. Ito, Kasem Mossavi, B. Behnke, Yasushi Mino, C. Gray, Mark A. Satterthwaite, V. V. Frolov, E. Myers, Soumya D. Mohanty, V. Parameshwaraiah, Benno Willke, N. A. Robertson, D. Hammer, Robert Stone, Kentaro Somiya, F. Seifert, Kenji Numata, Sarah Caudill, N. Zotov, Supriyo Sinha, Stanislav Babak, Alessandra Buonanno, Malcolm B. Gray, P. Raffai, Duncan A. Brown, P. Sarin, Lisa M. Goggin, K. Mason, S. R. P. Mohapatra, Martin P McHugh, Peter Kalmus, Sanjeev Dhurandhar, B. J. J. Slagmolen, R. Gouaty, B. Daudert, S. L. Danilishin, K. Flasch, R. M. Martin, Riccardo Bassiri, David Jones, G. S. Allen, K. L. Dooley, Marco Cavaglia, M. Scanlan, Xavier Siemens, E. Maros, A. E. Villar, Lisa Barsotti, Fumiko Kawazoe, A. Ivanov, A. W. Heptonstall, H. Radkins, Peter R. Saulson, Yi Chen, S. P. Vyachanin, A. Cumming, J. Thacker, R. Abbott, M. Brinkmann, Soma Mukherjee, Drew Keppel, Nergis Mavalvala, Zewu Yan, Jerome Degallaix, David Coward, B. Lantz, Evan Ochsner, Christian Röver, G. Mendell, A. J. Weinstein, I. Gholami, W. Wu, P. T. Beyersdorf, M. V. van der Sluys, J. Minelli, M. Landry, H. Rehbein, S. B. Anderson, Karel E. Urbanek, Antonio Lucianetti, A. M. Gretarsson, D. O. Bridges, A. Grant, L. Zhang, Ruslan Vaulin, David B. Tanner, J. Ulmen, Giuseppe Castaldi, R. M. S. Schofield, Tyson Littenberg, Keisuke Goda, M. Sung, G. P. Newton, M. Fyffe, D. S. Rabeling, Erik Katsavounidis, Matthew Benacquista, M. J. Lubinski, Badri Krishnan, Gabriela Gonzalez, J. M. Hallam, M. Pedraza, John G. Dwyer, Rajesh Kumar, Vladimir B. Braginsky, Maria Alessandra Papa, H. Vahlbruch, K. Riles, Benjamin J. Owen, K. Haughian, E. Espinoza, M. Weinert, C. M. Mow-Lowry, K. Mors, J. K. Blackburn, Christopher Wipf, Kirk McKenzie, John D. Scott, K. V. Tokmakov, Kazuhiro Hayama, N. Fotopoulos, R. A. Mercer, T. Etzel, B. F. Whiting, D. Talukder, C. Pankow, C. Veltkamp, Sheila Rowan, C. Van Den Broeck, K. A. Hodge, I. W. Harry, Martin Hewitson, S. Wen, C. T. Y. Chung, Michael E Zucker, Junwei Cao, Cheng Li, Kipp Cannon, R. S. Ottens, Chunnong Zhao, David H. Shoemaker, P. Lu, O. Burmeister, J. Slutsky, Imre Bartos, S. Goßler, B. Sorazu, H. Lin, Matthew P. Edgar, Marco Aurelio Diaz, V. Quetschke, Bangalore Suryanarayana Sathyaprakash, B. Johnson, D. Kasprzyk, Walter Winkler, A. S. Markosyan, E. Chalkley, A. Thüring, E. Black, J. R. Smith, R. Bork, Peter Fritschel, Harald Lück, R. M. Culter, H. Mukhopadhyay, T. Nash, S. C. McGuire, D. J. A. McKechan, Jesper Munch, A. C. Melissinos, G. H. Ogin, S. Giampanis, Ilya Mandel, T. Morioka, D. Muhammad, Ravi Kumar Kopparapu, P. Shawhan, R. J. S. Greenhalgh, T. Z. Summerscales, J. Heefner, R. Grosso, John A. Clark, P. Charlton, Gavin Davies, A. M. Cruise, Richard A. Matzner, S. Foley, B. Sears, Vicky Kalogera, A. C. Searle, I. A. Bilenko, V. Dergachev, David J. Ottaway, Vuk Mandic, Yaohui Fan, D. Hoak, Michele Vallisneri, H. J. Pletsch, C. Echols, Michael L. Gorodetsky, G. Traylor, J. A. Giaime, Ik Siong Heng, S. Steplewski, Thomas Corbitt, Emma L. Robinson, D. F. Menéndez, Jonah Kanner, Andreas Freise, Vincenzo Pierro, S. P. Tarabrin, Gregory Ely, John Nelson, J. C. Dumas, Albert Lazzarini, Matthew Pitkin, R. Taylor, Laura Cadonati, Tom Fricke, M. V. Plissi, R. Wooley, T. P. Bodiya, V. Kondrashov, K. Kokeyama, R. DeSalvo, E. Hirose, O. Punken, M. Frei, P. Baker, D. J. Hosken, J. G. Rollins, E. E. Doomes, H. Müller-Ebhardt, Jolien D. E. Creighton, Leo C. Stein, J. Garofoli, Susan M. Scott, Jon M. Miller, L. Sancho De La Jordana, G. Billingsley, Teviet Creighton, S. Caride, Lindy Blackburn, Jan Harms, Chad Hanna, S. J. Waldman, C. Wilkinson, K. Holt, Helena Armandula, V. Sandberg, Hartmut Grote, Evan Goetz, J. O'Dell, N. Rainer, Paul Roberts, S. Meshkov, Kevin M. Ryan, Neil J. Cornish, J. Myers, Shourov Chatterji, P. E. Lindquist, D. Fazi, Suvadeep Bose, Lutz Winkelmann, A. Franzen, Z. Márka, John Veitch, B. Moe, M. MacInnis, R. S. Amin, I. Wilmut, J. S. Kissel, Roger Jones, A. Lundgren, K. Kawabe, S. M. Aston, B. Rivera, Pablo Barriga, M. Mageswaran, M. C. Araya, P. G. Murray, J. H. Hough, Shantanu Desai, Kip S. Thorne, T. Chalermsongsak, Rana X. Adhikari, Gareth Jones, B. Machenschalk, Douglas R. Cook, S. Márka, A. Stroeer, Michele Zanolin, F. Donovan, T. Reed, Kenneth A. Strain, A. Perraca, A. Stochino, B. O'Reilly, G. D. Hammond, V. P. Mitrofanov, M. R. Smith, A. S. Sengupta, Yi Pan, Peter Aufmuth, Boris Hage, J. N. Marx, J. H. Clayton, Maria Ilaria Del Principe, H. Fehrmann, L. Tang, Alexander Khalaidovski, C. Robinson, Benjamin William Allen, Karsten Danzmann, Slawomir Gras, B. Bland, G. Brunet, Z. Raics, C. M. Reed, Stephen Fairhurst, J. Dueck, C. Aulbert, M. S. Meyer, D. B. Kozak, C. Vorvick, Z. Frei, Rainer Weiss, Seiji Kawamura, Maik Frede, R. W. P. Drever, Yoichi Aso, Reinhard Prix, A. Effler, Elizabeth Harstad, A. Weidner, P. Schwinberg, L. Wallace, R. Frey, Osamu Miyakawa, David H. Reitze, W. W. Johnson, H. Zur Mühlen, W. G. Anderson, P. J. King, B. Shapiro, J. Betzwieser, B. P. Abbott, E. K. Gustafson, H. Overmier, D. E. Clark, D. Sellers, A. G. Wiseman, Atsushi J. Nishizawa, Simon Chelkowski, S. Vass, M. Guenther, Jian Zhang, D. C. Coyne, Patrick Brady, David Blair, W. Kells, Lucía Santamaría, S. Kandhasamy, M. A. Barton, Roberto Conte, D. Barker, Scott Koranda, L. Matone, S. Roddy, D.B. DeBra, Chad Forrest, A. M. Sintes, Lee Samuel Finn, G. P. Szokoly, A. Sibley, Guenakh Mitselmakher, A. M. Sergeev, S. Grunewald, Innocenzo M. Pinto, F. Grimaldi, Thomas Cokelaer, Fabio Postiglione, P. Kwee, K. A. Thorne, F. Matichard, R. L. Savage, P. Armor, P. J. Veitch, T. Isogai, C. Torres, F. Y. Khalili, A. F. Brooks, C. N. Colacino, I. Yakushin, S. E. Whitcomb, S. Sakata, Rubab Khan, Miquel Trias, A. Mullavey, Richard O'Shaughnessy, B. Barr, P. Patel, Malik Rakhmanov, J. Worden, L. Williams, A. Rüdiger, R. Riesen, Roland Schilling, Y. Faltas, D. Ugolini, M. Lormand, A. Bullington, Rahul Biswas, L. Bogue, Jordan Camp, Matthew Evans, L. Cardenas, S. Klimenko, and The LIGO Scientific Collaboration
Subjects: Coalescence (physics), Physics, Nuclear and High Energy Physics, Gravitational wave, Astrophysics::High Energy Astrophysical Phenomena, X-ray binary, FOS: Physical sciences, Astronomy, General Relativity and Quantum Cosmology (gr-qc), Astrophysics, FORMS, General Relativity and Quantum Cosmology, LIGO, SYNTHESIS MODELS, Neutron star, Binary black hole, Binary star, CONSTRAINING POPULATION, Astrophysics::Solar and Stellar Astrophysics, Low Mass, QC, Astrophysics::Galaxy Astrophysics, QB
Abstract: We report on a search for gravitational waves from coalescing compact binaries, of total mass between 2 and 35M(circle dot), using LIGO observations between November 14, 2006 and May 18, 2007. No gravitational-wave signals were detected. We report upper limits on the rate of compact binary coalescence as a function of total mass. The LIGO cumulative 90%-confidence rate upper limits of the binary coalescence of neutron stars, black holes and black hole-neutron star systems are 1.4x10(-2), 7.3x10(-4) and 3.6x10(-3) yr(-1) L-10(-1), respectively, where L-10 is 10(10) times the blue solar luminosity.
Published: 2009

48. Einstein@Home search for periodic gravitational waves in early S5 LIGO data

Author: C. T. Y. Chung, Walter Winkler, Michael E Zucker, J. Dueck, H. Lin, Laura Cadonati, A. S. Markosyan, Harald Lück, H. Mukhopadhyay, C. Aulbert, Kipp Cannon, R. S. Ottens, S. C. McGuire, D. J. A. McKechan, S. Giampanis, Susan M. Scott, E. Chalkley, S. Kandhasamy, Teviet Creighton, P. Ehrens, Z. Frei, D. S. Rabeling, Ilya Mandel, Rana X. Adhikari, M. R. Smith, Vincenzo Galdi, Marco Aurelio Diaz, Chad Hanna, C. Wilkinson, R. L. Ward, A. S. Sengupta, V. Kondrashov, C. Echols, S. H. Huttner, Chunnong Zhao, K. Wette, Timothy Evans, D. Sigg, S. W. Ballmer, G. Moreno, Antonio Lucianetti, J. Ulmen, Kirk McKenzie, David H. Shoemaker, Sanichiro Yoshida, R. DeSalvo, Andrew Melatos, G. McIntyre, Richard A. Matzner, P. J. Sutton, J. H. Romie, R. J. S. Greenhalgh, Gareth Jones, B. Machenschalk, F. Donovan, P. Lu, O. Burmeister, Shantanu Desai, D. Barker, Kip S. Thorne, P. Shawhan, P. Charlton, B. Sorazu, A. Thüring, A. C. Melissinos, T. Z. Summerscales, Graham Woan, B. Schulz, S. Goßler, T. Chalermsongsak, A. Dietz, R. Taylor, Robert L. Byer, Stuart Reid, E. E. Doomes, Gavin Davies, Benno Willke, S. Roddy, L. Cunningham, John D. Scott, Bruce Allen, T. P. Bodiya, T. Reed, F. J. Raab, Tyson Littenberg, Badri Krishnan, B. Johnson, D. Kasprzyk, Alessandra Buonanno, B. Sears, Bernard F. Schutz, R. A. Mercer, Li Ju, Chad Forrest, M. A. Barton, Roman Schnabel, A. M. Sintes, C. M. Mow-Lowry, B. F. Whiting, V. V. Frolov, V. Parameshwaraiah, Helena Armandula, J. O'Dell, Ke-Xun Sun, N. Rainer, A. F. Brooks, J. Hanson, L. Sancho De La Jordana, Maria Ilaria Del Principe, Peter Fritschel, K. A. Hodge, I. Wilmut, Dustin Anderson, J. S. Kissel, I. A. Bilenko, V. Dergachev, David J. Ottaway, M. A. Arain, Gregory M. Harry, A. Stochino, S. L. Danilishin, K. L. Dooley, J. E. Brau, Guido Mueller, N. D. Smith, C. Van Den Broeck, A. A. van Veggel, D.B. DeBra, Lee Samuel Finn, Giuseppe Castaldi, V. P. Mitrofanov, Boris Hage, S. Saraf, R. Gustafson, Cheng Li, Vicky Kalogera, S. J. Waldman, D. Muhammad, Roger Jones, M. Bastarrika, Efim A. Khazanov, Moritz Mehmet, Lisa Barsotti, Supriyo Sinha, Stanislav Babak, A. J. Stein, M. Lei, Fabio Postiglione, P. Kwee, K. A. Thorne, F. Matichard, I. Yakushin, S. E. Whitcomb, M. Ito, Kevin M. Ryan, Duncan A. Brown, A. Cumming, Matthew P. Edgar, Yoichi Aso, L. Wallace, R. Frey, K. Haughian, P. J. Veitch, S. Penn, Pamela J. Russell, K. Kawabe, G. Allen, A. C. Searle, R. M. Culter, E. Hirose, Jesper Munch, S. E. Strigin, N. Fotopoulos, C. Barker, Atsushi J. Nishizawa, P. J. King, S. M. Aston, B. Rivera, Pablo Barriga, M. Mageswaran, B. Moe, J. Myers, Nick Leindecker, C. Veltkamp, B. Behnke, J. Zweizig, Kazuhiro Hayama, A. G. Wiseman, D. Talukder, C. Pankow, Stefan Hild, Andreas Freise, Vincenzo Pierro, H. R. Williams, A. Franzen, Matthew Pitkin, Shourov Chatterji, Pankaj Sarin, D. Fazi, Suvadeep Bose, Yaohui Fan, H. Müller-Ebhardt, H. J. Pletsch, T. Etzel, G. Traylor, J. Minelli, Thomas Corbitt, I. W. Harry, D. C. Coyne, Yasushi Mino, A. M. Gretarsson, I. W. Martin, R. Wooley, O. Punken, M. Frei, Z. Márka, Robert Stone, Roberto Conte, David Jones, S. Sakata, J. R. Taylor, M. C. Araya, Scott Koranda, S. Wen, Virginio Sannibale, David E. McClelland, Alberto Vecchio, H. Fehrmann, K. Flasch, L. Matone, Marco Cavaglia, L. Prokhorov, L. Tang, Jon M. Miller, J. K. Blackburn, A. Perreca, Guenakh Mitselmakher, Rubab Khan, Miquel Trias, A. Mullavey, Soumya D. Mohanty, Richard O'Shaughnessy, B. Barr, Martin P McHugh, B. J. J. Slagmolen, P. Patel, Malik Rakhmanov, J. Worden, A. W. Heptonstall, Peter R. Saulson, C. I. Torrie, G. Billingsley, Sheila Rowan, A. M. Sergeev, Mark A. Satterthwaite, J. Slutsky, Imre Bartos, C. Gray, J. Betzwieser, L. Williams, A. E. Villar, A. Sibley, N. Zotov, A. Ivanov, R. Abbott, C. Robinson, Riccardo Bassiri, V. Quetschke, Bangalore Suryanarayana Sathyaprakash, E. Myers, Kentaro Somiya, Evan Ochsner, B. Hughey, A. Rüdiger, H. Radkins, A. J. Weinstein, I. Gholami, W. Wu, P. T. Beyersdorf, M. V. van der Sluys, H. Overmier, E. Maros, Karsten Danzmann, S. P. Vyachanin, B. Lantz, R. Riesen, D. R. Ingram, E. Black, Roland Schilling, Phil Willems, J. R. Smith, R. Bork, A. Brummit, K. Mason, Kenji Numata, T. Nash, M. Brinkmann, Innocenzo M. Pinto, Slawomir Gras, M. Landry, F. Grimaldi, Nergis Mavalvala, Jerome Degallaix, J. Garofoli, G. H. Ogin, Sanjeev Dhurandhar, David Coward, D. Sellers, Thomas Cokelaer, Carlos Cepeda, Robert J. McCarthy, Linqing Wen, Christian Röver, Shuichi Sato, C. Messenger, Y. Faltas, Jan Harms, Lutz Winkelmann, Alexander Khalaidovski, Simon Chelkowski, M. Guenther, John Veitch, J. Heefner, R. Grosso, A. Grant, R. M. Martin, G. Mendell, R. M. S. Schofield, Evan Goetz, M. MacInnis, Sarah Caudill, Patrick Brady, L. Zhang, John A. Clark, Matthew Benacquista, Ping Koy Lam, Jolien D. E. Creighton, Lisa M. Goggin, S. Caride, R. Gouaty, B. Daudert, Paul Roberts, Lindy Blackburn, Karel E. Urbanek, K. Holt, D. O. Bridges, V. Sandberg, S. Meshkov, Keisuke Goda, D. Lodhia, Benjamin J. Owen, B. Bland, M. Scanlan, Xavier Siemens, G. Brunet, Seiji Kawamura, G. P. Newton, Reinhard Prix, A. Effler, Elizabeth Harstad, Erik Katsavounidis, M. Fyffe, Christopher Wipf, K. V. Tokmakov, T. Morioka, Ravi Kumar Kopparapu, K. Mailand, Maurizio Longo, M. J. Lubinski, Gabriela Gonzalez, J. M. Hallam, B. Shapiro, Osamu Miyakawa, David H. Reitze, Z. Raics, R. Mittleman, Nelson Christensen, Martin Hewitson, A. M. Cruise, John G. Dwyer, Rajesh Kumar, Vladimir B. Braginsky, H. Vahlbruch, K. Riles, V. Boschi, Joseph D. Romano, Jared Markowitz, S. Foley, Junwei Cao, Michele Vallisneri, Yi Chen, Stephen Fairhurst, E. Espinoza, M. Weinert, R. S. Amin, Hansheng Lei, K. Mors, Ik Siong Heng, S. Steplewski, Emma L. Robinson, Kasem Mossavi, G. P. Szokoly, Vuk Mandic, S. P. Tarabrin, Gregory Ely, John Nelson, J. A. Giaime, D. F. Menéndez, Jonah Kanner, J. C. Dumas, Albert Lazzarini, Tom Fricke, K. Kokeyama, P. Baker, S. Grunewald, D. J. Hosken, J. G. Rollins, Leo C. Stein, N. A. Robertson, D. Hammer, F. Seifert, R. L. Savage, P. Armor, S. R. P. Mohapatra, T. Isogai, Peter Kalmus, C. Torres, F. Y. Khalili, C. N. Colacino, I. Leonor, John K. Cannizzo, D. B. Kozak, S. B. Anderson, C. Vorvick, I. Duke, Maik Frede, A. Weidner, P. Schwinberg, H. Zur Mühlen, W. G. Anderson, A. L. Stuver, P. G. Murray, E. J. Daw, B. P. Abbott, E. K. Gustafson, D. E. Clark, S. Vass, Jian Zhang, K. D. Giardina, J. H. Hough, W. Kells, Lucía Santamaría, Douglas R. Cook, H. Rehbein, Ruslan Vaulin, Michele Zanolin, David B. Tanner, M. Sung, M. Pedraza, Maria Alessandra Papa, G. D. Hammond, H. Yamamoto, V. Raymond, N. A. Lockerbie, D. Hoyland, P. Savov, James Whelan, P. Ajith, Malcolm B. Gray, P. Raffai, Fumiko Kawazoe, J. Thacker, Soma Mukherjee, Drew Keppel, Zewu Yan, C. M. Reed, M. S. Meyer, S. Márka, A. Stroeer, Kenneth A. Strain, B. O'Reilly, Rainer Weiss, Yi Pan, R. W. P. Drever, W. W. Johnson, D. Hoak, Michael L. Gorodetsky, M. V. Plissi, David Blair, Jordan Camp, Hartmut Grote, Neil J. Cornish, P. E. Lindquist, Peter Aufmuth, J. N. Marx, Matthew Evans, L. Cardenas, J. H. Clayton, S. Klimenko, D. Ugolini, M. Lormand, A. Bullington, Rahul Biswas, L. Bogue, LSC Collaboration, The, Castaldi, G., Galdi, V., Pierro, V., Pinto, I. M., Principe, M., and The LIGO Scientific Collaboration
Subjects: Einstein@Home, Physics, Nuclear and High Energy Physics, Physics and Astronomy (miscellaneous), Gravitational wave, Frequency drift, FOS: Physical sciences, General Relativity and Quantum Cosmology (gr-qc), Astrophysics, General Relativity and Quantum Cosmology, LIGO, Neutron star, Amplitude, Pulsar, RADIATION, QC, QB, Nuclear and High Energy Physic, Dimensionless quantity
Abstract: This paper reports on an all-sky search for periodic gravitational waves from sources such as deformed isolated rapidly-spinning neutron stars. The analysis uses 840 hours of data from 66 days of the fifth LIGO science run (S5). The data was searched for quasi-monochromatic waves with frequencies f in the range from 50 Hz to 1500 Hz, with a linear frequency drift \dot{f} (measured at the solar system barycenter) in the range -f/\tau < \dot{f} < 0.1 f/\tau, for a minimum spin-down age \tau of 1000 years for signals below 400 Hz and 8000 years above 400 Hz. The main computational work of the search was distributed over approximately 100000 computers volunteered by the general public. This large computing power allowed the use of a relatively long coherent integration time of 30 hours while searching a large parameter space. This search extends Einstein@Home's previous search in LIGO S4 data to about three times better sensitivity. No statistically significant signals were found. In the 125 Hz to 225 Hz band, more than 90% of sources with dimensionless gravitational-wave strain tensor amplitude greater than 3e-24 would have been detected., Comment: 14 pages, 7 figures
Published: 2009

49. Search for gravitational wave ringdowns from perturbed black holes in LIGO S4 data

Author: Erik Katsavounidis, M. J. Lubinski, John G. Dwyer, Rajesh Kumar, Vladimir B. Braginsky, H. Vahlbruch, K. Riles, E. Espinoza, M. Weinert, K. Mors, R. L. Ward, Roman Schnabel, J. E. Brau, A. A. van Veggel, Efim A. Khazanov, Moritz Mehmet, H. R. Williams, Evan Ochsner, A. J. Weinstein, I. Gholami, W. Wu, P. T. Beyersdorf, M. V. van der Sluys, M. Landry, A. Grant, L. Zhang, Mark A. Satterthwaite, S. H. Huttner, N. A. Robertson, P. J. Sutton, J. H. Romie, L. Cunningham, J. Dueck, J. Garofoli, A. F. Brooks, F. J. Raab, Andrew Melatos, B. Schulz, N. Fotopoulos, C. Veltkamp, Benno Willke, S. Saraf, C. Aulbert, D. Hammer, F. Seifert, V. Kondrashov, J. Betzwieser, Jan Harms, A. Dietz, K. Mailand, Maurizio Longo, R. Gustafson, R. Mittleman, I. Yakushin, D. Hoak, Michael L. Gorodetsky, C. M. Reed, H. Overmier, E. Hirose, R. DeSalvo, Alessandra Buonanno, Nelson Christensen, S. E. Whitcomb, J. Myers, D. Sellers, S. R. P. Mohapatra, E. E. Doomes, S. E. Strigin, Z. Frei, Evan Goetz, Peter Kalmus, David Jones, Andreas Freise, Vincenzo Pierro, Marco Cavaglia, Laura Cadonati, M. Bastarrika, H. Müller-Ebhardt, Nick Leindecker, J. Zweizig, R. L. Savage, P. Armor, Shourov Chatterji, D. Fazi, Suvadeep Bose, Z. Márka, Simon Chelkowski, M. Guenther, M. S. Meyer, M. V. Plissi, Matthew Pitkin, Patrick Brady, L. Sancho De La Jordana, Jonah Kanner, A. W. Heptonstall, Peter R. Saulson, T. Isogai, Tyson Littenberg, J. R. Taylor, Paul Roberts, Hansheng Lei, Antonio Lucianetti, R. Wooley, J. C. Dumas, Jon M. Miller, G. Billingsley, R. J. S. Greenhalgh, O. Punken, R. Abbott, M. Frei, C. Torres, Gavin Davies, M. Ito, M. R. Smith, Guenakh Mitselmakher, A. S. Sengupta, S. Meshkov, C. Barker, J. Ulmen, Albert Lazzarini, B. Sears, S. Sakata, Walter Winkler, F. Y. Khalili, Rainer Weiss, B. Lantz, Badri Krishnan, Soumya D. Mohanty, Samuel J. Waldman, Vicky Kalogera, Rubab Khan, G. S. Allen, I. Leonor, John K. Cannizzo, Vincenzo Galdi, Miquel Trias, Tom Fricke, A. S. Markosyan, R. W. P. Drever, Atsushi J. Nishizawa, C. Gray, R. M. S. Schofield, N. Zotov, B. Behnke, Pankaj Sarin, Kevin M. Ryan, Matthew Benacquista, A. Mullavey, H. Lin, Yaohui Fan, K. Mason, Benjamin J. Owen, Harald Lück, Robert Stone, Sanjeev Dhurandhar, Richard O'Shaughnessy, B. Barr, P. Patel, Malik Rakhmanov, J. Worden, M. A. Barton, W. W. Johnson, E. Chalkley, C. M. Mow-Lowry, E. Myers, Christopher Wipf, K. V. Tokmakov, L. Williams, Martin Hewitson, A. Rüdiger, H. Fehrmann, R. M. Martin, K. Kokeyama, L. Tang, Junwei Cao, Susan M. Scott, A. M. Sergeev, D.B. DeBra, Sanichiro Yoshida, Teviet Creighton, I. Duke, Graham Woan, Robert L. Byer, C. N. Colacino, Kentaro Somiya, P. Baker, Kirk McKenzie, P. Shawhan, Roberto Conte, Scott Koranda, M. Scanlan, Xavier Siemens, R. Riesen, C. Messenger, Stuart Reid, Hartmut Grote, Martin P McHugh, H. Mukhopadhyay, Seiji Kawamura, B. J. J. Slagmolen, Reinhard Prix, A. Effler, Elizabeth Harstad, D. J. Hosken, Roland Schilling, S. L. Danilishin, P. Charlton, J. G. Rollins, David Blair, B. F. Whiting, L. Matone, Maria Ilaria Del Principe, Bernard F. Schutz, Fabio Postiglione, Li Ju, A. Franzen, S. C. McGuire, J. Heefner, K. L. Dooley, Chad Hanna, J. Hanson, Yi Chen, P. Kwee, K. A. Thorne, I. A. Bilenko, V. Dergachev, David J. Ottaway, Alberto Vecchio, Osamu Miyakawa, C. Robinson, Guido Mueller, Benjamin William Allen, R. Grosso, Riccardo Bassiri, D. J. A. McKechan, Lisa Barsotti, David H. Reitze, Leo C. Stein, C. Wilkinson, N. D. Smith, C. Van Den Broeck, John A. Clark, A. Sibley, F. Matichard, L. Prokhorov, Kenji Numata, E. Maros, Ping Koy Lam, A. J. Stein, S. Giampanis, T. Morioka, Ravi Kumar Kopparapu, Y. Faltas, Karsten Danzmann, D. B. Kozak, B. Sorazu, A. L. Stuver, E. J. Daw, P. J. Veitch, C. Echols, A. Cumming, A. Thüring, A. M. Cruise, C. Vorvick, Neil J. Cornish, C. T. Y. Chung, D. Ugolini, Michael E Zucker, Ilya Mandel, A. C. Melissinos, Michele Vallisneri, G. McIntyre, Alexander Khalaidovski, Ik Siong Heng, Slawomir Gras, S. Steplewski, M. Lormand, T. Z. Summerscales, B. Hughey, Emma L. Robinson, S. P. Tarabrin, P. E. Lindquist, John Nelson, J. Minelli, A. M. Gretarsson, Vitor Cardoso, Innocenzo M. Pinto, Vuk Mandic, R. Taylor, K. D. Giardina, P. Ehrens, Kipp Cannon, R. S. Ottens, J. A. Giaime, F. Grimaldi, Peter Aufmuth, B. Bland, G. Brunet, T. P. Bodiya, Thomas Cokelaer, M. A. Arain, Giuseppe Castaldi, J. K. Blackburn, Sheila Rowan, Maik Frede, A. Weidner, P. Schwinberg, J. N. Marx, Gregory M. Harry, D. F. Menéndez, K. Wette, Timothy Evans, D. Sigg, S. W. Ballmer, Richard A. Matzner, Z. Raics, C. I. Torrie, A. E. Villar, H. Zur Mühlen, W. G. Anderson, M. Lei, Helena Armandula, J. O'Dell, A. Bullington, Rahul Biswas, Ke-Xun Sun, G. Moreno, Yoichi Aso, Shantanu Desai, L. Bogue, Nergis Mavalvala, D. R. Ingram, Kip S. Thorne, L. Wallace, R. Frey, N. Rainer, T. Chalermsongsak, Phil Willems, A. Brummit, B. P. Abbott, Jerome Degallaix, K. Haughian, Marco Aurelio Diaz, E. K. Gustafson, D. E. Clark, H. Rehbein, S. B. Anderson, T. Reed, Carlos Cepeda, P. J. King, Robert J. McCarthy, Linqing Wen, A. G. Wiseman, Ruslan Vaulin, Jordan Camp, A. Perraca, A. Stochino, S. Vass, Shuichi Sato, Kazuhiro Hayama, Lutz Winkelmann, V. P. Mitrofanov, David B. Tanner, Jian Zhang, D. Lodhia, D. C. Coyne, K. A. Hodge, J. H. Clayton, W. Kells, S. Kandhasamy, I. W. Martin, Virginio Sannibale, David E. McClelland, V. Boschi, Joseph D. Romano, Jared Markowitz, Lucía Santamaría, Boris Hage, Stephen Fairhurst, John Veitch, D. Talukder, C. Pankow, Sarah Caudill, S. Foley, Lisa M. Goggin, R. Gouaty, B. Daudert, M. MacInnis, Kasem Mossavi, I. W. Harry, Cheng Li, M. Sung, Rana X. Adhikari, R. S. Amin, Gareth Jones, D. Barker, I. Wilmut, S. Wen, S. Roddy, B. Machenschalk, F. Donovan, J. S. Kissel, S. Penn, G. P. Szokoly, Peter Fritschel, Jolien D. E. Creighton, Pamela J. Russell, Roger Jones, Chad Forrest, S. Caride, Matthew Evans, L. Cardenas, M. Pedraza, A. M. Sintes, Lee Samuel Finn, D. Muhammad, S. Grunewald, Lindy Blackburn, S. Klimenko, K. Holt, Chunnong Zhao, Maria Alessandra Papa, K. Kawabe, David H. Shoemaker, Stefan Hild, S. M. Aston, B. Rivera, Pablo Barriga, A. C. Searle, Yasushi Mino, M. Mageswaran, V. Sandberg, H. J. Pletsch, S. Márka, P. Lu, O. Burmeister, G. Traylor, Thomas Corbitt, A. Stroeer, S. Goßler, Kenneth A. Strain, K. Flasch, B. Johnson, D. Kasprzyk, A. Ivanov, H. Radkins, B. O'Reilly, S. P. Vyachanin, M. Brinkmann, B. Moe, David Coward, Christian Röver, Yi Pan, D. S. Rabeling, M. C. Araya, John D. Scott, R. A. Mercer, Matthew P. Edgar, R. M. Culter, Jesper Munch, H. Yamamoto, V. Raymond, N. A. Lockerbie, D. Hoyland, P. Savov, James Whelan, P. Ajith, Malcolm B. Gray, P. Raffai, Fumiko Kawazoe, J. Thacker, Soma Mukherjee, Drew Keppel, Zewu Yan, P. G. Murray, J. H. Hough, Douglas R. Cook, Michele Zanolin, G. D. Hammond, G. Mendell, Karel E. Urbanek, D. O. Bridges, G. P. Newton, M. Fyffe, Gabriela Gonzalez, J. M. Hallam, B. Shapiro, T. Etzel, J. Slutsky, Imre Bartos, V. Quetschke, Bangalore Suryanarayana Sathyaprakash, E. Black, J. R. Smith, R. Bork, T. Nash, G. H. Ogin, V. V. Frolov, V. Parameshwaraiah, Supriyo Sinha, Stanislav Babak, Duncan A. Brown, Keisuke Goda, LSC Collaboration, The, Castaldi, G., Galdi, V., Pierro, V., Pinto, I. M., and Principe, M.
Subjects: Physics, Nuclear and High Energy Physics, Physics and Astronomy (miscellaneous), Gravitational wave, White hole, Astrophysics::High Energy Astrophysical Phenomena, FOS: Physical sciences, Primordial black hole, Astrophysics, General Relativity and Quantum Cosmology (gr-qc), Astrophysics::Cosmology and Extragalactic Astrophysics, LIGO, General Relativity and Quantum Cosmology, Black hole, Binary black hole, Stellar black hole, QC, Hawking radiation, QB, Nuclear and High Energy Physic
Abstract: According to general relativity a perturbed black hole will settle to a stationary configuration by the emission of gravitational radiation. Such a perturbation will occur, for example, in the coalescence of a black hole binary, following their inspiral and subsequent merger. At late times the waveform is a superposition of quasi-normal modes, which we refer to as the ringdown. The dominant mode is expected to be the fundamental mode, l=m=2. Since this is a well-known waveform, matched filtering can be implemented to search for this signal using LIGO data. We present a search for gravitational waves from black hole ringdowns in the fourth LIGO science run S4, during which LIGO was sensitive to the dominant mode of perturbed black holes with masses in the range of 10 Msun to 500 Msun, the regime of intermediate-mass black holes, to distances up to 300 Mpc. We present a search for gravitational waves from black hole ringdowns using data from S4. No gravitational wave candidates were found; we place a 90%-confidence upper limit on the rate of ringdowns from black holes with mass between 85 Msun and 390 Msun in the local universe, assuming a uniform distribution of sources, of 3.2 x 10^{-5} yr^{-1} Mpc^{-3} = 1.6 x 10^{-3}yr^{-1} L_{10}^{-1}, where L_{10} is 10^{10} times the solar blue-light luminosity., 8 pages, 6 figures
Published: 2009

50. All-sky LIGO search for periodic gravitational waves in the early fifth-science-run data

Author: C. Torres, C. Echols, R. Taylor, Malcolm B. Gray, T. P. Bodiya, P. Raffai, Seiji Kawamura, Reinhard Prix, A. Effler, Sanichiro Yoshida, Elizabeth Harstad, Helena Armandula, D. S. Rabeling, Graham Woan, J. O'Dell, Ke-Xun Sun, Osamu Miyakawa, David H. Reitze, N. Rainer, John D. Scott, Robert L. Byer, Stuart Reid, R. A. Mercer, J. Thacker, Soma Mukherjee, Drew Keppel, Zewu Yan, Kevin M. Ryan, Bernard F. Schutz, Li Ju, Ravi Kumar Kopparapu, J. Hanson, R. J. S. Greenhalgh, Rana X. Adhikari, Gareth Jones, B. Machenschalk, F. Donovan, Matthew P. Edgar, A. Franzen, Peter Aufmuth, Evan Ochsner, A. J. Weinstein, I. Gholami, W. Wu, Guido Mueller, Gianpietro Cagnoli, C. Gray, E. Myers, Soumya D. Mohanty, N. Zotov, K. Mason, Jesper Munch, Gavin Davies, A. M. Cruise, B. Sears, Vicky Kalogera, David Jones, Marco Cavaglia, P. T. Beyersdorf, M. V. van der Sluys, A. W. Heptonstall, Peter R. Saulson, R. Abbott, H. Lin, E. Chalkley, J. N. Marx, Kentaro Somiya, I. Leonor, John K. Cannizzo, Sanjeev Dhurandhar, P. Shawhan, M. Landry, P. Charlton, I. A. Bilenko, V. Dergachev, David J. Ottaway, R. M. Martin, E. Hirose, Kenji Numata, Vuk Mandic, M. Scanlan, Xavier Siemens, P. G. Murray, Laura Cadonati, I. Wilmut, F. Kawazoe, J. Garofoli, H. Bantilan, J. S. Kissel, A. Grant, D. Barker, A. F. Brooks, Yaohui Fan, B. Behnke, Carlos Cepeda, Robert J. McCarthy, Benno Willke, J. Clark, L. Ruet, J. H. Hough, Roger Jones, K. L. Dooley, Yi Chen, M. A. Barton, J. Myers, J. H. Clayton, Douglas R. Cook, Pankaj Sarin, I. Duke, Michele Zanolin, Shourov Chatterji, Alessandra Buonanno, J. A. Giaime, P. Ehrens, D.B. DeBra, Giuseppe Castaldi, I. Yakushin, D. Fazi, S. J. Waldman, Suvadeep Bose, S. Grunewald, K. Kawabe, S. M. Aston, B. Rivera, Linqing Wen, Pablo Barriga, M. Mageswaran, Andreas Freise, L. Zhang, Shuichi Sato, D. Lodhia, V. Boschi, Joseph D. Romano, S. Foley, R. L. Ward, T. Casebolt, P. J. Sutton, J. H. Romie, L. Cunningham, H. Müller-Ebhardt, Kasem Mossavi, A. L. Stuver, S. H. Huttner, S. E. Whitcomb, Susan M. Scott, Teviet Creighton, Chad Hanna, C. Wilkinson, S. Roddy, T. Petrie, Jon M. Miller, G. Billingsley, Chad Forrest, N. Fotopoulos, K. Wette, Z. Márka, Fabio Postiglione, Matthew Pitkin, J. Betzwieser, P. Kwee, Lisa Barsotti, I. Kozhevatov, F. J. Raab, R. Wooley, S. Saraf, R. Gustafson, Martin P McHugh, B. J. J. Slagmolen, Jolien D. E. Creighton, A. Dietz, D. B. Kozak, C. Vorvick, S. Giampanis, T. Hayler, Timothy Evans, A. M. Sintes, F. Matichard, Kazuhiro Hayama, Lindy Blackburn, M. Ramsunder, H. Yamamoto, C. Pankow, P. J. Veitch, H. Overmier, S. Kamat, Lee Samuel Finn, Riccardo Bassiri, K. Holt, D. Sigg, K. D. Giardina, B. Lantz, S. W. Ballmer, D. Meyers, P. Schwinberg, V. Sandberg, S. Wen, M. R. Smith, A. S. Sengupta, J. Dickson, C. I. Torrie, E. Maros, D. Sellers, Chunnong Zhao, S. Márka, J. Zweizig, David H. Shoemaker, Bence Kocsis, H. Zur Mühlen, W. G. Anderson, S. Sakata, Rubab Khan, Miquel Trias, R. M. S. Schofield, N. A. Lockerbie, D. R. Ingram, G. Moreno, Phil Willems, Simon Chelkowski, M. Guenther, P. Lu, O. Burmeister, C. Robinson, Jan Harms, Kenneth A. Strain, Matthew Benacquista, Benjamin William Allen, Tyson Littenberg, Karsten Danzmann, Badri Krishnan, B. P. Abbott, E. K. Gustafson, D. E. Clark, M. Ito, Antonio Lucianetti, A. Mullavey, H. Ward, F. Ya. Khalili, Richard O'Shaughnessy, B. Barr, P. Patel, Malik Rakhmanov, J. Worden, Benjamin J. Owen, Jonah Kanner, P. Savov, Slawomir Gras, James Whelan, K. Flasch, P. Ajith, J. C. Dumas, B. Johnson, L. Williams, D. Kasprzyk, A. Rüdiger, B. O'Reilly, C. Aulbert, Albert Lazzarini, M. Bastarrika, Yi Pan, Atsushi J. Nishizawa, Christopher Wipf, N. A. Robertson, S. Vass, Rainer Weiss, Jian Zhang, C. M. Mow-Lowry, S. Gossler, Patrick Brady, R. W. P. Drever, R. Riesen, Roland Schilling, K. V. Tokmakov, Evan Goetz, B. Moe, Cheng Li, Martin Hewitson, D. Hoak, W. Kells, Lucía Santamaría, A. M. Rogan, Junwei Cao, A. Miller, E. Haughian, B. F. Whiting, N. D. Smith, F. Seifert, Yoichi Aso, C. Van Den Broeck, L. Wallace, R. Frey, W. W. Johnson, Roberto Conte, Scott Koranda, L. Matone, Y. Faltas, Alexander Khalaidovski, Sarah Caudill, Lisa M. Goggin, A. Ivanov, C. Barker, Z. Frei, K. Kokeyama, Maria Ilaria Del Principe, John Veitch, Sascha Schediwy, M. V. Plissi, David Blair, Michael E Zucker, H. Radkins, Shantanu Desai, Kip S. Thorne, B. Bland, G. Brunet, R. Gouaty, B. Daudert, M. C. Araya, P. Baker, T. Reed, S. Meshkov, Jordan Camp, D. J. Hosken, S. P. Vyachanin, J. G. Rollins, M. Brinkmann, Alberto Vecchio, M. MacInnis, R. S. Amin, Kipp Cannon, R. S. Ottens, A. Sibley, Peter Kalmus, A. Perraca, V. P. Mitrofanov, P. J. King, A. G. Wiseman, Leo C. Stein, Kirk McKenzie, Hartmut Grote, Stephen Fairhurst, Boris Hage, Peter Fritschel, A. Cumming, D. Muhammad, S. Penn, Pamela J. Russell, Marco Aurelio Diaz, T. T. Fricke, Neil J. Cornish, P. E. Lindquist, A. C. Searle, K. A. Thorne, D. C. Coyne, J. Minelli, H. J. Pletsch, A. M. Gretarsson, Matthew Evans, L. Cardenas, G. S. Allen, Stefan Hild, G. Traylor, Thomas Corbitt, J. K. Blackburn, S. Caride, Hirotaka Takahashi, S. Klimenko, D. Ugolini, Sheila Rowan, B. Sorazu, M. Lormand, Guenakh Mitselmakher, Walter Winkler, A. S. Markosyan, H. Rehbein, Harald Lück, S. B. Anderson, A. Thüring, Ruslan Vaulin, David B. Tanner, H. Mukhopadhyay, S. C. McGuire, D. J. A. McKechan, A. Bullington, Rahul Biswas, A. M. Sergeev, L. Bogue, A. C. Melissinos, Ilya Mandel, M. Sung, Vitor Cardoso, T. Z. Summerscales, M. Pedraza, Maria Alessandra Papa, Richard A. Matzner, Innocenzo M. Pinto, F. Grimaldi, Thomas Cokelaer, T. Etzel, J. Slutsky, Imre Bartos, V. Quetschke, Bangalore Suryanarayana Sathyaprakash, E. Black, Martin M. Fejer, J. R. Smith, R. Bork, T. Nash, G. H. Ogin, John S. Markowitz, G. Mendell, K. Mailand, R. Mittleman, Roman Schnabel, J. E. Brau, A. A. van Veggel, Subhasish Mitra, Efim A. Khazanov, Moritz Mehmet, H. R. Williams, Keisuke Goda, Erik Katsavounidis, Nelson Christensen, M. J. Lubinski, John G. Dwyer, Vladimir B. Braginsky, H. Vahlbruch, K. Riles, E. Espinoza, M. Weinert, K. Mors, Karel E. Urbanek, G. P. Newton, M. Fyffe, Gabriela Gonzalez, J. M. Hallam, B. Shapiro, G. McIntyre, A. E. Villar, M. A. Arain, Gregory M. Harry, M. Lei, Nergis Mavalvala, Jerome Degallaix, I. W. Martin, Virginio Sannibale, David E. McClelland, V. V. Frolov, B. C. Barish, J. Heefner, C. Messenger, R. Grosso, V. Parameshwaraiah, R. M. Cutler, Supriyo Sinha, Stanislav Babak, Duncan A. Brown, Ik Siong Heng, Emma L. Robinson, Gregory Ely, John Nelson, V. Kondrashov, R. DeSalvo, E. E. Doomes, L. Sancho De La Jordana, R. L. Savage, P. Armor, The LIGO Scientific Collaboration, LVC Collaboration, The, Castaldi, G., Pinto, I. M., and Principe, M.
Subjects: Physics, Gravitational wave, media_common.quotation_subject, General Physics and Astronomy, Astronomy, Astrophysics, Radiation, LIGO, Physics and Astronomy (all), Neutron star, Stars, Quark star, Pulsar, Sky, QC, QB, media_common
Abstract: We report on an all-sky search with the LIGO detectors for periodic gravitational waves in the frequency range 50-1100Hz and with the frequency's time derivative in the range -5×10-9-0Hzs-1. Data from the first eight months of the fifth LIGO science run (S5) have been used in this search, which is based on a semicoherent method (PowerFlux) of summing strain power. Observing no evidence of periodic gravitational radiation, we report 95% confidence-level upper limits on radiation emitted by any unknown isolated rotating neutron stars within the search range. Strain limits below 10-24 are obtained over a 200-Hz band, and the sensitivity improvement over previous searches increases the spatial volume sampled by an average factor of about 100 over the entire search band. For a neutron star with nominal equatorial ellipticity of 10-6, the search is sensitive to distances as great as 500pc. © 2009 The American Physical Society.
Published: 2009

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