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196 results on '"Yakovleva, Anna"'

1. HIV and hepatitis C Virus in internally displaced people with and without injection drug use experience in the region of Shida Kartli, Georgia.

Author

Trovato, Adrian, Gogia, Maka, Aslanikashvili, Ana, Kasrashvili, Tamuna, Kovalenko, Ganna, Yakovleva, Anna, Skaathun, Britt, and Vasylyeva, Tetyana

Subjects
Displacement, Georgia, HCV, HIV, People who inject drugs, Humans, Female, Male, Hepatitis C, HIV Infections, Adult, Substance Abuse, Intravenous, Middle Aged, Georgia (Republic), Adolescent, Refugees, Young Adult, Prevalence, Health Knowledge, Attitudes, Practice, Hepacivirus
Abstract

OBJECTIVE: Internally displaced persons (IDPs) can have limited access to HIV and hepatitis C Virus (HCV) treatment and prevention. IDPs comprise > 7% of Georgian population but prevalence and levels of HIV and HCV knowledge in this population remain unknown. We tested 100 IDPs in Georgia for HIV and HCV, many of whom had drug injecting experience, and interviewed them about their migration experience, sexual and drug injecting practices, and HIV/HCV transmission knowledge. RESULTS: The average age of participants was 37.5 years (range 18-63); 31% were women. Almost half (N = 48) of participants reported ever injecting drugs; 17% of those (N = 8) started injecting drugs within the last year. Anti-HCV and HIV prevalence was 11% and 0%, respectively. Fewer people without drug use experience compared to people who inject drugs correctly answered all questions on the HIV knowledge test (13% vs. 35%, p = 0.015) or knew where to get tested for HIV (67% vs 98%, p

Published
2024

2. Phylodynamics and migration data help describe HIV transmission dynamics in internally displaced people who inject drugs in Ukraine

Author

Kovalenko, Ganna, Yakovleva, Anna, Smyrnov, Pavlo, Redlinger, Matthew, Tymets, Olga, Korobchuk, Anna, Kolodiazieva, Anna, Podolina, Anna, Cherniavska, Svitlana, Skaathun, Britt, Smith, Laramie R, Strathdee, Steffanie A, Wertheim, Joel O, Friedman, Samuel R, Bortz, Eric, Goodfellow, Ian, Meredith, Luke, and Vasylyeva, Tetyana I

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Genetics, Clinical Research, Drug Abuse (NIDA only), Infectious Diseases, Behavioral and Social Science, Health Services, Prevention, Sexually Transmitted Infections, HIV/AIDS, Substance Misuse, Infection, Good Health and Well Being, HIV, displacement, people who inject drugs, Ukraine, phylodynamics
Abstract

Internally displaced persons are often excluded from HIV molecular epidemiology surveillance due to structural, behavioral, and social barriers in access to treatment. We test a field-based molecular epidemiology framework to study HIV transmission dynamics in a hard-to-reach and highly stigmatized group, internally displaced people who inject drugs (IDPWIDs). We inform the framework by Nanopore generated HIV pol sequences and IDPWID migration history. In June-September 2020, we recruited 164 IDPWID in Odesa, Ukraine, and obtained 34 HIV sequences from HIV-infected participants. We aligned them to publicly available sequences (N = 359) from Odesa and IDPWID regions of origin and identified 7 phylogenetic clusters with at least 1 IDPWID. Using times to the most recent common ancestors of the identified clusters and times of IDPWID relocation to Odesa, we infer potential post-displacement transmission window when infections likely to happen to be between 10 and 21 months, not exceeding 4 years. Phylogeographic analysis of the sequence data shows that local people in Odesa disproportionally transmit HIV to the IDPWID community. Rapid transmissions post-displacement in the IDPWID community might be associated with slow progression along the HIV continuum of care: only 63% of IDPWID were aware of their status, 40% of those were in antiviral treatment, and 43% of those were virally suppressed. Such HIV molecular epidemiology investigations are feasible in transient and hard-to-reach communities and can help indicate best times for HIV preventive interventions. Our findings highlight the need to rapidly integrate Ukrainian IDPWID into prevention and treatment services following the dramatic escalation of the war in 2022.

Published
2023

4. Hepatitis C Virus in people with experience of injection drug use following their displacement to Southern Ukraine before 2020

Author

Yakovleva, Anna, Kovalenko, Ganna, Redlinger, Matthew, Smyrnov, Pavlo, Tymets, Olga, Korobchuk, Anna, Kotlyk, Lyudmyla, Kolodiazieva, Anna, Podolina, Anna, Cherniavska, Svitlana, Antonenko, Petro, Strathdee, Steffanie A, Friedman, Samuel R, Goodfellow, Ian, Wertheim, Joel O, Bortz, Eric, Meredith, Luke, and Vasylyeva, Tetyana I

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Clinical Sciences, Liver Disease, Digestive Diseases, Prevention, Hepatitis, Infectious Diseases, Hepatitis - C, Drug Abuse (NIDA only), Women's Health, Clinical Research, Chronic Liver Disease and Cirrhosis, Genetics, Substance Misuse, Emerging Infectious Diseases, Sexually Transmitted Infections, Infection, Good Health and Well Being, Humans, Hepacivirus, Ukraine, Cross-Sectional Studies, Phylogeny, Seroepidemiologic Studies, Bayes Theorem, HIV Infections, Substance Abuse, Intravenous, Hepatitis C, Prevalence, Hepatitis C virus, People who inject drugs, Displacement, Phylodynamics, Nanopore sequencing, Microbiology, Clinical sciences, Medical microbiology, Public health
Abstract

BackgroundDue to practical challenges associated with genetic sequencing in low-resource environments, the burden of hepatitis C virus (HCV) in forcibly displaced people is understudied. We examined the use of field applicable HCV sequencing methods and phylogenetic analysis to determine HCV transmission dynamics in internally displaced people who inject drugs (IDPWID) in Ukraine.MethodsIn this cross-sectional study, we used modified respondent-driven sampling to recruit IDPWID who were displaced to Odesa, Ukraine, before 2020. We generated partial and near full length genome (NFLG) HCV sequences using Oxford Nanopore Technology (ONT) MinION in a simulated field environment. Maximum likelihood and Bayesian methods were used to establish phylodynamic relationships.ResultsBetween June and September 2020, we collected epidemiological data and whole blood samples from 164 IDPWID (PNAS Nexus.2023;2(3):pgad008). Rapid testing (Wondfo® One Step HCV; Wondfo® One Step HIV1/2) identified an anti-HCV seroprevalence of 67.7%, and 31.1% of participants tested positive for both anti-HCV and HIV. We generated 57 partial or NFLG HCV sequences and identified eight transmission clusters, of which at least two originated within a year and a half post-displacement.ConclusionsLocally generated genomic data and phylogenetic analysis in rapidly changing low-resource environments, such as those faced by forcibly displaced people, can help inform effective public health strategies. For example, evidence of HCV transmission clusters originating soon after displacement highlights the importance of implementing urgent preventive interventions in ongoing situations of forced displacement.

Published
2023

5. Introduction and Establishment of SARS-CoV-2 Gamma Variant in New York City in Early 2021

Author

Vasylyeva, Tetyana I, Fang, Courtney E, Su, Michelle, Havens, Jennifer L, Parker, Edyth, Wang, Jade C, Zeller, Mark, Yakovleva, Anna, Hassler, Gabriel W, Chowdhury, Moinuddin A, Andersen, Kristian G, Hughes, Scott, and Wertheim, Joel O

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Prevention, Genetics, Good Health and Well Being, Humans, SARS-CoV-2, New York City, COVID-19, Phylogeny, Gamma variant, travel restrictions, public health, Biological Sciences, Medical and Health Sciences, Microbiology, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

BackgroundMonitoring the emergence and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants is an important public health objective. We investigated how the Gamma variant was established in New York City (NYC) in early 2021 in the presence of travel restrictions that aimed to prevent viral spread from Brazil, the country where the variant was first identified.MethodsWe performed phylogeographic analysis on 15 967 Gamma sequences sampled between 10 March and 1 May 2021, to identify geographic sources of Gamma lineages introduced into NYC. We identified locally circulating Gamma transmission clusters and inferred the timing of their establishment in NYC.ResultsWe identified 16 phylogenetically distinct Gamma clusters established in NYC (cluster sizes ranged 2-108 genomes); most of them were introduced from Florida and Illinois and only 1 directly from Brazil. By the time the first Gamma case was reported by genomic surveillance in NYC on 10 March, the majority (57%) of circulating Gamma lineages had already been established in the city for at least 2 weeks.ConclusionsAlthough travel from Brazil to the United States was restricted from May 2020 through the end of the study period, this restriction did not prevent Gamma from becoming established in NYC as most introductions occurred from domestic locations.

Published
2022

6. Tracking SARS-COV-2 variants using Nanopore sequencing in Ukraine in 2021

Author

Yakovleva, Anna, Kovalenko, Ganna, Redlinger, Matthew, Liulchuk, Mariia G, Bortz, Eric, Zadorozhna, Viktoria I, Scherbinska, Alla M, Wertheim, Joel O, Goodfellow, Ian, Meredith, Luke, and Vasylyeva, Tetyana I

Subjects
Biological Sciences, Health Sciences, Genetics, Emerging Infectious Diseases, Infectious Diseases, Bioengineering, Human Genome, Coronaviruses, Biotechnology, Nanotechnology, Good Health and Well Being, COVID-19, Humans, Nanopore Sequencing, SARS-CoV-2, Ukraine
Abstract

The use of real-time genomic epidemiology has enabled the tracking of the global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), informing evidence-based public health decision making. Ukraine has experienced four waves of the Coronavirus Disease 2019 (COVID-19) between spring 2020 and spring 2022. However, insufficient capacity for local genetic sequencing limited the potential application of SARS-CoV-2 genomic surveillance for public health response in the country. Herein, we report local sequencing of 103 SARS-CoV-2 genomes from patient samples collected in Kyiv in July-December 2021 using Oxford Nanopore technology. Together with other published Ukrainian SARS-CoV-2 genomes, our data suggest that the third wave of the epidemic in Ukraine (June-December 2021) was dominated by the Delta Variant of Concern (VOC). Our phylogeographic analysis revealed that in summer 2021 Delta VOC was introduced into Ukraine from multiple locations worldwide, with most introductions coming from Central and Eastern European countries. The wide geographic range of Delta introductions coincides with increased volume of travel to Ukraine particularly from locations outside of Europe in summer 2021. This study highlights the need to urgently integrate affordable and easily scaled pathogen sequencing technologies in locations with less developed genomic infrastructure, in order to support local public health decision making.

Published
2022

7. Developing Management and Implementation Mechanism for a Digital Supply System Transformation Programme in Construction Company

Author

Hayrapetyan, Diana, Yakovleva, Anna, Kacprzyk, Janusz, Series Editor, Gomide, Fernando, Advisory Editor, Kaynak, Okyay, Advisory Editor, Liu, Derong, Advisory Editor, Pedrycz, Witold, Advisory Editor, Polycarpou, Marios M., Advisory Editor, Rudas, Imre J., Advisory Editor, Wang, Jun, Advisory Editor, Bushuyev, Sergey, editor, Ding, Ronggui, editor, and Radujkovic, Mladen, editor

Published
2023
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8. Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

Author

Koshy, Cherian, Wise, Emma, Cortes, Nick, Lynch, Jessica, Kidd, Stephen, Mori, Matilde, Fairley, Derek J., Curran, Tanya, McKenna, James P., Adams, Helen, Fraser, Christophe, Golubchik, Tanya, Bonsall, David, Moore, Catrin, Caddy, Sarah L., Khokhar, Fahad A., Wantoch, Michelle, Reynolds, Nicola, Warne, Ben, Maksimovic, Joshua, Spellman, Karla, McCluggage, Kathryn, John, Michaela, Beer, Robert, Afifi, Safiah, Morgan, Sian, Marchbank, Angela, Price, Anna, Kitchen, Christine, Gulliver, Huw, Merrick, Ian, Southgate, Joel, Guest, Martyn, Munn, Robert, Workman, Trudy, Connor, Thomas R., Fuller, William, Bresner, Catherine, Snell, Luke B., Charalampous, Themoula, Nebbia, Gaia, Batra, Rahul, Edgeworth, Jonathan, Robson, Samuel C., Beckett, Angela, Loveson, Katie F., Aanensen, David M., Underwood, Anthony P., Yeats, Corin A., Abudahab, Khalil, Taylor, Ben E.W., Menegazzo, Mirko, Clark, Gemma, Smith, Wendy, Khakh, Manjinder, Fleming, Vicki M., Lister, Michelle M., Howson-Wells, Hannah C., Berry, Louise, Boswell, Tim, Joseph, Amelia, Willingham, Iona, Bird, Paul, Helmer, Thomas, Fallon, Karlie, Holmes, Christopher, Tang, Julian, Raviprakash, Veena, Campbell, Sharon, Sheriff, Nicola, Loose, Matthew W., Holmes, Nadine, Moore, Christopher, Carlile, Matthew, Wright, Victoria, Sang, Fei, Debebe, Johnny, Coll, Francesc, Signell, Adrian W., Betancor, Gilberto, Wilson, Harry D., Feltwell, Theresa, Houldcroft, Charlotte J., Eldirdiri, Sahar, Kenyon, Anita, Davis, Thomas, Pybus, Oliver, du Plessis, Louis, Zarebski, Alex, Raghwani, Jayna, Kraemer, Moritz, Francois, Sarah, Attwood, Stephen, Vasylyeva, Tetyana, Torok, M. Estee, Hamilton, William L., Goodfellow, Ian G., Hall, Grant, Jahun, Aminu S., Chaudhry, Yasmin, Hosmillo, Myra, Pinckert, Malte L., Georgana, Iliana, Yakovleva, Anna, Meredith, Luke W., Moses, Samuel, Lowe, Hannah, Ryan, Felicity, Fisher, Chloe L., Awan, Ali R., Boyes, John, Breuer, Judith, Harris, Kathryn Ann, Brown, Julianne Rose, Shah, Divya, Atkinson, Laura, Lee, Jack C.D., Alcolea-Medina, Adela, Moore, Nathan, Cortes, Nicholas, Williams, Rebecca, Chapman, Michael R., Levett, Lisa J., Heaney, Judith, Smith, Darren L., Bashton, Matthew, Young, Gregory R., Allan, John, Loh, Joshua, Randell, Paul A., Cox, Alison, Madona, Pinglawathee, Holmes, Alison, Bolt, Frances, Price, James, Mookerjee, Siddharth, Rowan, Aileen, Taylor, Graham P., Ragonnet-Cronin, Manon, Nascimento, Fabricia F., Jorgensen, David, Siveroni, Igor, Johnson, Rob, Boyd, Olivia, Geidelberg, Lily, Volz, Erik M., Brunker, Kirstyn, Smollett, Katherine L., Loman, Nicholas J., Quick, Joshua, McMurray, Claire, Stockton, Joanne, Nicholls, Sam, Rowe, Will, Poplawski, Radoslaw, Martinez-Nunez, Rocio T., Mason, Jenifer, Robinson, Trevor I., O'Toole, Elaine, Watts, Joanne, Breen, Cassie, Cowell, Angela, Ludden, Catherine, Sluga, Graciela, Machin, Nicholas W., Ahmad, Shazaad S.Y., George, Ryan P., Halstead, Fenella, Sivaprakasam, Venkat, Thomson, Emma C., Shepherd, James G., Asamaphan, Patawee, Niebel, Marc O., Li, Kathy K., Shah, Rajiv N., Jesudason, Natasha G., Parr, Yasmin A., Tong, Lily, Broos, Alice, Mair, Daniel, Nichols, Jenna, Carmichael, Stephen N., Nomikou, Kyriaki, Aranday-Cortes, Elihu, Johnson, Natasha, Starinskij, Igor, da Silva Filipe, Ana, Robertson, David L., Orton, Richard J., Hughes, Joseph, Vattipally, Sreenu, Singer, Joshua B., Hale, Antony D., Macfarlane-Smith, Louissa R., Harper, Katherine L., Taha, Yusri, Payne, Brendan A.I., Burton-Fanning, Shirelle, Waugh, Sheila, Collins, Jennifer, Eltringham, Gary, Templeton, Kate E., McHugh, Martin P., Dewar, Rebecca, Wastenge, Elizabeth, Dervisevic, Samir, Stanley, Rachael, Prakash, Reenesh, Stuart, Claire, Elumogo, Ngozi, Sethi, Dheeraj K., Meader, Emma J., Coupland, Lindsay J., Potter, Will, Graham, Clive, Barton, Edward, Padgett, Debra, Scott, Garren, Swindells, Emma, Greenaway, Jane, Nelson, Andrew, Yew, Wen C., Resende Silva, Paola C., Andersson, Monique, Shaw, Robert, Peto, Timothy, Justice, Anita, Eyre, David, Crooke, Derrick, Hoosdally, Sarah, Sloan, Tim J., Duckworth, Nichola, Walsh, Sarah, Chauhan, Anoop J., Glaysher, Sharon, Bicknell, Kelly, Wyllie, Sarah, Butcher, Ethan, Elliott, Scott, Lloyd, Allyson, Impey, Robert, Levene, Nick, Monaghan, Lynn, Bradley, Declan T., Allara, Elias, Pearson, Clare, Muir, Peter, Vipond, Ian B., Hopes, Richard, Pymont, Hannah M., Hutchings, Stephanie, Curran, Martin D., Parmar, Surendra, Lackenby, Angie, Mbisa, Tamyo, Platt, Steven, Miah, Shahjahan, Bibby, David, Manso, Carmen, Hubb, Jonathan, Chand, Meera, Dabrera, Gavin, Ramsay, Mary, Bradshaw, Daniel, Thornton, Alicia, Myers, Richard, Schaefer, Ulf, Groves, Natalie, Gallagher, Eileen, Lee, David, Williams, David, Ellaby, Nicholas, Harrison, Ian, Hartman, Hassan, Manesis, Nikos, Patel, Vineet, Bishop, Chloe, Chalker, Vicki, Osman, Husam, Bosworth, Andrew, Robinson, Esther, Holden, Matthew T.G., Shaaban, Sharif, Birchley, Alec, Adams, Alexander, Davies, Alisha, Gaskin, Amy, Plimmer, Amy, Gatica-Wilcox, Bree, McKerr, Caoimhe, Moore, Catherine, Williams, Chris, Heyburn, David, De Lacy, Elen, Hilvers, Ember, Downing, Fatima, Shankar, Giri, Jones, Hannah, Asad, Hibo, Coombes, Jason, Watkins, Joanne, Evans, Johnathan M., Fina, Laia, Gifford, Laura, Gilbert, Lauren, Graham, Lee, Perry, Malorie, Morgan, Mari, Bull, Matthew, Cronin, Michelle, Pacchiarini, Nicole, Craine, Noel, Jones, Rachel, Howe, Robin, Corden, Sally, Rey, Sara, Kumziene-Summerhayes, Sara, Taylor, Sarah, Cottrell, Simon, Jones, Sophie, Edwards, Sue, O’Grady, Justin, Page, Andrew J., Wain, John, Webber, Mark A., Mather, Alison E., Baker, David J., Rudder, Steven, Yasir, Muhammad, Thomson, Nicholas M., Aydin, Alp, Tedim, Ana P., Kay, Gemma L., Trotter, Alexander J., Gilroy, Rachel A.J., Alikhan, Nabil-Fareed, de Oliveira Martins, Leonardo, Le-Viet, Thanh, Meadows, Lizzie, Kolyva, Anastasia, Diaz, Maria, Bell, Andrew, Gutierrez, Ana Victoria, Charles, Ian G., Adriaenssens, Evelien M., Kingsley, Robert A., Casey, Anna, Simpson, David A., Molnar, Zoltan, Thompson, Thomas, Acheson, Erwan, Masoli, Jane A.H., Knight, Bridget A., Hattersley, Andrew, Ellard, Sian, Auckland, Cressida, Mahungu, Tabitha W., Irish-Tavares, Dianne, Haque, Tanzina, Bourgeois, Yann, Scarlett, Garry P., Partridge, David G., Raza, Mohammad, Evans, Cariad, Johnson, Kate, Liggett, Steven, Baker, Paul, Essex, Sarah, Lyons, Ronan A., Caller, Laura G., Castellano, Sergi, Williams, Rachel J., Kristiansen, Mark, Roy, Sunando, Williams, Charlotte A., Dyal, Patricia L., Tutill, Helena J., Panchbhaya, Yasmin N., Forrest, Leysa M., Niola, Paola, Findlay, Jacqueline, Brooks, Tony T., Gavriil, Artemis, Mestek-Boukhibar, Lamia, Weeks, Sam, Pandey, Sarojini, Berry, Lisa, Jones, Katie, Richter, Alex, Beggs, Andrew, Smith, Colin P., Bucca, Giselda, Hesketh, Andrew R., Harrison, Ewan M., Peacock, Sharon J., Palmer, Sophie, Churcher, Carol M., Bellis, Katherine L., Girgis, Sophia T., Naydenova, Plamena, Blane, Beth, Sridhar, Sushmita, Ruis, Chris, Forrest, Sally, Cormie, Claire, Gill, Harmeet K., Dias, Joana, Higginson, Ellen E., Maes, Mailis, Young, Jamie, Kermack, Leanne M., Hadjirin, Nazreen F., Aggarwal, Dinesh, Griffith, Luke, Swingler, Tracey, Davidson, Rose K., Rambaut, Andrew, Williams, Thomas, Balcazar, Carlos E., Gallagher, Michael D., O'Toole, Áine, Rooke, Stefan, Jackson, Ben, Colquhoun, Rachel, Ashworth, Jordan, Hill, Verity, McCrone, J.T., Scher, Emily, Yu, Xiaoyu, Williamson, Kathleen A., Stanton, Thomas D., Michell, Stephen L., Bewshea, Claire M., Temperton, Ben, Michelsen, Michelle L., Warwick-Dugdale, Joanna, Manley, Robin, Farbos, Audrey, Harrison, James W., Sambles, Christine M., Studholme, David J., Jeffries, Aaron R., Darby, Alistair C., Hiscox, Julian A., Paterson, Steve, Iturriza-Gomara, Miren, Jackson, Kathryn A., Lucaci, Anita O., Vamos, Edith E., Hughes, Margaret, Rainbow, Lucille, Eccles, Richard, Nelson, Charlotte, Whitehead, Mark, Turtle, Lance, Haldenby, Sam T., Gregory, Richard, Gemmell, Matthew, Kwiatkowski, Dominic, de Silva, Thushan I., Smith, Nikki, Angyal, Adrienn, Lindsey, Benjamin B., Groves, Danielle C., Green, Luke R., Wang, Dennis, Freeman, Timothy M., Parker, Matthew D., Keeley, Alexander J., Parsons, Paul J., Tucker, Rachel M., Brown, Rebecca, Wyles, Matthew, Constantinidou, Chrystala, Unnikrishnan, Meera, Ott, Sascha, Cheng, Jeffrey K.J., Bridgewater, Hannah E., Frost, Lucy R., Taylor-Joyce, Grace, Stark, Richard, Baxter, Laura, Alam, Mohammad T., Brown, Paul E., McClure, Patrick C., Chappell, Joseph G., Tsoleridis, Theocharis, Ball, Jonathan, Grammatopoulos, Dimitris, Buck, David, Todd, John A., Green, Angie, Trebes, Amy, MacIntyre-Cockett, George, de Cesare, Mariateresa, Langford, Cordelia, Alderton, Alex, Amato, Roberto, Goncalves, Sonia, Jackson, David K., Johnston, Ian, Sillitoe, John, Palmer, Steve, Lawniczak, Mara, Berriman, Matt, Danesh, John, Livett, Rich, Shirley, Lesley, Farr, Ben, Quail, Mike, Thurston, Scott, Park, Naomi, Betteridge, Emma, Weldon, Danni, Goodwin, Scott, Nelson, Rachel, Beaver, Charlotte, Letchford, Laura, Jackson, David A., Foulser, Luke, McMinn, Liz, Prestwood, Liam, Kay, Sally, Kane, Leanne, Dorman, Matthew J., Martincorena, Inigo, Puethe, Christoph, Keatley, Jon-Paul, Tonkin-Hill, Gerry, Smith, Christen, Jamrozy, Dorota, Beale, Mathew A., Patel, Minal, Ariani, Cristina, Spencer-Chapman, Michael, Drury, Eleanor, Lo, Stephanie, Rajatileka, Shavanthi, Scott, Carol, James, Keith, Buddenborg, Sarah K., Berger, Duncan J., Patel, Gaurang, Garcia-Casado, Maria V., Dibling, Thomas, McGuigan, Samantha, Rogers, Hazel A., Hunter, Adam D., Souster, Emily, Neaverson, Alexandra S., Volz, Erik, McCrone, John T., O’Toole, Áine, Johnson, Robert, Rey, Sara M., Nicholls, Samuel M., Colquhoun, Rachel M., Shepherd, James, Pascall, David J., Shah, Rajiv, Jesudason, Natasha, Li, Kathy, Jarrett, Ruth, Goodfellow, Ian, and Pybus, Oliver G.

Published
2021
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9. Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study

Author

Meredith, Luke W, Hamilton, William L, Warne, Ben, Houldcroft, Charlotte J, Hosmillo, Myra, Jahun, Aminu S, Curran, Martin D, Parmar, Surendra, Caller, Laura G, Caddy, Sarah L, Khokhar, Fahad A, Yakovleva, Anna, Hall, Grant, Feltwell, Theresa, Forrest, Sally, Sridhar, Sushmita, Weekes, Michael P, Baker, Stephen, Brown, Nicholas, Moore, Elinor, Popay, Ashley, Roddick, Iain, Reacher, Mark, Gouliouris, Theodore, Peacock, Sharon J, Dougan, Gordon, Török, M Estée, and Goodfellow, Ian

Published
2020
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10. Long-term outcomes in Juvenile Myositis patients

Author

Tsaltskan, Vladislav, Aldous, Annette, Serafi, Sam, Yakovleva, Anna, Sami, Heidi, Mamyrova, Gulnara, Targoff, Ira N., Schiffenbauer, Adam, Miller, Frederick W., Simmens, Samuel J., Curiel, Rodolfo, Jones, Olcay Y., and Rider, Lisa G.

Published
2020
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12. Additional file 1 of Hepatitis C Virus in people with experience of injection drug use following their displacement to Southern Ukraine before 2020

Author

Yakovleva, Anna, Kovalenko, Ganna, Redlinger, Matthew, Smyrnov, Pavlo, Tymets, Olga, Korobchuk, Anna, Kotlyk, Lyudmyla, Kolodiazieva, Anna, Podolina, Anna, Cherniavska, Svitlana, Antonenko, Petro, Strathdee, Steffanie A., Friedman, Samuel R., Goodfellow, Ian, Wertheim, Joel O., Bortz, Eric, Meredith, Luke, and Vasylyeva, Tetyana I.

Abstract

Additional file 1. Supplementary Methods and Figures.

Published
2023
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16. Phylodynamics and migration data help describe HIV transmission dynamics in internally displaced people who inject drugs in Ukraine

Author

Kovalenko, Ganna, primary, Yakovleva, Anna, additional, Smyrnov, Pavlo, additional, Redlinger, Matthew, additional, Tymets, Olga, additional, Korobchuk, Anna, additional, Kolodiazieva, Anna, additional, Podolina, Anna, additional, Cherniavska, Svitlana, additional, Skaathun, Britt, additional, Smith, Laramie R., additional, Strathdee, Steffanie A., additional, Wertheim, Joel O., additional, Friedman, Samuel R., additional, Bortz, Eric, additional, Goodfellow, Ian, additional, Meredith, Luke, additional, and Vasylyeva, Tetyana I., additional

Published
2022
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17. Simulation and research of cylindrical broach structures stress-strain state in solidworks system

Author

Lukina Svetlana, Yakovleva Anna, and Zimovets Olga

Subjects
Engineering (General). Civil engineering (General), TA1-2040
Abstract

The authors considered a methodology for the automated design of cylindrical broach structures consisting of the following stages: forming a 3D-parametric geometrical broach image, assessing a broach structure stress-strain state during operation. The paper presents the results of software implementation of the algorithm for forming a broach structure parametric model from 3D-geometrical prototypes in the system Solidworks. To assess a stress-strain state of tools with the numerical method of finite elements in Solidworks Simulation, the authors formed an analytical design model taking into account strain of geometric prototypes. A series of numerical experiments was aimed at researching a stress-strain state of broach teeth under cutting forces action. According to the results of numerical experiments, by means of the least square method the authors obtained analytical expressions to estimate the influence of geometrical and design parameters of the broach teeth structure on elastic displacements of cutting edges vertice and equivalent stresses of the most loaded teeth components. The authors developed recommendations on the change of the teeth section parameters allowing for the extension of the broach structure operation life and reducing the tool life consumption for the batch of parts.

Published
2019
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18. A2B-COVID: A Tool for Rapidly Evaluating Potential SARS-CoV-2 Transmission Events

Author

Illingworth, Christopher J. R., Hamilton, William L., Jackson, Christopher, Warne, Ben, Popay, Ashley, Meredith, Luke, Hosmillo, Myra, Jahun, Aminu, Fieldman, Tom, Routledge, Matthew, Houldcroft, Charlotte J., Caller, Laura, Caddy, Sarah, Yakovleva, Anna, Hall, Grant, Khokhar, Fahad A., Feltwell, Theresa, Pinckert, Malte L., Georgana, Iliana, Chaudhry, Yasmin, Curran, Martin, Parmar, Surendra, Sparkes, Dominic, Rivett, Lucy, Jones, Nick K., Sridhar, Sushmita, Forrest, Sally, Dymond, Tom, Grainger, Kayleigh, Workman, Chris, Gkrania-Klotsas, Effrossyni, Brown, Nicholas M., Weekes, Michael P., Baker, Stephen, Peacock, Sharon J., Gouliouris, Theodore, Goodfellow, Ian, De Angelis, Daniela, Torok, M. Estee, Illingworth, Christopher J. R., Hamilton, William L., Jackson, Christopher, Warne, Ben, Popay, Ashley, Meredith, Luke, Hosmillo, Myra, Jahun, Aminu, Fieldman, Tom, Routledge, Matthew, Houldcroft, Charlotte J., Caller, Laura, Caddy, Sarah, Yakovleva, Anna, Hall, Grant, Khokhar, Fahad A., Feltwell, Theresa, Pinckert, Malte L., Georgana, Iliana, Chaudhry, Yasmin, Curran, Martin, Parmar, Surendra, Sparkes, Dominic, Rivett, Lucy, Jones, Nick K., Sridhar, Sushmita, Forrest, Sally, Dymond, Tom, Grainger, Kayleigh, Workman, Chris, Gkrania-Klotsas, Effrossyni, Brown, Nicholas M., Weekes, Michael P., Baker, Stephen, Peacock, Sharon J., Gouliouris, Theodore, Goodfellow, Ian, De Angelis, Daniela, and Torok, M. Estee

Abstract

Identifying linked cases of infection is a critical component of the public health response to viral infectious diseases. In a clinical context, there is a need to make rapid assessments of whether cases of infection have arrived independently onto a ward, or are potentially linked via direct transmission. Viral genome sequence data are of great value in making these assessments, but are often not the only form of data available. Here, we describe A2B-COVID, a method for the rapid identification of potentially linked cases of COVID-19 infection designed for clinical settings. Our method combines knowledge about infection dynamics, data describing the movements of individuals, and evolutionary analysis of genome sequences to assess whether data collected from cases of infection are consistent or inconsistent with linkage via direct transmission. A retrospective analysis of data from two wards at Cambridge University Hospitals NHS Foundation Trust during the first wave of the pandemic showed qualitatively different patterns of linkage between cases on designated COVID-19 and non-COVID-19 wards. The subsequent real-time application of our method to data from the second epidemic wave highlights its value for monitoring cases of infection in a clinical context.

Published
2022

19. Introduction and Establishment of SARS-CoV-2 Gamma Variant in New York City in Early 2021

Author

Vasylyeva, Tetyana I., primary, Fang, Courtney E., additional, Su, Michelle, additional, Havens, Jennifer L., additional, Parker, Edyth, additional, Wang, Jade C., additional, Zeller, Mark, additional, Yakovleva, Anna, additional, Hassler, Gabriel W., additional, Chowdhury, Moinuddin A., additional, Andersen, Kristian G., additional, Hughes, Scott, additional, and Wertheim, Joel O., additional

Published
2022
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21. A2B-COVID: A Tool for Rapidly Evaluating Potential SARS-CoV-2 Transmission Events

Author

Illingworth, Christopher J R, primary, Hamilton, William L, additional, Jackson, Christopher, additional, Warne, Ben, additional, Popay, Ashley, additional, Meredith, Luke, additional, Hosmillo, Myra, additional, Jahun, Aminu, additional, Fieldman, Tom, additional, Routledge, Matthew, additional, Houldcroft, Charlotte J, additional, Caller, Laura, additional, Caddy, Sarah, additional, Yakovleva, Anna, additional, Hall, Grant, additional, Khokhar, Fahad A, additional, Feltwell, Theresa, additional, Pinckert, Malte L, additional, Georgana, Iliana, additional, Chaudhry, Yasmin, additional, Curran, Martin, additional, Parmar, Surendra, additional, Sparkes, Dominic, additional, Rivett, Lucy, additional, Jones, Nick K, additional, Sridhar, Sushmita, additional, Forrest, Sally, additional, Dymond, Tom, additional, Grainger, Kayleigh, additional, Workman, Chris, additional, Gkrania-Klotsas, Effrossyni, additional, Brown, Nicholas M, additional, Weekes, Michael P, additional, Baker, Stephen, additional, Peacock, Sharon J, additional, Gouliouris, Theodore, additional, Goodfellow, Ian, additional, Angelis, Daniela De, additional, and Török, M Estée, additional

Published
2022
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24. Patterns of within-host genetic diversity in SARS-CoV-2

Author

Tonkin-Hill, Gerry, Martincorena, Inigo, Amato, Roberto, Lawson, Andrew RJ, Gerstung, Moritz, Johnston, Ian, Jackson, David K, Park, Naomi, Lensing, Stefanie V, Quail, Michael A, Gonçalves, Sónia, Ariani, Cristina, Spencer Chapman, Michael, Hamilton, William L, Meredith, Luke W, Hall, Grant, Jahun, Aminu S, Chaudhry, Yasmin, Hosmillo, Myra, Pinckert, Malte L, Georgana, Iliana, Yakovleva, Anna, Caller, Laura G, Caddy, Sarah L, Feltwell, Theresa, Khokhar, Fahad A, Houldcroft, Charlotte J, Curran, Martin D, Parmar, Surendra, Alderton, Alex, Nelson, Rachel, Harrison, Ewan M, Sillitoe, John, Bentley, Stephen D, Barrett, Jeffrey C, Torok, M Estee, Goodfellow, Ian G, Langford, Cordelia, Kwiatkowski, Dominic, The COVID-19 Genomics UK (COG-UK) Consortium, Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg, McCann, Clare, Tonkin-Hill, Gerry [0000-0003-4397-2224], Gerstung, Moritz [0000-0001-6709-963X], Pinckert, Malte [0000-0002-6072-5949], Caddy, Sarah [0000-0002-9790-7420], Torok, Estee [0000-0001-9098-8590], Apollo - University of Cambridge Repository, Jackson, David K [0000-0002-8090-9462], Spencer Chapman, Michael [0000-0002-5320-8193], Hamilton, William L [0000-0002-3330-353X], Hall, Grant [0000-0003-3928-3979], Jahun, Aminu S [0000-0002-4585-1701], Hosmillo, Myra [0000-0002-3514-7681], Georgana, Iliana [0000-0002-8976-1177], Caddy, Sarah L [0000-0002-9790-7420], Houldcroft, Charlotte J [0000-0002-1833-5285], Torok, M Estee [0000-0001-9098-8590], Goodfellow, Ian G [0000-0002-9483-510X], and Lawson, Andrew Rj [0000-0003-3592-1005]

Subjects
Mutation rate, global health, medicine.disease_cause, Negative selection, 0302 clinical medicine, genetics, Biology (General), Phylogeny, 0303 health sciences, Mutation, Phylogenetic tree, General Neuroscience, C100, transmission, General Medicine, C700, C900, 3. Good health, Host-Pathogen Interactions, Medicine, epidemiology, Research Article, Lineage (genetic), QH301-705.5, Science, mutational spectrum, Genomics, Genome, Viral, Biology, General Biochemistry, Genetics and Molecular Biology, within-host, 03 medical and health sciences, The COVID-19 Genomics UK (COG-UK) Consortium, genomics, medicine, Humans, Pandemics, Allele frequency, 030304 developmental biology, Genetic diversity, Base Sequence, General Immunology and Microbiology, SARS-CoV-2, Wellcome Sanger Institute COVID-19 Surveillance Team, COVID-19, Genetic Variation, Genetics and Genomics, B900, Epidemiology and Global Health, Evolutionary biology, Other, 030217 neurology & neurosurgery
Abstract

Monitoring the spread of SARS-CoV-2 and reconstructing transmission chains has become a major public health focus for many governments around the world. The modest mutation rate and rapid transmission of SARS-CoV-2 prevents the reconstruction of transmission chains from consensus genome sequences, but within-host genetic diversity could theoretically help identify close contacts. Here we describe the patterns of within-host diversity in 1181 SARS-CoV-2 samples sequenced to high depth in duplicate. 95.1% of samples show within-host mutations at detectable allele frequencies. Analyses of the mutational spectra revealed strong strand asymmetries suggestive of damage or RNA editing of the plus strand, rather than replication errors, dominating the accumulation of mutations during the SARS-CoV-2 pandemic. Within- and between-host diversity show strong purifying selection, particularly against nonsense mutations. Recurrent within-host mutations, many of which coincide with known phylogenetic homoplasies, display a spectrum and patterns of purifying selection more suggestive of mutational hotspots than recombination or convergent evolution. While allele frequencies suggest that most samples result from infection by a single lineage, we identify multiple putative examples of co-infection. Integrating these results into an epidemiological inference framework, we find that while sharing of within-host variants between samples could help the reconstruction of transmission chains, mutational hotspots and rare cases of superinfection can confound these analyses., eLife digest The COVID-19 pandemic has had major health impacts across the globe. The scientific community has focused much attention on finding ways to monitor how the virus responsible for the pandemic, SARS-CoV-2, spreads. One option is to perform genetic tests, known as sequencing, on SARS-CoV-2 samples to determine the genetic code of the virus and to find any differences or mutations in the genes between the viral samples. Viruses mutate within their hosts and can develop into variants that are able to more easily transmit between hosts. Genetic sequencing can reveal how genetically similar two SARS-CoV-2 samples are. But tracking how SARS-CoV-2 moves from one person to the next through sequencing can be tricky. Even a sample of SARS-CoV-2 viruses from the same individual can display differences in their genetic material or within-host variants. Could genetic testing of within-host variants shed light on factors driving SARS-CoV-2 to evolve in humans? To get to the bottom of this, Tonkin-Hill, Martincorena et al. probed the genetics of SARS-CoV-2 within-host variants using 1,181 samples. The analyses revealed that 95.1% of samples contained within-host variants. A number of variants occurred frequently in many samples, which were consistent with mutational hotspots in the SARS-CoV-2 genome. In addition, within-host variants displayed mutation patterns that were similar to patterns found between infected individuals. The shared within-host variants between samples can help to reconstruct transmission chains. However, the observed mutational hotspots and the detection of multiple strains within an individual can make this challenging. These findings could be used to help predict how SARS-CoV-2 evolves in response to interventions such as vaccines. They also suggest that caution is needed when using information on within-host variants to determine transmission between individuals.

Published
2021

25. Temporal trends of hepatitis C virus transmission in internally displaced people who inject drugs in Odessa, Ukraine

Author

Yakovleva, Anna, primary, Kovalenko, Ganna, additional, Redlinger, Matthew, additional, Smyrnov, Pavlo, additional, Tymets, Olga, additional, Korobchuk, Ania, additional, Kotlyk, Lyudmyla, additional, Kolodyazeva, Ganna, additional, Podolina, Ganna, additional, Chernyavskaya, Svetlana, additional, Strathdee, Steffanie A., additional, Friedman, Samuel R, additional, Goodfellow, Ian, additional, Wertheim, Joel O., additional, Bortz, Eric, additional, Meredith, Luke, additional, and Vasylyeva, Tetyana I, additional

Published
2021
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27. Combined Point-of-Care Nucleic Acid and Antibody Testing for SARS-CoV-2 following Emergence of D614G Spike Variant

Author

Baker, Stephen, Bradley, John, Dougan, Gordon, Goodfellow, Ian, Gupta, Ravi, Lehner, Paul J., Lyons, Paul, Matheson, Nicholas J., Smith, Kenneth G.C., Toshner, Mark, Weekes, Michael P., Brown, Nick, Curran, Martin, Palmar, Surendra, Zhang, Hongyi, Enoch, David, Chapman, Daniel, Shaw, Ashley, Jose, Sherly, Bermperi, Areti, Zerrudo, Julie Ann, Kourampa, Evgenia, Watson, Laura, Worsley, Jieniean, Saunders, Caroline, de Jesus, Ranalie, Domingo, Jason, Pasquale, Ciro, Vergese, Bensi, Vargas, Phoebe, Fabiculana, Marivic, Perales, Marlyn, Mynott, Lee, Blake, Elizabeth, Bates, Amy, Vallier, Anne-Laure, Williams, Alexandra, Phillips, David, Chiu, Edmund, Overhill, Alex, Ramenatte, Nicola, Sipple, Jamal, Frost, Steven, Knock, Helena, Hardy, Richard, Foster, Emily, Davidson, Fiona, Rundell, Viona, Bundi, Purity, Abeseabe, Richmond, Clark, Sarah, Vicente, Isabel, Elmer, Anne, Ribeiro, Carla, Kourampa, Jenny, Kennet, Jane, Rowlands, Jane, Meadows, Anne, O’Brien, Criona, Rastall, Rebecca, Crucusio, Cherry, Hewitt, Sarah, Price, Jane, Calder, Jo, Canna, Laura, Bucke, Ashlea, Tordesillas, Hugo, Harris, Julie, Ruffolo, Valentina, Graves, Barbara, Butcher, Helen, Caputo, Daniela, Le Gresley, Emma, Dunmore, Benjamin J., Martin, Jennifer, Legchenko, Ekaterina, Treacy, Carmen, Huang, Christopher, Wood, Jennifer, Sutcliffe, Rachel, Hodgson, Josh, Shih, Joy, Graf, Stefan, Tong, Zhen, Mescia, Federica, Tilly, Tobias, O’Donnell, Ciara, Hunter, Kelvin, Pointon, Linda, Pond, Nicole, Wylot, Marta, Jones, Emma, Fawke, Stuart, Bullman, Ben, Turner, Lori, Jarvis, Isobel, Omarjee, Ommar, De Sa, Aloka, Marsden, Joe, Betancourt, Ariana, Perera, Marianne, Epping, Maddie, Richoz, Nathan, Bower, Georgie, Sharma, Rahul, Nice, Francesca, Huhn, Oisin, Savoinykh Yarkoni, Natalia, Romashova, Nika, Lewis, Daniel, Hinch, Andrew, Cossetti, Chiara, Strezlecki, Mateusz, Grenfell, Richard, Stark, Hannah, Walker, Neil, Stirrups, Kathy, Ovington, Nigel, Dewhust, Eleanor, Li, Emily, Papadia, Sofia, Kingston, Nathalie, Lever, Andrew, Torok, Estee, Hamilton, William, Hall, Grant, Jahun, Aminu, Chaudhry, Yasmin, Pinckert, Malte, Georgana, Iliana, Yakovleva, Anna, Caller, Laura, Caddy, Sarah, Feltwell, Theresa, Khokhar, Fahad, Meredith, Luke, Holdcroft, Charlotte, Parmar, Surendra, Mlcochova, Petra, Collier, Dami, Ritchie, Allyson, Assennato, Sonny M., Hosmillo, Myra, Goel, Neha, Meng, Bo, Chatterjee, Krishna, Mendoza, Vivien, Temperton, Nigel, Kiss, Leo, James, Leo C., Ciazynska, Katarzyna A., Xiong, Xiaoli, Briggs, John A.G., Nathan, James A., Bergamaschi, Laura, Barmpounakis, Petros, Demeris, Nikos, Skells, Richard, Lyons, Paul A., Baker, Steven, Allain, Jean Pierre, Bousfield, Rachel, Wilson, Michael, Sparkes, Dominic, Amoroso, Glenn, Gkrania-Klotsas, Effrosyni, Hardwick, Susie, Boyle, Adrian, and Gupta, Ravindra K.

Published
2020
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28. Genomic epidemiology of COVID-19 in care homes in the east of England

Author

Hamilton, William L, Tonkin-Hill, Gerry, Smith, Emily R, Aggarwal, Dinesh, Houldcroft, Charlotte J, Warne, Ben, Meredith, Luke W, Hosmillo, Myra, Jahun, Aminu S, Curran, Martin D, Parmar, Surendra, Caller, Laura G, Caddy, Sarah L, Khokhar, Fahad A, Yakovleva, Anna, Hall, Grant, Feltwell, Theresa, Pinckert, Malte L, Georgana, Iliana, Chaudhry, Yasmin, Brown, Colin S, Gonçalves, Sonia, Amato, Roberto, Harrison, Ewan M, Brown, Nicholas M, Beale, Mathew A, Spencer Chapman, Michael, Jackson, David K, Johnston, Ian, Alderton, Alex, Sillitoe, John, Langford, Cordelia, Dougan, Gordon, Peacock, Sharon J, Kwiatowski, Dominic P, Goodfellow, Ian G, Torok, M Estee, The COVID-19 Genomics Consortium UK, Allan, John, Bashton, Matthew, Loh, Joshua, Nelson, Andrew, Smith, Darren L., Yew, Wen Chyin, Young, Gregory R., Hamilton, William L [0000-0002-3330-353X], Tonkin-Hill, Gerry [0000-0003-4397-2224], Aggarwal, Dinesh [0000-0002-5938-8172], Houldcroft, Charlotte J [0000-0002-1833-5285], Hosmillo, Myra [0000-0002-3514-7681], Jahun, Aminu S [0000-0002-4585-1701], Caddy, Sarah L [0000-0002-9790-7420], Hall, Grant [0000-0003-3928-3979], Georgana, Iliana [0000-0002-8976-1177], Brown, Nicholas M [0000-0002-6657-300X], Beale, Mathew A [0000-0002-4740-3187], Spencer Chapman, Michael [0000-0002-5320-8193], Jackson, David K [0000-0002-8090-9462], Peacock, Sharon J [0000-0002-1718-2782], Goodfellow, Ian G [0000-0002-9483-510X], Torok, M Estee [0000-0001-9098-8590], and Apollo - University of Cambridge Repository

Subjects
Male, 0301 basic medicine, Time Factors, Care homes, Disease Outbreaks, Infectious Disease Transmission, Professional-to-Patient, 0302 clinical medicine, Epidemiology, Global health, Medicine, Infection control, 030212 general & internal medicine, Biology (General), Aged, 80 and over, education.field_of_study, Transmission (medicine), General Neuroscience, General Medicine, 3. Good health, Virus, England, Female, epidemiology, Sequence Analysis, Research Article, medicine.medical_specialty, Infectious Disease Transmission, Patient-to-Professional, Coronavirus disease 2019 (COVID-19), QH301-705.5, Science, Population, Polymorphism, Single Nucleotide, B700, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Environmental health, genomics, Humans, education, General Immunology and Microbiology, business.industry, SARS-CoV-2, Outbreak, COVID-19, Genetics and Genomics, C400, Nursing Homes, 030104 developmental biology, Epidemiology and Global Health, business
Abstract

COVID-19 poses a major challenge to care homes, as SARS-CoV-2 is readily transmitted and causes disproportionately severe disease in older people. Here, 1167 residents from 337 care homes were identified from a dataset of 6600 COVID-19 cases from the East of England. Older age and being a care home resident were associated with increased mortality. SARS-CoV-2 genomes were available for 700 residents from 292 care homes. By integrating genomic and temporal data, 409 viral clusters within the 292 homes were identified, indicating two different patterns – outbreaks among care home residents and independent introductions with limited onward transmission. Approximately 70% of residents in the genomic analysis were admitted to hospital during the study, providing extensive opportunities for transmission between care homes and hospitals. Limiting viral transmission within care homes should be a key target for infection control to reduce COVID-19 mortality in this population.

Published
2021

29. Superspreaders drive the largest outbreaks of hospital onset COVID-19 infections

Author

Illingworth, Christopher JR, primary, Hamilton, William L, additional, Warne, Ben, additional, Routledge, Matthew, additional, Popay, Ashley, additional, Jackson, Chris, additional, Fieldman, Tom, additional, Meredith, Luke W, additional, Houldcroft, Charlotte J, additional, Hosmillo, Myra, additional, Jahun, Aminu S, additional, Caller, Laura G, additional, Caddy, Sarah L, additional, Yakovleva, Anna, additional, Hall, Grant, additional, Khokhar, Fahad A, additional, Feltwell, Theresa, additional, Pinckert, Malte L, additional, Georgana, Iliana, additional, Chaudhry, Yasmin, additional, Curran, Martin D, additional, Parmar, Surendra, additional, Sparkes, Dominic, additional, Rivett, Lucy, additional, Jones, Nick K, additional, Sridhar, Sushmita, additional, Forrest, Sally, additional, Dymond, Tom, additional, Grainger, Kayleigh, additional, Workman, Chris, additional, Ferris, Mark, additional, Gkrania-Klotsas, Effrossyni, additional, Brown, Nicholas M, additional, Weekes, Michael P, additional, Baker, Stephen, additional, Peacock, Sharon J, additional, Goodfellow, Ian G, additional, Gouliouris, Theodore, additional, de Angelis, Daniela, additional, and Török, M Estée, additional

Published
2021
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31. Author response: Superspreaders drive the largest outbreaks of hospital onset COVID-19 infections

Author

Illingworth, Christopher JR, primary, Hamilton, William L, additional, Warne, Ben, additional, Routledge, Matthew, additional, Popay, Ashley, additional, Jackson, Chris, additional, Fieldman, Tom, additional, Meredith, Luke W, additional, Houldcroft, Charlotte J, additional, Hosmillo, Myra, additional, Jahun, Aminu S, additional, Caller, Laura G, additional, Caddy, Sarah L, additional, Yakovleva, Anna, additional, Hall, Grant, additional, Khokhar, Fahad A, additional, Feltwell, Theresa, additional, Pinckert, Malte L, additional, Georgana, Iliana, additional, Chaudhry, Yasmin, additional, Curran, Martin D, additional, Parmar, Surendra, additional, Sparkes, Dominic, additional, Rivett, Lucy, additional, Jones, Nick K, additional, Sridhar, Sushmita, additional, Forrest, Sally, additional, Dymond, Tom, additional, Grainger, Kayleigh, additional, Workman, Chris, additional, Ferris, Mark, additional, Gkrania-Klotsas, Effrossyni, additional, Brown, Nicholas M, additional, Weekes, Michael P, additional, Baker, Stephen, additional, Peacock, Sharon J, additional, Goodfellow, Ian G, additional, Gouliouris, Theodore, additional, de Angelis, Daniela, additional, and Török, M Estée, additional

Published
2021
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32. Screening of healthcare workers for SARS-CoV-2 highlights the role of asymptomatic carriage in COVID-19 transmission

Author

Rivett, Lucy, Sridhar, Sushmita, Sparkes, Dominic, Routledge, Matthew, Jones, Nick K, Forrest, Sally, Young, Jamie, Pereira-Dias, Joana, Hamilton, William L, Ferris, Mark, Torok, M Estee, Meredith, Luke, Collaboration, The CITIID-NIHR COVID-19 BioResource, Curran, Martin D, Fuller, Stewart, Chaudhry, Afzal, Shaw, Ashley, Samworth, Richard J, Bradley, John R, Dougan, Gordon, Smith, Kenneth GC, Lehner, Paul J, Matheson, Nicholas J, Wright, Giles, Goodfellow, Ian G, Baker, Stephen, Weekes, Michael P, Gupta, Ravi, Lyons, Paul A, Toshner, Mark, Warne, Ben, Bartholdson Scott, Josefin, Cormie, Claire, Gill, Harmeet, Kean, Iain, Maes, Mailis, Reynolds, Nicola, Wantoch, Michelle, Caddy, Sarah, Caller, Laura, Feltwell, Theresa, Hall, Grant, Hosmillo, Myra, Houldcroft, Charlotte, Jahun, Aminu, Khokhar, Fahad, Yakovleva, Anna, Butcher, Helen, Caputo, Daniela, Clapham-Riley, Debra, Dolling, Helen, Furlong, Anita, Graves, Barbara, Gresley, Emma Le, Kingston, Nathalie, Papadia, Sofia, Stark, Hannah, Stirrups, Kathleen E, Webster, Jennifer, Calder, Joanna, Harris, Julie, Hewitt, Sarah, Kennet, Jane, Meadows, Anne, Rastall, Rebecca, Brien, Criona O, Price, Jo, Publico, Cherry, Rowlands, Jane, Ruffolo, Valentina, Tordesillas, Hugo, Brookes, Karen, Canna, Laura, Cruz, Isabel, Dempsey, Katie, Elmer, Anne, Escoffery, Naidine, Jones, Heather, Ribeiro, Carla, Saunders, Caroline, Wright, Angela, Nyagumbo, Rutendo, Roberts, Anne, Bucke, Ashlea, Hargreaves, Simone, Johnson, Danielle, Narcorda, Aileen, Read, Debbie, Sparke, Christian, Warboys, Lucy, Lagadu, Kirsty, Mactavous, Lenette, Gould, Tim, Raine, Tim, Mather, Claire, Ramenatte, Nicola, Vallier, Anne-Laure, Kasanicki, Mary, Eames, Penelope-Jane, McNicholas, Chris, Thake, Lisa, Bartholomew, Neil, Brown, Nick, Parmar, Surendra, Zhang, Hongyi, Bowring, Ailsa, Martell, Geraldine, Quinnell, Natalie, Wright, Jo, Murphy, Helen, Dunmore, Benjamin J, Legchenko, Ekaterina, Gräf, Stefan, Huang, Christopher, Hodgson, Josh, Hunter, Kelvin, Martin, Jennifer, Mescia, Federica, O'Donnell, Ciara, Pointon, Linda, Shih, Joy, Sutcliffe, Rachel, Tilly, Tobias, Tong, Zhen, Treacy, Carmen, Wood, Jennifer, Bergamaschi, Laura, Betancourt, Ariana, Bowyer, Georgie, De Sa, Aloka, Epping, Maddie, Hinch, Andrew, Huhn, Oisin, Jarvis, Isobel, Lewis, Daniel, Marsden, Joe, McCallum, Simon, Nice, Francescsa, Rivett, Lucy [0000-0002-2781-9345], Lehner, Paul J [0000-0001-9383-1054], Matheson, Nicholas J [0000-0002-3318-1851], Goodfellow, Ian G [0000-0002-9483-510X], Weekes, Michael P [0000-0003-3196-5545], and Apollo - University of Cambridge Repository

Subjects
Epidemiology and Global Health, SARS-CoV-2, infectious disease, education, occupational health, virus diseases, COVID-19, Human Biology and Medicine, Research Article, virology, emerging pathogens, Human, Virus
Abstract

Funder: Addenbrooke's Charitable Trust, Cambridge University Hospitals; FundRef: http://dx.doi.org/10.13039/501100002927, Significant differences exist in the availability of healthcare worker (HCW) SARS-CoV-2 testing between countries, and existing programmes focus on screening symptomatic rather than asymptomatic staff. Over a 3 week period (April 2020), 1032 asymptomatic HCWs were screened for SARS-CoV-2 in a large UK teaching hospital. Symptomatic staff and symptomatic household contacts were additionally tested. Real-time RT-PCR was used to detect viral RNA from a throat+nose self-swab. 3% of HCWs in the asymptomatic screening group tested positive for SARS-CoV-2. 17/30 (57%) were truly asymptomatic/pauci-symptomatic. 12/30 (40%) had experienced symptoms compatible with coronavirus disease 2019 (COVID-19)>7 days prior to testing, most self-isolating, returning well. Clusters of HCW infection were discovered on two independent wards. Viral genome sequencing showed that the majority of HCWs had the dominant lineage B∙1. Our data demonstrates the utility of comprehensive screening of HCWs with minimal or no symptoms. This approach will be critical for protecting patients and hospital staff.

Published
2020
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33. Superspreaders drive the largest outbreaks of hospital onset COVID-19 infections

Author

Illingworth, Christopher J. R., Hamilton, William L., Warne, Ben, Routledge, Matthew, Popay, Ashley, Jackson, Chris, Fieldman, Tom, Meredith, Luke W., Houldcroft, Charlotte J., Hosmillo, Myra, Jahun, Aminu S., Caller, Laura G., Caddy, Sarah L., Yakovleva, Anna, Hall, Grant, Khokhar, Fahad A., Feltwell, Theresa, Pinckert, Malte L., Georgana, Iliana, Chaudhry, Yasmin, Curran, Martin D., Parmar, Surendra, Sparkes, Dominic, Rivett, Lucy, Jones, Nick K., Sridhar, Sushmita, Forrest, Sally, Dymond, Tom, Grainger, Kayleigh, Workman, Chris, Ferris, Mark, Gkrania-Klotsas, Effrossyni, Brown, Nicholas M., Weekes, Michael P., Baker, Stephen, Peacock, Sharon J., Goodfellow, Ian G., Gouliouris, Theodore, de Angelis, Daniela, Torok, M. Estee, Illingworth, Christopher J. R., Hamilton, William L., Warne, Ben, Routledge, Matthew, Popay, Ashley, Jackson, Chris, Fieldman, Tom, Meredith, Luke W., Houldcroft, Charlotte J., Hosmillo, Myra, Jahun, Aminu S., Caller, Laura G., Caddy, Sarah L., Yakovleva, Anna, Hall, Grant, Khokhar, Fahad A., Feltwell, Theresa, Pinckert, Malte L., Georgana, Iliana, Chaudhry, Yasmin, Curran, Martin D., Parmar, Surendra, Sparkes, Dominic, Rivett, Lucy, Jones, Nick K., Sridhar, Sushmita, Forrest, Sally, Dymond, Tom, Grainger, Kayleigh, Workman, Chris, Ferris, Mark, Gkrania-Klotsas, Effrossyni, Brown, Nicholas M., Weekes, Michael P., Baker, Stephen, Peacock, Sharon J., Goodfellow, Ian G., Gouliouris, Theodore, de Angelis, Daniela, and Torok, M. Estee

Abstract

SARS-CoV-2 is notable both for its rapid spread, and for the heterogeneity of its patterns of transmission, with multiple published incidences of superspreading behaviour. Here, we applied a novel network reconstruction algorithm to infer patterns of viral transmission occurring between patients and health care workers (HCWs) in the largest clusters of COVID-19 infection identified during the first wave of the epidemic at Cambridge University Hospitals NHS Foundation Trust, UK. Based upon dates of individuals reporting symptoms, recorded individual locations, and viral genome sequence data, we show an uneven pattern of transmission between individuals, with patients being much more likely to be infected by other patients than by HCWs. Further, the data were consistent with a pattern of superspreading, whereby 21% of individuals caused 80% of transmission events. Our study provides a detailed retrospective analysis of nosocomial SARS-CoV-2 transmission, and sheds light on the need for intensive and pervasive infection control procedures.

Published
2021

37. Superspreaders drive the largest outbreaks of hospital onset COVID-19 infection

Author

Illingworth, Chris, primary, Hamilton, William, additional, Warne, Ben, additional, Routledge, Matthew, additional, Popay, Ashley, additional, jackson, christopher, additional, Fieldman, Tom, additional, Meredith, Luke W., additional, Houldcroft, Charlotte J., additional, Hosmillo, Myra, additional, Jahun, Aminu S., additional, Caller, Laura G., additional, Caddy, Sarah L., additional, Yakovleva, Anna, additional, Hall, Grant, additional, Khokhar, Fahad A., additional, Feltwell, Theresa, additional, Pinckert, Malte L., additional, Georgana, Iliana, additional, Chaudhry, Yasmin, additional, Curran, Martin D., additional, Parmar, Surendra, additional, Sparkes, Dominic, additional, Rivett, Lucy, additional, Jones, Nick K., additional, Sridhar, Sushmita, additional, Forrest, Sally, additional, Dymond, Tom, additional, Grainger, Kayleigh, additional, Workman, Chris, additional, Gkrania-Klotsas, Effrossyni, additional, Brown, Nicholas M., additional, Baker, Stephen, additional, Weekes, Michael P., additional, Peacock, Sharon J., additional, Goodfellow, Ian, additional, Gouliouris, Theodore, additional, de Angelis, Daniela, additional, and Török, Estée, additional

Published
2021
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39. Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

Author

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

Published
2021
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40. A2B-COVID: A method for evaluating potential SARS-CoV-2 transmission events

Author

Illingworth, Christopher J. R., primary, Hamilton, William L., additional, Jackson, Chris, additional, Popay, Ashley, additional, Meredith, Luke, additional, Houldcroft, Charlotte J., additional, Hosmillo, Myra, additional, Jahun, Aminu, additional, Routledge, Matthew, additional, Warne, Ben, additional, Caller, Laura, additional, Caddy, Sarah, additional, Yakovleva, Anna, additional, Hall, Grant, additional, Khokhar, Fahad A., additional, Feltwell, Theresa, additional, Pinckert, Malte L., additional, Georgana, Iliana, additional, Chaudhry, Yasmin, additional, Curran, Martin, additional, Parmar, Surendra, additional, Sparkes, Dominic, additional, Rivett, Lucy, additional, Jones, Nick K., additional, Sridhar, Sushmita, additional, Forrest, Sally, additional, Dymond, Tom, additional, Grainger, Kayleigh, additional, Workman, Chris, additional, Gkrania-Klotsas, Effrossyni, additional, Brown, Nicholas M., additional, Weekes, Michael P., additional, Baker, Stephen, additional, Peacock, Sharon J., additional, Gouliouris, Theodore, additional, Goodfellow, Ian, additional, Angelis, Daniela De, additional, and Török, M. Estée, additional

Published
2020
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41. Successful treatment of COVID-19 with remdesivir in the absence of humoral immunity

Author

Buckland, Matthew S, primary, Galloway, James, additional, Fhogartaig, Caoimhe Nic, additional, Meredith, Luke, additional, Provine, Nicholas M., additional, Bloor, Stuart, additional, Ogbe, Ane, additional, Zelek, Wioleta M., additional, Smielewska, Anna, additional, Yakovleva, Anna, additional, Mann, Tiffeney, additional, Bergamaschi, Laura, additional, Turner, Lorinda, additional, Mescia, Frederica, additional, Toonen, Erik J.M., additional, Hackstein, Carl-Philipp, additional, Akther, Hossain Delowar, additional, Vieira, Vinicius Adriano, additional, Ceron-Gutierrez, Lourdes, additional, Periselneris, Jimstan, additional, Kiani-Alikhan, Sorena, additional, Grigoriadou, Sofia, additional, Vaghela, Devan, additional, Lear, Sara E., additional, Torok, Estee, additional, Hamilton, William L., additional, Quick, Josh, additional, Stockton, Joanne, additional, Nelson, Peter, additional, Hunter, Michael, additional, Coulter, Tanya I, additional, Devlin, Lisa, additional, Bradley, John, additional, Smith, Ken, additional, Ouwehand, Willem, additional, Estcourt, Lise, additional, Simmonds, Heli Harvala, additional, Roberts, Dave, additional, Wilkinson, Ian, additional, Screaton, Nick, additional, Loman, Nick, additional, Lyons, Paul, additional, Doffinger, Rainer, additional, Morgan, Paul, additional, Goodfellow, Ian, additional, Klenerman, Paul, additional, Lehner, Paul, additional, Matheson, Nick, additional, and Thaventhiran, James, additional

Published
2020
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43. Combined Point-of-Care Nucleic Acid and Antibody Testing for SARS-CoV-2 following Emergence of D614G Spike Variant

Author

Mlcochova, Petra, primary, Collier, Dami, additional, Ritchie, Allyson, additional, Assennato, Sonny M., additional, Hosmillo, Myra, additional, Goel, Neha, additional, Meng, Bo, additional, Chatterjee, Krishna, additional, Mendoza, Vivien, additional, Temperton, Nigel, additional, Kiss, Leo, additional, James, Leo C., additional, Ciazynska, Katarzyna A., additional, Xiong, Xiaoli, additional, Briggs, John A.G., additional, Nathan, James A., additional, Mescia, Federica, additional, Bergamaschi, Laura, additional, Zhang, Hongyi, additional, Barmpounakis, Petros, additional, Demeris, Nikos, additional, Skells, Richard, additional, Lyons, Paul A., additional, Bradley, John, additional, Baker, Steven, additional, Allain, Jean Pierre, additional, Smith, Kenneth G.C., additional, Bousfield, Rachel, additional, Wilson, Michael, additional, Sparkes, Dominic, additional, Amoroso, Glenn, additional, Gkrania-Klotsas, Effrosyni, additional, Hardwick, Susie, additional, Boyle, Adrian, additional, Goodfellow, Ian, additional, Gupta, Ravindra K., additional, Baker, Stephen, additional, Dougan, Gordon, additional, Gupta, Ravi, additional, Lehner, Paul J., additional, Lyons, Paul, additional, Matheson, Nicholas J., additional, Toshner, Mark, additional, Weekes, Michael P., additional, Brown, Nick, additional, Curran, Martin, additional, Palmar, Surendra, additional, Enoch, David, additional, Chapman, Daniel, additional, Shaw, Ashley, additional, Jose, Sherly, additional, Bermperi, Areti, additional, Zerrudo, Julie Ann, additional, Kourampa, Evgenia, additional, Watson, Laura, additional, Worsley, Jieniean, additional, Saunders, Caroline, additional, de Jesus, Ranalie, additional, Domingo, Jason, additional, Pasquale, Ciro, additional, Vergese, Bensi, additional, Vargas, Phoebe, additional, Fabiculana, Marivic, additional, Perales, Marlyn, additional, Mynott, Lee, additional, Blake, Elizabeth, additional, Bates, Amy, additional, Vallier, Anne-Laure, additional, Williams, Alexandra, additional, Phillips, David, additional, Chiu, Edmund, additional, Overhill, Alex, additional, Ramenatte, Nicola, additional, Sipple, Jamal, additional, Frost, Steven, additional, Knock, Helena, additional, Hardy, Richard, additional, Foster, Emily, additional, Davidson, Fiona, additional, Rundell, Viona, additional, Bundi, Purity, additional, Abeseabe, Richmond, additional, Clark, Sarah, additional, Vicente, Isabel, additional, Elmer, Anne, additional, Ribeiro, Carla, additional, Kourampa, Jenny, additional, Kennet, Jane, additional, Rowlands, Jane, additional, Meadows, Anne, additional, O’Brien, Criona, additional, Rastall, Rebecca, additional, Crucusio, Cherry, additional, Hewitt, Sarah, additional, Price, Jane, additional, Calder, Jo, additional, Canna, Laura, additional, Bucke, Ashlea, additional, Tordesillas, Hugo, additional, Harris, Julie, additional, Ruffolo, Valentina, additional, Graves, Barbara, additional, Butcher, Helen, additional, Caputo, Daniela, additional, Le Gresley, Emma, additional, Dunmore, Benjamin J., additional, Martin, Jennifer, additional, Legchenko, Ekaterina, additional, Treacy, Carmen, additional, Huang, Christopher, additional, Wood, Jennifer, additional, Sutcliffe, Rachel, additional, Hodgson, Josh, additional, Shih, Joy, additional, Graf, Stefan, additional, Tong, Zhen, additional, Tilly, Tobias, additional, O’Donnell, Ciara, additional, Hunter, Kelvin, additional, Pointon, Linda, additional, Pond, Nicole, additional, Wylot, Marta, additional, Jones, Emma, additional, Fawke, Stuart, additional, Bullman, Ben, additional, Turner, Lori, additional, Jarvis, Isobel, additional, Omarjee, Ommar, additional, De Sa, Aloka, additional, Marsden, Joe, additional, Betancourt, Ariana, additional, Perera, Marianne, additional, Epping, Maddie, additional, Richoz, Nathan, additional, Bower, Georgie, additional, Sharma, Rahul, additional, Nice, Francesca, additional, Huhn, Oisin, additional, Savoinykh Yarkoni, Natalia, additional, Romashova, Nika, additional, Lewis, Daniel, additional, Hinch, Andrew, additional, Cossetti, Chiara, additional, Strezlecki, Mateusz, additional, Grenfell, Richard, additional, Stark, Hannah, additional, Walker, Neil, additional, Stirrups, Kathy, additional, Ovington, Nigel, additional, Dewhust, Eleanor, additional, Li, Emily, additional, Papadia, Sofia, additional, Kingston, Nathalie, additional, Lever, Andrew, additional, Torok, Estee, additional, Hamilton, William, additional, Hall, Grant, additional, Jahun, Aminu, additional, Chaudhry, Yasmin, additional, Pinckert, Malte, additional, Georgana, Iliana, additional, Yakovleva, Anna, additional, Caller, Laura, additional, Caddy, Sarah, additional, Feltwell, Theresa, additional, Khokhar, Fahad, additional, Meredith, Luke, additional, Holdcroft, Charlotte, additional, and Parmar, Surendra, additional

Published
2020
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44. Correction: Safety and immunogenicity of the Na-GST-1 hookworm vaccine in Brazilian and American adults

Author

Diemert, David J., primary, Freire, Janaína, additional, Valente, Vanderson, additional, Fraga, Carlo Geraldo, additional, Talles, Frederico, additional, Grahek, Shannon, additional, Campbell, Doreen, additional, Jariwala, Amar, additional, Periago, Maria Victoria, additional, Enk, Martin, additional, Gazzinelli, Maria Flávia, additional, Bottazzi, Maria Elena, additional, Hamilton, Robert, additional, Brelsford, Jill, additional, Yakovleva, Anna, additional, Li, Guangzhao, additional, Peng, Jin, additional, Correa-Oliveira, Rodrigo, additional, Hotez, Peter, additional, and Bethony, Jeffrey, additional

Published
2020
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46. Rapid implementation of real-time SARS-CoV-2 sequencing to investigate healthcare-associated COVID-19 infections

Author

Meredith, Luke W., primary, Hamilton, William L., additional, Warne, Ben, additional, Houldcroft, Charlotte J., additional, Hosmillo, Myra, additional, Jahun, Aminu S., additional, Curran, Martin D., additional, Parmar, Surendra, additional, Caller, Laura G., additional, Caddy, Sarah L., additional, Khokhar, Fahad A., additional, Yakovleva, Anna, additional, Hall, Grant, additional, Feltwell, Theresa, additional, Forrest, Sally, additional, Sridhar, Sushmita, additional, Weekes, Michael P., additional, Baker, Stephen, additional, Brown, Nicholas, additional, Moore, Elinor, additional, Popay, Ashley, additional, Roddick, Iain, additional, Reacher, Mark, additional, Gouliouris, Theodore, additional, Peacock, Sharon J., additional, Dougan, Gordon, additional, Török, M. Estée, additional, and Goodfellow, Ian, additional

Published
2020
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47. Prospects for power supply infrastructure enhancement

Author

Kosygina Anna Vladimirovna, Dolmatov Ilya Alexeevich, Yakovleva Anna Yuryevna, Gavrikova Elizaveta, and Volkova Irina

Subjects
business.industry, Telecommunications, business, Power (physics)
Abstract

Traditional retail electricity market models transform under the condition of new technologies development and institutional changes in countries and worldwide. New models of the retail electricity market need to be adopted to recent requirements made by different stakeholders. The purpose of this study is to advance the understanding of transformation of the electricity retail market in different countries through introducing a uniform framework for comparison. The findings provide insights for experts and authorities on how the changes in the dynamic environment led to the emergence of new market models in six surveyed countries. Specific features of different models are highlighted to ensure optimal working conditions and incorporation with managerial practices in the industry as well as to help policy makers to understand what additional measures may boost the competition in retail electricity markets.

Published
2021
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48. [Untitled]

Author

Yakovleva, Anna

Subjects
clientelism, institute of distributing economy, paternalism, social justice, socio-economic inequality, Russian model of statehood, collectivism
Abstract

The article is devoted to the problem of the institutional specifics of socio-economic inequality in Russia. The article focuses on political, economic and ideological factors that determined the sociocultural features of the institutionalization of socio-economic inequality in Russian society.

Published
2019
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49. ИНСТИТУЦИОНАЛЬНЫЕ ТРАНСФОРМАЦИИ КАК СПОСОБ ПРЕОДОЛЕНИЯ СОЦИАЛЬНО-ЭКОНОМИЧЕСКОГО НЕРАВЕНСТВА В СОВРЕМЕННОЙ РОССИИ

Author

Yakovleva, Anna

Subjects
state, institutional transformations, socio-economic inequality, civil society, Russia
Abstract

The article identifies the main areas of activity aimed at changing the institutional environment of Russian society, generating socio-economic inequality. It seems that the key actors in the fight against poverty and socio-economic inequality should be the state and civil society. It is concluded that currently Russia has a request for changes in the system of public administration, for the implementation of the principle of social justice and the formation of real legal institutions in the state. The latter is possible only under condition of functioning of institutes of civil society.

Published
2019
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