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1. SARS-CoV-2 Testing in the Community: Testing Positive Samples with the TaqMan SARS-CoV-2 Mutation Panel To Find Variants in Real Time

Author: Ashford, Fiona, Best, Angus, Dunn, Steven J, Ahmed, Zahra, Siddiqui, Henna, Melville, Jordan, Wilkinson, Samuel, Mirza, Jeremy, Cumley, Nicola, Stockton, Joanne, Ferguson, Jack, Wheatley, Lucy, Ratcliffe, Elizabeth, Casey, Anna, Plant, Tim, Aggarwal, Dinesh, Blane, Beth, Brooks, Ellena, Carabelli, Alessandro M, Churcher, Carol M, Galai, Katerina, Girgis, Sophia T, Gupta, Ravi K, Hadjirin, Nazreen F, Leek, Danielle, Ludden, Catherine, McManus, Georgina M, Palmer, Sophie, Peacock, Sharon J, Smith, Kim S, Allara, Elias, Bibby, David, Bishop, Chloe, Bosworth, Andrew, Bradshaw, Daniel, Chalker, Vicki, Chand, Meera, Dabrera, Gavin, Ellaby, Nicholas, Gallagher, Eileen, Groves, Natalie, Harrison, Ian, Hartman, Hassan, Hopes, Richard, Hubb, Jonathan, Hutchings, Stephanie, Lackenby, Angie, Ledesma, Juan, Lee, David, Manesis, Nikos, Manso, Carmen, Mbisa, Tamyo, Miah, Shahjahan, Muir, Peter, Myers, Richard, Osman, Husam, Patel, Vineet, Pearson, Clare, Platt, Steven, Pymont, Hannah M, Ramsay, Mary, Robinson, Esther, Schaefer, Ulf, Thornton, Alicia, Twohig, Katherine A, Vipond, Ian B, Williams, David, Hamilton, William L, Warne, Ben, Aigrain, Louise, Alderton, Alex, Amato, Roberto, Ariani, Cristina V, Barrett, Jeff, Bassett, Andrew R, Beale, Mathew A, Beaver, Charlotte, Bellis, Katherine L, Betteridge, Emma, Bonfield, James, Bronner, Iraad F, Chapman, Michael HS, Danesh, John, Davies, Robert, Dorman, Matthew J, Drury, Eleanor, Durham, Jillian, Farr, Ben W, Foulser, Luke, Goncalves, Sonia, Goodwin, Scott, Gourtovaia, Marina, Harrison, Ewan M, Jackson, David K, James, Keith, Jamrozy, Dorota, Johnston, Ian, Kane, Leanne, Kay, Sally, and Keatley, Jon-Paul
Subjects: Human Genome, Prevention, Biodefense, Genetics, Lung, Vaccine Related, Emerging Infectious Diseases, Good Health and Well Being, COVID-19, COVID-19 Testing, Humans, Mutation, SARS-CoV-2, COVID-19 Genomics UK (COG-UK) Consortium, PCR, SNPs, genome sequencing, genotyping, real time, variants of concern, Biological Sciences, Agricultural and Veterinary Sciences, Medical and Health Sciences, Microbiology
Abstract: Genome sequencing is a powerful tool for identifying SARS-CoV-2 variant lineages; however, there can be limitations due to sequence dropout when used to identify specific key mutations. Recently, ThermoFisher Scientific has developed genotyping assays to help bridge the gap between testing capacity and sequencing capability to generate real-time genotyping results based on specific variants. Over a 6-week period during the months of April and May 2021, we set out to assess the ThermoFisher TaqMan mutation panel genotyping assay, initially for three mutations of concern and then for an additional two mutations of concern, against SARS-CoV-2-positive clinical samples and the corresponding COVID-19 Genomics UK Consortium (COG-UK) sequencing data. We demonstrate that genotyping is a powerful in-depth technique for identifying specific mutations, is an excellent complement to genome sequencing, and has real clinical health value potential, allowing laboratories to report and take action on variants of concern much more quickly.
Published: 2022

2. Antibiotic resistance determination using Enterococcus faecium whole-genome sequences: a diagnostic accuracy study using genotypic and phenotypic data

Author: Coll, Francesc, Gouliouris, Theodore, Blane, Beth, Yeats, Corin A, Raven, Kathy E, Ludden, Catherine, Khokhar, Fahad A, Wilson, Hayley J, Roberts, Leah W, Harrison, Ewan M, Horner, Carolyne S, Le, Thi Hoi, Nguyen, Thi Hoa, Nguyen, Vu Trung, Brown, Nicholas M, Holmes, Mark A, Parkhill, Julian, Estee Török, Mili, and Peacock, Sharon J
Published: 2024
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3. The impact of viral mutations on recognition by SARS-CoV-2 specific T cells

Author: de Silva, Thushan I, Liu, Guihai, Lindsey, Benjamin B, Dong, Danning, Moore, Shona C, Hsu, Nienyun Sharon, Shah, Dhruv, Wellington, Dannielle, Mentzer, Alexander J, Angyal, Adrienn, Brown, Rebecca, Parker, Matthew D, Ying, Zixi, Yao, Xuan, Turtle, Lance, Dunachie, Susanna, Aanensen, David M, Abudahab, Khalil, Adams, Helen, Adams, Alexander, Afifi, Safiah, Aggarwal, Dinesh, Ahmad, Shazaad SY, Aigrain, Louise, Alcolea-Medina, Adela, Alikhan, Nabil-Fareed, Allara, Elias, Amato, Roberto, Annett, Tara, Aplin, Stephen, Ariani, Cristina V, Asad, Hibo, Ash, Amy, Ashfield, Paula, Ashford, Fiona, Atkinson, Laura, Attwood, Stephen W, Auckland, Cressida, Aydin, Alp, Baker, David J, Baker, Paul, Balcazar, Carlos E, Ball, Jonathan, Barrett, Jeffrey C, Barrow, Magdalena, Barton, Edward, Bashton, Matthew, Bassett, Andrew R, Batra, Rahul, Baxter, Chris, Bayzid, Nadua, Beaver, Charlotte, Beckett, Angela H, Beckwith, Shaun M, Bedford, Luke, Beer, Robert, Beggs, Andrew, Bellis, Katherine L, Berry, Louise, Bertolusso, Beatrice, Best, Angus, Betteridge, Emma, Bibby, David, Bicknell, Kelly, Binns, Debbie, Birchley, Alec, Bird, Paul W, Bishop, Chloe, Blacow, Rachel, Blakey, Victoria, Blane, Beth, Bolt, Frances, Bonfield, James, Bonner, Stephen, Bonsall, David, Boswell, Tim, Bosworth, Andrew, Bourgeois, Yann, Boyd, Olivia, Bradley, Declan T, Breen, Cassie, Bresner, Catherine, Breuer, Judith, Bridgett, Stephen, Bronner, Iraad F, Brooks, Ellena, Broos, Alice, Brown, Julianne R, Bucca, Giselda, Buchan, Sarah L, Buck, David, Bull, Matthew, Burns, Phillipa J, Burton-Fanning, Shirelle, Byaruhanga, Timothy, Byott, Matthew, Campbell, Sharon, Carabelli, Alessandro M, Cargill, James S, and Carlile, Matthew
Subjects: Infectious Diseases, Prevention, Vaccine Related, Biodefense, Immunization, Emerging Infectious Diseases, Clinical Research, Good Health and Well Being, COVID-19 Genomics UK (COG-UK) Consortium, ISARIC4C Investigators, Immune response, Immunology, Molecular biology, Phylogenetics, Virology
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 recognize 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.
Published: 2021

4. Evaluating the impact of genomic epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) on hospital infection prevention and control decisions

Author: Blane, Beth, primary, Raven, Kathy E., additional, Brown, Nicholas M., additional, Harrison, Ewan M., additional, Coll, Francesc, additional, Thaxter, Rachel, additional, Enoch, David A., additional, Gouliouris, Theodore, additional, Leek, Danielle, additional, Girgis, Sophia T., additional, Akram, Asha, additional, Matuszewska, Marta, additional, Rhodes, Paul, additional, Parkhill, Julian, additional, and Peacock, Sharon J., additional
Published: 2024
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5. Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

Author: Aggarwal, Dinesh, Warne, Ben, Jahun, Aminu S., Hamilton, William L., Fieldman, Thomas, du Plessis, Louis, Hill, Verity, Blane, Beth, Watkins, Emmeline, Wright, Elizabeth, Hall, Grant, Ludden, Catherine, Myers, Richard, Hosmillo, Myra, Chaudhry, Yasmin, Pinckert, Malte L., Georgana, Iliana, Izuagbe, Rhys, Leek, Danielle, Nsonwu, Olisaeloka, Hughes, Gareth J., Packer, Simon, Page, Andrew J., Metaxaki, Marina, Fuller, Stewart, Weale, Gillian, Holgate, Jon, Brown, Christopher A., Howes, Rob, McFarlane, Duncan, Dougan, Gordon, Pybus, Oliver G., Angelis, Daniela De, Maxwell, Patrick H., Peacock, Sharon J., Weekes, Michael P., Illingworth, Chris, Harrison, Ewan M., Matheson, Nicholas J., and Goodfellow, Ian G.
Published: 2022
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6. The impact of viral mutations on recognition by SARS-CoV-2 specific T cells

Author: Aanensen, David M., Abudahab, Khalil, Adams, Helen, Adams, Alexander, Afifi, Safiah, Aggarwal, Dinesh, Ahmad, Shazaad S.Y., Aigrain, Louise, Alcolea-Medina, Adela, Alikhan, Nabil-Fareed, Allara, Elias, Amato, Roberto, Annett, Tara, Aplin, Stephen, Ariani, Cristina V., Asad, Hibo, Ash, Amy, Ashfield, Paula, Ashford, Fiona, Atkinson, Laura, Attwood, Stephen W., Auckland, Cressida, Aydin, Alp, Baker, David J., Baker, Paul, Balcazar, Carlos E., Ball, Jonathan, Barrett, Jeffrey C., Barrow, Magdalena, Barton, Edward, Bashton, Matthew, Bassett, Andrew R., Batra, Rahul, Baxter, Chris, Bayzid, Nadua, Beaver, Charlotte, Beckett, Angela H., Beckwith, Shaun M., Bedford, Luke, Beer, Robert, Beggs, Andrew, Bellis, Katherine L., Berry, Louise, Bertolusso, Beatrice, Best, Angus, Betteridge, Emma, Bibby, David, Bicknell, Kelly, Binns, Debbie, Birchley, Alec, Bird, Paul W., Bishop, Chloe, Blacow, Rachel, Blakey, Victoria, Blane, Beth, Bolt, Frances, Bonfield, James, Bonner, Stephen, Bonsall, David, Boswell, Tim, Bosworth, Andrew, Bourgeois, Yann, Boyd, Olivia, Bradley, Declan T., Breen, Cassie, Bresner, Catherine, Breuer, Judith, Bridgett, Stephen, Bronner, Iraad F., Brooks, Ellena, Broos, Alice, Brown, Julianne R., Bucca, Giselda, Buchan, Sarah L., Buck, David, Bull, Matthew, Burns, Phillipa J., Burton-Fanning, Shirelle, Byaruhanga, Timothy, Byott, Matthew, Campbell, Sharon, Carabelli, Alessandro M., Cargill, James S., Carlile, Matthew, Carvalho, Silvia F., Casey, Anna, Castigador, Anibolina, Catalan, Jana, Chalker, Vicki, Chaloner, Nicola J., Chand, Meera, Chappell, Joseph G., Charalampous, Themoula, Chatterton, Wendy, Chaudhry, Yasmin, Churcher, Carol M., Clark, Gemma, Clarke, Phillip, Cogger, Benjamin J., Cole, Kevin, Collins, Jennifer, Colquhoun, Rachel, Connor, Thomas R., Cook, Kate F., Coombes, Jason, Corden, Sally, Cormie, Claire, Cortes, Nicholas, Cotic, Marius, Cotton, Seb, Cottrell, Simon, Coupland, Lindsay, Cox, MacGregor, Cox, Alison, Craine, Noel, Crawford, Liam, Cross, Aidan, Crown, Matthew R., Crudgington, Dorian, Cumley, Nicola, Curran, Tanya, Curran, Martin D., da Silva Filipe, Ana, Dabrera, Gavin, Darby, Alistair C., Davidson, Rose K., Davies, Alisha, Davies, Robert M., Davis, Thomas, de Angelis, Daniela, De Lacy, Elen, de Oliveira Martins, Leonardo, Debebe, Johnny, Denton-Smith, Rebecca, Dervisevic, Samir, Dewar, Rebecca, Dey, Jayasree, Dias, Joana, Dobie, Donald, Dorman, Matthew J., Downing, Fatima, Driscoll, Megan, du Plessis, Louis, Duckworth, Nichola, Durham, Jillian, Eastick, Kirstine, Easton, Lisa J., Eccles, Richard, Edgeworth, Jonathan, Edwards, Sue, El Bouzidi, Kate, Eldirdiri, Sahar, Ellaby, Nicholas, Elliott, Scott, Eltringham, Gary, Ensell, Leah, Erkiert, Michelle J., Zamudio, Marina Escalera, Essex, Sarah, Evans, Johnathan M., Evans, Cariad, Everson, William, Fairley, Derek J., Fallon, Karlie, Fanaie, Arezou, Farr, Ben W., Fearn, Christopher, Feltwell, Theresa, Ferguson, Lynne, Fina, Laia, Flaviani, Flavia, Fleming, Vicki M., Forrest, Sally, Foster-Nyarko, Ebenezer, Foulkes, Benjamin H., Foulser, Luke, Fragakis, Mireille, Frampton, Dan, Francois, Sarah, Fraser, Christophe, Freeman, Timothy M., Fryer, Helen, Fuchs, Marc, Fuller, William, Gajee, Kavitha, Galai, Katerina, Gallagher, Abbie, Gallagher, Eileen, Gallagher, Michael D., Gallis, Marta, Gaskin, Amy, Gatica-Wilcox, Bree, Geidelberg, Lily, Gemmell, Matthew, Georgana, Iliana, George, Ryan P., Gifford, Laura, Gilbert, Lauren, Girgis, Sophia T., Glaysher, Sharon, Goldstein, Emily J., Golubchik, Tanya, Gomes, Andrea N., Gonçalves, Sónia, Goodfellow, Ian G., Goodwin, Scott, Goudarzi, Salman, Gourtovaia, Marina, Graham, Clive, Graham, Lee, Grant, Paul R., Green, Luke R., Green, Angie, Greenaway, Jane, Gregory, Richard, Guest, Martyn, Gunson, Rory N., Gupta, Ravi K., Gutierrez, Bernardo, Haldenby, Sam T., Hamilton, William L., Hansford, Samantha E., Haque, Tanzina, Harris, Kathryn A., Harrison, Ian, Harrison, Ewan M., Hart, Jennifer, Hartley, John A., Harvey, William T., Harvey, Matthew, Hassan-Ibrahim, Mohammed O., Heaney, Judith, Helmer, Thomas, Henderson, John H., Hesketh, Andrew R., Hey, Jessica, Heyburn, David, Higginson, Ellen E., Hill, Verity, Hill, Jack D., Hilson, Rachel A., Hilvers, Ember, Holden, Matthew T.G., Hollis, Amy, Holmes, Christopher W., Holmes, Nadine, Holmes, Alison H., Hopes, Richard, Hornsby, Hailey R., Hosmillo, Myra, Houlihan, Catherine, Howson-Wells, Hannah C., Hubb, Jonathan, Huckson, Hannah, Hughes, Warwick, Hughes, Joseph, Hughes, Margaret, Hutchings, Stephanie, Idle, Giles, Illingworth, Chris J., Impey, Robert, Irish-Tavares, Dianne, Iturriza-Gomara, Miren, Izuagbe, Rhys, Jackson, Chris, Jackson, Ben, Jackson, Leigh M., Jackson, Kathryn A., Jackson, David K., Jahun, Aminu S., James, Victoria, James, Keith, Jeanes, Christopher, Jeffries, Aaron R., Jeremiah, Sarah, Jermy, Andrew, John, Michaela, Johnson, Rob, Johnson, Kate, Johnston, Ian, Jones, Owen, Jones, Sophie, Jones, Hannah, Jones, Christopher R., Jones, Neil, Joseph, Amelia, Judges, Sarah, Kay, Gemma L., Kay, Sally, Keatley, Jon-Paul, Keeley, Alexander J., Kenyon, Anita, Kermack, Leanne M., Khakh, Manjinder, Kidd, Stephen P., Kimuli, Maimuna, Kirk, Stuart, Kitchen, Christine, Kitchman, Katie, Knight, Bridget A., Koshy, Cherian, Kraemer, Moritz U.G., Kumziene-Summerhayes, Sara, Kwiatkowski, Dominic, Lackenby, Angie, Laing, Kenneth G., Lampejo, Temi, Langford, Cordelia F., Lavin, Deborah, Lawton, Andrew I., Lee, Jack, Lee, David, Lensing, Stefanie V., Leonard, Steven, Levett, Lisa J., Le-Viet, Thanh, Lewis, Jonathan, Lewis, Kevin, Liddle, Jennifier, Liggett, Steven, Lillie, Patrick J., Lister, Michelle M., Livett, Rich, Lo, Stephanie, Loman, Nicholas J., Loose, Matthew W., Louka, Stavroula F., Loveson, Katie F., Lowdon, Sarah, Lowe, Hannah, Lowe, Helen L., Lucaci, Anita O., Ludden, Catherine, Lynch, Jessica, Lyons, Ronan A., Lythgoe, Katrina, Machin, Nicholas W., MacIntyre-Cockett, George, Mack, Andrew, Macklin, Ben, Maclean, Alasdair, Macnaughton, Emily, Madona, Pinglawathee, Maes, Mailis, Maftei, Laurentiu, Mahanama, Adhyana I.K., Mahungu, Tabitha W., Mair, Daniel, Maksimovic, Joshua, Malone, Cassandra S., Maloney, Daniel, Manesis, Nikos, Manley, Robin, Mantzouratou, Anna, Marchbank, Angela, Mariappan, Arun, Martincorena, Inigo, Martinez Nunez, Rocio T., Mather, Alison E., Maxwell, Patrick, Mayhew, Megan, Mbisa, Tamyo, McCann, Clare M., McCarthy, Shane A., McCluggage, Kathryn, McClure, Patrick C., McCrone, J.T., McHugh, Martin P., McKenna, James P., McKerr, Caoimhe, McManus, Georgina M., McMurray, Claire L., McMurray, Claire, McNally, Alan, Meadows, Lizzie, Medd, Nathan, Megram, Oliver, Menegazzo, Mirko, Merrick, Ian, Michell, Stephen L., Michelsen, Michelle L., Mirfenderesky, Mariyam, Mirza, Jeremy, Miskelly, Julia, Moles-Garcia, Emma, Moll, Robin J., Molnar, Zoltan, Monahan, Irene M., Mondani, Matteo, Mookerjee, Siddharth, Moore, Christopher, Moore, Jonathan, Moore, Nathan, Moore, Catherine, Morcrette, Helen, Morgan, Sian, Morgan, Mari, Mori, Matilde, Morriss, Arthur, Moses, Samuel, Mower, Craig, Muir, Peter, Mukaddas, Afrida, Munemo, Florence, Munn, Robert, Murray, Abigail, Murray, Leanne J., Murray, Darren R., Mutingwende, Manasa, Myers, Richard, Nastouli, Eleni, Nebbia, Gaia, Nelson, Andrew, Nelson, Charlotte, Nicholls, Sam, Nichols, Jenna, Nicodemi, Roberto, Nomikou, Kyriaki, O’Grady, Justin, O'Brien, Sarah, Odedra, Mina, Ohemeng-Kumi, Natasha, Oliver, Karen, Orton, Richard J., Osman, Husam, xeine O'Toole, Pacchiarini, Nicole, Padgett, Debra, Page, Andrew J., Park, Emily J., Park, Naomi R., Parmar, Surendra, Partridge, David G., Pascall, David, Patel, Amita, Patel, Bindi, Paterson, Steve, Payne, Brendan A.I., Peacock, Sharon J., Pearson, Clare, Pelosi, Emanuela, Percival, Benita, Perkins, Jon, Perry, Malorie, Pinckert, Malte L., Platt, Steven, Podplomyk, Olga, Pohare, Manoj, Pond, Marcus, Pope, Cassie F., Poplawski, Radoslaw, Powell, Jessica, Poyner, Jennifer, Prestwood, Liam, Price, Anna, Price, James R., Prieto, Jacqui A., Pritchard, David T., Prosolek, Sophie J., Pugh, Georgia, Pusok, Monika, Pybus, Oliver G., Pymont, Hannah M., Quail, Michael A., Quick, Joshua, Radulescu, Clara, Raghwani, Jayna, Ragonnet-Cronin, Manon, Rainbow, Lucille, Rajan, Diana, Rajatileka, Shavanthi, Ramadan, Newara A., Rambaut, Andrew, Ramble, John, Randell, Paul A., Randell, Paul, Ratcliffe, Liz, Raviprakash, Veena, Raza, Mohammad, Redshaw, Nicholas M., Rey, Sara, Reynolds, Nicola, Richter, Alex, Robertson, David L., Robinson, Esther, Robson, Samuel C., Rogan, Fiona, Rooke, Stefan, Rowe, Will, Roy, Sunando, Rudder, Steven, Ruis, Chris, Rushton, Steven, Ryan, Felicity, Saeed, Kordo, Samaraweera, Buddhini, Sambles, Christine M., Sanderson, Roy, Sanderson, Theo, Sang, Fei, Sass, Thea, Scher, Emily, Scott, Garren, Scott, Carol, Sehmi, Jasveen, Shaaban, Sharif, Shah, Divya, Shaw, Jessica, Shelest, Ekaterina, Shepherd, James G., Sheridan, Liz A., Sheriff, Nicola, Shirley, Lesley, Sillitoe, John, Silviera, Siona, Simpson, David A., Singh, Aditi, Singleton, Dawn, Skvortsov, Timofey, Sloan, Tim J., Sluga, Graciela, Smith, Ken, Smith, Kim S., Smith, Perminder, Smith, Darren L., Smith, Louise, Smith, Colin P., Smith, Nikki, Smollett, Katherine L., Snell, Luke B., Somassa, Thomas, Southgate, Joel, Spellman, Karla, Spencer Chapman, Michael H., Spurgin, Lewis G., Spyer, Moira J., Stanley, Rachael, Stanley, William, Stanton, Thomas D., Starinskij, Igor, Stockton, Joanne, Stonehouse, Susanne, Storey, Nathaniel, Studholme, David J., Sudhanva, Malur, Swindells, Emma, Taha, Yusri, Tan, Ngee Keong, Tang, Julian W., Tang, Miao, Taylor, Ben E.W., Taylor, Joshua F., Taylor, Sarah, Temperton, Ben, Templeton, Kate E., Thomas, Claire, Thomson, Laura, Thomson, Emma C., Thornton, Alicia, Thurston, Scott A.J., Todd, John A., Tomb, Rachael, Tong, Lily, Tonkin-Hill, Gerry, Torok, M. Estee, Tovar-Corona, Jaime M., Trebes, Amy, Trotter, Alexander J., Tsatsani, Ioulia, Turnbull, Robyn, Twohig, Katherine A., Umpleby, Helen, Underwood, Anthony P., Vamos, Edith E., Vasylyeva, Tetyana I., Vattipally, Sreenu, Vernet, Gabrielle, Vipond, Barry B., Volz, Erik M., Walsh, Sarah, Wang, Dennis, Warne, Ben, Warwick-Dugdale, Joanna, Wastnedge, Elizabeth, Watkins, Joanne, Watson, Louisa K., Waugh, Sheila, Webster, Hermione J., Weldon, Danni, Westwick, Elaine, Whalley, Thomas, Wheeler, Helen, Whitehead, Mark, Whiteley, Max, Whitwham, Andrew, Wierzbicki, Claudia, Willford, Nicholas J., Williams, Lesley-Anne, Williams, Rebecca, Williams, Cheryl, Williams, Chris, Williams, Charlotte A., Williams, Rachel J., Williams, Thomas, Williams, Catryn, Williamson, Kathleen A., Wilson-Davies, Eleri, Witele, Eric, Withell, Karen T., Witney, Adam A., Wolverson, Paige, Wong, Nick, Workman, Trudy, Wright, Victoria, Wright, Derek W., Wyatt, Tim, Wyllie, Sarah, Xu-McCrae, Li, Yavus, Mehmet, Yaze, Geraldine, Yeats, Corin A., Yebra, Gonzalo, Yew, Wen C., Young, Gregory R., Young, Jamie, Zarebski, Alex E., Zhang, Peijun, Baillie, J. Kenneth, Semple, Malcolm G., Openshaw, Peter J.M., Carson, Gail, Alex, Beatrice, Andrikopoulos, Petros, Bach, Benjamin, Barclay, Wendy S., Bogaert, Debby, Chechi, Kanta, Cooke, Graham S., Docherty, Annemarie B., Correia, Gonçalo dos Santos, Dumas, Marc-Emmanuel, Dunning, Jake, Fletcher, Tom, Green, Christopher A., Greenhalf, William, Griffin, Julian L., Gupta, Rishi K., Harrison, Ewen M., Hiscox, Julian A., Wai Ho, Antonia Ying, Horby, Peter W., Ijaz, Samreen, Khoo, Saye, Klenerman, Paul, Law, Andrew, Lewis, Matthew R., Liggi, Sonia, Lim, Wei Shen, Maslen, Lynn, Mentzer, Alexander J., Merson, Laura, Meynert, Alison M., Noursadeghi, Mahdad, Olanipekun, Michael, Osagie, Anthonia, Palmarini, Massimo, Palmieri, Carlo, Paxton, William A., Pollakis, Georgios, Price, Nicholas, Russell, Clark D., Sancho-Shimizu, Vanessa, Sands, Caroline J., Scott, Janet T., Sigfrid, Louise, Solomon, Tom, Sriskandan, Shiranee, Stuart, David, Summers, Charlotte, Swann, Olivia V., Takats, Zoltan, Takis, Panteleimon, Tedder, Richard S., Thompson, A.A. Roger, Thwaites, Ryan S., Zambon, Maria, Hardwick, Hayley, Donohue, Chloe, Griffiths, Fiona, Oosthuyzen, Wilna, Donegan, Cara, Spencer, Rebecca G., Dalton, Jo, Girvan, Michelle, Saviciute, Egle, Roberts, Stephanie, Harrison, Janet, Marsh, Laura, Connor, Marie, Halpin, Sophie, Jackson, Clare, Gamble, Carrol, Plotkin, Daniel, Lee, James, Leeming, Gary, Wham, Murray, Clohisey, Sara, Hendry, Ross, Scott-Brown, James, Shaw, Victoria, McDonald, Sarah E., Keating, Seán, Ahmed, Katie A., Armstrong, Jane A., Ashworth, Milton, Asiimwe, Innocent G., Bakshi, Siddharth, Barlow, Samantha L., Booth, Laura, Brennan, Benjamin, Bullock, Katie, Catterall, Benjamin W.A., Clark, Jordan J., Clarke, Emily A., Cole, Sarah, Cooper, Louise, Cox, Helen, Davis, Christopher, Dincarslan, Oslem, Dunn, Chris, Dyer, Philip, Elliott, Angela, Evans, Anthony, Finch, Lorna, Fisher, Lewis W.S., Foster, Terry, Garcia-Dorival, Isabel, Gunning, Philip, Hartley, Catherine, Jensen, Rebecca L., Jones, Christopher B., Jones, Trevor R., Khandaker, Shadia, King, Katharine, Kiy, Robyn T., Koukorava, Chrysa, Lake, Annette, Lant, Suzannah, Latawiec, Diane, Lavelle-Langham, Lara, Lefteri, Daniella, Lett, Lauren, Livoti, Lucia A., Mancini, Maria, McDonald, Sarah, McEvoy, Laurence, McLauchlan, John, Metelmann, Soeren, Miah, Nahida S., Middleton, Joanna, Mitchell, Joyce, Moore, Shona C., Murphy, Ellen G., Penrice-Randal, Rebekah, Pilgrim, Jack, Prince, Tessa, Reynolds, Will, Ridley, P. Matthew, Sales, Debby, Shaw, Victoria E., Shears, Rebecca K., Small, Benjamin, Subramaniam, Krishanthi S., Szemiel, Agnieska, Taggart, Aislynn, Tanianis-Hughes, Jolanta, Thomas, Jordan, Trochu, Erwan, van Tonder, Libby, Wilcock, Eve, Zhang, J. Eunice, Flaherty, Lisa, Maziere, Nicole, Cass, Emily, Carracedo, Alejandra Doce, Carlucci, Nicola, Holmes, Anthony, Massey, Hannah, Murphy, Lee, Wrobel, Nicola, McCafferty, Sarah, Morrice, Kirstie, MacLean, Alan, Adeniji, Kayode, Agranoff, Daniel, Agwuh, Ken, Ail, Dhiraj, Aldera, Erin L., Alegria, Ana, Allen, Sam, Angus, Brian, Ashish, Abdul, Atkinson, Dougal, Bari, Shahedal, Barlow, Gavin, Barnass, Stella, Barrett, Nicholas, Bassford, Christopher, Basude, Sneha, Baxter, David, Beadsworth, Michael, Bernatoniene, Jolanta, Berridge, John, Berry, Colin, Best, Nicola, Bothma, Pieter, Chadwick, David, Brittain-Long, Robin, Bulteel, Naomi, Burden, Tom, Burtenshaw, Andrew, Caruth, Vikki, Chambler, Duncan, Chee, Nigel, Child, Jenny, Chukkambotla, Srikanth, Clark, Tom, Collini, Paul, Cosgrove, Catherine, Cupitt, Jason, Cutino-Moguel, Maria-Teresa, Dark, Paul, Dawson, Chris, Donnison, Phil, Douthwaite, Sam, Drummond, Andrew, DuRand, Ingrid, Dushianthan, Ahilanadan, Dyer, Tristan, Eziefula, Chi, Fegan, Chrisopher, Finn, Adam, Fullerton, Duncan, Garg, Sanjeev, Garg, Atul, Gkrania-Klotsas, Effrossyni, Godden, Jo, Goldsmith, Arthur, Hardy, Elaine, Hartshorn, Stuart, Harvey, Daniel, Havalda, Peter, Hawcutt, Daniel B., Hobrok, Maria, Hodgson, Luke, Hormis, Anil, Jacobs, Michael, Jain, Susan, Jennings, Paul, Kaliappan, Agilan, Kasipandian, Vidya, Kegg, Stephen, Kelsey, Michael, Kendall, Jason, Kerrison, Caroline, Kerslake, Ian, Koch, Oliver, Koduri, Gouri, Koshy, George, Laha, Shondipon, Laird, Steven, Larkin, Susan, Leiner, Tamas, Lillie, Patrick, Limb, James, Linnett, Vanessa, Little, Jeff, Lyttle, Mark, MacMahon, Michael, MacNaughton, Emily, Mankregod, Ravish, Masson, Huw, Matovu, Elijah, McCullough, Katherine, McEwen, Ruth, Meda, Manjula, Mills, Gary, Minton, Jane, Mohandas, Kavya, Mok, Quen, Moon, James, Moore, Elinoor, Morgan, Patrick, Morris, Craig, Mortimore, Katherine, Mpenge, Mbiye, Mulla, Rohinton, Murphy, Michael, Nagel, Megan, Nagarajan, Thapas, Nelson, Mark, Norris, Lillian, O'Shea, Matthew K., Otahal, Igor, Ostermann, Marlies, Pais, Mark, Panchatsharam, Selva, Papakonstantinou, Danai, Paraiso, Hassan, Patel, Brij, Pattison, Natalie, Pepperell, Justin, Peters, Mark, Phull, Mandeep, Pintus, Stefania, Pooni, Jagtur Singh, Planche, Tim, Post, Frank, Price, David, Prout, Rachel, Rae, Nikolas, Reschreiter, Henrik, Reynolds, Tim, Richardson, Neil, Roberts, Mark, Roberts, Devender, Rose, Alistair, Rousseau, Guy, Ruge, Bobby, Ryan, Brendan, Saluja, Taranprit, Schmid, Matthias L., Shah, Aarti, Shanmuga, Prad, Sharma, Anil, Shawcross, Anna, Sizer, Jeremy, Shankar-Hari, Manu, Smith, Richard, Snelson, Catherine, Spittle, Nick, Staines, Nikki, Stambach, Tom, Stewart, Richard, Subudhi, Pradeep, Szakmany, Tamas, Tatham, Kate, Thomas, Jo, Thompson, Chris, Thompson, Robert, Tridente, Ascanio, Tupper-Carey, Darell, Twagira, Mary, Vallotton, Nick, Vancheeswaran, Rama, Vincent-Smith, Lisa, Visuvanathan, Shico, Vuylsteke, Alan, Waddy, Sam, Wake, Rachel, Walden, Andrew, Welters, Ingeborg, Whitehouse, Tony, Whittaker, Paul, Whittington, Ashley, Papineni, Padmasayee, Wijesinghe, Meme, Williams, Martin, Wilson, Lawrence, Winchester, Stephen, Wiselka, Martin, Wolverson, Adam, Wootton, Daniel G., Workman, Andrew, Yates, Bryan, Young, Peter, de Silva, Thushan I., Liu, Guihai, Lindsey, Benjamin B., Dong, Danning, Hsu, Nienyun Sharon, Shah, Dhruv, Wellington, Dannielle, Angyal, Adrienn, Brown, Rebecca, Parker, Matthew D., Ying, Zixi, Yao, Xuan, Turtle, Lance, Dunachie, Susanna, Maini, Mala K., Ogg, Graham, Knight, Julian C., Peng, Yanchun, Rowland-Jones, Sarah L., and Dong, Tao
Published: 2021
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7. Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study

Author: Koshy, Cherian, Ash, Amy, Wise, Emma, Moore, Nathan, Mori, Matilde, Cortes, Nick, Lynch, Jessica, Kidd, Stephen, Fairley, Derek J, Curran, Tanya, McKenna, James P, Adams, Helen, Fraser, Christophe, Golubchik, Tanya, Bonsall, David, Hassan-Ibrahim, Mohammed O, Malone, Cassandra S, Cogger, Benjamin J, 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, Patel, Amita, Charalampous, Themoula, Nebbia, Gaia, Batra, Rahul, Edgeworth, Jonathan, Robson, Samuel C, Beckett, Angela H, Aanensen, David M, Underwood, Anthony P, Yeats, Corin A, Abudahab, Khalil, Taylor, Ben EW, 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, Jones, Carl, Holmes, Christopher, Bird, Paul, Helmer, Thomas, Fallon, Karlie, Tang, Julian, Raviprakash, Veena, Campbell, Sharon, Sheriff, Nicola, Blakey, Victoria, Williams, Lesley-Anne, 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, Eldirdiri, Sahar, Kenyon, Anita, Davis, Thomas, Pybus, Oliver G, du Plessis, Louis, Zarebski, Alex E, Raghwani, Jayna, Kraemer, Moritz UG, Francois, Sarah, Attwood, Stephen W, Vasylyeva, Tetyana I, Escalera Zamudio, Marina, Gutierrez, Bernardo, Torok, M. Estee, Hamilton, William L, Goodfellow, Ian G, Hall, Grant, Jahun, Aminu S, Chaudhry, Yasmin, Hosmillo, Myra, Pinckert, Malte L, Georgana, Iliana, Moses, Samuel, Lowe, Hannah, Bedford, Luke, Moore, Jonathan, Stonehouse, Susanne, Fisher, Chloe L, Awan, Ali R, BoYes, John, Breuer, Judith, Harris, Kathryn Ann, Brown, Julianne Rose, Shah, Divya, Atkinson, Laura, Lee, Jack CD, Storey, Nathaniel, Flaviani, Flavia, Alcolea-Medina, Adela, Williams, Rebecca, Vernet, Gabrielle, Chapman, Michael R, Levett, Lisa J, Heaney, Judith, Chatterton, Wendy, Pusok, Monika, Xu-McCrae, Li, Smith, Darren L, Bashton, Matthew, Young, Gregory R, Holmes, Alison, Randell, Paul Anthony, Cox, Alison, Madona, Pinglawathee, Bolt, Frances, Price, James, Mookerjee, Siddharth, Ragonnet-Cronin, Manon, Nascimento, Fabricia F., Jorgensen, David, Siveroni, Igor, Johnson, Rob, Boyd, Olivia, Geidelberg, Lily, Volz, Erik M, Rowan, Aileen, Taylor, Graham P, Smollett, Katherine L, Loman, Nicholas J, Quick, Joshua, McMurray, Claire, Stockton, Joanne, Nicholls, Sam, Rowe, Will, Poplawski, Radoslaw, McNally, Alan, Martinez Nunez, Rocio T, Mason, Jenifer, Robinson, Trevor I, O'Toole, Elaine, Watts, Joanne, Breen, Cassie, Cowell, Angela, Sluga, Graciela, Machin, Nicholas W, Ahmad, Shazaad S Y, George, Ryan P, Halstead, Fenella, Sivaprakasam, Venkat, Hogsden, Wendy, Illingworth, Chris J, Jackson, Chris, Thomson, Emma C, Shepherd, James G, Asamaphan, Patawee, Niebel, Marc O, Li, Kathy K, Shah, Rajiv N, Jesudason, Natasha G, 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, Nickbakhsh, Seema, Hale, Antony D, Macfarlane-Smith, Louissa R, Harper, Katherine L, Carden, Holli, Taha, Yusri, Payne, Brendan AI, Burton-Fanning, Shirelle, Waugh, Sheila, Collins, Jennifer, Eltringham, Gary, Rushton, Steven, O'Brien, Sarah, Bradley, Amanda, Maclean, Alasdair, Mollett, Guy, Blacow, Rachel, Templeton, Kate E, McHugh, Martin P, Dewar, Rebecca, Wastenge, Elizabeth, Dervisevic, Samir, Stanley, Rachael, Meader, Emma J, Coupland, Lindsay, Smith, Louise, Graham, Clive, Barton, Edward, Padgett, Debra, Scott, Garren, Swindells, Emma, Greenaway, Jane, Nelson, Andrew, McCann, Clare M, Yew, Wen C, Andersson, Monique, Peto, Timothy, Justice, Anita, Eyre, David, Crook, Derrick, Sloan, Tim J, Duckworth, Nichola, Walsh, Sarah, Chauhan, Anoop J, Glaysher, Sharon, Bicknell, Kelly, Wyllie, Sarah, Elliott, Scott, Lloyd, Allyson, Impey, Robert, Levene, Nick, Monaghan, Lynn, Bradley, Declan T, Wyatt, Tim, Allara, Elias, Pearson, Clare, Osman, Husam, Bosworth, Andrew, Robinson, Esther, 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, Ledesma, Juan, Twohig, Katherine A, 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, Mather, Alison E, Baker, David J, Rudder, Steven, Aydin, Alp, Kay, Gemma L, Trotter, Alexander J, Alikhan, Nabil-Fareed, de Oliveira Martins, Leonardo, Le-Viet, Thanh, Meadows, Lizzie, Casey, Anna, Ratcliffe, Liz, Simpson, David A, Molnar, Zoltan, Thompson, Thomas, Acheson, Erwan, Masoli, Jane AH, Knight, Bridget A, Ellard, Sian, Auckland, Cressida, Jones, Christopher R, Mahungu, Tabitha W, Irish-Tavares, Dianne, Haque, Tanzina, Hart, Jennifer, Witele, Eric, Fenton, Melisa Louise, Dadrah, Ashok, Symmonds, Amanda, Saluja, Tranprit, Bourgeois, Yann, Scarlett, Garry P, Loveson, Katie F, Goudarzi, Salman, Fearn, Christopher, Cook, Kate, Dent, Hannah, Paul, Hannah, Partridge, David G, Raza, Mohammad, Evans, Cariad, Johnson, Kate, Liggett, Steven, Baker, Paul, Bonner, Stephen, Essex, Sarah, Lyons, Ronan A, Saeed, Kordo, Mahanama, Adhyana I.K, Samaraweera, Buddhini, Silveira, Siona, Pelosi, Emanuela, Wilson-Davies, Eleri, Williams, Rachel J, Kristiansen, Mark, Roy, Sunando, Williams, Charlotte A, Cotic, Marius, Bayzid, Nadua, Westhorpe, Adam P, Hartley, John A, Jannoo, Riaz, Lowe, Helen L, Karamani, Angeliki, Ensell, Leah, Prieto, Jacqui A, Jeremiah, Sarah, Grammatopoulos, Dimitris, Pandey, Sarojini, Berry, Lisa, Jones, Katie, Richter, Alex, Beggs, Andrew, Best, Angus, Percival, Benita, Mirza, Jeremy, Megram, Oliver, Mayhew, Megan, Crawford, Liam, Ashcroft, Fiona, Moles-Garcia, Emma, Cumley, Nicola, Smith, Colin P, Bucca, Giselda, Hesketh, Andrew R, Blane, Beth, Girgis, Sophia T, Leek, Danielle, Sridhar, Sushmita, Forrest, Sally, Cormie, Claire, Gill, Harmeet K, Dias, Joana, Higginson, Ellen E, Maes, Mailis, Young, Jamie, Kermack, Leanne M, Gupta, Ravi Kumar, Ludden, Catherine, Peacock, Sharon J, Palmer, Sophie, Churcher, Carol M, Hadjirin, Nazreen F, Carabelli, Alessandro M, Brooks, Ellena, Smith, Kim S, Galai, Katerina, McManus, Georgina M, Ruis, Chris, Davidson, Rose K, Rambaut, Andrew, Williams, Thomas, Balcazar, Carlos E, Gallagher, Michael D, O'Toole, Áine, Rooke, Stefan, Hill, Verity, 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, Wierzbicki, Claudia, Webster, Hermione J, 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, Whiteley, Max, Zhang, Peijun, Gallis, Marta, Louka, Stavroula F, 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, Aggarwal, Dinesh, Cerda, Alberto C, Merrill, Tammy V, Wilson, Rebekah E, McClure, Patrick C, Chappell, Joseph G, Tsoleridis, Theocharis, Ball, Jonathan, Buck, David, Todd, John A, Green, Angie, Trebes, Amy, MacIntyre-Cockett, George, de Cesare, Mariateresa, Alderton, Alex, Amato, Roberto, Ariani, Cristina V, Beale, Mathew A, Beaver, Charlotte, Bellis, Katherine L, Betteridge, Emma, Bonfield, James, Danesh, John, Dorman, Matthew J, Drury, Eleanor, Farr, Ben W, Foulser, Luke, Goncalves, Sonia, Goodwin, Scott, Gourtovaia, Marina, Harrison, Ewan M, Jackson, David K, Jamrozy, Dorota, Johnston, Ian, Kane, Leanne, Kay, Sally, Keatley, Jon-Paul, Kwiatkowski, Dominic, Langford, Cordelia F, Lawniczak, Mara, Letchford, Laura, Livett, Rich, Lo, Stephanie, Martincorena, Inigo, McGuigan, Samantha, Nelson, Rachel, Palmer, Steve, Park, Naomi R, Patel, Minal, Prestwood, Liam, Puethe, Christoph, Quail, Michael A, Rajatileka, Shavanthi, Scott, Carol, Shirley, Lesley, Sillitoe, John, Spencer Chapman, Michael H, Thurston, Scott AJ, Tonkin-Hill, Gerry, Weldon, Danni, Rajan, Diana, Bronner, Iraad F, Aigrain, Louise, Redshaw, Nicholas M, Lensing, Stefanie V, Davies, Robert, Whitwham, Andrew, Liddle, Jennifier, Lewis, Kevin, Tovar-Corona, Jaime M, Leonard, Steven, Durham, Jillian, Bassett, Andrew R, McCarthy, Shane, Moll, Robin J, James, Keith, Oliver, Karen, Makunin, Alex, Barrett, Jeff, Gunson, Rory N, Graham, Mark S, Sudre, Carole H, May, Anna, Antonelli, Michela, Murray, Benjamin, Varsavsky, Thomas, Kläser, Kerstin, Canas, Liane S, Molteni, Erika, Modat, Marc, Drew, David A, Nguyen, Long H, Polidori, Lorenzo, Selvachandran, Somesh, Hu, Christina, Capdevila, Joan, Hammers, Alexander, Chan, Andrew T, Wolf, Jonathan, Spector, Tim D, Steves, Claire J, and Ourselin, Sebastien
Published: 2021
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8. The clinical, genomic, and microbiological profile of invasive multi-drug resistant Escherichia coli in a major teaching hospital in the United Kingdom

Author: Hamilton, William L., primary, Coscione, Suny, additional, Maes, Mailis, additional, Warne, Ben, additional, Pike, Lindsay J., additional, Khokhar, Fahad A., additional, Blane, Beth, additional, Brown, Nicholas M., additional, Gouliouris, Theodore, additional, Dougan, Gordon, additional, Török, M. Estée, additional, and Baker, Stephen, additional
Published: 2023
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9. A common protocol for the simultaneous processing of multiple clinically relevant bacterial species for whole genome sequencing

Author: Raven, Kathy E., Girgis, Sophia T., Akram, Asha, Blane, Beth, Leek, Danielle, Brown, Nicholas, and Peacock, Sharon J.
Published: 2021
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10. The composition and functional protein subsystems of the human nasal microbiome in granulomatosis with polyangiitis: a pilot study

Author: Wagner, Josef, Harrison, Ewan M., Martinez Del Pero, Marcos, Blane, Beth, Mayer, Gert, Leierer, Johannes, Gopaluni, Seerapani, Holmes, Mark A., Parkhill, Julian, Peacock, Sharon J., Jayne, David R. W., and Kronbichler, Andreas
Published: 2019
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11. Dissemination of carbapenemase-producing Enterobacterales in Ireland from 2012 to 2017: a retrospective genomic surveillance study

Author: Hadjirin, Nazreen F., primary, van Tonder, Andries J., additional, Blane, Beth, additional, Lees, John A., additional, Kumar, Narender, additional, Delappe, Niall, additional, Brennan, Wendy, additional, McGrath, Elaine, additional, Parkhill, Julian, additional, Cormican, Martin, additional, Peacock, Sharon J., additional, and Ludden, Catherine, additional
Published: 2023
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12. Large-Scale Evaluation of a Rapid Fully Automated Analysis Platform to Detect and Refute Outbreaks Based on MRSA Genome Comparisons

Author: Raven, Kathy E., primary, Bragin, Eugene, additional, Blane, Beth, additional, Leek, Danielle, additional, Kumar, Narender, additional, Rhodes, Paul A., additional, Enoch, David A., additional, Thaxter, Rachel, additional, Brown, Nicholas M., additional, Parkhill, Julian, additional, and Peacock, Sharon J., additional
Published: 2022
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13. Characteristics of Staphylococcus aureus Isolated from Patients in Busia County Referral Hospital, Kenya

Author: Obanda, Benear Apollo, primary, Cook, Elizabeth A. J., additional, Fèvre, Eric M., additional, Bebora, Lilly, additional, Ogara, William, additional, Wang, Shu-Hua, additional, Gebreyes, Wondwossen, additional, Ngetich, Ronald, additional, Wandede, Dolphine, additional, Muyodi, Johnstone, additional, Blane, Beth, additional, Coll, Francesc, additional, Harrison, Ewan M., additional, Peacock, Sharon J., additional, and Gitao, George C., additional
Published: 2022
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14. Multi-Drug Resistant Staphylococcus aureus Carriage in Abattoir Workers in Busia, Kenya

Author: Obanda, Benear Apollo, primary, Gibbons, Cheryl L., additional, Fèvre, Eric M., additional, Bebora, Lilly, additional, Gitao, George, additional, Ogara, William, additional, Wang, Shu-Hua, additional, Gebreyes, Wondwossen, additional, Ngetich, Ronald, additional, Blane, Beth, additional, Coll, Francesc, additional, Harrison, Ewan M., additional, Kariuki, Samuel, additional, Peacock, Sharon J., additional, and Cook, Elizabeth A. J., additional
Published: 2022
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15. Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission

Author: Aggarwal, Dinesh, Page, Andrew J., Schaefer, Ulf, Savva, George M., Myers, Richard, Volz, Erik, Ellaby, Nicholas, Platt, Steven, Groves, Natalie, Gallagher, Eileen, Tumelty, Niamh M., Le Viet, Thanh, Hughes, Gareth J., Chen, Cong, Turner, Charlie, Logan, Sophie, Harrison, Abbie, The COVID-19 Genomics UK (COG, Ash, Amy, Wise, Emma, Moore, Nathan, Mori, Matilde, Cortes, Nick, Lynch, Jessica, Kidd, Stephen, Fairley, Derek J., Curran, Tanya, McKenna, James P., Adams, Helen, Fraser, Christophe, Golubchik, Tanya, Bonsall, David, Hassan-Ibrahim, Mohammed O., Malone, Cassandra S., Cogger, Benjamin J., 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., Patel, Amita, Charalampous, Themoula, Nebbia, Gaia, Batra, Rahul, Edgeworth, Jonathan, Robson, Samuel C., Beckett, Angela H., 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, Jones, Carl, Holmes, Christopher, Bird, Paul, Helmer, Thomas, Fallon, Karlie, Tang, Julian, Raviprakash, Veena, Campbell, Sharon, Sheriff, Nicola, Blakey, Victoria, Williams, Lesley-Anne, 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., Eldirdiri, Sahar, Kenyon, Anita, Davis, Thomas, Pybus, Oliver G., du Plessis, Louis, Zarebski, Alex E., Raghwani, Jayna, Kraemer, Moritz U. G., Francois, Sarah, Attwood, Stephen W., Vasylyeva, Tetyana I., Zamudio, Marina Escalera, Gutierrez, Bernardo, Torok, M. Estee, Hamilton, William L., Goodfellow, Ian G., Hall, Grant, Jahun, Aminu S., Chaudhry, Yasmin, Hosmillo, Myra, Pinckert, Malte L., Georgana, Iliana, Moses, Samuel, Lowe, Hannah, Bedford, Luke, Moore, Jonathan, Stonehouse, Susanne, Fisher, Chloe L., Awan, Ali R., BoYes, John, Breuer, Judith, Harris, Kathryn A., Brown, Julianne R., Shah, Divya, Atkinson, Laura, Lee, Jack C. D., Storey, Nathaniel, Flaviani, Flavia, Alcolea-Medina, Adela, Williams, Rebecca, Vernet, Gabrielle, Chapman, Michael R., Levett, Lisa J., Heaney, Judith, Chatterton, Wendy, Pusok, Monika, Xu-McCrae, Li, Smith, Darren, Bashton, Matthew, Young, Greg, Holmes, Alison, Randell, Paul A., Cox, Alison, Madona, Pinglawathee, Bolt, Frances, Price, James, Mookerjee, Siddharth, Ragonnet-Cronin, Manon, Nascimento, Fabricia F., Jorgensen, David, Siveroni, Igor, Johnson, Rob, Boyd, Olivia, Geidelberg, Lily, Volz, Erik M., Rowan, Aileen, Taylor, Graham P., Smollett, Katherine L., Loman, Nicholas J., Quick, Joshua, McMurray, Claire, Stockton, Joanne, Nicholls, Sam, Rowe, Will, Poplawski, Radoslaw, McNally, Alan, Nunez, Rocio T. Martinez, Mason, Jenifer, Robinson, Trevor I., O’Toole, Elaine, Watts, Joanne, Breen, Cassie, Cowell, Angela, Sluga, Graciela, Machin, Nicholas W., Ahmad, Shazaad S. Y., George, Ryan P., Halstead, Fenella, Sivaprakasam, Venkat, Hogsden, Wendy, Illingworth, Chris J., Jackson, Chris, Thomson, Emma C., Shepherd, James G., Asamaphan, Patawee, Niebel, Marc O., Li, Kathy K., Shah, Rajiv N., Jesudason, Natasha G., 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., Nickbakhsh, Seema, Hale, Antony D., Macfarlane-Smith, Louissa R., Harper, Katherine L., Carden, Holli, Taha, Yusri, Payne, Brendan A. I., Burton-Fanning, Shirelle, Waugh, Sheila, Collins, Jennifer, Eltringham, Gary, Rushton, Steven, O’Brien, Sarah, Bradley, Amanda, Maclean, Alasdair, Mollett, Guy, Blacow, Rachel, Templeton, Kate E., McHugh, Martin P., Dewar, Rebecca, Wastenge, Elizabeth, Dervisevic, Samir, Stanley, Rachael, Meader, Emma J., Coupland, Lindsay, Smith, Louise, Graham, Clive, Barton, Edward, Padgett, Debra, Scott, Garren, Swindells, Emma, Greenaway, Jane, Nelson, Andrew, McCann, Clare, Yew, Wen Chyin, Andersson, Monique, Peto, Timothy, Justice, Anita, Eyre, David, Crook, Derrick, Sloan, Tim J., Duckworth, Nichola, Walsh, Sarah, Chauhan, Anoop J., Glaysher, Sharon, Bicknell, Kelly, Wyllie, Sarah, Elliott, Scott, Lloyd, Allyson, Impey, Robert, Levene, Nick, Monaghan, Lynn, Bradley, Declan T., Wyatt, Tim, Allara, Elias, Pearson, Clare, Osman, Husam, Bosworth, Andrew, Robinson, Esther, Muir, Peter, Vipond, Ian B., Hopes, Richard, Pymont, Hannah M., Hutchings, Stephanie, Curran, Martin D., Parmar, Surendra, Lackenby, Angie, Mbisa, Tamyo, Miah, Shahjahan, Bibby, David, Manso, Carmen, Hubb, Jonathan, Dabrera, Gavin, Ramsay, Mary, Bradshaw, Daniel, Thornton, Alicia, Lee, David, Williams, David, Harrison, Ian, Hartman, Hassan, Manesis, Nikos, Patel, Vineet, Bishop, Chloe, Chalker, Vicki, Ledesma, Juan, Twohig, Katherine A., 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, Mather, Alison E., Baker, David J., Rudder, Steven, Aydin, Alp, Kay, Gemma L., Trotter, Alexander J., Alikhan, Nabil-Fareed, de Oliveira Martins, Leonardo, Le-Viet, Thanh, Meadows, Lizzie, Casey, Anna, Ratcliffe, Liz, Simpson, David A., Molnar, Zoltan, Thompson, Thomas, Acheson, Erwan, Masoli, Jane A. H., Knight, Bridget A., Ellard, Sian, Auckland, Cressida, Jones, Christopher R., Mahungu, Tabitha W., Irish-Tavares, Dianne, Haque, Tanzina, Hart, Jennifer, Witele, Eric, Fenton, Melisa L., Dadrah, Ashok, Symmonds, Amanda, Saluja, Tranprit, Bourgeois, Yann, Scarlett, Garry P., Loveson, Katie F., Goudarzi, Salman, Fearn, Christopher, Cook, Kate, Dent, Hannah, Paul, Hannah, Partridge, David G., Raza, Mohammad, Evans, Cariad, Johnson, Kate, Liggett, Steven, Baker, Paul, Bonner, Stephen, Essex, Sarah, Lyons, Ronan A., Saeed, Kordo, Mahanama, Adhyana I. K., Samaraweera, Buddhini, Silveira, Siona, Pelosi, Emanuela, Wilson-Davies, Eleri, Williams, Rachel J., Kristiansen, Mark, Roy, Sunando, Williams, Charlotte A., Cotic, Marius, Bayzid, Nadua, Westhorpe, Adam P., Hartley, John A., Jannoo, Riaz, Lowe, Helen L., Karamani, Angeliki, Ensell, Leah, Prieto, Jacqui A., Jeremiah, Sarah, Grammatopoulos, Dimitris, Pandey, Sarojini, Berry, Lisa, Jones, Katie, Richter, Alex, Beggs, Andrew, Best, Angus, Percival, Benita, Mirza, Jeremy, Megram, Oliver, Mayhew, Megan, Crawford, Liam, Ashcroft, Fiona, Moles-Garcia, Emma, Cumley, Nicola, Smith, Colin P., Bucca, Giselda, Hesketh, Andrew R., Blane, Beth, Girgis, Sophia T., Leek, Danielle, Sridhar, Sushmita, Forrest, Sally, Cormie, Claire, Gill, Harmeet K., Dias, Joana, Higginson, Ellen E., Maes, Mailis, Young, Jamie, Kermack, Leanne M., Gupta, Ravi K., Ludden, Catherine, Peacock, Sharon J., Palmer, Sophie, Churcher, Carol M., Hadjirin, Nazreen F., Carabelli, Alessandro M., Brooks, Ellena, Smith, Kim S., Galai, Katerina, McManus, Georgina M., Ruis, Chris, Davidson, Rose K., Rambaut, Andrew, Williams, Thomas, Balcazar, Carlos E., Gallagher, Michael D., O’Toole, Áine, Rooke, Stefan, Hill, Verity, 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, Wierzbicki, Claudia, Webster, Hermione J., 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, Whiteley, Max, Zhang, Peijun, Gallis, Marta, Louka, Stavroula F., 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., Cerda, Alberto C., Merrill, Tammy V., Wilson, Rebekah E., McClure, Patrick C., Chappell, Joseph G., Tsoleridis, Theocharis, Ball, Jonathan, Buck, David, Todd, John A., Green, Angie, Trebes, Amy, MacIntyre-Cockett, George, de Cesare, Mariateresa, Alderton, Alex, Amato, Roberto, Ariani, Cristina V., Beale, Mathew A., Beaver, Charlotte, Bellis, Katherine L., Betteridge, Emma, Bonfield, James, Danesh, John, Dorman, Matthew J., Drury, Eleanor, Farr, Ben W., Foulser, Luke, Goncalves, Sonia, Goodwin, Scott, Gourtovaia, Marina, Harrison, Ewan M., Jackson, David K., Jamrozy, Dorota, Johnston, Ian, Kane, Leanne, Kay, Sally, Keatley, Jon-Paul, Kwiatkowski, Dominic, Langford, Cordelia F., Lawniczak, Mara, Letchford, Laura, Livett, Rich, Lo, Stephanie, Martincorena, Inigo, McGuigan, Samantha, Nelson, Rachel, Palmer, Steve, Park, Naomi R., Patel, Minal, Prestwood, Liam, Puethe, Christoph, Quail, Michael A., Rajatileka, Shavanthi, Scott, Carol, Shirley, Lesley, Sillitoe, John, Chapman, Michael H. Spencer, Thurston, Scott A. J., Tonkin-Hill, Gerry, Weldon, Danni, Rajan, Diana, Bronner, Iraad F., Aigrain, Louise, Redshaw, Nicholas M., Lensing, Stefanie V., Davies, Robert, Whitwham, Andrew, Liddle, Jennifier, Lewis, Kevin, Tovar-Corona, Jaime M., Leonard, Steven, Durham, Jillian, Bassett, Andrew R., McCarthy, Shane, Moll, Robin J., James, Keith, Oliver, Karen, Makunin, Alex, Barrett, Jeff, Gunson, Rory N., Koshy, Cherian, Chand, Meera, Aggarwal, Dinesh [0000-0002-5938-8172], Page, Andrew J [0000-0001-6919-6062], Volz, Erik [0000-0001-6268-8937], Tumelty, Niamh M [0000-0002-9894-6034], Le Viet, Thanh [0000-0002-2106-8130], Hughes, Gareth J [0000-0002-3781-0117], Harrison, Abbie [0000-0002-7435-9994], Peacock, Sharon J [0000-0002-1718-2782], and Apollo - University of Cambridge Repository
Subjects: 631/326/1762, 631/326/325/2483, General Physics and Astronomy, 45/23, Genome, Viral, General Biochemistry, Genetics and Molecular Biology, COVID-19 Genomics UK (COG-UK) Consortium, Communicable Diseases, Imported, Humans, 631/326/596/4130, Travel, Multidisciplinary, Science & Technology, 45, SARS-CoV-2, article, COVID-19, General Chemistry, Genomics, A300, C700, 692/700/478/174, B900, Multidisciplinary Sciences, England, Quarantine, Science & Technology - Other Topics, Health Impact Assessment, Contact Tracing, Travel-Related Illness, human activities
Abstract: Mitigation of SARS-CoV-2 transmission from international travel is a priority. We evaluated the effectiveness of travellers being required to quarantine for 14-days on return to England in Summer 2020. We identified 4,207 travel-related SARS-CoV-2 cases and their contacts, and identified 827 associated SARS-CoV-2 genomes. Overall, quarantine was associated with a lower rate of contacts, and the impact of quarantine was greatest in the 16-20 age-group. 186 SARS-CoV-2 genomes were sufficiently unique to identify travel-related clusters. Fewer genomically-linked cases were observed for index cases who returned from countries with quarantine requirement compared to countries with no quarantine requirement. This difference was explained by fewer importation events per identified genome for these cases, as opposed to fewer onward contacts per case. Overall, our study demonstrates that a 14-day quarantine period reduces, but does not completely eliminate, the onward transmission of imported cases, mainly by dissuading travel to countries with a quarantine requirement., We thank members of the COVID-19 Genomics Consortium UK and Test and Trace contact tracers for their contributions to generating the data used in this study. We thank the Sanger Covid Team for assisting with Samples and Logistics. We thank Sarah Mitchell from the Department of Plant Sciences, University of Cambridge, for direction on statistical analysis. DA is a Clinical PhD Fellow and gratefully supported by the Wellcome Trust (Grant number: 222903/Z/21/Z). EMH is supported by a UK Research and Innovation (UKRI) Fellowship: MR/S00291X/1. AJP, TLV, GMS gratefully acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC); their research was funded by the BBSRC Institute Strategic Programme Microbes in the Food Chain BB/R012504/1 and its constituent project BBS/E/F/000PR10352, also Quadram Institute Bioscience BBSRC funded Core Capability Grant (project number BB/CCG1860/1). The COVID-19 Genomics UK (COG-UK) Consortium 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. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Published: 2022

16. Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning

Author: Nickbakhsh, Sema, Hughes, Joseph, Christofidis, Nicolaos, Griffiths, Emily, Shaaban, Sharif, Enright, Jessica, Smollett, Katherine, Nomikou, Kyriaki, Palmalux, Natasha, Tong, Lily, Carmichael, Stephen, Sreenu, Vattipally B., Orton, Richard, Goldstein, Emily J., Tomb, Rachael M., Robson, Samuel C., Connor, Thomas R., Loman, Nicholas J., Golubchik, Tanya, Nunez, Rocio T. Martinez, Bonsall, David, Rambaut, Andrew, Snell, Luke B., Livett, Rich, Ludden, Catherine, Corden, Sally, Nastouli, Eleni, Nebbia, Gaia, Johnston, Ian, Lythgoe, Katrina, Torok, M. Estee, Goodfellow, Ian G., Prieto, Jacqui A., Saeed, Kordo, Jackson, David K., Houlihan, Catherine, Frampton, Dan, Hamilton, William L., Witney, Adam A., Bucca, Giselda, Pope, Cassie F., Moore, Catherine, Thomson, Emma C., Harrison, Ewan M., Smith, Colin P., Rogan, Fiona, Beckwith, Shaun M., Murray, Abigail, Singleton, Dawn, Eastick, Kirstine, Sheridan, Liz A., Randell, Paul, Jackson, Leigh M., Ariani, Cristina V., Gonçalves, Sónia, Fairley, Derek J., Loose, Matthew W., Watkins, Joanne, Moses, Samuel, Nicholls, Sam, Bull, Matthew, Amato, Roberto, Smith, Darren L., Aanensen, David M., Barrett, Jeffrey C., Aggarwal, Dinesh, Shepherd, James G., Curran, Martin D., Parmar, Surendra, Parker, Matthew D., Williams, Catryn, Glaysher, Sharon, Underwood, Anthony P., Bashton, Matthew, Pacchiarini, Nicole, Loveson, Katie F., Byott, Matthew, Carabelli, Alessandro M., Templeton, Kate E., de Silva, Thushan I., Wang, Dennis, Langford, Cordelia F., Sillitoe, John, Gunson, Rory N., Cottrell, Simon, O?Grady, Justin, Kwiatkowski, Dominic, Lillie, Patrick J., Cortes, Nicholas, Moore, Nathan, Thomas, Claire, Burns, Phillipa J., Mahungu, Tabitha W., Liggett, Steven, Beckett, Angela H., Holden, Matthew T. G., Levett, Lisa J., Osman, Husam, Hassan-Ibrahim, Mohammed O., Simpson, David A., Chand, Mrera, Gupta, Ravi K., Darby, Alistair C., Paterson, Steve, Pybus, Oliver G., Volz, Erik M., de Angelis, Daniela, Robertson, David L., Page, Andrew J., Martincorena, Inigo, Aigrain, Louise, Bassett, Andrew R., Wong, Nick, Taha, Yusri, Erkiert, Michelle J., Chapman, Michael H. Spencer, Dewar, Rebecca, McHugh, Martin P., Mookerjee, Siddharth, Aplin, Stephen, Harvey, Matthew, Sass, Thea, Umpleby, Helen, Wheeler, Helen, McKenna, James P., Warne, Ben, Taylor, Joshua F., Chaudhry, Yasmin, Izuagbe, Rhys, Jahun, Aminu S., Young, Gregory R., McMurray, Claire, McCann, Clare M., Nelson, Andrew, Elliott, Scott, Lowe, Hannah, Price, Anna, Crown, Matthew R., Rey, Sara, Roy, Sunando, Temperton, Ben, Hesketh, Andrew R., Laing, Kenneth G., Monahan, Irene M., Heaney, Judith, Pelosi, Emanuela, Silviera, Siona, Wilson-Davies, Eleri, Fryer, Helen, Adams, Helen, du Plessis, Louis, Johnson, Rob, Harvey, William T., Orton, Richard J., Spurgin, Lewis G., Bourgeois, Yann, Ruis, Chris, O?Toole, Áine, Gourtovaia, Marina, Sanderson, Theo, Fraser, Christophe, Edgeworth, Jonathan, Breuer, Judith, Michell, Stephen L., Todd, John A., John, Michaela, Buck, David, Gajee, Kavitha, Kay, Gemma L., Peacock, Sharon J., Heyburn, David, Kitchman, Katie, McNally, Alan, Pritchard, David T., Dervisevic, Samir, Muir, Peter, Robinson, Esther, Vipond, Barry B., Ramadan, Newara A., Jeanes, Christopher, Weldon, Danni, Catalan, Jana, Jones, Neil, da Silva Filipe, Ana, Williams, Chris, Fuchs, Marc, Miskelly, Julia, Jeffries, Aaron R., Oliver, Karen, Park, Naomi R., Ash, Amy, Koshy, Cherian, Barrow, Magdalena, Buchan, Sarah L., Mantzouratou, Anna, Clark, Gemma, Holmes, Christopher W., Campbell, Sharon, Davis, Thomas, Tan, Ngee Keong, Brown, Julianne R., Harris, Kathryn A., Kidd, Stephen P., Grant, Paul R., Xu-McCrae, Li, Cox, Alison, Madona, Pinglawathee, Pond, Marcus, Randell, Paul A., Withell, Karen T., Williams, Cheryl, Graham, Clive, Denton-Smith, Rebecca, Swindells, Emma, Turnbull, Robyn, Sloan, Tim J., Bosworth, Andrew, Hutchings, Stephanie, Pymont, Hannah M., Casey, Anna, Ratcliffe, Liz, Jones, Christopher R., Knight, Bridget A., Haque, Tanzina, Hart, Jennifer, Irish-Tavares, Dianne, Witele, Eric, Mower, Craig, Watson, Louisa K., Collins, Jennifer, Eltringham, Gary, Crudgington, Dorian, Macklin, Ben, Iturriza-Gomara, Miren, Lucaci, Anita O., McClure, Patrick C., Carlile, Matthew, Holmes, Nadine, Moore, Christopher, Storey, Nathaniel, Rooke, Stefan, Yebra, Gonzalo, Craine, Noel, Perry, Malorie, Alikhan, Nabil-Fareed, Bridgett, Stephen, Cook, Kate F., Fearn, Christopher, Goudarzi, Salman, Lyons, Ronan A., Williams, Thomas, Haldenby, Sam T., Durham, Jillian, Leonard, Steven, Davies, Robert M., Batra, Rahul, Blane, Beth, Spyer, Moira J., Smith, Perminder, Yavus, Mehmet, Williams, Rachel J., Mahanama, Adhyana I. K., Samaraweera, Buddhini, Girgis, Sophia T., Hansford, Samantha E., Green, Angie, Beaver, Charlotte, Bellis, Katherine L., Dorman, Matthew J., Kay, Sally, Prestwood, Liam, Rajatileka, Shavanthi, Quick, Joshua, Poplawski, Radoslaw, Reynolds, Nicola, Mack, Andrew, Morriss, Arthur, Whalley, Thomas, Patel, Bindi, Georgana, Iliana, Hosmillo, Myra, Pinckert, Malte L., Stockton, Joanne, Henderson, John H., Hollis, Amy, Stanley, William, Yew, Wen C., Myers, Richard, Thornton, Alicia, Adams, Alexander, Annett, Tara, Asad, Hibo, Birchley, Alec, Coombes, Jason, Evans, Johnathan M., Fina, Laia, Gatica-Wilcox, Bree, Gilbert, Lauren, Graham, Lee, Hey, Jessica, Hilvers, Ember, Jones, Sophie, Jones, Hannah, Kumziene-Summerhayes, Sara, McKerr, Caoimhe, Powell, Jessica, Pugh, Georgia, Taylor, Sarah, Trotter, Alexander J., Williams, Charlotte A., Kermack, Leanne M., Foulkes, Benjamin H., Gallis, Marta, Hornsby, Hailey R., Louka, Stavroula F., Pohare, Manoj, Wolverson, Paige, Zhang, Peijun, MacIntyre-Cockett, George, Trebes, Amy, Moll, Robin J., Ferguson, Lynne, Maclean, Alasdair, Tomb, Rachael, Starinskij, Igor, Thomson, Laura, Southgate, Joel, Kraemer, Moritz U. G., Raghwani, Jayna, Zarebski, Alex E., Boyd, Olivia, Geidelberg, Lily, Illingworth, Chris J., Jackson, Chris, Pascall, David, Vattipally, Sreenu, Freeman, Timothy M., Hsu, Sharon N., Lindsey, Benjamin B., James, Keith, Lewis, Kevin, Tonkin-Hill, Gerry, Tovar-Corona, Jaime M., Cox, MacGregor, Abudahab, Khalil, Menegazzo, Mirko, Taylor, Ben E. W., Yeats, Corin A., Mukaddas, Afrida, Wright, Derek W., de Oliveira Martins, Leonardo, Colquhoun, Rachel, Hill, Verity, Jackson, Ben, McCrone, J. T., Medd, Nathan, Scher, Emily, Keatley, Jon-Paul, Curran, Tanya, Morgan, Sian, Maxwell, Patrick, Smith, Ken, Eldirdiri, Sahar, Kenyon, Anita, Holmes, Alison H., Price, James R., Wyatt, Tim, Mather, Alison E., SkvortsovHartley, Timofey John A., Guest, Martyn, Kitchen, Christine, Merrick, Ian, Munn, Robert, Bertolusso, Beatrice, Lynch, Jessica, Vernet, Gabrielle, Kirk, Stuart, Wastnedge, Elizabeth, Stanley, Rachael, Idle, Giles, Bradley, Declan T., Poyner, Jennifer, Mori, Matilde, Jones, Owen, Wright, Victoria, Brooks, Ellena, Churcher, Carol M., Fragakis, Mireille, Galai, Katerina, Jermy, Andrew, Judges, Sarah, McManus, Georgina M., Smith, Kim S., Westwick, Elaine, Attwood, Stephen W., Bolt, Frances, Davies, Alisha, De Lacy, Elen, Downing, Fatima, Edwards, Sue, Meadows, Lizzie, Jeremiah, Sarah, Smith, Nikki, Foulser, Luke, Charalampous, Themoula, Patel, Amita, Berry, Louise, Boswell, Tim, Fleming, Vicki M., Howson-Wells, Hannah C., Joseph, Amelia, Khakh, Manjinder, Lister, Michelle M., Bird, Paul W., Fallon, Karlie, Helmer, Thomas, McMurray, Claire L., Odedra, Mina, Shaw, Jessica, Tang, Julian W., Willford, Nicholas J., Blakey, Victoria, Raviprakash, Veena, Sheriff, Nicola, Williams, Lesley-Anne, Feltwell, Theresa, Bedford, Luke, Cargill, James S., Hughes, Warwick, Moore, Jonathan, Stonehouse, Susanne, Atkinson, Laura, Lee, Jack C. D., Shah, Divya, Alcolea-Medina, Adela, Ohemeng-Kumi, Natasha, Ramble, John, Sehmi, Jasveen, Williams, Rebecca, Chatterton, Wendy, Pusok, Monika, Everson, William, Castigador, Anibolina, Macnaughton, Emily, El Bouzidi, Kate, Lampejo, Temi, Sudhanva, Malur, Breen, Cassie, Sluga, Graciela, Ahmad, Shazaad S. Y., George, Ryan P., Machin, Nicholas W., Binns, Debbie, James, Victoria, Blacow, Rachel, Coupland, Lindsay, Smith, Louise, Barton, Edward, Padgett, Debra, Scott, Garren, Cross, Aidan, Mirfenderesky, Mariyam, Greenaway, Jane, Cole, Kevin, Clarke, Phillip, Duckworth, Nichola, Walsh, Sarah, Bicknell, Kelly, Impey, Robert, Wyllie, Sarah, Hopes, Richard, Bishop, Chloe, Chalker, Vicki, Harrison, Ian, Gifford, Laura, Molnar, Zoltan, Auckland, Cressida, Evans, Cariad, Johnson, Kate, Partridge, David G., Raza, Mohammad, Baker, Paul, Bonner, Stephen, Essex, Sarah, Murray, Leanne J., Lawton, Andrew I., Burton-Fanning, Shirelle, Payne, Brendan A. I., Waugh, Sheila, Gomes, Andrea N., Kimuli, Maimuna, Murray, Darren R., Ashfield, Paula, Dobie, Donald, Ashford, Fiona, Best, Angus, Crawford, Liam, Cumley, Nicola, Mayhew, Megan, Megram, Oliver, Mirza, Jeremy, Moles-Garcia, Emma, Percival, Benita, Driscoll, Megan, Ensell, Leah, Lowe, Helen L., Maftei, Laurentiu, Mondani, Matteo, Chaloner, Nicola J., Cogger, Benjamin J., Easton, Lisa J., Huckson, Hannah, Lewis, Jonathan, Lowdon, Sarah, Malone, Cassandra S., Munemo, Florence, Mutingwende, Manasa, Nicodemi, Roberto, Podplomyk, Olga, Somassa, Thomas, Beggs, Andrew, Richter, Alex, Cormie, Claire, Dias, Joana, Forrest, Sally, Higginson, Ellen E., Maes, Mailis, Young, Jamie, Davidson, Rose K., Jackson, Kathryn A., Turtle, Lance, Keeley, Alexander J., Ball, Jonathan, Byaruhanga, Timothy, Chappell, Joseph G., Dey, Jayasree, Hill, Jack D., Park, Emily J., Fanaie, Arezou, Hilson, Rachel A., Yaze, Geraldine, Lo, Stephanie, Afifi, Safiah, Beer, Robert, Maksimovic, Joshua, McCluggage, Kathryn, Spellman, Karla, Bresner, Catherine, Fuller, William, Marchbank, Angela, Workman, Trudy, Shelest, Ekaterina, Debebe, Johnny, Sang, Fei, Zamudio, Marina Escalera, Francois, Sarah, Gutierrez, Bernardo, Vasylyeva, Tetyana I., Flaviani, Flavia, Ragonnet-Cronin, Manon, Smollett, Katherine L., Broos, Alice, Mair, Daniel, Nichols, Jenna, Tsatsani, Ioulia, O?Brien, Sarah, Rushton, Steven, Sanderson, Roy, Perkins, Jon, Cotton, Seb, Gallagher, Abbie, Allara, Elias, Pearson, Clare, Bibby, David, Dabrera, Gavin, Ellaby, Nicholas, Gallagher, Eileen, Hubb, Jonathan, Lackenby, Angie, Lee, David, Manesis, Nikos, Mbisa, Tamyo, Platt, Steven, Twohig, Katherine A., Morgan, Mari, Aydin, Alp, Baker, David J., Foster-Nyarko, Ebenezer, Prosolek, Sophie J., Rudder, Steven, Baxter, Chris, Carvalho, SÃlvia F., Lavin, Deborah, Mariappan, Arun, Radulescu, Clara, Singh, Aditi, Tang, Miao, Morcrette, Helen, Bayzid, Nadua, Cotic, Marius, Balcazar, Carlos E., Gallagher, Michael D., Maloney, Daniel, Stanton, Thomas D., Williamson, Kathleen A., Manley, Robin, Michelsen, Michelle L., Sambles, Christine M., Studholme, David J., Warwick-Dugdale, Joanna, Eccles, Richard, Gemmell, Matthew, Gregory, Richard, Hughes, Margaret, Nelson, Charlotte, Rainbow, Lucille, Vamos, Edith E., Webster, Hermione J., Whitehead, Mark, Wierzbicki, Claudia, Angyal, Adrienn, Green, Luke R., Whiteley, Max, Betteridge, Emma, Bronner, Iraad F., Farr, Ben W., Goodwin, Scott, Lensing, Stefanie V., McCarthy, Shane A., Quail, Michael A., Rajan, Diana, Redshaw, Nicholas M., Scott, Carol, Shirley, Lesley, Thurston, Scott A. J., Rowe, Will, Gaskin, Amy, Le-Viet, Thanh, Bonfield, James, Liddle, Jennifier, Whitwham, Andrew, Templeton, Kate, Milosevic, Catriona, Thomson, Emma, Illingworth, Christopher J. R., Smith-Palmer, Alison, Nickbakhsh, Sema [0000-0001-9543-7536], Sreenu, Vattipally B [0000-0001-6673-4697], Orton, Richard [0000-0002-3389-4325], Thomson, Emma [0000-0003-1482-0889], Robertson, David L [0000-0001-6338-0221], Apollo - University of Cambridge Repository, University of St Andrews. St Andrews Bioinformatics Unit, University of St Andrews. Infection and Global Health Division, University of St Andrews. Biomedical Sciences Research Complex, and University of St Andrews. School of Medicine
Subjects: 631/114/739, Multidisciplinary, Universities, SARS-CoV-2, article, COVID-19, QH426 Genetics, 3rd-DAS, Genomics, C400, 692/700/478/174, United States, Disease Outbreaks, B900, Health Planning, SDG 3 - Good Health and Well-being, 692/699/255/2514, 631/114/2397, RA0421, RA0421 Public health. Hygiene. Preventive Medicine, Humans, 631/181/457, QH426
Abstract: Funding: The CVR authors are supported by the Medical Research Council [MC_UU_12014/12 and MC_UU_12018/12]. 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) [Grant code: MC_PC_19027], and Genome Research Limited, operating as the Wellcome Sanger Institute. Whole genome sequencing of SARS-CoV-2 has occurred at an unprecedented scale, and can be exploited for characterising outbreak risks at the fine-scale needed to inform control strategies. One setting at continued risk of COVID-19 outbreaks are higher education institutions, associated with student movements at the start of term, close living conditions within residential halls, and high social contact rates. Here we analysed SARS-CoV-2 whole genome sequences in combination with epidemiological data to investigate a large cluster of student cases associated with University of Glasgow accommodation in autumn 2020, Scotland. We identified 519 student cases of SARS-CoV-2 infection associated with this large cluster through contact tracing data, with 30% sequencing coverage for further analysis. We estimated at least 11 independent introductions of SARS-CoV-2 into the student population, with four comprising the majority of detected cases and consistent with separate outbreaks. These four outbreaks were curtailed within a week following implementation of control measures. The impact of student infections on the local community was short-term despite an underlying increase in community infections. Our study highlights the need for context-specific information in the formation of public health policy for higher educational settings. Publisher PDF
Published: 2022

17. COVID-19 due to the B.1.617.2 (Delta) variant compared to B.1.1.7 (Alpha) variant of SARS-CoV-2: a prospective observational cohort study

Author: Kläser, Kerstin, Molteni, Erika, Graham, Mark, Canas, Liane S., Österdahl, Marc F., Antonelli, Michela, Chen, Liyuan, Deng, Jie, Murray, Benjamin, Kerfoot, Eric, Wolf, Jonathan, May, Anna, Fox, Ben, Capdevila, Joan, Aanensen, David M., Abudahab, Khalil, Adams, Helen, Adams, Alexander, Afifi, Safiah, Aggarwal, Dinesh, Ahmad, Shazaad S. Y., Aigrain, Louise, Alcolea-Medina, Adela, Alikhan, Nabil-Fareed, Allara, Elias, Amato, Roberto, Angyal, Adrienn, Annett, Tara, Aplin, Stephen, Ariani, Cristina V., Asad, Hibo, Ash, Amy, Ashfield, Paula, Ashford, Fiona, Atkinson, Laura, Attwood, Stephen W., Auckland, Cressida, Aydin, Alp, Baker, David J., Baker, Paul, Balcazar, Carlos E., Ball, Jonathan, Barrett, Jeffrey C., Barrow, Magdalena, Barton, Edward, Bashton, Matthew, Bassett, Andrew R., Batra, Rahul, Baxter, Chris, Bayzid, Nadua, Beaver, Charlotte, Beckett, Angela H., Beckwith, Shaun M., Bedford, Luke, Beer, Robert, Beggs, Andrew, Bellis, Katherine L., Berry, Louise, Bertolusso, Beatrice, Best, Angus, Betteridge, Emma, Bibby, David, Bicknell, Kelly, Binns, Debbie, Birchley, Alec, Bird, Paul W., Bishop, Chloe, Blacow, Rachel, Blakey, Victoria, Blane, Beth, Bolt, Frances, Bonfield, James, Bonner, Stephen, Bonsall, David, Boswell, Tim, Bosworth, Andrew, Bourgeois, Yann, Boyd, Olivia, Bradley, Declan T., Breen, Cassie, Bresner, Catherine, Breuer, Judith, Bridgett, Stephen, Bronner, Iraad F., Brooks, Ellena, Broos, Alice, Brown, Julianne R., Bucca, Giselda, Buchan, Sarah L., Buck, David, Bull, Matthew, Burns, Phillipa J., Burton-Fanning, Shirelle, Byaruhanga, Timothy, Byott, Matthew, Campbell, Sharon, Carabelli, Alessandro M., Cargill, James S., Carlile, Matthew, Carvalho, Sílvia F., Casey, Anna, Castigador, Anibolina, Catalan, Jana, Chalker, Vicki, Chaloner, Nicola J., Chand, Meera, Chappell, Joseph G., Charalampous, Themoula, Chatterton, Wendy, Chaudhry, Yasmin, Churcher, Carol M., Clark, Gemma, Clarke, Phillip, Cogger, Benjamin J., Cole, Kevin, Collins, Jennifer, Colquhoun, Rachel, Connor, Thomas R., Cook, Kate F., Coombes, Jason, Corden, Sally, Cormie, Claire, Cortes, Nicholas, Cotic, Marius, Cotton, Seb, Cottrell, Simon, Coupland, Lindsay, Cox, MacGregor, Cox, Alison, Craine, Noel, Crawford, Liam, Cross, Aidan, Crown, Matthew, Crudgington, Dorian, Cumley, Nicola, Curran, Tanya, Curran, Martin D., da Silva Filipe, Ana, Dabrera, Gavin, Darby, Alistair C., Davidson, Rose K., Davies, Alisha, Davies, Robert M., Davis, Thomas, de Angelis, Daniela, De Lacy, Elen, de Oliveira Martins, Leonardo, de Silva, Thushan I., Debebe, Johnny, Denton-Smith, Rebecca, Dervisevic, Samir, Dewar, Rebecca, Dey, Jayasree, Dias, Joana, Dobie, Donald, Dorman, Matthew J., Downing, Fatima, Driscoll, Megan, du Plessis, Louis, Duckworth, Nichola, Durham, Jillian, Eastick, Kirstine, Easton, Lisa J., Eccles, Richard, Edgeworth, Jonathan, Edwards, Sue, Bouzidi, Kate El, Eldirdiri, Sahar, Ellaby, Nicholas, Elliott, Scott, Eltringham, Gary, Ensell, Leah, Erkiert, Michelle J., Zamudio, Marina Escalera, Essex, Sarah, Evans, Johnathan M., Evans, Cariad, Everson, William, Fairley, Derek J., Fallon, Karlie, Fanaie, Arezou, Farr, Ben W., Fearn, Christopher, Feltwell, Theresa, Ferguson, Lynne, Fina, Laia, Flaviani, Flavia, Fleming, Vicki M., Forrest, Sally, Foster-Nyarko, Ebenezer, Foulkes, Benjamin H., Foulser, Luke, Fragakis, Mireille, Frampton, Dan, Francois, Sarah, Fraser, Christophe, Freeman, Timothy M., Fryer, Helen, Fuchs, Marc, Fuller, William, Gajee, Kavitha, Galai, Katerina, Gallagher, Abbie, Gallagher, Eileen, Gallagher, Michael D., Gallis, Marta, Gaskin, Amy, Gatica-Wilcox, Bree, Geidelberg, Lily, Gemmell, Matthew, Georgana, Iliana, George, Ryan P., Gifford, Laura, Gilbert, Lauren, Girgis, Sophia T., Glaysher, Sharon, Goldstein, Emily J., Golubchik, Tanya, Gomes, Andrea N., Gonçalves, Sónia, Goodfellow, Ian G., Goodwin, Scott, Goudarzi, Salman, Gourtovaia, Marina, Graham, Clive, Graham, Lee, Grant, Paul R., Green, Luke R., Green, Angie, Greenaway, Jane, Gregory, Richard, Guest, Martyn, Gunson, Rory N., Gupta, Ravi K., Gutierrez, Bernardo, Haldenby, Sam T., Hamilton, William L., Hansford, Samantha E., Haque, Tanzina, Harris, Kathryn A., Harrison, Ian, Harrison, Ewan M., Hart, Jennifer, Hartley, John A., Harvey, William T., Harvey, Matthew, Hassan-Ibrahim, Mohammed O., Heaney, Judith, Helmer, Thomas, Henderson, John, Hesketh, Andrew R., Hey, Jessica, Heyburn, David, Higginson, Ellen E., Hill, Verity, Hill, Jack D., Hilson, Rachel A., Hilvers, Ember, Holden, Matthew T. G., Hollis, Amy, Holmes, Christopher W., Holmes, Nadine, Holmes, Alison H., Hopes, Richard, Hornsby, Hailey R., Hosmillo, Myra, Houlihan, Catherine, Howson-Wells, Hannah C., Hsu, Sharon N., Hubb, Jonathan, Huckson, Hannah, Hughes, Warwick, Hughes, Joseph, Hughes, Margaret, Hutchings, Stephanie, Idle, Giles, Illingworth, Chris J., Impey, Robert, Irish-Tavares, Dianne, Iturriza-Gomara, Miren, Izuagbe, Rhys, Jackson, Chris, Jackson, Ben, Jackson, Leigh M., Jackson, Kathryn A., Jackson, David K., Jahun, Aminu S., James, Victoria, James, Keith, Jeanes, Christopher, Jeffries, Aaron R., Jeremiah, Sarah, Jermy, Andrew, John, Michaela, Johnson, Rob, Johnson, Kate, Johnston, Ian, Jones, Owen, Jones, Sophie, Jones, Hannah, Jones, Christopher R., Jones, Neil, Joseph, Amelia, Judges, Sarah, Kay, Gemma L., Kay, Sally, Keatley, Jon-Paul, Keeley, Alexander J., Kenyon, Anita, Kermack, Leanne M., Khakh, Manjinder, Kidd, Stephen P., Kimuli, Maimuna, Kirk, Stuart, Kitchen, Christine, Kitchman, Katie, Knight, Bridget A., Koshy, Cherian, Kraemer, Moritz U. G., Kumziene-Summerhayes, Sara, Kwiatkowski, Dominic, Lackenby, Angie, Laing, Kenneth G., Lampejo, Temi, Langford, Cordelia F., Lavin, Deborah, Lawton, Andrew I., Lee, Jack C. D., Lee, David, Lensing, Stefanie V., Leonard, Steven, Levett, Lisa J., Le-Viet, Thanh, Lewis, Jonathan, Lewis, Kevin, Liddle, Jennifier, Liggett, Steven, Lillie, Patrick J., Lindsey, Benjamin B., Lister, Michelle M., Livett, Rich, Lo, Stephanie, Loman, Nicholas J., Loose, Matthew W., Louka, Stavroula F., Loveson, Katie F., Lowdon, Sarah, Lowe, Hannah, Lowe, Helen L., Lucaci, Anita O., Ludden, Catherine, Lynch, Jessica, Lyons, Ronan A., Lythgoe, Katrina, Machin, Nicholas W., MacIntyre-Cockett, George, Mack, Andrew, Macklin, Ben, Maclean, Alasdair, Macnaughton, Emily, Madona, Pinglawathee, Maes, Mailis, Maftei, Laurentiu, Mahanama, Adhyana I. K., Mahungu, Tabitha W., Mair, Daniel, Maksimovic, Joshua, Malone, Cassandra S., Maloney, Daniel, Manesis, Nikos, Manley, Robin, Mantzouratou, Anna, Marchbank, Angela, Mariappan, Arun, Martincorena, Inigo, Nunez, Rocio T. Martinez, Mather, Alison E., Maxwell, Patrick, Mayhew, Megan, Mbisa, Tamyo, McCann, Clare, McCarthy, Shane A., McCluggage, Kathryn, McClure, Patrick C., McCrone, J. T., McHugh, Martin P., McKenna, James P., McKerr, Caoimhe, McManus, Georgina M., McMurray, Claire L., McMurray, Claire, McNally, Alan, Meadows, Lizzie, Medd, Nathan, Megram, Oliver, Menegazzo, Mirko, Merrick, Ian, Michell, Stephen L., Michelsen, Michelle L., Mirfenderesky, Mariyam, Mirza, Jeremy, Miskelly, Julia, Moles-Garcia, Emma, Moll, Robin J., Molnar, Zoltan, Monahan, Irene M., Mondani, Matteo, Mookerjee, Siddharth, Moore, Christopher, Moore, Jonathan, Moore, Nathan, Moore, Catherine, Morcrette, Helen, Morgan, Sian, Morgan, Mari, Mori, Matilde, Morriss, Arthur, Moses, Samuel, Mower, Craig, Muir, Peter, Mukaddas, Afrida, Munemo, Florence, Munn, Robert, Murray, Abigail, Murray, Leanne J., Murray, Darren R., Mutingwende, Manasa, Myers, Richard, Nastouli, Eleni, Nebbia, Gaia, Nelson, Andrew, Nelson, Charlotte, Nicholls, Sam, Nichols, Jenna, Nicodemi, Roberto, Nomikou, Kyriaki, O’Grady, Justin, O’Brien, Sarah, Odedra, Mina, Ohemeng-Kumi, Natasha, Oliver, Karen, Orton, Richard J., Osman, Husam, O’Toole, Áine, Pacchiarini, Nicole, Padgett, Debra, Page, Andrew J., Park, Emily J., Park, Naomi R., Parker, Matthew D., Parmar, Surendra, Partridge, David G., Pascall, David, Patel, Amita, Patel, Bindi, Paterson, Steve, Payne, Brendan A. I., Peacock, Sharon J., Pearson, Clare, Pelosi, Emanuela, Percival, Benita, Perkins, Jon, Perry, Malorie, Pinckert, Malte L., Platt, Steven, Podplomyk, Olga, Pohare, Manoj, Pond, Marcus, Pope, Cassie F., Poplawski, Radoslaw, Powell, Jessica, Poyner, Jennifer, Prestwood, Liam, Price, Anna, Price, James R., Prieto, Jacqui A., Pritchard, David T., Prosolek, Sophie J., Pugh, Georgia, Pusok, Monika, Pybus, Oliver G., Pymont, Hannah M., Quail, Michael A., Quick, Joshua, Radulescu, Clara, Raghwani, Jayna, Ragonnet-Cronin, Manon, Rainbow, Lucille, Rajan, Diana, Rajatileka, Shavanthi, Ramadan, Newara A., Rambaut, Andrew, Ramble, John, Randell, Paul A., Randell, Paul, Ratcliffe, Liz, Raviprakash, Veena, Raza, Mohammad, Redshaw, Nicholas M., Rey, Sara, Reynolds, Nicola, Richter, Alex, Robertson, David L., Robinson, Esther, Robson, Samuel C., Rogan, Fiona, Rooke, Stefan, Rowe, Will, Roy, Sunando, Rudder, Steven, Ruis, Chris, Rushton, Steven, Ryan, Felicity, Saeed, Kordo, Samaraweera, Buddhini, Sambles, Christine M., Sanderson, Roy, Sanderson, Theo, Sang, Fei, Sass, Thea, Scher, Emily, Scott, Garren, Scott, Carol, Sehmi, Jasveen, Shaaban, Sharif, Shah, Divya, Shaw, Jessica, Shelest, Ekaterina, Shepherd, James G., Sheridan, Liz A., Sheriff, Nicola, Shirley, Lesley, Sillitoe, John, Silviera, Siona, Simpson, David A., Singh, Aditi, Singleton, Dawn, Skvortsov, Timofey, Sloan, Tim J., Sluga, Graciela, Smith, Ken, Smith, Kim S., Smith, Perminder, Smith, Darren, Smith, Louise, Smith, Colin P., Smith, Nikki, Smollett, Katherine L., Snell, Luke B., Somassa, Thomas, Southgate, Joel, Spellman, Karla, Chapman, Michael H. Spencer, Spurgin, Lewis G., Spyer, Moira J., Stanley, Rachael, Stanley, William, Stanton, Thomas D., Starinskij, Igor, Stockton, Joanne, Stonehouse, Susanne, Storey, Nathaniel, Studholme, David J., Sudhanva, Malur, Swindells, Emma, Taha, Yusri, Tan, Ngee Keong, Tang, Julian W., Tang, Miao, Taylor, Ben E. W., Taylor, Joshua F., Taylor, Sarah, Temperton, Ben, Templeton, Kate E., Thomas, Claire, Thomson, Laura, Thomson, Emma C., Thornton, Alicia, Thurston, Scott A. J., Todd, John A., Tomb, Rachael, Tong, Lily, Tonkin-Hill, Gerry, Torok, M. Estee, Tovar-Corona, Jaime M., Trebes, Amy, Trotter, Alexander J., Tsatsani, Ioulia, Turnbull, Robyn, Turtle, Lance, Twohig, Katherine A., Umpleby, Helen, Underwood, Anthony P., Vamos, Edith E., Vasylyeva, Tetyana I., Vattipally, Sreenu, Vernet, Gabrielle, Vipond, Barry B., Volz, Erik M., Walsh, Sarah, Wang, Dennis, Warne, Ben, Warwick-Dugdale, Joanna, Wastnedge, Elizabeth, Watkins, Joanne, Watson, Louisa K., Waugh, Sheila, Webster, Hermione J., Weldon, Danni, Westwick, Elaine, Whalley, Thomas, Wheeler, Helen, Whitehead, Mark, Whiteley, Max, Whitwham, Andrew, Wierzbicki, Claudia, Willford, Nicholas J., Williams, Lesley-Anne, Williams, Rebecca, Williams, Cheryl, Williams, Chris, Williams, Charlotte A., Williams, Rachel J., Williams, Thomas, Williams, Catryn, Williamson, Kathleen A., Wilson-Davies, Eleri, Witele, Eric, Withell, Karen T., Witney, Adam A., Wolverson, Paige, Wong, Nick, Workman, Trudy, Wright, Victoria, Wright, Derek W., Wyatt, Tim, Wyllie, Sarah, Xu-McCrae, Li, Yavus, Mehmet, Yaze, Geraldine, Yeats, Corin A., Yebra, Gonzalo, Yew, Wen Chyin, Young, Greg, Young, Jamie, Zarebski, Alex E., Zhang, Peijun, Modat, Marc, Hammers, Alexander, Spector, Tim D., Steves, Claire J., Sudre, Carole H., Ourselin, Sebastien, Duncan, Emma L., Radiology and nuclear medicine, Peacock, Sharon [0000-0002-1718-2782], and Apollo - University of Cambridge Repository
Subjects: B900, Adult, Multidisciplinary, SARS-CoV-2, SARS-CoV-2/genetics, Reinfection, B100, COVID-19, Humans, C500, Prospective Studies, Hepatitis D, COVID-19/epidemiology
Abstract: The Delta (B.1.617.2) variant was the predominant UK circulating SARS-CoV-2 strain between May and December 2021. How Delta infection compares with previous variants is unknown. This prospective observational cohort study assessed symptomatic adults participating in the app-based COVID Symptom Study who tested positive for SARS-CoV-2 from May 26 to July 1, 2021 (Delta overwhelmingly the predominant circulating UK variant), compared (1:1, age- and sex-matched) with individuals presenting from December 28, 2020 to May 6, 2021 (Alpha (B.1.1.7) the predominant variant). We assessed illness (symptoms, duration, presentation to hospital) during Alpha- and Delta-predominant timeframes; and transmission, reinfection, and vaccine effectiveness during the Delta-predominant period. 3581 individuals (aged 18 to 100 years) from each timeframe were assessed. The seven most frequent symptoms were common to both variants. Within the first 28 days of illness, some symptoms were more common with Delta versus Alpha infection (including fever, sore throat, and headache) and some vice versa (dyspnoea). Symptom burden in the first week was higher with Delta versus Alpha infection; however, the odds of any given symptom lasting ≥ 7 days was either lower or unchanged. Illness duration ≥ 28 days was lower with Delta versus Alpha infection, though unchanged in unvaccinated individuals. Hospitalisation for COVID-19 was unchanged. The Delta variant appeared more (1.49) transmissible than Alpha. Re-infections were low in all UK regions. Vaccination markedly reduced the risk of Delta infection (by 69-84%). We conclude that COVID-19 from Delta or Alpha infections is similar. The Delta variant is more transmissible than Alpha; however, current vaccines showed good efficacy against disease. This research framework can be useful for future comparisons with new emerging variants.
Published: 2022

18. Significant variability exists in the cytotoxicity of global methicillin-resistant Staphylococcus aureus lineages

Author: Laabei, Maisem, primary, Peacock, Sharon J., additional, Blane, Beth, additional, Baines, Sarah L., additional, Howden, Benjamin P., additional, Stinear, Timothy P., additional, and Massey, Ruth C., additional
Published: 2021
Full Text: View/download PDF

19. Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

Author: Aggarwal, Dinesh, Warne, Ben, Jahun, Aminu, Hamilton, William, Fieldman, Thomas, Plessis, Louis, Hill, Verity, Blane, Beth, Watkins, Emmeline, Wright, Elizabeth, Hall, Grant, Ludden, Catherine, Myers, Richard, Hosmillo, Myra, Goodfellow, Yasmin, Pinckert, Malte, Georgana, Iliana, Izuagbe, Rhys, Leek, Danielle, Nsonwu, Olisaeloka, Hughes, Gareth, Packer, Simon, Page, Andrew, Metaxaki, Marina, Fuller, Stewart, Weale, Gillian, Holgate, Jon, Howes, Rob, McFarlane, Duncan, Dougan, Gordon, Pybus, Oliver, Angelis, Daniela De, Maxwell, Patrick, Peacock, Sharon, Weekes, Michael, Illingworth, Chris, Harrison, Ewan, Matheson, Nicholas, Goodfellow, Ian, The COVID-19 Genomics UK (COG-UK) Consortium, Bashton, Matthew, Smith, Darren, Young, Greg, Nelson, Andrew, and McCann, Clare
Subjects: medicine.medical_specialty, Transmission (mechanics), Geography, law, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Epidemiology, medicine, B100, C500, Computational biology, C700, law.invention
Abstract: Understanding the drivers for spread of SARS-CoV-2 in higher education settings is important to limit transmission between students, and onward spread into at-risk populations. In this study, we prospectively sequenced 482 SARS-CoV-2 isolates derived from asymptomatic student screening and symptomatic testing of students and staff at the University of Cambridge from 5 October to 6 December 2020. We performed a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. After a limited number of viral introductions into the university, the majority of student cases were linked to a single genetic cluster, likely dispersed across the university following social gatherings at a venue outside the university. We identified considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and dramatically reduced following a national lockdown. We observed that transmission clusters were largely segregated within the university or within the community. This study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics.
Published: 2021

20. Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 variant of concern 202012/01 (B.1.1.7): an exploratory analysis of a randomised controlled trial

Author: Emary, Katherine RW, Golubchik, Tanya, Aley, Parvinder K, Ariani, Cristina V, Angus, Brian, Bibi, Sagida, Blane, Beth, Bonsall, David, Cicconi, Paola, Charlton, Sue, Clutterbuck, Elizabeth A, Collins, Andrea M, Cox, Tony, Darton, Thomas C, Dold, Christina, Douglas, Alexander D, Duncan, Christopher JA, Ewer, Katie J, Flaxman, Amy L, Faust, Saul N, Ferreira, Daniela M, Feng, Shuo, Finn, Adam, Folegatti, Pedro M, Fuskova, Michelle, Galiza, Eva, Goodman, Anna L, Green, Catherine M, Green, Christopher A, Greenland, Melanie, Hallis, Bassam, Heath, Paul T, Hay, Jodie, Hill, Helen C, Jenkin, Daniel, Kerridge, Simon, Lazarus, Rajeka, Libri, Vincenzo, Lillie, Patrick J, Ludden, Catherine, Marchevsky, Natalie G, Minassian, Angela M, McGregor, Alastair C, Mujadidi, Yama F, Phillips, Daniel J, Plested, Emma, Pollock, Katrina M, Robinson, Hannah, Smith, Andrew, Song, Rinn, Snape, Matthew D, Sutherland, Rebecca K, Thomson, Emma C, Toshner, Mark, Turner, David PJ, Vekemans, Johan, Villafana, Tonya L, Williams, Christopher J, Hill, Adrian VS, Lambe, Teresa, Gilbert, Sarah C, Voysey, Merryn, Ramasamy, Maheshi N, Pollard, Andrew J, COVID-19 Genomics UK Consortium, AMPHEUS Project, Oxford COVID-19 Vaccine Trial Group, Toshner, Mark [0000-0002-3969-6143], and Apollo - University of Cambridge Repository
Subjects: Adult, Male, COVID-19 Vaccines, Adolescent, SARS-CoV-2, COVID-19, Middle Aged, Viral Load, Antibodies, Neutralizing, United Kingdom, Young Adult, COVID-19 Nucleic Acid Testing, ChAdOx1 nCoV-19, Humans, Female, Single-Blind Method, Nucleic Acid Amplification Techniques, Pandemics
Abstract: BACKGROUND: A new variant of SARS-CoV-2, B.1.1.7, emerged as the dominant cause of COVID-19 disease in the UK from November, 2020. We report a post-hoc analysis of the efficacy of the adenoviral vector vaccine, ChAdOx1 nCoV-19 (AZD1222), against this variant. METHODS: Volunteers (aged ≥18 years) who were enrolled in phase 2/3 vaccine efficacy studies in the UK, and who were randomly assigned (1:1) to receive ChAdOx1 nCoV-19 or a meningococcal conjugate control (MenACWY) vaccine, provided upper airway swabs on a weekly basis and also if they developed symptoms of COVID-19 disease (a cough, a fever of 37·8°C or higher, shortness of breath, anosmia, or ageusia). Swabs were tested by nucleic acid amplification test (NAAT) for SARS-CoV-2 and positive samples were sequenced through the COVID-19 Genomics UK consortium. Neutralising antibody responses were measured using a live-virus microneutralisation assay against the B.1.1.7 lineage and a canonical non-B.1.1.7 lineage (Victoria). The efficacy analysis included symptomatic COVID-19 in seronegative participants with a NAAT positive swab more than 14 days after a second dose of vaccine. Participants were analysed according to vaccine received. Vaccine efficacy was calculated as 1 - relative risk (ChAdOx1 nCoV-19 vs MenACWY groups) derived from a robust Poisson regression model. This study is continuing and is registered with ClinicalTrials.gov, NCT04400838, and ISRCTN, 15281137. FINDINGS: Participants in efficacy cohorts were recruited between May 31 and Nov 13, 2020, and received booster doses between Aug 3 and Dec 30, 2020. Of 8534 participants in the primary efficacy cohort, 6636 (78%) were aged 18-55 years and 5065 (59%) were female. Between Oct 1, 2020, and Jan 14, 2021, 520 participants developed SARS-CoV-2 infection. 1466 NAAT positive nose and throat swabs were collected from these participants during the trial. Of these, 401 swabs from 311 participants were successfully sequenced. Laboratory virus neutralisation activity by vaccine-induced antibodies was lower against the B.1.1.7 variant than against the Victoria lineage (geometric mean ratio 8·9, 95% CI 7·2-11·0). Clinical vaccine efficacy against symptomatic NAAT positive infection was 70·4% (95% CI 43·6-84·5) for B.1.1.7 and 81·5% (67·9-89·4) for non-B.1.1.7 lineages. INTERPRETATION: ChAdOx1 nCoV-19 showed reduced neutralisation activity against the B.1.1.7 variant compared with a non-B.1.1.7 variant in vitro, but the vaccine showed efficacy against the B.1.1.7 variant of SARS-CoV-2. FUNDING: UK Research and Innovation, National Institute for Health Research (NIHR), Coalition for Epidemic Preparedness Innovations, NIHR Oxford Biomedical Research Centre, Thames Valley and South Midlands NIHR Clinical Research Network, and AstraZeneca.
Published: 2021

21. Defining nosocomial transmission of Escherichia coli and antimicrobial resistance genes: a genomic surveillance study

Author: Ludden, Catherine, primary, Coll, Francesc, additional, Gouliouris, Theodore, additional, Restif, Olivier, additional, Blane, Beth, additional, Blackwell, Grace A, additional, Kumar, Narender, additional, Naydenova, Plamena, additional, Crawley, Charles, additional, Brown, Nicholas M, additional, Parkhill, Julian, additional, and Peacock, Sharon J, additional
Published: 2021
Full Text: View/download PDF

22. Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7

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

Author: Graham, Mark S, primary, Sudre, Carole H, additional, May, Anna, additional, Antonelli, Michela, additional, Murray, Benjamin, additional, Varsavsky, Thomas, additional, Kläser, Kerstin, additional, Canas, Liane S, additional, Molteni, Erika, additional, Modat, Marc, additional, Drew, David A, additional, Nguyen, Long H, additional, Polidori, Lorenzo, additional, Selvachandran, Somesh, additional, Hu, Christina, additional, Capdevila, Joan, additional, Hammers, Alexander, additional, Chan, Andrew T, additional, Wolf, Jonathan, additional, Spector, Tim D, additional, Steves, Claire J, additional, Ourselin, Sebastien, additional, Koshy, Cherian, additional, Ash, Amy, additional, Wise, Emma, additional, Moore, Nathan, additional, Mori, Matilde, additional, Cortes, Nick, additional, Lynch, Jessica, additional, Kidd, Stephen, additional, Fairley, Derek J, additional, Curran, Tanya, additional, McKenna, James P, additional, Adams, Helen, additional, Fraser, Christophe, additional, Golubchik, Tanya, additional, Bonsall, David, additional, Hassan-Ibrahim, Mohammed O, additional, Malone, Cassandra S, additional, Cogger, Benjamin J, 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, Price, Anna, additional, Kitchen, Christine, additional, Gulliver, Huw, additional, Merrick, Ian, additional, Southgate, Joel, additional, Guest, Martyn, additional, Munn, Robert, additional, Workman, Trudy, additional, Connor, Thomas R, additional, Fuller, William, additional, Bresner, Catherine, additional, Snell, Luke B, additional, Patel, Amita, additional, Charalampous, Themoula, additional, Nebbia, Gaia, additional, Batra, Rahul, additional, Edgeworth, Jonathan, additional, Robson, Samuel C, additional, Beckett, Angela H, additional, Aanensen, David M, additional, Underwood, Anthony P, additional, Yeats, Corin A, additional, Abudahab, Khalil, additional, Taylor, Ben EW, 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, Jones, Carl, additional, Holmes, Christopher, additional, Bird, Paul, additional, Helmer, Thomas, additional, Fallon, Karlie, additional, Tang, Julian, additional, Raviprakash, Veena, additional, Campbell, Sharon, additional, Sheriff, Nicola, additional, Blakey, Victoria, additional, Williams, Lesley-Anne, 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, Eldirdiri, Sahar, additional, Kenyon, Anita, additional, Davis, Thomas, additional, Pybus, Oliver G, additional, du Plessis, Louis, additional, Zarebski, Alex E, additional, Raghwani, Jayna, additional, Kraemer, Moritz UG, additional, Francois, Sarah, additional, Attwood, Stephen W, additional, Vasylyeva, Tetyana I, additional, Escalera Zamudio, Marina, additional, Gutierrez, Bernardo, 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, Moses, Samuel, additional, Lowe, Hannah, additional, Bedford, Luke, additional, Moore, Jonathan, additional, Stonehouse, Susanne, 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 CD, additional, Storey, Nathaniel, additional, Flaviani, Flavia, additional, Alcolea-Medina, Adela, additional, Williams, Rebecca, additional, Vernet, Gabrielle, additional, Chapman, Michael R, additional, Levett, Lisa J, additional, Heaney, Judith, additional, Chatterton, Wendy, additional, Pusok, Monika, additional, Xu-McCrae, Li, additional, Smith, Darren L, additional, Bashton, Matthew, additional, Young, Gregory R, additional, Holmes, Alison, additional, Randell, Paul Anthony, additional, Cox, Alison, additional, Madona, Pinglawathee, additional, Bolt, Frances, additional, Price, James, additional, Mookerjee, Siddharth, additional, Ragonnet-Cronin, Manon, additional, Nascimento, Fabricia F., additional, Jorgensen, David, additional, Siveroni, Igor, additional, Johnson, Rob, additional, Boyd, Olivia, additional, Geidelberg, Lily, additional, Volz, Erik M, additional, Rowan, Aileen, additional, Taylor, Graham P, additional, Smollett, Katherine L, additional, Loman, Nicholas J, additional, Quick, Joshua, additional, McMurray, Claire, additional, Stockton, Joanne, additional, Nicholls, Sam, additional, Rowe, Will, additional, Poplawski, Radoslaw, additional, McNally, Alan, 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, Sluga, Graciela, additional, Machin, Nicholas W, additional, Ahmad, Shazaad S Y, additional, George, Ryan P, additional, Halstead, Fenella, additional, Sivaprakasam, Venkat, additional, Hogsden, Wendy, additional, Illingworth, Chris J, additional, Jackson, Chris, additional, Thomson, Emma C, additional, Shepherd, James G, additional, Asamaphan, Patawee, additional, Niebel, Marc O, additional, Li, Kathy K, additional, Shah, Rajiv N, additional, Jesudason, Natasha G, 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, da Silva Filipe, Ana, additional, Robertson, David L, additional, Orton, Richard J, additional, Hughes, Joseph, additional, Vattipally, Sreenu, additional, Singer, Joshua B, additional, Nickbakhsh, Seema, additional, Hale, Antony D, additional, Macfarlane-Smith, Louissa R, additional, Harper, Katherine L, additional, Carden, Holli, additional, Taha, Yusri, additional, Payne, Brendan AI, additional, Burton-Fanning, Shirelle, additional, Waugh, Sheila, additional, Collins, Jennifer, additional, Eltringham, Gary, additional, Rushton, Steven, additional, O'Brien, Sarah, additional, Bradley, Amanda, additional, Maclean, Alasdair, additional, Mollett, Guy, additional, Blacow, Rachel, additional, Templeton, Kate E, additional, McHugh, Martin P, additional, Dewar, Rebecca, additional, Wastenge, Elizabeth, additional, Dervisevic, Samir, additional, Stanley, Rachael, additional, Meader, Emma J, additional, Coupland, Lindsay, additional, Smith, Louise, additional, Graham, Clive, additional, Barton, Edward, additional, Padgett, Debra, additional, Scott, Garren, additional, Swindells, Emma, additional, Greenaway, Jane, additional, Nelson, Andrew, additional, McCann, Clare M, additional, Yew, Wen C, additional, Andersson, Monique, additional, Peto, Timothy, additional, Justice, Anita, additional, Eyre, David, additional, Crook, Derrick, additional, Sloan, Tim J, additional, Duckworth, Nichola, additional, Walsh, Sarah, additional, Chauhan, Anoop J, additional, Glaysher, Sharon, additional, Bicknell, Kelly, additional, Wyllie, Sarah, additional, Elliott, Scott, additional, Lloyd, Allyson, additional, Impey, Robert, additional, Levene, Nick, additional, Monaghan, Lynn, additional, Bradley, Declan T, additional, Wyatt, Tim, additional, Allara, Elias, additional, Pearson, Clare, additional, Osman, Husam, additional, Bosworth, Andrew, additional, Robinson, Esther, 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, Ledesma, Juan, additional, Twohig, Katherine A, 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, Bull, Matthew, additional, Cronin, Michelle, additional, Pacchiarini, Nicole, 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, Mather, Alison E, additional, Baker, David J, additional, Rudder, Steven, additional, Aydin, Alp, additional, Kay, Gemma L, additional, Trotter, Alexander J, additional, Alikhan, Nabil-Fareed, additional, de Oliveira Martins, Leonardo, additional, Le-Viet, Thanh, additional, Meadows, Lizzie, additional, Casey, Anna, additional, Ratcliffe, Liz, additional, Simpson, David A, additional, Molnar, Zoltan, additional, Thompson, Thomas, additional, Acheson, Erwan, additional, Masoli, Jane AH, additional, Knight, Bridget A, additional, Ellard, Sian, additional, Auckland, Cressida, additional, Jones, Christopher R, additional, Mahungu, Tabitha W, additional, Irish-Tavares, Dianne, additional, Haque, Tanzina, additional, Hart, Jennifer, additional, Witele, Eric, additional, Fenton, Melisa Louise, additional, Dadrah, Ashok, additional, Symmonds, Amanda, additional, Saluja, Tranprit, additional, Bourgeois, Yann, additional, Scarlett, Garry P, additional, Loveson, Katie F, additional, Goudarzi, Salman, additional, Fearn, Christopher, additional, Cook, Kate, additional, Dent, Hannah, additional, Paul, Hannah, additional, Partridge, David G, additional, Raza, Mohammad, additional, Evans, Cariad, additional, Johnson, Kate, additional, Liggett, Steven, additional, Baker, Paul, additional, Bonner, Stephen, additional, Essex, Sarah, additional, Lyons, Ronan A, additional, Saeed, Kordo, additional, Mahanama, Adhyana I.K, additional, Samaraweera, Buddhini, additional, Silveira, Siona, additional, Pelosi, Emanuela, additional, Wilson-Davies, Eleri, additional, Williams, Rachel J, additional, Kristiansen, Mark, additional, Roy, Sunando, additional, Williams, Charlotte A, additional, Cotic, Marius, additional, Bayzid, Nadua, additional, Westhorpe, Adam P, additional, Hartley, John A, additional, Jannoo, Riaz, additional, Lowe, Helen L, additional, Karamani, Angeliki, additional, Ensell, Leah, additional, Prieto, Jacqui A, additional, Jeremiah, Sarah, additional, Grammatopoulos, Dimitris, additional, Pandey, Sarojini, additional, Berry, Lisa, additional, Jones, Katie, additional, Richter, Alex, additional, Beggs, Andrew, additional, Best, Angus, additional, Percival, Benita, additional, Mirza, Jeremy, additional, Megram, Oliver, additional, Mayhew, Megan, additional, Crawford, Liam, additional, Ashcroft, Fiona, additional, Moles-Garcia, Emma, additional, Cumley, Nicola, additional, Smith, Colin P, additional, Bucca, Giselda, additional, Hesketh, Andrew R, additional, Blane, Beth, additional, Girgis, Sophia T, additional, Leek, Danielle, additional, Sridhar, Sushmita, 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, Gupta, Ravi Kumar, additional, Ludden, Catherine, additional, Peacock, Sharon J, additional, Palmer, Sophie, additional, Churcher, Carol M, additional, Hadjirin, Nazreen F, additional, Carabelli, Alessandro M, additional, Brooks, Ellena, additional, Smith, Kim S, additional, Galai, Katerina, additional, McManus, Georgina M, additional, Ruis, Chris, additional, Davidson, Rose K, additional, Rambaut, Andrew, additional, Williams, Thomas, additional, Balcazar, Carlos E, additional, Gallagher, Michael D, additional, O'Toole, Áine, additional, Rooke, Stefan, additional, Hill, Verity, 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, Wierzbicki, Claudia, additional, Webster, Hermione J, 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, Whiteley, Max, additional, Zhang, Peijun, additional, Gallis, Marta, additional, Louka, Stavroula F, 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, Aggarwal, Dinesh, additional, Cerda, Alberto C, additional, Merrill, Tammy V, additional, Wilson, Rebekah E, additional, McClure, Patrick C, additional, Chappell, Joseph G, additional, Tsoleridis, Theocharis, additional, Ball, Jonathan, additional, Buck, David, additional, Todd, John A, additional, Green, Angie, additional, Trebes, Amy, additional, MacIntyre-Cockett, George, additional, de Cesare, Mariateresa, additional, Alderton, Alex, additional, Amato, Roberto, additional, Ariani, Cristina V, additional, Beale, Mathew A, additional, Beaver, Charlotte, additional, Bellis, Katherine L, additional, Betteridge, Emma, additional, Bonfield, James, additional, Danesh, John, additional, Dorman, Matthew J, additional, Drury, Eleanor, additional, Farr, Ben W, additional, Foulser, Luke, additional, Goncalves, Sonia, additional, Goodwin, Scott, additional, Gourtovaia, Marina, additional, Harrison, Ewan M, additional, Jackson, David K, additional, Jamrozy, Dorota, additional, Johnston, Ian, additional, Kane, Leanne, additional, Kay, Sally, additional, Keatley, Jon-Paul, additional, Kwiatkowski, Dominic, additional, Langford, Cordelia F, additional, Lawniczak, Mara, additional, Letchford, Laura, additional, Livett, Rich, additional, Lo, Stephanie, additional, Martincorena, Inigo, additional, McGuigan, Samantha, additional, Nelson, Rachel, additional, Palmer, Steve, additional, Park, Naomi R, additional, Patel, Minal, additional, Prestwood, Liam, additional, Puethe, Christoph, additional, Quail, Michael A, additional, Rajatileka, Shavanthi, additional, Scott, Carol, additional, Shirley, Lesley, additional, Sillitoe, John, additional, Spencer Chapman, Michael H, additional, Thurston, Scott AJ, additional, Tonkin-Hill, Gerry, additional, Weldon, Danni, additional, Rajan, Diana, additional, Bronner, Iraad F, additional, Aigrain, Louise, additional, Redshaw, Nicholas M, additional, Lensing, Stefanie V, additional, Davies, Robert, additional, Whitwham, Andrew, additional, Liddle, Jennifier, additional, Lewis, Kevin, additional, Tovar-Corona, Jaime M, additional, Leonard, Steven, additional, Durham, Jillian, additional, Bassett, Andrew R, additional, McCarthy, Shane, additional, Moll, Robin J, additional, James, Keith, additional, Oliver, Karen, additional, Makunin, Alex, additional, Barrett, Jeff, additional, and Gunson, Rory N, additional
Published: 2021
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24. Definition of a genetic relatedness cutoff to exclude recent transmission of meticillin-resistant Staphylococcus aureus: a genomic epidemiology analysis

Author: Coll, Francesc, Raven, Kathy E, Knight, Gwenan M, Blane, Beth, Harrison, Ewan M, Leek, Danielle, Enoch, David A, Brown, Nicholas M, Parkhill, Julian, and Peacock, Sharon J
Abstract: BACKGROUND: Whole-genome sequencing (WGS) can be used in genomic epidemiology investigations to confirm or refute outbreaks of bacterial pathogens, and to support targeted and efficient infection control interventions. We aimed to define a genetic relatedness cutoff, quantified as a number of single-nucleotide polymorphisms (SNP), for meticillin-resistant Staphylococcus aureus (MRSA), above which recent (ie, within 6 months) patient-to-patient transmission could be ruled out. METHODS: We did a retrospective genomic and epidemiological analysis of MRSA data from two prospective observational cohort studies in the UK to establish SNP cutoffs for genetic relatedness, above which recent transmission was unlikely. We used three separate approaches to calculate these thresholds. First, we applied a linear mixed model to estimate the S aureus substitution rate and 95th percentile within-host diversity in a cohort in which multiple isolates were sequenced per individual. Second, we applied a simulated transmission model to this same genomic dataset. Finally, in a second cohort, we determined the genetic distance (ie, the number of SNPs) that would capture 95% of epidemiologically linked cases. We applied the three approaches to both whole-genome and core-genome sequences. FINDINGS: In the linear mixed model, the estimated substitution rate was roughly 5 whole-genome SNPs (wgSNPs) or 3 core-genome SNPs (cgSNPs) per genome per year, and the 95th percentile within-host diversity was 19 wgSNPs or 10 cgSNPs. The combined SNP cutoffs for detection of MRSA transmission within 6 months per this model were thus 24 wgSNPs or 13 cgSNPs. The simulated transmission model suggested that cutoffs of 17 wgSNPs or 12 cgSNPs would detect 95% of MRSA transmission events within the same timeframe. Finally, in the second cohort, cutoffs of 22 wgSNPs or 11 cgSNPs captured 95% of epidemiologically linked cases within 6 months. INTERPRETATION: On the basis of our results, we propose conservative cutoffs of 25 wgSNPs or 15 cgSNPS above which transmission of MRSA within the previous 6 months can be ruled out. These cutoffs could potentially be used as part of a genomic sequencing approach to the management of outbreaks of MRSA in conjunction with traditional epidemiological techniques. FUNDING: UK Department of Health, Wellcome Trust, UK National Institute for Health Research.
Published: 2020

25. 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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26. Defining metrics for whole-genome sequence analysis of MRSA in clinical practice

Author: Raven, Kathy E, Blane, Beth, Kumar, Narender, Leek, Danielle, Bragin, Eugene, Coll, Francesc, Parkhill, Julian, Peacock, Sharon J, Parkhill, Julian [0000-0002-7069-5958], Peacock, Sharon [0000-0002-1718-2782], and Apollo - University of Cambridge Repository
Subjects: Methicillin-Resistant Staphylococcus aureus, Whole Genome Sequencing, translational, Computational Biology, High-Throughput Nucleotide Sequencing, MRSA, Staphylococcal Infections, Polymorphism, Single Nucleotide, United Kingdom, Workflow, quality metrics, Bacterial Proteins, whole-genome sequencing, Humans, Penicillin-Binding Proteins
Abstract: Bacterial sequencing will become increasingly adopted in routine microbiology laboratories. Here, we report the findings of a technical evaluation of almost 800 clinical methicillin-resistant Staphylococcus aureus (MRSA) isolates, in which we sought to define key quality metrics to support MRSA sequencing in clinical practice. We evaluated the accuracy of mapping to a generic reference versus clonal complex (CC)-specific mapping, which is more computationally challenging. Focusing on isolates that were genetically related (50 bp apart to identify same-species contamination for MRSA. These metrics were combined into a quality-control (QC) flowchart to determine whether sequence runs and individual clinical isolates passed QC, which could be adapted by future automated analysis systems to enable rapid hands-off sequence analysis by clinical laboratories.
Published: 2020
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27. A One Health Study of the Genetic Relatedness of Klebsiella pneumoniae and Their Mobile Elements in the East of England

Author: Ludden, Catherine, Moradigaravand, Danesh, Jamrozy, Dorota, Gouliouris, Theodore, Blane, Beth, Naydenova, Plamena, Hernandez-Garcia, Juan, Wood, Paul, Hadjirin, Nazreen, Radakovic, Milorad, Crawley, Charles, Brown, Nicholas M, Holmes, Mark, Parkhill, Julian, Peacock, Sharon J, Ludden, Catherine [0000-0001-9503-0744], Hernandez-Garcia, Juan [0000-0001-5932-9327], Holmes, Mark [0000-0002-5454-1625], Parkhill, Julian [0000-0002-7069-5958], Peacock, Sharon [0000-0002-1718-2782], and Apollo - University of Cambridge Repository
Subjects: Cross Infection, Microbial Sensitivity Tests, United Kingdom, beta-Lactamases, Anti-Bacterial Agents, Klebsiella Infections, Klebsiella pneumoniae, Cross-Sectional Studies, England, genomics, surveillance, Animals, Humans, Cattle, One Health, antimicrobial resistance, Articles and Commentaries, Klebsiella pneumonia
Abstract: Background Klebsiella pneumoniae is a human, animal, and environmental commensal and a leading cause of nosocomial infections, which are often caused by multiresistant strains. We evaluate putative sources of K. pneumoniae that are carried by and infect hospital patients. Methods We conducted a 6-month survey on 2 hematology wards at Addenbrooke’s Hospital, Cambridge, United Kingdom, in 2015 to isolate K. pneumoniae from stool, blood, and the environment. We conducted cross-sectional surveys of K. pneumoniae from 29 livestock farms, 97 meat products, the hospital sewer, and 20 municipal wastewater treatment plants in the East of England between 2014 and 2015. Isolates were sequenced and their genomes compared. Results Klebsiella pneumoniae was isolated from stool of 17/149 (11%) patients and 18/922 swabs of their environment, together with 1 bloodstream infection during the study and 4 others over a 24-month period. Each patient carried 1 or more lineages that was unique to them, but 2 broad environmental contamination events and patient–environment transmission were identified. Klebsiella pneumoniae was isolated from cattle, poultry, hospital sewage, and 12/20 wastewater treatment plants. There was low genetic relatedness between isolates from patients/their hospital environment vs isolates from elsewhere. Identical genes encoding cephalosporin resistance were carried by isolates from humans/environment and elsewhere but were carried on different plasmids. Conclusion We identified no patient-to-patient transmission and no evidence for livestock as a source of K. pneumoniae infecting humans. However, our findings reaffirm the importance of the hospital environment as a source of K. pneumoniae associated with serious human infection., A One Health genomic survey of Klebsiella pneumoniae demonstrated transmission between patients and their ward environment but no evidence to implicate livestock as a source of K. pneumoniae or their mobile genetic elements encoding antibiotic resistance.
Published: 2020

28. The Emergence of Successful Streptococcus pyogenes Lineages through Convergent Pathways of Capsule Loss and Recombination Directing High Toxin Expression

Author: Turner, Claire E., primary, Holden, Matthew T. G., additional, Blane, Beth, additional, Horner, Carolyne, additional, Peacock, Sharon J., additional, and Sriskandan, Shiranee, additional
Published: 2019
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29. Pilot Evaluation of a Fully Automated Bioinformatics System for Analysis of Methicillin-Resistant Staphylococcus aureus Genomes and Detection of Outbreaks

Author: Brown, Nicholas M., primary, Blane, Beth, additional, Raven, Kathy E., additional, Kumar, Narender, additional, Leek, Danielle, additional, Bragin, Eugene, additional, Rhodes, Paul A., additional, Enoch, David A., additional, Thaxter, Rachel, additional, Parkhill, Julian, additional, and Peacock, Sharon J., additional
Published: 2019
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30. Methodology for Whole-Genome Sequencing of Methicillin-Resistant Staphylococcus aureus Isolates in a Routine Hospital Microbiology Laboratory

Author: Raven, Kathy E, Blane, Beth, Leek, Danielle, Churcher, Carol, Kokko-Gonzales, Paula, Pugazhendhi, Dhamayanthi, Fraser, Louise, Betley, Jason, Parkhill, Julian, Peacock, Sharon J, Parkhill, Julian [0000-0002-7069-5958], and Apollo - University of Cambridge Repository
Subjects: Methicillin-Resistant Staphylococcus aureus, Microbiological Techniques, clinical application, Whole Genome Sequencing, whole-genome sequencing, Diagnostic Tests, Routine, Humans, MRSA, Staphylococcal Infections, Laboratories, Hospital, Genome, Bacterial, Multilocus Sequence Typing
Abstract: There is growing evidence for the value of bacterial whole-genome sequencing in hospital outbreak investigations. Our aim was to develop methods that support efficient and accurate low-throughput clinical sequencing of methicillin-resistant Staphylococcus aureus (MRSA) isolates. Using a test panel of 25 MRSA isolates previously associated with outbreak investigations, we devised modifications to library preparation that reduced the processing time by 1 hour. We determined the maximum number of isolates that could be sequenced per run using an Illumina MiniSeq platform and a 13-hour (overnight) run time, which equated to 21 MRSA isolates and 3 controls (no template, positive, and negative). Repeatability and reproducibility assays based on this sequencing methodology demonstrated 100% accuracy in assigning species and sequence type (ST) and in detecting mecA Established genetic relatedness between isolates was recapitulated. Quality control (QC) metrics were evaluated over nine sequencing runs. Of the test panel MRSA genomes, 168/173 (97%) passed QC metrics based on the correct species assigned, detection of mecA and ST, and depth/coverage metrics. An evaluation of contamination in these 9 runs showed that positive and negative controls and test MRSA sequence files contained
Published: 2019

31. One Health study of the genetic relatedness of Klebsiella pneumoniae and their mobile elements in the East of England

Author: Ludden, Catherine, Moradigaravand, Danesh, Jamrozy, Dorota, Gouliouris, Theodore, Blane, Beth, Naydenova, Plamena, Hernandez-Garcia, Juan, Wood, Paul, Hadjirin, Nazreen, Radakovic, Milorad, Crawley, Charles, Brown, Nicholas M., Holmes, Mark A., Parkhill, Julian, and Peacock, Sharon J
Subjects: Klebsiella pneumoniae, genomics, surveillance, One Health, antimicrobial resistance
Abstract: Klebsiella pneumoniae is a human, animal and environmental commensal and a leading cause of nosocomial infections, which are often caused by multi-resistant strains that are challenging to treat. We conducted a One Health evaluation of putative sources of K. pneumoniae that are carried by, and infect hospital patients. This combined data from a six-month study on two haematology wards at Addenbrooke’s Hospital, Cambridge, in 2015 to isolate K. pneumoniae from stool, blood and the environment, and a cross-sectional survey of K. pneumoniae from 29 livestock farms, 97 meat products, the hospital sewer and 20 municipal wastewater treatment plants in the East of England between 2014 and 2015. K. pneumoniae was isolated from stools of 17/149 (11%) patients and 18/922 swabs of their environment, together with one patient bloodstream infection during the study and 4 others over a 24-month period. Each patient carried one or more lineages that was unique to them, but two broad environmental contamination events and patient-environmental transmission were identified. K. pneumoniae was isolated from cattle and poultry, hospital sewage and 12/20 wastewater plants. There was low genetic relatedness between isolates from patients/their hospital environment versus isolates from elsewhere. Identical genes encoding cephalosporin resistance were carried by isolates from different reservoirs, but were carried on different plasmids by isolates from patients/their environment versus elsewhere. We identified no patient-to-patient transmission and no evidence for livestock as a source of K. pneumoniae infecting humans, but our findings reaffirm the importance of the hospital environment as a source of K. pneumoniae associated with serious human infection.
Published: 2019

32. Prospective genomic surveillance of methicillin-resistant Staphylococcus aureus (MRSA) associated with bloodstream infection, England, 1 October 2012 to 30 September 2013

Author: Toleman, Michelle S, Reuter, Sandra, Jamrozy, Dorota, Wilson, Hayley J, Blane, Beth, Harrison, Ewan M, Coll, Francesc, Hope, Russell J, Kearns, Angela, Parkhill, Julian, Peacock, Sharon J, Török, M Estée, Harrison, Ewan [0000-0003-2720-0507], Parkhill, Julian [0000-0002-7069-5958], Peacock, Sharon [0000-0002-1718-2782], and Apollo - University of Cambridge Repository
Subjects: Adult, Male, Methicillin-Resistant Staphylococcus aureus, bacteraemia, Adolescent, Bacteremia, MRSA, Disease Outbreaks, Cohort Studies, Humans, Public Health Surveillance, Prospective Studies, Child, Phylogeny, Aged, Aged, 80 and over, Cross Infection, Molecular Epidemiology, Whole Genome Sequencing, public health, Infant, Newborn, Infant, Sequence Analysis, DNA, biochemical phenomena, metabolism, and nutrition, Middle Aged, Staphylococcal Infections, bacterial infections and mycoses, England, whole-genome sequencing, Child, Preschool, Epidemiological Monitoring, surveillance, Feasibility Studies, epidemiology, Female, WGS, Genome, Bacterial
Abstract: BackgroundMandatory reporting of methicillin-resistant Staphylococcus aureus (MRSA) bloodstream infections (BSI) has occurred in England for over 15years. Epidemiological information is recorded, but routine collection of isolates for characterisation has not been routinely undertaken. Ongoing developments in whole-genome sequencing (WGS) have demonstrated its value in outbreak investigations and for determining the spread of antimicrobial resistance and bacterial population structure. Benefits of adding genomics to routine epidemiological MRSA surveillance are unknown.AimTo determine feasibility and potential utility of adding genomics to epidemiological surveillance of MRSA.MethodsWe conducted an epidemiological and genomic survey of MRSA BSI in England over a 1-year period (1 October 2012--30 September 2013).ResultsDuring the study period, 903 cases of MRSA BSI were reported; 425 isolates were available for sequencing of which, 276 (65%) were clonal complex (CC) 22. Addition of 64 MRSA genomes from published outbreak investigations showed that the study genomes could provide context for outbreak isolates and supported cluster identification. Comparison to other MRSA genome collections demonstrated variation in clonal diversity achieved through different sampling strategies and identified potentially high-risk clones e.g. USA300 and local expansion of CC5 MRSA in South West England.ConclusionsWe demonstrate the potential utility of combined epidemiological and genomic MRSA BSI surveillance to determine the national population structure of MRSA, contextualise previous MRSA outbreaks, and detect potentially high-risk lineages. These findings support the integration of epidemiological and genomic surveillance for MRSA BSI as a step towards a comprehensive surveillance programme in England.
Published: 2019
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33. MOESM4 of The composition and functional protein subsystems of the human nasal microbiome in granulomatosis with polyangiitis: a pilot study

Author: Wagner, Josef, Harrison, Ewan, Pero, Marcos Martinez Del, Blane, Beth, Mayer, Gert, Leierer, Johannes, Seerapani Gopaluni, Holmes, Mark, Parkhill, Julian, Peacock, Sharon, Jayne, David, and Kronbichler, Andreas
Subjects: stomatognathic system, macromolecular substances
Abstract: Additional file 4: Figure S4. Heatmap analysis with annotation for disease duration in months and active GPA and inactive GPA disease stage using top 28 species with a minimum abundance of 0.5% in at least one sample in the bacterial 16S rRNA dataset. (PDF 75 kb)
Published: 2019
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34. Genomic Surveillance of <named-content content-type='genus-species'>Enterococcus faecium</named-content> Reveals Limited Sharing of Strains and Resistance Genes between Livestock and Humans in the United Kingdom

Author: Gouliouris, Theodore, Raven, Kathy E, Ludden, Catherine, Blane, Beth, Corander, Jukka, Horner, Carolyne S, Hernandez-Garcia, Juan, Wood, Paul, Hadjirin, Nazreen F, Radakovic, Milorad, Holmes, Mark A, De Goffau, Marcus, Brown, Nicholas M, Parkhill, Julian, Peacock, Sharon J, Parkhill, Julian [0000-0002-7069-5958], and Apollo - University of Cambridge Repository
Subjects: vancomycin resistant, Farms, Genotype, Swine, Enterococcus faecium, Microbial Sensitivity Tests, Wastewater, Polymorphism, Single Nucleotide, Microbiology, Vancomycin-Resistant Enterococci, Clinical Science and Epidemiology, Drug Resistance, Multiple, Bacterial, parasitic diseases, Prevalence, Animals, Humans, One Health, Gram-Positive Bacterial Infections, Phylogeny, Whole Genome Sequencing, vancomycin-resistant, Vancomycin Resistance, United Kingdom, QR1-502, Anti-Bacterial Agents, Meat Products, livestock, genome sequencing, Cross-Sectional Studies, Epidemiological Monitoring, Genome, Bacterial, Research Article
Abstract: The rise in rates of human infection caused by vancomycin-resistant Enterococcus faecium (VREfm) strains between 1988 to the 2000s in Europe was suggested to be associated with acquisition from livestock. As a result, the European Union banned the use of the glycopeptide drug avoparcin as a growth promoter in livestock feed. While some studies reported a decrease in VREfm in livestock, others reported no reduction. Here, we report the first livestock VREfm prevalence survey in the UK since 2003 and the first large-scale study using whole-genome sequencing to investigate the relationship between E. faecium strains in livestock and humans. We found a low prevalence of VREfm in retail meat and limited evidence for recent sharing of strains between livestock and humans with bloodstream infection. There was evidence for limited sharing of genes encoding antibiotic resistance between these reservoirs, a finding which requires further research., Vancomycin-resistant Enterococcus faecium (VREfm) is a major cause of nosocomial infection and is categorized as high priority by the World Health Organization global priority list of antibiotic-resistant bacteria. In the past, livestock have been proposed as a putative reservoir for drug-resistant E. faecium strains that infect humans, and isolates of the same lineage have been found in both reservoirs. We undertook cross-sectional surveys to isolate E. faecium (including VREfm) from livestock farms, retail meat, and wastewater treatment plants in the United Kingdom. More than 600 isolates from these sources were sequenced, and their relatedness and antibiotic resistance genes were compared with genomes of almost 800 E. faecium isolates from patients with bloodstream infection in the United Kingdom and Ireland. E. faecium was isolated from 28/29 farms; none of these isolates were VREfm, suggesting a decrease in VREfm prevalence since the last UK livestock survey in 2003. However, VREfm was isolated from 1% to 2% of retail meat products and was ubiquitous in wastewater treatment plants. Phylogenetic comparison demonstrated that the majority of human and livestock-related isolates were genetically distinct, although pig isolates from three farms were more genetically related to human isolates from 2001 to 2004 (minimum of 50 single-nucleotide polymorphisms [SNPs]). Analysis of accessory (variable) genes added further evidence for distinct niche adaptation. An analysis of acquired antibiotic resistance genes and their variants revealed limited sharing between humans and livestock. Our findings indicate that the majority of E. faecium strains infecting patients are largely distinct from those from livestock in this setting, with limited sharing of strains and resistance genes.
Published: 2018

35. Genomic surveillance of Enterococcus faecium reveals limited sharing of strains and resistance genes between livestock and humans

Author: Gouliouris, Theodore, Raven, Kathy E., Ludden, Catherine, Blane, Beth, Corander, Jukka, Horner, Carolyne, Hernandez-Garcia, Juan, Wood, Paul, Hadjirin, Nazreen, Radakovic, Milorad, Holmes, Mark A., Goffau, Marcus de, Brown, Nicholas M., Parkhill, Julian, and Peacock, Sharon J
Subjects: livestock, genome sequencing, vancomycin resistant, Enterococcus faecium, vancomycin-resistant, One Health
Abstract: Vancomycin-resistant Enterococcus faecium (VREfm) is a major cause ofnosocomial infection and is categorized as high priority by the World Health Organizationglobal priority list of antibiotic-resistant bacteria. In the past, livestock havebeen proposed as a putative reservoir for drug-resistant E. faecium strains that infecthumans, and isolates of the same lineage have been found in both reservoirs. Weundertook cross-sectional surveys to isolate E. faecium (including VREfm) from livestockfarms, retail meat, and wastewater treatment plants in the United Kingdom.More than 600 isolates from these sources were sequenced, and their relatednessand antibiotic resistance genes were compared with genomes of almost 800 E. faeciumisolates from patients with bloodstream infection in the United Kingdom andIreland. E. faecium was isolated from 28/29 farms; none of these isolates wereVREfm, suggesting a decrease in VREfm prevalence since the last UK livestock surveyin 2003. However, VREfm was isolated from 1% to 2% of retail meat products andwas ubiquitous in wastewater treatment plants. Phylogenetic comparison demonstratedthat the majority of human and livestock-related isolates were geneticallydistinct, although pig isolates from three farms were more genetically related to humanisolates from 2001 to 2004 (minimum of 50 single-nucleotide polymorphisms[SNPs]). Analysis of accessory (variable) genes added further evidence for distinctniche adaptation. An analysis of acquired antibiotic resistance genes and their variantsrevealed limited sharing between humans and livestock. Our findings indicatethat the majority of E. faecium strains infecting patients are largely distinct fromthose from livestock in this setting, with limited sharing of strains and resistancegenes.
Published: 2018

36. Are commercial providers a viable option for clinical bacterial sequencing?

Author: Raven, Kathy, Blane, Beth, Churcher, Carol, Parkhill, Julian, Peacock, Sharon J, Parkhill, Julian [0000-0002-7069-5958], Peacock, Sharon [0000-0002-1718-2782], and Apollo - University of Cambridge Repository
Subjects: DNA, Bacterial, Methicillin-Resistant Staphylococcus aureus, Whole Genome Sequencing, MRSA, Sequence Analysis, DNA, Contract Services, Staphylococcal Infections, Polymorphism, Single Nucleotide, United Kingdom, Disease Outbreaks, clinical application, whole-genome sequencing, Humans, Genome, Bacterial, Multilocus Sequence Typing
Abstract: Bacterial whole-genome sequencing in the clinical setting has the potential to bring major improvements to infection control and clinical practice. Sequencing instruments are not currently available in the majority of routine microbiology laboratories worldwide, but an alternative is to use external sequencing providers. To foster discussion around this we investigated whether send-out services were a viable option. Four providers offering MiSeq sequencing were selected based on cost and evaluated based on the service provided and sequence data quality. DNA was prepared from five methicillin-resistant Staphylococcus aureus (MRSA) isolates, four of which were investigated during a previously published outbreak in the UK together with a reference MRSA isolate (ST22 HO 5096 0412). Cost of sequencing per isolate ranged from £155 to £342 and turnaround times from DNA postage to arrival of sequence data ranged from 12 to 63 days. Comparison of commercially generated genomes against the original sequence data demonstrated very high concordance, with no more than one single nucleotide polymorphism (SNP) difference on core genome mapping between the original sequences and the new sequence for all four providers. Multilocus sequence type could not be assigned based on assembly for the two cheapest sequence providers due to fragmented assemblies probably caused by a lower output of sequence data per isolate. Our results indicate that external providers returned highly accurate genome data, but that improvements are required in turnaround time to make this a viable option for use in clinical practice.
Published: 2018

37. Genomic surveillance of Escherichia coli in municipal wastewater treatment plants as an indicator of clinically relevant pathogens and their resistance genes

Author: Raven, Kathy E., primary, Ludden, Catherine, additional, Gouliouris, Theodore, additional, Blane, Beth, additional, Naydenova, Plamena, additional, Brown, Nicholas M., additional, Parkhill, Julian, additional, and Peacock, Sharon J., additional
Published: 2019
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38. Detection of vancomycin-resistant Enterococcus faecium hospital-adapted lineages in municipal wastewater treatment plants indicates widespread distribution and release into the environment

Author: Gouliouris, Theodore, primary, Raven, Kathy E., additional, Moradigaravand, Danesh, additional, Ludden, Catherine, additional, Coll, Francesc, additional, Blane, Beth, additional, Naydenova, Plamena, additional, Horner, Carolyne, additional, Brown, Nicholas M., additional, Corander, Jukka, additional, Limmathurotsakul, Direk, additional, Parkhill, Julian, additional, and Peacock, Sharon J., additional
Published: 2019
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39. 176. THE COMPOSITION OF THE HUMAN NASAL MICROBIOME IN GRANULOMATOSIS WITH POLYANGIITIS: A PILOT STUDY

Author: Kronbichler, Andreas, primary, Wagner, Josef, additional, Harrison, Ewan, additional, Pero, Marcos Martinez Del, additional, Blane, Beth, additional, Mayer, Gert, additional, Leierer, Johannes, additional, Gopaluni, Seerapani, additional, Holmes, Mark, additional, Parkhill, Julian, additional, Peacock, Sharon, additional, and Jayne, David, additional
Published: 2019
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40. One Health Genomic Surveillance of Escherichia coli Demonstrates Distinct Lineages and Mobile Genetic Elements in Isolates from Humans versus Livestock

Author: Ludden, Catherine, primary, Raven, Kathy E., additional, Jamrozy, Dorota, additional, Gouliouris, Theodore, additional, Blane, Beth, additional, Coll, Francesc, additional, de Goffau, Marcus, additional, Naydenova, Plamena, additional, Horner, Carolyne, additional, Hernandez-Garcia, Juan, additional, Wood, Paul, additional, Hadjirin, Nazreen, additional, Radakovic, Milorad, additional, Brown, Nicholas M., additional, Holmes, Mark, additional, Parkhill, Julian, additional, and Peacock, Sharon J., additional
Published: 2019
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41. Prospective genomic surveillance of methicillin-resistant Staphylococcus aureus (MRSA) associated with bloodstream infection, England, 1 October 2012 to 30 September 2013

Author: Toleman, Michelle S, primary, Reuter, Sandra, additional, Jamrozy, Dorota, additional, Wilson, Hayley J, additional, Blane, Beth, additional, Harrison, Ewan M, additional, Coll, Francesc, additional, Hope, Russell J, additional, Kearns, Angela, additional, Parkhill, Julian, additional, Peacock, Sharon J, additional, and Török, M Estée, additional
Published: 2019
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42. Within-host evolution of Enterococcus faecium during longitudinal carriage and transition to bloodstream infection in immunocompromised patients

Author: Moradigaravand, Danesh, Gouliouris, Theodore, Blane, Beth, Naydenova, Plamena, Ludden, Catherine, Crawley, Charles, Brown, Nicholas M, Török, M Estée, Parkhill, Julian, Peacock, Sharon J, Ludden, Catherine [0000-0001-9503-0744], Parkhill, Julian [0000-0002-7069-5958], Peacock, Sharon [0000-0002-1718-2782], and Apollo - University of Cambridge Repository
Subjects: Within-host evolution, lcsh:QH426-470, Research, lcsh:R, Enterococcus faecium, lcsh:Medicine, Bacteremia, Genome sequencing, Polymorphism, Single Nucleotide, Evolution, Molecular, lcsh:Genetics, Immunocompromised Host, Drug Resistance, Bacterial, Humans, Genome, Bacterial, Gram-Positive Bacterial Infections
Abstract: Background Enterococcus faecium is a leading cause of hospital-acquired infection, particularly in the immunocompromised. Here, we use whole genome sequencing of E. faecium to study within-host evolution and the transition from gut carriage to invasive disease. Methods We isolated and sequenced 180 E. faecium from four immunocompromised patients who developed bloodstream infection during longitudinal surveillance of E. faecium in stool and their immediate environment. Results A phylogenetic tree based on single nucleotide polymorphisms (SNPs) in the core genome of the 180 isolates demonstrated several distinct clones. This was highly concordant with the population structure inferred by Bayesian methods, which contained four main BAPS (Bayesian Analysis of Population Structure) groups. The majority of isolates from each patient resided in a single group, but all four patients also carried minority populations in stool from multiple phylogenetic groups. Bloodstream isolates from each case belonged to a single BAPS group, which differed in all four patients. Analysis of 87 isolates (56 from blood) belonging to a single BAPS group that were cultured from the same patient over 54 days identified 30 SNPs in the core genome (nine intergenic, 13 non-synonymous, eight synonymous), and 250 accessory genes that were variably present. Comparison of these genetic variants in blood isolates versus those from stool or environment did not identify any variants associated with bloodstream infection. The substitution rate for these isolates was estimated to be 128 (95% confidence interval 79.82 181.77) mutations per genome per year, more than ten times higher than previous estimates for E. faecium. Within-patient variation in vancomycin resistance associated with vanA was common and could be explained by plasmid loss, or less often by transposon loss. Conclusions These findings demonstrate the diversity of E. faecium carriage by individual patients and significant within-host diversity of E. faecium, but do not provide evidence for adaptive genetic variation associated with invasion. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0507-0) contains supplementary material, which is available to authorized users.
Published: 2017

43. Genomic Surveillance of Enterococcus faecium Reveals Limited Sharing of Strains and Resistance Genes between Livestock and Humans in the United Kingdom

Author: Gouliouris, Theodore, primary, Raven, Kathy E., additional, Ludden, Catherine, additional, Blane, Beth, additional, Corander, Jukka, additional, Horner, Carolyne S., additional, Hernandez-Garcia, Juan, additional, Wood, Paul, additional, Hadjirin, Nazreen F., additional, Radakovic, Milorad, additional, Holmes, Mark A., additional, de Goffau, Marcus, additional, Brown, Nicholas M., additional, Parkhill, Julian, additional, and Peacock, Sharon J., additional
Published: 2018
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44. Nasal carriage of Staphylococcus pseudintermedius in patients with granulomatosis with polyangiitis

Author: Kronbichler, Andreas, primary, Blane, Beth, additional, Holmes, Mark A, additional, Wagner, Josef, additional, Parkhill, Julian, additional, Peacock, Sharon J, additional, Jayne, David R W, additional, and Harrison, Ewan M, additional
Published: 2018
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45. Additional file 2: Figures S1â S6. of Whole genome sequencing reveals high-resolution epidemiological links between clinical and environmental Klebsiella pneumoniae

Author: Chakkaphan Runcharoen, Danesh Moradigaravand, Blane, Beth, Suporn Paksanont, Jeeranan Thammachote, Suthatip Anun, Parkhill, Julian, Narisara Chantratita, and Peacock, Sharon
Abstract: Figures and descriptions of Supplemental Figures S1â S6 mentioned throughout the manuscript. (DOCX 1927Â kb)
Published: 2017
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46. Additional file 3: Figure S1. of Whole genome sequencing of ESBL-producing Escherichia coli isolated from patients, farm waste and canals in Thailand

Author: Chakkaphan Runcharoen, Raven, Kathy, Reuter, Sandra, Kallonen, Teemu, Suporn Paksanont, Jeeranan Thammachote, Suthatip Anun, Blane, Beth, Parkhill, Julian, Peacock, Sharon, and Narisara Chantratita
Abstract: Predominant STs of ESBL-producing E. coli isolated from clinical and environmental origins in Thailand. Graph showing the prevalence of the eight most frequently identified STs among each of the clinical or environmental Thai ESBL-producing E. coli isolates, split by source of isolation. The total adds up to 12 since four of the top eight most frequent in each category did not overlap. The presence of all isolates in each of the 12 STs is shown. Figure S2. Phylogeny of CTX-M genes identified in Thai ESBL-producing E. coli. Phylogeny of the seven CTX-M gene variants identified in the 149 study genomes. Figure S3. Phylogeny of Thai ESBL-producing E. coli in a global context. Maximum-likelihood tree of the 149 study genomes and 514 global genomes based on 222,900 SNPs in the 1983 core genes. Inner ring shows origin of isolate, middle ring shows country of isolation and outer ring indicates the study isolates (black). Scale bar indicates ~ 20,000 SNPs. Figure S4. Virulence gene comparison between ST131 and non-ST131 isolates. Graph showing the prevalence of virulence factors in ST131 (n 26) compared to non-ST131 (n 123) in the study isolates. Using Fisher’s exact test at a p value of 0.05, only those factors over-represented between the two groups are shown. (DOCX 2381 kb)
Published: 2017
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47. Transmission of methicillin-resistant $\textit{Staphylococcus aureus}$ in long-term care facilities and their related healthcare networks

Author: Harrison, Ewan, Ludden, Catherine, Brodrick, Hayley J, Blane, Beth, Brennan, Gráinne, Morris, Dearbháile, Coll, Francesc, Reuter, Sandra, Brown, Nicholas M, Holmes, Mark, O’Connell, Brian, Parkhill, Julian, Török, M Estee, Cormican, Martin, Peacock, Sharon, Harrison, Ewan [0000-0003-2720-0507], Ludden, Catherine [0000-0001-9503-0744], Holmes, Mark [0000-0002-5454-1625], Parkhill, Julian [0000-0002-7069-5958], Peacock, Sharon [0000-0002-1718-2782], and Apollo - University of Cambridge Repository
Subjects: nursing home, $\textit{Staphylococcus aureus}$, whole-genome sequencing, transmission, MRSA, biochemical phenomena, metabolism, and nutrition, bacterial infections and mycoses, molecular epidemiology, long-term care facilities
Abstract: $\textbf{Background:}$ Long-term care facilities (LTCF) are potential reservoirs for methicillin-resistant $\textit{Staphylococcus aureus}$ (MRSA), control of which may reduce MRSA transmission and infection elsewhere in the healthcare system. Whole-genome sequencing (WGS) has been used successfully to understand MRSA epidemiology and transmission in hospitals and has the potential to identify transmission between these and LTCF. $\textbf{Methods:}$ Two prospective observational studies of MRSA carriage were conducted in LTCF in England and Ireland. MRSA isolates were whole-genome sequenced and analyzed using established methods. Genomic data were available for MRSA isolated in the local healthcare systems (isolates submitted by hospitals and general practitioners). $\textbf{Results:}$ We sequenced a total of 181 MRSA isolates from the two study sites. The majority of MRSA were multilocus sequence type (ST)22. WGS identified one likely transmission event between residents in the English LTCF and three putative transmission events in the Irish LTCF. WGS also identified closely related isolates present in colonized Irish residents and their immediate environment. Based on phylogenetic reconstruction, closely related MRSA clades were identified between the LTCF and their healthcare referral network, together with putative MRSA acquisition by LTCF residents during hospital admission. $\textbf{Conclusions:}$ These data confirm that MRSA is transmitted between residents of LTCF and is both acquired and transmitted to others in referral hospitals and beyond. Our data present compelling evidence for the importance of environmental contamination in MRSA transmission, reinforcing the importance of environmental cleaning. The use of WGS in this study highlights the need to consider infection control in hospitals and community healthcare facilities as a continuum., UKCRC Translational Infection Research (TIR) Initiative, Medical Research Council (Grant ID: G1000803), Biotechnology and Biological Sciences Research Council, National Institute for Health Research, Chief Scientist Office of the Scottish Government Health Directorate, Hospital Infection Society (Major Research Grant), Wellcome Trust (Grant ID: 098051), Academy of Medical Sciences, Health Foundation, National Institute for Health Research Cambridge Biomedical Research Centre, This is the final version of the article. It first appeared from BioMed Central via http://dx.doi.org/10.1186/s13073-016-0353-5
Published: 2016
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48. Transmission of methicillin-resistant Staphylococcus aureus in long-term care facilities and their related healthcare networks

Author: Harrison, Ewan M, Ludden, Catherine, Brodrick, Hayley J, Blane, Beth, Brennan, Gráinne, Morris, Dearbháile, Coll, Francesc, Reuter, Sandra, Brown, Nicholas M, Holmes, Mark A, O'Connell, Brian, Parkhill, Julian, Török, M Estee, Cormican, Martin, Peacock, Sharon J, Harrison, Ewan [0000-0003-2720-0507], Ludden, Catherine [0000-0001-9503-0744], Holmes, Mark [0000-0002-5454-1625], Parkhill, Julian [0000-0002-7069-5958], Peacock, Sharon [0000-0002-1718-2782], and Apollo - University of Cambridge Repository
Subjects: Adult, DNA, Bacterial, Male, Methicillin-Resistant Staphylococcus aureus, Staphylococcus aureus, MRSA, Genetics, Transmission, Humans, Genetics(clinical), Prospective Studies, Molecular Biology, Aged, Aged, 80 and over, Whole-genome sequencing, Cross Infection, Infection Control, Long-term care facilities, Nursing home, Research, High-Throughput Nucleotide Sequencing, Middle Aged, Staphylococcal Infections, biochemical phenomena, metabolism, and nutrition, bacterial infections and mycoses, Long-Term Care, United Kingdom, Molecular epidemiology, Health Facility Environment, Molecular Medicine, Female, Multilocus Sequence Typing
Abstract: Background Long-term care facilities (LTCF) are potential reservoirs for methicillin-resistant Staphylococcus aureus (MRSA), control of which may reduce MRSA transmission and infection elsewhere in the healthcare system. Whole-genome sequencing (WGS) has been used successfully to understand MRSA epidemiology and transmission in hospitals and has the potential to identify transmission between these and LTCF. Methods Two prospective observational studies of MRSA carriage were conducted in LTCF in England and Ireland. MRSA isolates were whole-genome sequenced and analyzed using established methods. Genomic data were available for MRSA isolated in the local healthcare systems (isolates submitted by hospitals and general practitioners). Results We sequenced a total of 181 MRSA isolates from the two study sites. The majority of MRSA were multilocus sequence type (ST)22. WGS identified one likely transmission event between residents in the English LTCF and three putative transmission events in the Irish LTCF. WGS also identified closely related isolates present in colonized Irish residents and their immediate environment. Based on phylogenetic reconstruction, closely related MRSA clades were identified between the LTCF and their healthcare referral network, together with putative MRSA acquisition by LTCF residents during hospital admission. Conclusions These data confirm that MRSA is transmitted between residents of LTCF and is both acquired and transmitted to others in referral hospitals and beyond. Our data present compelling evidence for the importance of environmental contamination in MRSA transmission, reinforcing the importance of environmental cleaning. The use of WGS in this study highlights the need to consider infection control in hospitals and community healthcare facilities as a continuum. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0353-5) contains supplementary material, which is available to authorized users.
Published: 2016

49. Genomic survey of Clostridium difficile reservoirs in the East of England implicates environmental contamination of wastewater treatment plants by clinical lineages

Author: Moradigaravand, Danesh, primary, Gouliouris, Theodore, additional, Ludden, Catherine, additional, Reuter, Sandra, additional, Jamrozy, Dorota, additional, Blane, Beth, additional, Naydenova, Plamena, additional, Judge, Kim, additional, H. Aliyu, Sani, additional, F. Hadjirin, Nazreen, additional, A. Holmes, Mark, additional, Török, Estée, additional, M. Brown, Nicholas, additional, Parkhill, Julian, additional, and Peacock, Sharon, additional
Published: 2018
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50. Systematic Surveillance Detects Multiple Silent Introductions and Household Transmission of Methicillin-Resistant Staphylococcus aureus USA300 in the East of England

Author: Toleman, Michelle S, Reuter, Sandra, Coll, Francesc, Harrison, Ewan M, Blane, Beth, Brown, Nicholas M, Török, M Estée, Parkhill, Julian, Peacock, Sharon J, Harrison, Ewan [0000-0003-2720-0507], Parkhill, Julian [0000-0002-7069-5958], Peacock, Sharon [0000-0002-1718-2782], and Apollo - University of Cambridge Repository
Subjects: Adult, Male, Methicillin-Resistant Staphylococcus aureus, Staphylococcus aureus, Adolescent, Genotype, MRSA, molecular epidemiology, Young Adult, Disease Transmission, Infectious, Humans, Prospective Studies, Child, skin and connective tissue diseases, health care economics and organizations, Aged, Aged, 80 and over, Family Health, Family Characteristics, USA300, Sequence Analysis, DNA, Middle Aged, Staphylococcal Infections, biochemical phenomena, metabolism, and nutrition, bacterial infections and mycoses, England, whole-genome sequencing, Child, Preschool, Epidemiological Monitoring, Female
Abstract: BACKGROUND: The spread of USA300 methicillin-resistant Staphylococcus aureus (MRSA) across the United States resulted in an epidemic of infections. In Europe, only sporadic cases or small clusters of USA300 infections are described, and its prevalence in England is unknown. We conducted prospective surveillance for USA300 in the east of England. METHODS: We undertook a 12-month prospective observational cohort study of all individuals with MRSA isolated from community and hospital samples submitted to a microbiology laboratory. At least 1 MRSA isolate from each individual underwent whole-genome sequencing. USA300 was identified on the basis of sequence analysis, and phylogenetic comparisons were made between these and USA300 genomes from the United States. RESULTS: Between April 2012 and April 2013, we sequenced 2283 MRSA isolates (detected during carriage screening and in clinical samples) from 1465 individuals. USA300 was isolated from 24 cases (1.6%). Ten cases (42%) had skin and soft tissue infection, and 2 cases had invasive disease. Phylogenetic analyses identified multiple introductions and household transmission of USA300. CONCLUSIONS: Use of a diagnostic laboratory as a sentinel for surveillance has identified repeated introductions of USA300 in eastern England in 2012-2013, with evidence for limited transmission. Our results show how systematic surveillance could provide an early warning of strain emergence and dissemination.
Published: 2016

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