Items where Author is "The COVID-19 Genomics UK (COG-UK) Consortium, "

Article

Cook, Kate F,, Beckett, Angela H., Glaysher, Sharon, Goudarzi, Salman, Fearn, Christopher, Loveson, Katie F., Elliott, Scott, Wyllie, Sarah, Lloyd, Allyson, Bicknell, Kelly, Lumley, Sally, Chauhan, Anoop J., Robson, Samuel C., The COVID-19 Genomics UK (COG-UK) Consortium, , Smith, Darren, Bashton, Matthew, Young, Greg, McCann, Clare, Nelson, Andrew, Crown, Matthew, Henderson, John, Hollis, Amy, Stanley, William and Yew, Wen Chyin (2023) Multiple pathways of SARS-CoV-2 nosocomial transmission uncovered by integrated genomic and epidemiological analyses during the second wave of the COVID-19 pandemic in the UK. Frontiers in Cellular and Infection Microbiology, 12. p. 1066390. ISSN 2235-2988

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., Orton, Alexandra, Douthwaite, Julie, Rees, Steve, Brown, Christopher, Clark, Roger, Jones, Daniel R., Kuenzi, Fred, Rankin, Jennifer, Waddell, Ian, Maxwell, Patrick, Matheson, Nicholas, Abell, Chris, Braithwaite, Vickie, Brierley, Craig, Crowcroft, Jon, Dahal, Aastha, Faulkner, Kathryn, Glover, Michael, Goodfellow, Ian, Greatorex, Jane, James, Laura, Lehner, Paul, Leslie, Ian, Liddell, Kathleen, Margolis, Ben, Morgan, Sally, Sheridan, Linda, Valletta, Sally, Vignoles, Anna, Vinnell, Martin, Wills, Mark, Hilborne, Sarah, Berry, Sarah, Kahkeshi, Mahin Bagheri, Hancock, Dawn, Winster, Jennifer, Enright, Jessica, Samworth, Richard, Samtani, Vijay, Ahmadi-Assalemi, Gabriela, Feather, Tom, Goodall, Robin, Hoensch, Steve, Johnson, Dean, Hunt, Martin, Mathieson, Nick, Nikitina, Katya, Sheldrake, Zara, Keen, Martin, Sato, Aris, Connor, David, Tolhurst, Jonathan, Williman, Jack, Hollamby, Victoria, Jordan, Sinead, Fatseas, Tania, Taylor, Peter, Georgiou, Christine, Caspersz, Michelle, McNulty, Claire, Davies, Richard, Clarke, Rebecca, Danaei, Darius, Dyer, Rory, Glew, Rob, Lambson, Oliver, Gibbs, Karen, Mozdzen, Barbara, Raub, Gabor, Radecki, Asako, White, Phil, Hughes, Robert, Gransden, Lucie, Ceaser, Matt, Sing, Robert, Wilson, Karl, Parlikad, Ajith, Dhada, Maharshi, Ridgman, Tom, Mungovan, Diane, Matthews, Steve, Searle, Paul, Mills, John, Neely, Andy, Henderson, Robert, Murphy, Edna, Russell, Matthew, Freeling, Anthony, Poppitt, Steve, Tynan, Jo, Knapton, James, Marchetti, Filippo, Angelis, Daniela De, Feltwell, Theresa, Hadjirin, Nazreen F., Hamilton, William L., Jahun, Aminu, Pinckert, Malte, Shaw, Ashley, Chaudhry, Afzal, Brown, Nicholas M., Mactavous, Lenette, Hannan, Sophie, Hosaja, Aleksandra, Leong, Clare, Wright, Jo, Quinnell, Natalie, Workman, Chris, Ferris, Mark, Wright, Giles, Wright, Elizabeth, Aggarwal, Dinesh, Brooks, Ellena, Carabelli, Alessandro M., Churcher, Carol M., Galai, Katerina, Girgis, Sophia T., Gupta, Ravi K., 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, 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., 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 H. S., Danesh, John, Davies, Robert, Dorman, Matthew J., Drury, Eleanor, Durham, Jillian, Farr, Ben W., Foulser, Luke, Goncalves, Sonia, Goodwin, Scott, Gourtovaia, Marina, Jackson, David K., James, Keith, Jamrozy, Dorota, Johnston, Ian, Kane, Leanne, Kay, Sally, Keatley, Jon-Paul, Kwiatkowski, Dominic, Langford, Cordelia F., Lawniczak, Mara, Lensing, Stefanie V., Leonard, Steven, Letchford, Laura, Lewis, Kevin, Liddle, Jennifier, Livett, Rich, Lo, Stephanie, Makunin, Alex, Martincorena, Inigo, McCarthy, Shane, McGuigan, Samantha, Moll, Robin J., Nelson, Rachel, Oliver, Karen, Palmer, Steve, Park, Naomi R., Patel, Minal, Prestwood, Liam, Puethe, Christoph, Quail, Michael A., Rajan, Diana, Rajatileka, Shavanthi, Redshaw, Nicholas M., Scott, Carol, Shirley, Lesley, Sillitoe, John, Thurston, Scott A. J., Tonkin-Hill, Gerry, Tovar-Corona, Jaime M., Weldon, Danni, Whitwham, Andrew, Hosmillo, Myra, Attwood, Stephen W., du Plessis, Louis, Zamudio, Marina Escalera, Francois, Sarah, Gutierrez, Bernardo, Kraemer, Moritz U. G., Raghwani, Jayna, Vasylyeva, Tetyana I., Zarebski, Alex E., Alikhan, Nabil-Fareed, Aydin, Alp, Baker, David J., de Oliveira Martins, Leonardo, Kay, Gemma L., Le-Viet, Thanh, Mather, Alison E., Meadows, Lizzie, O’Grady, Justin, Rudder, Steven, Trotter, Alexander J., Illingworth, Chris J., Jackson, Chris, Aranday-Cortes, Elihu, Asamaphan, Patawee, Broos, Alice, Carmichael, Stephen N., da Silva Filipe, Ana, Hughes, Joseph, Jesudason, Natasha G., Johnson, Natasha, Li, Kathy K., Mair, Daniel, Nichols, Jenna, Nickbakhsh, Seema, Niebel, Marc O., Nomikou, Kyriaki, Orton, Richard J., Robertson, David L., Shah, Rajiv N., Shepherd, James G., Singer, Joshua B., Starinskij, Igor, Thomson, Emma C., Tong, Lily, Vattipally, Sreenu, Ash, Amy, Koshy, Cherian, Cortes, Nick, Kidd, Stephen, Lynch, Jessica, Moore, Nathan, Mori, Matilde, Wise, Emma, Curran, Tanya, Fairley, Derek J., McKenna, James P., Adams, Helen, Bonsall, David, Fraser, Christophe, Golubchik, Tanya, Cogger, Benjamin J., Hassan-Ibrahim, Mohammed O., Malone, Cassandra S., Reynolds, Nicola, Wantoch, Michelle, Afifi, Safiah, Beer, Robert, John, Michaela, Maksimovic, Joshua, McCluggage, Kathryn, Morgan, Sian, Spellman, Karla, Bresner, Catherine, Connor, Thomas R., Fuller, William, Guest, Martyn, Gulliver, Huw, Kitchen, Christine, Marchbank, Angela, Merrick, Ian, Munn, Robert, Price, Anna, Southgate, Joel, Workman, Trudy, Patel, Amita, Snell, Luke B., Batra, Rahul, Charalampous, Themoula, Edgeworth, Jonathan, Nebbia, Gaia, Beckett, Angela H., Robson, Samuel C., Aanensen, David M., Abudahab, Khalil, Menegazzo, Mirko, Taylor, Ben E. W., Underwood, Anthony P., Yeats, Corin A., Berry, Louise, Boswell, Tim, Clark, Gemma, Fleming, Vicki M., Howson-Wells, Hannah C., Jones, Carl, Joseph, Amelia, Khakh, Manjinder, Lister, Michelle M., Smith, Wendy, Willingham, Iona, Bird, Paul, Fallon, Karlie, Helmer, Thomas, Holmes, Christopher, Tang, Julian, Blakey, Victoria, Campbell, Sharon, Raviprakash, Veena, Sheriff, Nicola, Williams, Lesley-Anne, Carlile, Matthew, Debebe, Johnny, Holmes, Nadine, Loose, Matthew W., Moore, Christopher, Sang, Fei, Wright, Victoria, Coll, Francesc, Betancor, Gilberto, Signell, Adrian W., Wilson, Harry D., Davis, Thomas, Eldirdiri, Sahar, Kenyon, Anita, Torok, M. Estee, Lowe, Hannah, Moses, Samuel, Bedford, Luke, Moore, Jonathan, Stonehouse, Susanne, Awan, Ali R., Fisher, Chloe L., BoYes, John, Atkinson, Laura, Breuer, Judith, Brown, Julianne R., Harris, Kathryn A., Lee, Jack C. D., Shah, Divya, Storey, Nathaniel, Flaviani, Flavia, Alcolea-Medina, Adela, Vernet, Gabrielle, Williams, Rebecca, Chapman, Michael R., Chatterton, Wendy, Heaney, Judith, Levett, Lisa J., Pusok, Monika, Xu-McCrae, Li, Bashton, Matthew, Smith, Darren, Young, Greg, Bolt, Frances, Cox, Alison, Holmes, Alison, Madona, Pinglawathee, Mookerjee, Siddharth, Price, James, Randell, Paul A., Boyd, Olivia, Nascimento, Fabricia F., Geidelberg, Lily, Johnson, Rob, Jorgensen, David, Ragonnet-Cronin, Manon, Rowan, Aileen, Siveroni, Igor, Taylor, Graham P., Volz, Erik M., Smollett, Katherine L., Loman, Nicholas J., McMurray, Claire, McNally, Alan, Nicholls, Sam, Poplawski, Radoslaw, Quick, Joshua, Rowe, Will, Stockton, Joanne, Nunez, Rocio T. Martinez, Breen, Cassie, Cowell, Angela, Mason, Jenifer, O’Toole, Elaine, Robinson, Trevor I., Watts, Joanne, Sluga, Graciela, Ahmad, Shazaad S. Y., George, Ryan P., Machin, Nicholas W., Halstead, Fenella, Hogsden, Wendy, Sivaprakasam, Venkat, Carden, Holli, Hale, Antony D., Harper, Katherine L., Macfarlane-Smith, Louissa R., Burton-Fanning, Shirelle, Collins, Jennifer, Eltringham, Gary, Payne, Brendan AI., Taha, Yusri, Waugh, Sheila, O’Brien, Sarah, Rushton, Steven, Blacow, Rachel, Bradley, Amanda, Maclean, Alasdair, Mollett, Guy, Dewar, Rebecca, McHugh, Martin P., Templeton, Kate E., Wastenge, Elizabeth, Coupland, Lindsay, Dervisevic, Samir, Meader, Emma J., Stanley, Rachael, Smith, Louise, Barton, Edward, Graham, Clive, Padgett, Debra, Scott, Garren, Greenaway, Jane, Swindells, Emma, McCann, Clare, Nelson, Andrew, Yew, Wen Chyin, Andersson, Monique, Crook, Derrick, Eyre, David, Justice, Anita, Peto, Timothy, Duckworth, Nichola, Sloan, Tim J., Walsh, Sarah, Bicknell, Kelly, Chauhan, Anoop J., Elliott, Scott, Glaysher, Sharon, Impey, Robert, Lloyd, Allyson, Wyllie, Sarah, Levene, Nick, Monaghan, Lynn, Bradley, Declan T., Wyatt, Tim, Curran, Martin D., Parmar, Surendra, Holden, Matthew T. G., Shaaban, Sharif, Adams, Alexander, Asad, Hibo, Birchley, Alec, Bull, Matthew, Coombes, Jason, Corden, Sally, Cottrell, Simon, Craine, Noel, Cronin, Michelle, Davies, Alisha, Lacy, Elen De, Downing, Fatima, Edwards, Sue, Evans, Johnathan M., Fina, Laia, Gaskin, Amy, Gatica-Wilcox, Bree, Gifford, Laura, Gilbert, Lauren, Graham, Lee, Heyburn, David, Hilvers, Ember, Howe, Robin, Jones, Hannah, Jones, Rachel, Jones, Sophie, Kumziene-SummerhaYes, Sara, McKerr, Caoimhe, Moore, Catherine, Morgan, Mari, Pacchiarini, Nicole, Perry, Malorie, Plimmer, Amy, Rey, Sara, Shankar, Giri, Taylor, Sarah, Watkins, Joanne, Williams, Chris, Casey, Anna, Ratcliffe, Liz, Acheson, Erwan, Molnar, Zoltan, Simpson, David A., Thompson, Thomas, Auckland, Cressida, Ellard, Sian, Jones, Christopher R., Knight, Bridget A., Masoli, Jane A. H., Haque, Tanzina, Hart, Jennifer, Irish-Tavares, Dianne, Mahungu, Tabitha W., Witele, Eric, Dadrah, Ashok, Fenton, Melisa L., Saluja, Tranprit, Symmonds, Amanda, Bourgeois, Yann, Scarlett, Garry P., Cook, Kate, Dent, Hannah, Fearn, Christopher, Goudarzi, Salman, Loveson, Katie F., Paul, Hannah, Evans, Cariad, Johnson, Kate, Partridge, David G., Raza, Mohammad, Baker, Paul, Bonner, Stephen, Essex, Sarah, Liggett, Steven, Lyons, Ronan A., Mahanama, Adhyana I. K., Saeed, Kordo, Samaraweera, Buddhini, Silveira, Siona, Wilson-Davies, Eleri, Emanuela, P., Bayzid, Nadua, Cotic, Marius, Ensell, Leah, Hartley, John A., Jannoo, Riaz, Karamani, Angeliki, Kristiansen, Mark, Lowe, Helen L., Roy, Sunando, Westhorpe, Adam P., Williams, Rachel J., Williams, Charlotte A., Jeremiah, Sarah, Prieto, Jacqui A., Berry, Lisa, Grammatopoulos, Dimitris, Jones, Katie, Pandey, Sarojini, Beggs, Andrew, Richter, Alex, Ashcroft, Fiona, Best, Angus, Crawford, Liam, Cumley, Nicola, Mayhew, Megan, Megram, Oliver, Mirza, Jeremy, Moles-Garcia, Emma, Percival, Benita, Bucca, Giselda, Hesketh, Andrew R., Smith, Colin P., Davidson, Rose K., Balcazar, Carlos E., Gallagher, Michael D., O’Toole, Áine, Rambaut, Andrew, Rooke, Stefan, Stanton, Thomas D., Williams, Thomas, Williamson, Kathleen A., Bewshea, Claire M., Farbos, Audrey, Harrison, James W., Jeffries, Aaron R., Manley, Robin, Michell, Stephen L., Michelsen, Michelle L., Sambles, Christine M., Studholme, David J., Temperton, Ben, Warwick-Dugdale, Joanna, Darby, Alistair C., Eccles, Richard, Gemmell, Matthew, Gregory, Richard, Haldenby, Sam T., Hiscox, Julian A., Hughes, Margaret, Iturriza-Gomara, Miren, Jackson, Kathryn A., Lucaci, Anita O., Nelson, Charlotte, Paterson, Steve, Rainbow, Lucille, Turtle, Lance, Vamos, Edith E., Webster, Hermione J., Whitehead, Mark, Wierzbicki, Claudia, Angyal, Adrienn, Brown, Rebecca, de Silva, Thushan I., Freeman, Timothy M., Gallis, Marta, Green, Luke R., Groves, Danielle C., Keeley, Alexander J., Lindsey, Benjamin B., Louka, Stavroula F., Parker, Matthew D., Parsons, Paul J., Smith, Nikki, Tucker, Rachel M., Wang, Dennis, Whiteley, Max, Wyles, Matthew, Zhang, Peijun, Alam, Mohammad T., Baxter, Laura, Bridgewater, Hannah E., Brown, Paul E., Cheng, Jeffrey K. J., Constantinidou, Chrystala, Frost, Lucy R., Ott, Sascha, Stark, Richard, Taylor-Joyce, Grace, Unnikrishnan, Meera, Cerda, Alberto C., Merrill, Tammy V., Wilson, Rebekah E., Ball, Jonathan, Chappell, Joseph G., McClure, Patrick C., Tsoleridis, Theocharis, Buck, David, de Cesare, Mariateresa, Green, Angie, MacIntyre-Cockett, George, Todd, John A., Trebes, Amy, Gunson, Rory N., Cormie, Claire, Dias, Joana, Forrest, Sally, Gill, Harmeet K., Higginson, Ellen E., Kermack, Leanne M., Maes, Mailis, Ruis, Chris, Sridhar, Sushmita, Young, Jamie, 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., Goodfellow, Ian G., The Cambridge Covid-19 testing Centre, , University of Cambridge Asymptomatic COVID-19 Screening Programm, and The COVID-19 Genomics UK (COG-UK) Consortium, (2022) Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission. Nature Communications, 13 (1). p. 751. ISSN 2041-1723

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., The COVID-19 Genomics UK (COG-UK) Consortium, , Templeton, Kate, Gunson, Rory N., da Silva Filipe, Ana, Milosevic, Catriona, Thomson, Emma, Robertson, David L., Holden, Matthew T.G., Illingworth, Christopher J.R., Smith-Palmer, Alison, Smith, Darren, Bashton, Matthew, Young, Greg, McCann, Clare, Nelson, Andrew, Crown, Matthew, Henderson, John and Yew, Wen Chyin (2022) Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning. Scientific Reports, 12 (1). p. 11735. ISSN 2045-2322

Eales, Oliver, Page, Andrew J., de Oliveira Martins, Leonardo, Wang, Haowei, Bodinier, Barbara, Haw, David, Jonnerby, Jakob, Atchison, Christina, The COVID-19 Genomics UK (COG-UK) Consortium, , Ashby, Deborah, Barclay, Wendy, Taylor, Graham, Cooke, Graham, Ward, Helen, Darzi, Ara, Riley, Steven, Chadeau-Hyam, Marc, Donnelly, Christl A., Elliott, Paul, Smith, Darren, Bashton, Matthew, McCann, Clare, Nelson, Andrew, Crown, Matthew, Henderson, John, Hollis, Amy, Stanley, William and Yew, Wen Chyin (2022) SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2. BMC Infectious Diseases, 22 (1). p. 647. ISSN 1471-233

Zhao, Lele, Hall, Matthew, de Cesare, Mariateresa, MacIntyre-Cockett, George, Lythgoe, Katrina, Fraser, Christophe, Bonsall, David, Golubchik, Tanya, Ferretti, Luca, The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg and McCann, Clare (2022) The mutational spectrum of SARS-CoV-2 genomic and antigenomic RNA. Proceedings of the Royal Society B: Biological Sciences, 289 (1987). p. 20221747. ISSN 0962-8452

Brunner, F.S., Brown, M.R., Bassano, I., Denise, H., Khalifa, M.S., Wade, M.J., van Aerle, R., Kevill, J.L., Jones, D.L., Farkas, K., Jeffries, A.R., Cairns, E., Wierzbicki, C., Paterson, S., Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg, McCann, Clare and The COVID-19 Genomics UK (COG-UK) Consortium, (2022) City-wide wastewater genomic surveillance through the successive emergence of SARS-CoV-2 Alpha and Delta variants. Water Research, 226. p. 119306. ISSN 0043-1354

Hettle, David, Hutchings, Stephanie, Muir, Peter, Moran, Ed, Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg, McCann, Clare and The COVID-19 Genomics UK (COG-UK) Consortium, (2022) Persistent SARS-CoV-2 infection in immunocompromised patients facilitates rapid viral evolution: Retrospective cohort study and literature review. Clinical Infection in Practice, 16. p. 100210. ISSN 2590-1702

McCrone, John T., Hill, Verity, Bajaj, Sumali, Pena, Rosario Evans, Lambert, Ben C., Inward, Rhys, Bhatt, Samir, Volz, Erik, Ruis, Christopher, Dellicour, Simon, Baele, Guy, Zarebski, Alexander E., Sadilek, Adam, Wu, Neo, Schneider, Aaron, Ji, Xiang, Raghwani, Jayna, Jackson, Ben, Colquhoun, Rachel, O’Toole, Áine, Peacock, Thomas P., Twohig, Kate, Thelwall, Simon, Dabrera, Gavin, Myers, Richard, Faria, Nuno R., Huber, Carmen, Bogoch, Isaac I., Khan, Kamran, du Plessis, Louis, Barrett, Jeffrey C., Aanensen, David M., Barclay, Wendy S., Chand, Meera, Connor, Thomas, Loman, Nicholas J., Suchard, Marc A., Pybus, Oliver G., Rambaut, Andrew, Kraemer, Moritz U. G., Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg, McCann, Clare and The COVID-19 Genomics UK (COG-UK) Consortium, (2022) Context-specific emergence and growth of the SARS-CoV-2 Delta variant. Nature, 610 (7930). pp. 154-160. ISSN 0028-0836

Hinch, Robert, Panovska-Griffiths, Jasmina, Probert, William J. M., Ferretti, Luca, Wymant, Chris, Di Lauro, Francesco, Baya, Nikolas, Ghafari, Mahan, Abeler-Dörner, Lucie, Fraser, Christophe, Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg, McCann, Clare and The COVID-19 Genomics UK (COG-UK) Consortium, (2022) Estimating SARS-CoV-2 variant fitness and the impact of interventions in England using statistical and geo-spatial agent-based models. Philosophical Transactions of the Royal Society A: Mathematical Physical and Engineering Sciences, 380 (2233). p. 20210304. ISSN 1364-503X

Panovska-Griffiths, J., Swallow, B., Hinch, R., Cohen, J., Rosenfeld, K., Stuart, R. M., Ferretti, L., Di Lauro, F., Wymant, C., Izzo, A., Waites, W., Viner, R., Bonell, C., Fraser, C., Klein, D., Kerr, C. C., Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg, McCann, Claire and The COVID-19 Genomics UK (COG-UK) Consortium, (2022) Statistical and agent-based modelling of the transmissibility of different SARS-CoV-2 variants in England and impact of different interventions. Philosophical Transactions of the Royal Society A: Mathematical Physical and Engineering Sciences, 380 (2233). p. 20210315. ISSN 1364-503X

Willett, Brian J., Grove, Joe, MacLean, Oscar A., Wilkie, Craig, De Lorenzo, Giuditta, Furnon, Wilhelm, Cantoni, Diego, Scott, Sam, Logan, Nicola, Ashraf, Shirin, Manali, Maria, Szemiel, Agnieszka, Cowton, Vanessa, Vink, Elen, Harvey, William T., Davis, Chris, Asamaphan, Patawee, Smollett, Katherine, Tong, Lily, Orton, Richard, Hughes, Joseph, Holland, Poppy, Silva, Vanessa, Pascall, David J., Puxty, Kathryn, da Silva Filipe, Ana, Yebra, Gonzalo, Shaaban, Sharif, Holden, Matthew T.G., Pinto, Rute Maria, Gunson, Rory, Templeton, Kate, Murcia, Pablo R., Patel, Arvind H., Klenerman, Paul, Dunachie, Susanna, PITCH Consortium, , The COVID-19 Genomics UK (COG-UK) Consortium, , Haughney, John, Robertson, David L., Palmarini, Massimo, Ray, Surajit, Thomson, Emma C., Smith, Darren, Young, Greg, Bashton, Matthew, McCann, Clare, Henderson, John, Crown, Matthew and Yew, Wen Chyin (2022) Publisher Correction: SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway (Nature Microbiology, (2022), 7, 8, (1161-1179), 10.1038/s41564-022-01143-7). Nature Microbiology, 7 (10). p. 1709. ISSN 2058-5276

Hill, Verity, Du Plessis, Louis, Peacock, Thomas P, Aggarwal, Dinesh, Colquhoun, Rachel, Carabelli, Alesandro M, Ellaby, Nicholas, Gallagher, Eileen, Groves, Natalie, Jackson, Ben, McCrone, J T, O’Toole, Áine, Price, Anna, Sanderson, Theo, Scher, Emily, Southgate, Joel, Volz, Erik, Barclay, Wendy S, Barrett, Jeffrey C, Chand, Meera, Connor, Thomas, Goodfellow, Ian, Gupta, Ravindra K, Harrison, Ewan M, Loman, Nicholas, Myers, Richard, Robertson, David L, Pybus, Oliver G, Rambaut, Andrew, Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg, McCann, Clare and The COVID-19 Genomics UK (COG-UK) Consortium, (2022) The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK. Virus Evolution, 8 (2). veac080. ISSN 2057-1577

Dolton, Garry, Rius, Cristina, Hasan, Md Samiul, Wall, Aaron, Szomolay, Barbara, Behiry, Enas, Whalley, Thomas, Southgate, Joel, Fuller, Anna, Morin, Théo, Topley, Katie, Tan, Li Rong, Goulder, Philip J.R., Spiller, Owen B., Rizkallah, Pierre J., Jones, Lucy C., Connor, Thomas R., Sewell, Andrew K., Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg, McCann, Clare and The COVID-19 Genomics UK (COG-UK) Consortium, (2022) Emergence of immune escape at dominant SARS-CoV-2 killer T cell epitope. Cell, 185 (16). 2936-2951.e19. ISSN 0092-8674

Willett, Brian J., Grove, Joe, MacLean, Oscar A., Wilkie, Craig, de Lorenzo, Giuditta, Furnon, Wilhelm, Cantoni, Diego, Scott, Sam, Logan, Nicola, Ashraf, Shirin, Manali, Maria, Szemiel, Agnieszka, Cowton, Vanessa, Vink, Elen, Harvey, William T., Davis, Chris, Asamaphan, Patawee, Smollett, Katherine, Tong, Lily, Orton, Richard, Hughes, Joseph, Holland, Poppy, Silva, Vanessa, Pascall, David J., Puxty, Kathryn, da Silva Filipe, Ana, Yebra, Gonzalo, Shaaban, Sharif, Holden, Matthew T. G., Pinto, Rute Maria, Gunson, Rory, Templeton, Kate, Murcia, Pablo R., Patel, Arvind H., Klenerman, Paul, Dunachie, Susanna, PITCH Consortium, , The COVID-19 Genomics UK (COG-UK) Consortium, , Haughney, John, Robertson, David L., Palmarini, Massimo, Ray, Surajit, Thomson, Emma C., Smith, Darren, Young, Greg, Bashton, Matthew, McCann, Clare, Henderson, John, Crown, Matthew and Yew, Wen Chyin (2022) SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nature Microbiology, 7 (8). pp. 1161-1179. ISSN 2058-5276

Krutikov, Maria, Stirrup, Oliver, Nacer-Laidi, Hadjer, Azmi, Borscha, Fuller, Chris, Tut, Gokhan, Palmer, Tom, Shrotri, Madhumita, Irwin-Singer, Aidan, Baynton, Verity, Hayward, Andrew, Moss, Paul, Copas, Andrew, Shallcross, Laura, The COVID-19 Genomics UK (COG-UK) Consortium, , Smith, Darren, Bashton, Matthew, McCann, Clare, Young, Greg, Nelson, Andrew, Crown, Matthew, Henderson, John, Hollis, Amy, Stanley, William and Yew, Wen Chyin (2022) Outcomes of SARS-CoV-2 omicron infection in residents of long-term care facilities in England (VIVALDI): a prospective, cohort study. The Lancet Healthy Longevity, 3 (5). e347-e355. ISSN 2666-7568

Blackstone, James, Stirrup, Oliver, Mapp, Fiona, Panca, Monica, Copas, Andrew, Flowers, Paul, Hockey, Leanne, Price, James, Partridge, David, Peters, Christine, de Silva, Thushan, Nebbia, Gaia, Snell, Luke B, McComish, Rachel, Breuer, Judith, The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, McCann, Clare, Nelson, Andrew, Smith, Darren and Young, Greg (2022) Protocol for the COG-UK hospital-onset COVID-19 infection (HOCI) multicentre interventional clinical study: evaluating the efficacy of rapid genome sequencing of SARS-CoV-2 in limiting the spread of COVID-19 in UK NHS hospitals. BMJ Open, 12 (4). e052514. ISSN 2044-6055

Nyberg, Tommy, Ferguson, Neil M., Nash, Sophie G., Webster, Harriet H., Flaxman, Seth, Andrews, Nick, Hinsley, Wes, Bernal, Jamie Lopez, Kall, Meaghan, Bhatt, Samir, Blomquist, Paula, Zaidi, Asad, Volz, Erik, Aziz, Nurin Abdul, Harman, Katie, Funk, Sebastian, Abbott, Sam, Hope, Russell, Charlett, Andre, Chand, Meera, Ghani, Azra C., Seaman, Shaun R., Dabrera, Gavin, De Angelis, Daniela, Presanis, Anne M., Thelwall, Simon, Nyberg, Tommy, Ferguson, Neil M., Nash, Sophie G., Webster, Harriet H., Flaxman, Seth, Andrews, Nick, Hinsley, Wes, Lopez Bernal, Jamie, Kall, Meaghan, Bhatt, Samir, Blomquist, Paula, Zaidi, Asad, Volz, Erik, Abdul Aziz, Nurin, Harman, Katie, Funk, Sebastian, Abbott, Sam, Hope, Russell, Charlett, Andre, Chand, Meera, Ghani, Azra C., Seaman, Shaun R., Dabrera, Gavin, De Angelis, Daniela, Presanis, Anne M., Thelwall, Simon, The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, McCann, Clare, Smith, Darren, Young, Greg and Nelson, Andrew (2022) Comparative analysis of the risks of hospitalisation and death associated with SARS-CoV-2 omicron (B.1.1.529) and delta (B.1.617.2) variants in England: a cohort study. The Lancet, 399 (10332). pp. 1303-1312. ISSN 0140-6736

Chadeau-Hyam, Marc, Wang, Haowei, Eales, Oliver, Haw, David, Bodinier, Barbara, Whitaker, Matthew, Walters, Caroline E, Ainslie, Kylie E C, Atchison, Christina, Fronterre, Claudio, Diggle, Peter J, Page, Andrew J, Trotter, Alexander J, Ashby, Deborah, Barclay, Wendy, Taylor, Graham, Cooke, Graham, Ward, Helen, Darzi, Ara, Riley, Steven, Donnelly, Christl A, Elliott, Paul, The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Smith, Darren, Young, Greg, Nelson, Andrew and McCann, Clare (2022) SARS-CoV-2 infection and vaccine effectiveness in England (REACT-1): a series of cross-sectional random community surveys. The Lancet Respiratory Medicine, 10 (4). pp. 355-366. ISSN 2213-2600

Wright, Derek W., Harvey, William T., Hughes, Joseph, Cox, MacGregor, Peacock, Thomas P., Colquhoun, Rachel, Jackson, Ben, Orton, Richard, Nielsen, Morten, Hsu, Nienyun Sharon, Harrison, Ewan M., de Silva, Thushan I., Rambaut, Andrew, Peacock, Sharon J., Robertson, David L., Carabelli, Alessandro M., The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Smith, Darren, Young, Greg, Nelson, Andrew and McCann, Clare (2022) Tracking SARS-CoV-2 Mutations & Variants Through the COG-UK-Mutation Explorer. Virus Evolution, 8 (1). veac023. ISSN 2057-1577

Snell, Luke B, Wang, Wenjuan, Alcolea-Medina, Adela, Charalampous, Themoula, Batra, Rahul, de Jongh, Leonardo, Higgins, Finola, Nebbia, Gaia, Wang, Yanzhong, Edgeworth, Jonathan, Curcin, Vasa, The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Smith, Darren and Crown, Matthew (2022) Descriptive comparison of admission characteristics between pandemic waves and multivariable analysis of the association of the Alpha variant (B.1.1.7 lineage) of SARS-CoV-2 with disease severity in inner London. BMJ Open, 12 (2). e055474. ISSN 2044-6055

Aggarwal, Dinesh, Myers, Richard, Hamilton, William L, Bharucha, Tehmina, Tumelty, Niamh M, Brown, Colin S, Meader, Emma J, Connor, Tom, Smith, Darren L, Bradley, Declan T, Robson, Samuel, Bashton, Matthew, Shallcross, Laura, Zambon, Maria, Goodfellow, Ian, Chand, Meera, O'Grady, Justin, Török, M Estée, Peacock, Sharon J, Page, Andrew J, The COVID-19 Genomics UK (COG-UK) Consortium, , Allan, John, Loh, Joshua, Nelson, Andrew, Yew, Wen C. and Young, Gregory R. (2022) The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities. The Lancet Microbe, 3 (2). e151-e158. ISSN 2666-5247

Boshier, Florencia A. T., Pang, Juanita, Penner, Justin, Parker, Matthew, Alders, Nele, Bamford, Alasdair, Grandjean, Louis, Grunewald, Stephanie, Hatcher, James, Best, Timothy, Dalton, Caroline, Bynoe, Patricia Dyal, Frauenfelder, Claire, Köeglmeier, Jutta, Myerson, Phoebe, Roy, Sunando, Williams, Rachel, Silva, Thushan I., Goldstein, Richard A., Breuer, Judith, The COVID-19 Genomics UK (COG-UK) Consortium, , Allan, John, Bashton, Matthew, Loh, Joshua, Nelson, Andrew, Smith, Darren L., Yew, Wen Chyin and Young, Gregory R. (2022) Evolution of viral variants in remdesivir‐treated and untreated SARS‐CoV‐2‐infected pediatrics patients. Journal of Medical Virology, 94 (1). pp. 161-172. ISSN 0146-6615

Twohig, Katherine A, Nyberg, Tommy, Zaidi, Asad, Thelwall, Simon, Sinnathamby, Mary A, Aliabadi, Shirin, Seaman, Shaun R, Harris, Ross J, Hope, Russell, Lopez-bernal, Jamie, Gallagher, Eileen, Charlett, Andre, De Angelis, Daniela, Presanis, Anne M, Dabrera, Gavin, The COVID-19 Genomics UK (COG-UK) Consortium, , Koshy, Cherian, Ash, Amy, Wise, Emma, Moore, Nathan, Mori, Matilde, Cortes, Nick, Lynch, Jessica, Kidd, Stephen, Fairley, Derek, Curran, Tanya, Mckenna, James, Adams, Helen, Fraser, Christophe, Golubchik, Tanya, Bonsall, David, Hassan-ibrahim, Mohammed, Malone, Cassandra, Cogger, Benjamin, Wantoch, Michelle, Reynolds, Nicola, Warne, Ben, Maksimovic, Joshua, Spellman, Karla, McCluggage, Kathryn, John, Michaela, Beer, Robert, Afifi, Safiah, Morgan, Sian, Marchbank, Angela, Smith, Darren, Bashton, Matthew, Young, Greg, Nelson, Andrew, McCann, Clare and Yew, Wen Chyin (2022) Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study. The Lancet Infectious Diseases, 22 (1). pp. 35-42. ISSN 1473-3099

Allen, Hester, Vusirikala, Amoolya, Flannagan, Joe, Twohig, Katherine A., Zaidi, Asad, Chudasama, Dimple, Lamagni, Theresa, Groves, Natalie, Turner, Charlie, Rawlinson, Christopher, Lopez-Bernal, Jamie, Harris, Ross, Charlett, Andre, Dabrera, Gavin, Kall, Meaghan, The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Nelson, Andrew, Smith, Darren, Young, Greg and McCann, Clare (2022) Household transmission of COVID-19 cases associated with SARS-CoV-2 delta variant (B.1.617.2): national case-control study. The Lancet Regional Health - Europe, 12. p. 100252. ISSN 2666-7762

Francis, Rodric V., Billam, Harriet, Clarke, Mitch, Yates, Carl, Tsoleridis, Theocharis, Berry, Louise, Mahida, Nikunj, Irving, William L., Moore, Christopher, Holmes, Nadine, Ball, Jonathan K., Loose, Matthew, McClure, C. Patrick, The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Smith, Darren, Young, Greg, McCann, Clare and Nelson, Andrew (2022) The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks. The Journal of Infectious Diseases, 225 (1). pp. 10-18. ISSN 0022-1899

Vöhringer, Harald S., Sanderson, Theo, Sinnott, Matthew, De Maio, Nicola, Nguyen, Thuy, Goater, Richard, Schwach, Frank, Harrison, Ian, Hellewell, Joel, Ariani, Cristina V., Gonçalves, Sonia, Jackson, David K., Johnston, Ian, Jung, Alexander W., Saint, Callum, Sillitoe, John, Suciu, Maria, Goldman, Nick, Panovska-Griffiths, Jasmina, Birney, Ewan, Volz, Erik, Funk, Sebastian, Kwiatkowski, Dominic, Chand, Meera, Martincorena, Inigo, Barrett, Jeffrey C., Gerstung, Moritz, The Wellcome Sanger Institute Covid-19 Surveillance Team, , The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, McCann, Clare, Nelson, Andrew, Smith, Darren and Young, Greg (2021) Genomic reconstruction of the SARS-CoV-2 epidemic in England. Nature, 600 (7889). pp. 506-511. ISSN 0028-0836

Mashe, Tapfumanei, Takawira, Faustinos Tatenda, de Oliveira Martins, Leonardo, Gudza-Mugabe, Muchaneta, Chirenda, Joconiah, Munyanyi, Manes, Chaibva, Blessmore V., Tarupiwa, Andrew, Gumbo, Hlanai, Juru, Agnes, Nyagupe, Charles, Ruhanya, Vurayai, Phiri, Isaac, Manangazira, Portia, Goredema, Alexander, Danda, Sydney, Chabata, Israel, Jonga, Janet, Munharira, Rutendo, Masunda, Kudzai, Mukeredzi, Innocent, Mangwanya, Douglas, Trotter, Alex, Le Viet, Thanh, Rudder, Steven, Kay, Gemma, Baker, David, Thilliez, Gaetan, Gutierrez, Ana Victoria, O'Grady, Justin, Hove, Maxwell, Mutapuri-Zinyowera, Sekesai, Page, Andrew J., Kingsley, Robert A., Mhlanga, Gibson, The COVID-19 Genomics UK (COG-UK) Consortium, , SARS-CoV-2 Research Group, , Bashton, Matthew, Nelson, Andrew, McCann, Clare, Smith, Darren and Young, Greg (2021) Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data. The Lancet Global Health, 9 (12). e1658-e1666. ISSN 2214-109X

Nicholls, Samuel M., Poplawski, Radoslaw, Bull, Matthew J., Underwood, Anthony, Chapman, Michael, Abu-Dahab, Khalil, Taylor, Ben, Colquhoun, Rachel M., Rowe, Will P. M., Jackson, Ben, Hill, Verity, O’Toole, Áine, Rey, Sara, Southgate, Joel, Amato, Roberto, Livett, Rich, Gonçalves, Sónia, Harrison, Ewan M., Peacock, Sharon J., Aanensen, David M., Rambaut, Andrew, Connor, Thomas R., Loman, Nicholas J., The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg and McCann, Clare (2021) CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance. Genome Biology, 22 (1). p. 196. ISSN 1474-760X

de Silva, Thushan, 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, Bashton, Matthew, McCann, Clare, Nelson, Andrew, Smith, Darren, Yew, Wen Chyin, Young, Greg, The COVID-19 Genomics UK (COG-UK) Consortium, and ISARIC4C Investigators, (2021) The impact of viral mutations on recognition by SARS-CoV-2 specific T cells. iScience, 24 (11). p. 103353. ISSN 2589-0042

Jackson, Ben, Boni, Maciej F., Bull, Matthew J., Colleran, Amy, Colquhoun, Rachel M., Darby, Alistair C., Haldenby, Sam, Hill, Verity, Lucaci, Anita, McCrone, John T., Nicholls, Samuel M., O’Toole, Áine, Pacchiarini, Nicole, Poplawski, Radoslaw, Scher, Emily, Todd, Flora, Webster, Hermione J., Whitehead, Mark, Wierzbicki, Claudia, Loman, Nicholas J., Connor, Thomas R., Robertson, David L., Pybus, Oliver G., Rambaut, Andrew, The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg and McCann, Clare (2021) Generation and transmission of inter-lineage recombinants in the SARS-CoV-2 pandemic. Cell, 184 (20). 5179-5188.e8. ISSN 0092-8674

Stirrup, Oliver, Boshier, Florencia, Venturini, Cristina, Guerra-Assunção, José Afonso, Alcolea-Medina, Adela, Beckett, Angela, Charalampous, Themoula, da Silva Filipe, Ana, Glaysher, Sharon, Khan, Tabassum, Kulasegaran Shylini, Raghavendran, Kele, Beatrix, Monahan, Irene, Mollett, Guy, Parker, Matthew, Pelosi, Emanuela, Randell, Paul, Roy, Sunando, Taylor, Joshua, Weller, Sophie, Wilson-Davies, Eleri, Wade, Phillip, Williams, Rachel, Copas, Andrew, Cutino-Moguel, Maria-Teresa, Freemantle, Nick, Hayward, Andrew C, Holmes, Alison, Hughes, Joseph, Mahungu, Tabitha, Nebbia, Gaia, Partridge, David, Pope, Cassie, Price, James, Robson, Samuel, Saeed, Kordo, de Silva, Thushan, Snell, Luke, Thomson, Emma, Witney, Adam A, Breuer, Judith, Bashton, Matthew, Nelson, Andrew, McCann, Clare, Young, Greg, Smith, Darren and The COVID-19 Genomics UK (COG-UK) Consortium, (2021) SARS-CoV-2 lineage B.1.1.7 is associated with greater disease severity among hospitalised women but not men: multicentre cohort study. BMJ Open Respiratory Research, 8 (1). e001029. ISSN 2052-4439

Mishra, Swapnil, Mindermann, Sören, Sharma, Mrinank, Whittaker, Charles, Mellan, Thomas A, Wilton, Thomas, Klapsa, Dimitra, Mate, Ryan, Fritzsche, Martin, Zambon, Maria, Ahuja, Janvi, Howes, Adam, Miscouridou, Xenia, Nason, Guy P, Ratmann, Oliver, Semenova, Elizaveta, Leech, Gavin, Sandkühler, Julia Fabienne, Rogers-Smith, Charlie, Vollmer, Michaela, Unwin, H Juliette T, Gal, Yarin, Chand, Meera, Gandy, Axel, Martin, Javier, Volz, Erik, Ferguson, Neil M, Bhatt, Samir, Brauner, Jan M, Flaxman, Seth, The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg and McCann, Clare (2021) Changing composition of SARS-CoV-2 lineages and rise of Delta variant in England. EClinicalMedicine, 39. p. 101064. ISSN 2589-5370

Wenlock, R.D., Tausan, M., Mann, R., Garr, W., Preston, R., Arnold, A., Hoban, J., Webb, L., Quick, C., Beckett, A., Loveson, K., Glaysher, S., Elliott, S., Malone, C., Cogger, B., Easton, L., The COVID-19 Genomics UK (COG-UK) Consortium, , Allan, John, Bashton, Matthew, Loh, Joshua, Nelson, Andrew, Smith, Darren L., Yew, Wen Chyin, Young, Gregory R., Robson, S.C., Hassan-Ibrahim, M.O. and Sargent, C. (2021) Nosocomial or not? A combined epidemiological and genomic investigation to understand hospital-acquired COVID-19 infection on an elderly care ward. Infection Prevention in Practice, 3 (3). p. 100165. ISSN 2590-0889

Leary, Shay, Gaudieri, Silvana, Parker, Matthew D., Chopra, Abha, James, Ian, Pakala, Suman, Alves, Eric, John, Mina, Lindsey, Benjamin B., Keeley, Alexander J., Rowland-Jones, Sarah L., Swanson, Maurice S., Ostrov, David A., Bubenik, Jodi L., Das, Suman R., Sidney, John, Sette, Alessandro, The COVID-19 Genomics UK (COG-UK) Consortium, , De Silva, Thushan, Phillips, Elizabeth, Mallal, Simon, Smith, Darren, Bashton, Matthew, Young, Greg, Nelson, Andrew, McCann, Clare and Yew, Wen Chyin (2021) Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level. Pathogens and Immunity, 6 (2). pp. 27-49. ISSN 2469-2964

Tonkin-Hill, Gerry, Martincorena, Inigo, Amato, Roberto, Lawson, Andrew RJ, Gerstung, Moritz, Johnston, Ian, Jackson, David K, Park, Naomi, Lensing, Stefanie V, Quail, Michael A, Gonçalves, Sónia, Ariani, Cristina, Spencer Chapman, Michael, Hamilton, William L, Meredith, Luke W, Hall, Grant, Jahun, Aminu S, Chaudhry, Yasmin, Hosmillo, Myra, Pinckert, Malte L, Georgana, Iliana, Yakovleva, Anna, Caller, Laura G, Caddy, Sarah L, Feltwell, Theresa, Khokhar, Fahad A, Houldcroft, Charlotte J, Curran, Martin D, Parmar, Surendra, Alderton, Alex, Nelson, Rachel, Harrison, Ewan M, Sillitoe, John, Bentley, Stephen D, Barrett, Jeffrey C, Torok, M Estee, Goodfellow, Ian G, Langford, Cordelia, Kwiatkowski, Dominic, The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg and McCann, Clare (2021) Patterns of within-host genetic diversity in SARS-CoV-2. eLife, 10. ISSN 2050-084X

Harvey, William T., Carabelli, Alessandro M., Jackson, Ben, Gupta, Ravindra K., Thomson, Emma C., Harrison, Ewan M., Ludden, Catherine, Reeve, Richard, Rambaut, Andrew, Peacock, Sharon J., Robertson, David L., The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg and McCann, Clare (2021) SARS-CoV-2 variants, spike mutations and immune escape. Nature Reviews Microbiology, 19 (7). pp. 409-424. ISSN 1740-1526

Stirrup, Oliver, Hughes, Joseph, Parker, Matthew, Partridge, David G, Shepherd, James G, Blackstone, James, Coll, Francesc, Keeley, Alexander, Lindsey, Benjamin B, Marek, Aleksandra, Peters, Christine, Singer, Joshua B, Tamuri, Asif, de Silva, Thushan I, Thomson, Emma C, Breuer, Judith, The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg and McCann, Clare (2021) Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data. eLife, 10. ISSN 2050-084X

Meng, Bo, Kemp, Steven A, Papa, Guido, Datir, Rawlings, Ferreira, Isabella A.T.M., Marelli, Sara, Harvey, William T., Lytras, Spyros, Mohamed, Ahmed, Gallo, Giulia, Thakur, Nazia, Collier, Dami A., Mlcochova, Petra, The COVID-19 Genomics UK (COG-UK) Consortium, , Bailey, Dalan, Gupta, Ravindra K., Smith, Darren, Bashton, Matthew, Nelson, Andrew, Young, Greg, McCann, Clare and Yew, Wen Chyin (2021) Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. Cell Reports, 35 (13). p. 109292. ISSN 2211-1247

Chappell, Joseph G., Tsoleridis, Theocharis, Clark, Gemma, Berry, Louise, Holmes, Nadine, Moore, Christopher, Carlile, Matthew, Sang, Fei, Debebe, Bisrat J., Wright, Victoria, Irving, William L., Thomson, Brian J., Boswell, Timothy C. J., Willingham, Iona, Joseph, Amelia, Smith, Wendy, Khakh, Manjinder, Fleming, Vicki M., Lister, Michelle M., Howson-Wells, Hannah C., Holmes, Edward C., Loose, Matthew W., Ball, Jonathan K., McClure, C. Patrick, The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg and McCann, Clare (2021) Retrospective screening of routine respiratory samples revealed undetected community transmission and missed intervention opportunities for SARS-CoV-2 in the United Kingdom. Journal of General Virology, 102 (6). 001595. ISSN 0022-1317

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 (2021) Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission. Research Square Platform. pp. 1-25. (Submitted)

O'Toole, Áine, Hill, Verity, Pybus, Oliver G., Watts, Alexander, Bogoch, Issac I., Khan, Kamran, Messina, Jane P., Tegally, Houriiyah, Lessells, Richard R., Giandhari, Jennifer, Pillay, Sureshnee, Tumedi, Kefentse Arnold, Nyepetsi, Gape, Kebabonye, Malebogo, Matsheka, Maitshwarelo, Mine, Madisa, Tokajian, Sima, Hassan, Hamad, Salloum, Tamara, Merhi, Georgi, Koweyes, Jad, Geoghegan, Jemma L., de Ligt, Joep, Ren, Xiaoyun, Storey, Matthew, Freed, Nikki E., Pattabiraman, Chitra, Prasad, Pramada, Desai, Anita S., Vasanthapuram, Ravi, Schulz, Thomas F., Steinbrück, Lars, Stadler, Tanja, Parisi, Antonio, Bianco, Angelica, García de Viedma, Darío, Buenestado-Serrano, Sergio, Borges, Vítor, Isidro, Joana, Duarte, Sílvia, Gomes, João Paulo, Zuckerman, Neta S., Mandelboim, Michal, Mor, Orna, Seemann, Torsten, Arnott, Alicia, Draper, Jenny, Gall, Mailie, Rawlinson, William, Deveson, Ira, Schlebusch, Sanmarié, McMahon, Jamie, Leong, Lex, Lim, Chuan Kok, Chironna, Maria, Loconsole, Daniela, Bal, Antonin, Josset, Laurence, Holmes, Edward, St. George, Kirsten, Lasek-Nesselquist, Erica, Sikkema, Reina S., Oude Munnink, Bas, Koopmans, Marion, Brytting, Mia, Sudha rani, V., Pavani, S., Smura, Teemu, Heim, Albert, Kurkela, Satu, Umair, Massab, Salman, Muhammad, Bartolini, Barbara, Rueca, Martina, Drosten, Christian, Wolff, Thorsten, Silander, Olin, Eggink, Dirk, Reusken, Chantal, Vennema, Harry, Park, Aekyung, Carrington, Christine, Sahadeo, Nikita, Carr, Michael, Gonzalez, Gabo, de Oliveira, Tulio, Faria, Nuno, Rambaut, Andrew, Kraemer, Moritz U. G., The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Smith, Darren, Young, Greg, McCann, Clare and Nelson, Andrew (2021) Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2. Wellcome Open Research, 6. p. 121. ISSN 2398-502X

Volz, Erik, Mishra, Swapnil, Chand, Meera, Barrett, Jeffrey C., Johnson, Robert, Geidelberg, Lily, Hinsley, Wes R., Laydon, Daniel J., Dabrera, Gavin, O’Toole, Áine, Amato, Robert, Ragonnet-Cronin, Manon, Harrison, Ian, Jackson, Ben, Ariani, Cristina V., Boyd, Olivia, Loman, Nicholas J., McCrone, John T., Gonçalves, Sónia, Jorgensen, David, Myers, Richard, Hill, Verity, Jackson, David K., Gaythorpe, Katy, Groves, Natalie, Sillitoe, John, Kwiatkowski, Dominic P., Koshy, Cherian, Ash, Amy, Wise, Emma, Moore, Nathan, Mori, Matilde, Cortes, Nick, Lynch, Jessica, Kidd, Stephen, Fairley, Derek J., Curran, Tanya, McKenna, James P., Fraser, Christophe, Adams, Helen, The COVID-19 Genomics UK (COG-UK) Consortium, , Smith, Darren L., Bashton, Matthew, Young, Gregory R., Nelson, Andrew, McCann, Clare M., Yew, Wen Chyin, Jones, Hannah, Flaxman, Seth, Ratmann, Oliver, Bhatt, Samir, Hopkins, Susan, Gandy, Axel, Rambaut, Andrew and Ferguson, Neil M. (2021) Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. Nature, 593 (7858). pp. 266-269. ISSN 0028-0836

Lythgoe, Katrina A., Hall, Matthew, Ferretti, Luca, de Cesare, Mariateresa, MacIntyre-Cockett, George, Trebes, Amy, Andersson, Monique, Otecko, Newton, Wise, Emma L., Moore, Nathan, Lynch, Jessica, Kidd, Stephen, Cortes, Nicholas, Mori, Matilde, Williams, Rebecca, Vernet, Gabrielle, Justice, Anita, Green, Angie, Nicholls, Samuel M., Ansari, M. Azim, Abeler-Dörner, Lucie, Moore, Catrin E., Peto, Timothy E. A., Eyre, David W., Shaw, Robert, Simmonds, Peter, Buck, David, Todd, John A., Connor, Thomas R., Ashraf, Shirin, da Silva Filipe, Ana, Shepherd, James, Thomson, Emma C., Bonsall, David, Fraser, Christophe, Golubchik, Tanya, Bashton, Matthew, Nelson, Andrew, Smith, Darren, Young, Greg, Oxford Virus Sequencing Analysis Group (OVSG), and The COVID-19 Genomics UK (COG-UK) Consortium, (2021) SARS-CoV-2 within-host diversity and transmission. Science, 372 (6539). eabg0821. ISSN 0036-8075

Parker, Matthew D., Lindsey, Benjamin B., Leary, Shay, Gaudieri, Silvana, Chopra, Abha, Wyles, Matthew, Angyal, Adrienn, Green, Luke R., Parsons, Paul, Tucker, Rachel M., Brown, Rebecca, Groves, Danielle, Johnson, Katie, Carrilero, Laura, Heffer, Joe, Partridge, David G., Evans, Cariad, Raza, Mohammad, Keeley, Alexander J., Smith, Nikki, Filipe, Ana Da Silva, Shepherd, James G., Davis, Chris, Bennett, Sahan, Sreenu, Vattipally B., Kohl, Alain, Aranday-Cortes, Elihu, Tong, Lily, Nichols, Jenna, Thomson, Emma C., Wang, Dennis, Mallal, Simon, de Silva, Thushan I., The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Young, Greg, Allan, John, Loh, Joshua, Nelson, Andrew, Smith, Darren and Yew, Wen Chyin (2021) Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data. Genome Research, 31 (4). pp. 645-658. ISSN 1088-9051

Darlix, Jean-Luc EPH, Harper, Helen, Burridge, Amanda, Winfield, Mark, Finn, Adam, Davidson, Andrew, Matthews, David, Hutchings, Stephanie, Vipond, Barry, Jain, Nisha, The COVID-19 Genomics UK (COG-UK) Consortium, , Allan, John, Bashton, Matthew, Loh, Joshua, Nelson, Andrew, Smith, Darren L., Yew, Wen Chyin, Young, Gregory R., Edwards, Keith and Barker, Gary (2021) Detecting SARS-CoV-2 variants with SNP genotyping. PLoS ONE, 16 (2). e0243185. ISSN 1932-6203