Accès ouvert déclaré
2022
article
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
Oliver Eales, Andrew J. Page, Leonardo de Oliveira Martins, Haowei Wang, Barbara Bodinier, David Haw, Jakob Jonnerby, Christina Atchison, Samuel C. Robson, Thomas R. Connor, Nicholas J. Loman, Tanya Golubchik, Rocio T. Martinez Nunez, David Bonsall, Andrew Rambaut, Luke B. Snell, Rich Livett, Catherine Ludden, Sally Corden, Eleni Nastouli, Gaia Nebbia, Ian Johnston, Katrina Lythgoe, M. Estée Török, Ian Goodfellow, Jacqui Prieto, Kordo Saeed, David K. Jackson, Catherine Houlihan, Dan Frampton, William L. Hamilton, Adam A. Witney, Giselda Bucca, Cassie F. Pope, Catherine Moore, Emma C. Thomson, Ewan M. Harrison, Colin P. Smith, Fiona Rogan, Shaun M. Beckwith, Abigail Murray, Dawn Singleton, Kirstine Eastick, Liz A. Sheridan, Paul Randell, Leigh Jackson, Cristina V. Ariani, Sónia Gonçalves, Derek Fairley, Matthew Loose, Joanne Watkins, Samuel Moses, Sam Nicholls, Matthew Bull, Roberto Amato, Darren Smith, David M. Aanensen, Jeffrey C. Barrett, Dinesh Aggarwal, James G. Shepherd, Martin D. Curran, Surendra Parmar, Catryn Williams, Sharon Glaysher, Anthony P. Underwood, Matthew Bashton, Nicole Pacchiarini, Katie F. Loveson, Matthew Byott, Alessandro M. Carabelli, Kate Templeton, Thushan I. de Silva, Dennis Wang, Cordelia F. Langford, John Sillitoe, Rory Gunson, Simon Cottrell, Justin O’Grady, Dominic Kwiatkowski, Patrick Lillie, Nicholas Cortes, Nathan Moore, Claire Thomas, Phillipa Burns, Tabitha Mahungu, Steven Liggett, Angela H. Beckett, Matthew T. G. Holden, Lisa J. Levett, Husam Osman, Mohammed O. Hassan-Ibrahim, David Simpson, Meera Chand, Ravi Gupta, Alistair C. Darby, Steve Paterson, Oliver G. Pybus, Erik Volz, Daniela De Angelis, David L. Robertson, Iñigo Martincorena, Louise Aigrain, Andrew R. Bassett, Nick Wong, Yusri Taha, Michelle J. Erkiert, Michael H. Spencer Chapman, Rebecca Dewar, M. McHugh, Siddharth Mookerjee, Stephen Aplin, Matthew Harvey, Thea Sass, Helen Umpleby, Helen Wheeler, James McKenna, Ben Warne, Joshua F. Taylor, Yasmin Chaudhry, Rhys Izuagbe, Aminu S. Jahun, Gregory R. Young, Claire McMurray, Clare M. McCann, Andrew Nelson, Scott Elliott, Hannah Lowe, Anna Price, Matthew Crown, Sara Rey, Sunando Roy, Ben Temperton, Sharif Shaaban, Andrew R. Hesketh, Kenneth G. Laing, Irene M. Monahan, Judith Heaney, Emanuela Pelosi, Siona Silviera, Eleri Wilson-Davies, Helen Fryer, Helen Adams, Louis du Plessis, Rob Johnson, William T. Harvey, Joseph Hughes, Richard Orton, Lewis G. Spurgin, Yann Bourgeois, Chris Ruis, Áine O’Toole, Marina Gourtovaia, Theo Sanderson, Christophe Fraser, Jonathan Edgeworth, Judith Breuer, Stephen L. Michell, John A. Todd, John P.T. Mo, David Buck, Kavitha Gajee, Gemma L. Kay, Sharon J. Peacock, David Heyburn, Katie Kitchman, Alan McNally, David T. Pritchard, Samir Dervisevic, Peter Muir, Esther Robinson, Barry Vipond, Newara Ramadan, Christopher Jeanes, Danni Weldon, Jana Catalan, Neil Jones, Ana da Silva Filipe, Chris Williams, Marc Fuchs, Julia Miskelly, Aaron R. Jeffries, Karen Oliver, Naomi R. Park, Amy Ash, Cherian Koshy, Magdalena Barrow, Sarah L. Buchan, Anna Mantzouratou, Gemma Clark, Christopher W. Holmes, Thomas Davis, Ngee Keong Tan, Julianne R. Brown, Kathryn Harris, Stephen P. Kidd, Paul R. Grant, Li Xu-McCrae, Alison D. Cox, Pinglawathee Madona, Marcus Pond, Karen T. Withell, Cheryl Williams, Clive Graham, Rebecca Denton-Smith, Emma Swindells, Robyn Turnbull, Tim J. Sloan, Andrew Bosworth, Stephanie Hutchings, Hannah M. Pymont, Anna Casey, Liz Ratcliffe, Christopher R. Jones, Bridget Knight, Tanzina Haque, Jennifer Hart, Dianne Irish-Tavares, Eric Witele, Craig Mower, Louisa K. Watson, Jennifer Collins, Gary Eltringham, Dorian Crudgington, Ben Macklin, Miren Iturriza‐Gómara, Anita O. Lucaci, C. Patrick McClure, Matthew Carlile, Nadine Holmes, Christopher Moore, Nathaniel Storey, Stefan Rooke, Gonzalo Yebra, Noel Craine, Malorie Perry, Nabil-Fareed Alikhan, Stephen Bridgett, Kate F. Cook, Christopher Fearn, Salman Goudarzi, Ronan A Lyons, Thomas Williams, Sam Haldenby, Jillian Durham, Steven Leonard, Robert M. Davies, Rahul Batra, Beth Blane, Moira Spyer, Perminder Smith, Mehmet Yavus, Rachel Williams, Adhyana I. K. Mahanama, Buddhini Samaraweera, Sophia T. Girgis, Samantha E. Hansford, Angie Green, Charlotte Beaver, Katherine L. Bellis, Matthew J. Dorman, Sally Kay, Liam Prestwood, Shavanthi Rajatileka, Joshua Quick, Radoslaw Poplawski, Nicola Reynolds, Andrew Mack, Arthur Morriss, Thomas Whalley, Bindi Patel, Iliana Georgana, Myra Hosmillo, Malte L. Pinckert, Joanne Stockton, John Henderson, Amy Hollis, William T. Stanley, Wen C. Yew, Richard Myers, Alicia Thornton, Alexander Adams, Tara Annett, Hibo Asad, Alec Birchley, Jason Coombes, Johnathan M. Evans, Laia Fina, Bree Gatica-Wilcox, Lauren Gilbert, Lee Graham, Jessica Hey, Ember Hilvers, Sophie Jones, Hannah Jones, Sara Kumziene-Summerhayes, Caoimhe McKerr, Jessica Powell, Georgia Pugh, Sarah Taylor, Alexander J. Trotter, Charlotte A. Williams, Leanne M. Kermack, Benjamin H. Foulkes, Marta Gallis, Hailey Hornsby, Stavroula F. Louka, Manoj Pohare, Paige Wolverson, Peijun Zhang, George MacIntyre-Cockett, Amy Trebes, Robin J. Moll, Lynne Ferguson, Emily J. Goldstein, Alasdair Maclean, Rachael Tomb, Igor Starinskij, Joel Southgate, Moritz U. G. Kraemer, Jayna Raghwani, Alex E. Zarebski, Olivia Boyd, Lily Geidelberg, Chris J. Illingworth, Chris Jackson, David J. Pascall, Vattipally B. Sreenu, Timothy M. Freeman, Sharon N. Hsu, Benjamin B. Lindsey, Keith James, Kevin Lewis, Gerry Tonkin‐Hill, Jaime M. Tovar-Corona, MacGregor Cox, Khalil Abudahab, Mirko Menegazzo, Ben E. W. Taylor MEng, Corin Yeats, Afrida Mukaddas, Derek Wright, Rachel Colquhoun, Verity Hill, Ben Jackson, J. T. McCrone, Nathan Medd, Emily Scher, Jon-Paul Keatley, Tanya Curran, Sian Morgan, Patrick H. Maxwell, Kenneth G. C. Smith, Sahar Eldirdiri, Anita Kenyon, Alison Holmes, James Price, Tim Wyatt, Alison E. Mather, Timofey Skvortsov, John A. Hartley, Martyn F. Guest, Christine Kitchen, Ian Merrick, Robert J. Munn, Beatrice Bertolusso, Jessica Lynch, Gabrielle Vernet, Stuart A. Kirk, Elizabeth Wastnedge, Rachael Stanley, Giles Idle, Declan Bradley, Jennifer Poyner, Matilde Mori, Owen R. Jones, Victoria Wright, Ellena Brooks, Carol Churcher, Mireille Fragakis, Katerina Galai, Andrew Jermy, Sarah Judges, Georgina M. McManus, Kim S. Smith, Elaine Westwick, Stephen W. Attwood, Frances Bolt, Alisha Davies, Elen De Lacy, Fatima Downing, Sue Edwards, Lizzie Meadows, Sarah Jeremiah, Luke Foulser, Themoula Charalampous, Amita Patel, Louise Berry, Tim Boswell, Vicki M. Fleming, Hannah C. Howson‐Wells, Amelia Joseph, Manjinder Khakh, Michelle M. Lister, Paul Bird, Karlie Fallon, Thomas Helmer, Mina Odedra, Jessica R. Shaw, Julian W. Tang, Nicholas J. Willford, Victoria Blakey, Veena Raviprakash, Nicola Sheriff, Lesley-Anne Williams, Theresa Feltwell, Luke Bedford, James S. Cargill, Warwick Hughes, Jonathan P. Moore, Susanne Stonehouse, Laura Atkinson, Jack C. D. Lee, Divya Shah, Adela Alcolea-Medina, Natasha Ohemeng-Kumi, John Ramble, Jasveen Sehmi, Rebecca Williams, Wendy Chatterton, Monika Pusok, William V. Everson, Anibolina Castigador, Emily MacNaughton, Kate El Bouzidi, Temi Lampejo, Malur Sudhanva, Cassie Breen, Graciela Sluga, Shazaad Ahmad, Ryan P. George, Nicholas W. Machin, Debbie Binns, Victoria James, Rachel Blacow, Lindsay Coupland, Louise Smith, Edward Barton, Debra Padgett, Garren Scott, Aidan Cross, Mariyam Mirfenderesky, Jane Greenaway, Kevin Cole, Phillip Clarke, Nichola Duckworth, Sarah Walsh, Kelly Bicknell, Robert Impey, Sarah Wyllie, Richard Hopes, Chloe Bishop, Vicki Chalker, Ian Harrison, Laura Gifford, Zoltán Molnár, Cressida Auckland, Cariad Evans, KATE JOHNSON, David G. Partridge, Mohammad Raza, Paul Baker, Stephen Bonner, Sarah Essex, Leanne J. Murray, Andrew I. Lawton, Shirelle Burton-Fanning, Brendan Payne, Sheila Waugh, Andrea N. Gomes, Maimuna Kimuli, Darren R. Murray, Paula Ashfield, Donald Dobie, Fiona Ashford, Angus Best, Liam Crawford, Nicola Cumley, Megan Mayhew, Oliver Megram, Jeremy Mirza, Emma Moles-Garcia, Benita Percival, Megan Driscoll, Leah Ensell, Helen L. Lowe, Laurentiu Maftei, Matteo Mondani, Nicola J. Chaloner, Benjamin J. Cogger, Lisa J. Easton, Hannah Huckson, J. R. Lewis, Sarah Lowdon, Cassandra S. Malone, Florence Munemo, Manasa Mutingwende, Roberto Nicodemi, Olga Podplomyk, Thomas Somassa, Andrew D. Beggs, Alex Richter, Claire Cormie, Joana Angélica Andrade Dias, Ellen E. Higginson, Mailis Maes, Jamie Young, Rose K. Davidson, Kathryn Jackson, Lance Turtle, Alexander J. Keeley, Jonathan K. Ball, Timothy Byaruhanga, Joseph Chappell, Jayasree Dey, Jack D. Hill, Emily J. Park, Arezou Fanaie, Rachel A. Hilson, Geraldine Yaze, Stephanie W. Lo, Safiah Afifi, Robert Beer, Joshua Maksimovic, Kathryn McCluggage, Karla Spellman, Catherine Bresner, William Fuller, Angela Marchbank, Trudy Workman, Ekaterina Shelest, Johnny Debebe, Fei Sang, Marina Escalera Zamudio, Sarah François, Bernardo Gutiérrez, Tetyana I. Vasylyeva, Flavia Flaviani, Manon Ragonnet‐Cronin, Katherine Smollett, Alice Broos, Daniel Mair, Jenna Nichols, Kyriaki Nomikou, L. Tong, Ioulia Tsatsani, Prof Sarah O’Brien, Steven Rushton, Roy Sanderson, Jon Perkins, Seb Cotton, Abbie Gallagher, Elias Allara, Clare Pearson, David Bibby, Gavin Dabrera, Nicholas Ellaby, Eileen Gallagher, Jonathan Hubb, Angie Lackenby, David Lee, Nikos Manesis, Tamyo Mbisa, Steven G. Platt, Katherine A. Twohig, Mari Morgan, Alp Aydin, David Baker, Ebenezer Foster-Nyarko, Sophie J. Prosolek, Steven Rudder, Chris Baxter, Silvia Carvalho, Deborah Lavin, Arun Mariappan, Clara Radulescu, Aditi Singh, Miao Tang, Helen Morcrette, Nadua Bayzid, Marius Cotic, Carlos E. Balcazar, Daniel Maloney, Kathleen A. Williamson, Robin Manley, Michelle L. Michelsen, Christine Sambles, David J. Studholme, Joanna Warwick-Dugdale, Richard Eccles, Matthew Gemmell, Richard D. Gregory, Margaret Hughes, Charlotte Nelson, Lucille Rainbow, Edith E. Vamos, Hermione J. Webster, Mark Whitehead, Claudia Wierzbicki, Adrienn Angyal, Luke R. Green, Max Whiteley, Emma Betteridge, Iraad F. Bronner, Ben W. Farr, Scott Goodwin, Stefanie V. Lensing, Shane McCarthy, Michael A. Quail, Diana Rajan, Nicholas Redshaw, Lesley Shirley, Scott A. J. Thurston, Will Rowe, Amy Gaskin, Thanh Le-Viet, James Bonfield, Jennifier Liddle, Andrew Whitwham, Deborah Ashby, William Barclay, Graham P. Taylor, Graham Cooke, Helen Ward, Ara Darzi, Steven Riley, Marc Chadeau‐Hyam, Christl A. Donnelly, Paul Elliott
25Citations signalées — pas une note de qualité
11Institutions déclarées
1Pays d’affiliation déclarés
Résumé fourni par la source
BACKGROUND: Since the emergence of SARS-CoV-2, evolutionary pressure has driven large increases in the transmissibility of the virus. However, with increasing levels of immunity through vaccination and natural infection the evolutionary pressure will switch towards immune escape. Genomic surveillance in regions of high immunity is crucial in detecting emerging variants that can more successfully navigate the immune landscape. METHODS: We present phylogenetic relationships and lineage dynamics within England (a country with high levels of immunity), as inferred from a random community sample of individuals who provided a self-administered throat and nose swab for rt-PCR testing as part of the REal-time Assessment of Community Transmission-1 (REACT-1) study. During round 14 (9 September-27 September 2021) and 15 (19 October-5 November 2021) lineages were determined for 1322 positive individuals, with 27.1% of those which reported their symptom status reporting no symptoms in the previous month. RESULTS: We identified 44 unique lineages, all of which were Delta or Delta sub-lineages, and found a reduction in their mutation rate over the study period. The proportion of the Delta sub-lineage AY.4.2 was increasing, with a reproduction number 15% (95% CI 8-23%) greater than the most prevalent lineage, AY.4. Further, AY.4.2 was less associated with the most predictive COVID-19 symptoms (p = 0.029) and had a reduced mutation rate (p = 0.050). Both AY.4.2 and AY.4 were found to be geographically clustered in September but this was no longer the case by late October/early November, with only the lineage AY.6 exhibiting clustering towards the South of England. CONCLUSIONS: As SARS-CoV-2 moves towards endemicity and new variants emerge, genomic data obtained from random community samples can augment routine surveillance data without the potential biases introduced due to higher sampling rates of symptomatic individuals.
Ce résumé expose les affirmations des auteurs. BNTIC ne l’interprète pas comme une validation indépendante des résultats.
Contrôle bibliographique ouvert
DOI retrouvé dans Crossref DOI retrouvé ; titre concordant.
- Titre Crossref
- 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
- Date Crossref
- 27/07/2022
- Éditeur
- Springer Science and Business Media LLC
- Type
- journal-article
Ce recoupement confirme des métadonnées liées au DOI. Il ne confirme ni la méthode ni les conclusions de l’étude et ne compte pas comme une seconde source scientifique indépendante.
Institutions déclarées
Une affiliation ne permet pas de déduire la nationalité d’un auteur.
Sujets associés
SARS-CoV-2 and COVID-19 Researchvaccines and immunoinformatics approachesRespiratory viral infections research