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ArticlesPeer ReviewedFull Text
Viral burden is associated with age, vaccination, and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection-related sampling bias
Author / Creator:Fryer, Helen R. ; Golubchik, Tanya ; Hall, Matthew ; Fraser, Christophe ; Hinch, Robert ; Ferretti, Luca ; Thomson, Laura ; Nurtay, Anel ; Pellis, Lorenzo ; House, Thomas ; MacIntyre-Cockett, George ; Trebes, Amy ; Buck, David ; Piazza, Paolo ; Green, Angie ; Lonie, Lorne J ; Smith, Darren ; Bashton, Matthew ; Crown, Matthew ; Nelson, Andrew ; McCann, Clare M. ; Adnan Tariq, Mohammed ; Elstob, Claire J. ; Nunes Dos Santos, Rui ; Richards, Zack ; Xhang, Xin ; Hawley, Joseph ; Lee, Mark R. ; Carrillo-Barragan, Priscilla ; Chapman, Isobel ; Harthern-Flint, Sarah ; Bonsall, David ; Lythgoe, Katrina A.
Publisher:United States: Public Library of Science
Journal title:PLoS pathogens, 2023-08, Vol.19 (8), p.e1011461
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ArticlesPeer ReviewedFull Text
Tracking SARS-CoV-2 mutations and variants through the COG-UK-Mutation Explorer
Author / Creator: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
Publisher:UK: Oxford University Press
Journal title:Virus evolution, 2022-01, Vol.8 (1), p.veac023
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ArticlesPeer ReviewedFull Text
CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance
Author / Creator: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.
Publisher:England: BioMed Central
Journal title:Genome Biology, 2021-07, Vol.22 (1), p.196-196, Article 196
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ArticlesPeer ReviewedFull Text
Lineage frequency time series reveal elevated levels of genetic drift in SARS-CoV-2 transmission in England
Author / Creator:Yu, QinQin ; Ascensao, Joao A. ; Okada, Takashi ; Boyd, Olivia ; Volz, Erik ; Hallatschek, Oskar
Publisher:United States: Public Library of Science
Journal title:PLoS pathogens, 2024-04, Vol.20 (4), p.e1012090-e1012090
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ArticlesPeer ReviewedFull Text
Characterising within-hospitalSARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves
Author / Creator:Lindsey, Benjamin B ; Villabona-Arenas, Ch Julián ; Campbell, Finlay ; Keeley, Alexander J ; Parker, Matthew D ; Shah, Dhruv R ; Parsons, Helena ; Zhang, Peijun ; Kakkar, Nishchay ; Gallis, Marta ; Foulkes, Benjamin H ; Wolverson, Paige ; Louka, Stavroula F ; Christou, Stella ; State, Amy ; Johnson, Katie ; Raza, Mohammad ; Hsu, Sharon ; Jombart, Thibaut ; Cori, Anne ; Evans, Cariad M ; Partridge, David G ; Atkins, Katherine E ; Hué, Stéphane ; de Silva, Thushan I
Publisher:England: Nature Portfolio
Journal title:Nature communications, 2022-02, Vol.13 (1), p.671-11
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ArticlesPeer ReviewedFull Text
The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: A genomics-based retrospective cohort analysis
Author / Creator:Pascall, David J. ; Vink, Elen ; Blacow, Rachel ; Bulteel, Naomi ; Campbell, Alasdair ; Campbell, Robyn ; Clifford, Sarah ; Davis, Chris ; da Silva Filipe, Ana ; El Sakka, Noha ; Fjodorova, Ludmila ; Forrest, Ruth ; Goldstein, Emily ; Gunson, Rory ; Haughney, John ; Holden, Matthew T. G. ; Honour, Patrick ; Hughes, Joseph ; James, Edward ; Lewis, Tim ; Lycett, Samantha ; MacLean, Oscar ; McHugh, Martin ; Mollett, Guy ; Onishi, Yusuke ; Parcell, Ben ; Ray, Surajit ; Robertson, David L. ; Shabaan, Sharif ; Shepherd, James G. ; Smollett, Katherine ; Templeton, Kate ; Wastnedge, Elizabeth ; Wilkie, Craig ; Williams, Thomas ; Thomson, Emma C.
Publisher:United States: Public Library of Science
Journal title:PloS one, 2023-04, Vol.18 (4), p.e0284187-e0284187
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ArticlesPeer ReviewedFull Text
Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data
Author / Creator: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
Publisher:England: eLife Sciences Publications Ltd
Journal title:eLife, 2021-06, Vol.10
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ArticlesPeer ReviewedFull Text
Combining viral genomics and clinical data to assess risk factors for severe COVID-19 (mortality, ICU admission, or intubation) amongst hospital patients in a large acute UK NHS hospital Trust
Author / Creator:Foxley-Marrable, Max ; D’Cruz, Leon ; Meredith, Paul ; Glaysher, Sharon ; Beckett, Angela H. ; Goudarzi, Salman ; Fearn, Christopher ; Cook, Kate F. ; Loveson, Katie F. ; Dent, Hannah ; Paul, Hannah ; Elliott, Scott ; Wyllie, Sarah ; Lloyd, Allyson ; Bicknell, Kelly ; Lumley, Sally ; McNicholas, James ; Prytherch, David ; Lundgren, Andrew ; Graur, Or ; Chauhan, Anoop J. ; Robson, Samuel C.
Publisher:United States: Public Library of Science
Journal title:PloS one, 2023-03, Vol.18 (3), p.e0283447-e0283447
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ArticlesPeer ReviewedFull Text
Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, prospective study
Author / Creator:Stirrup, Oliver ; Blackstone, James ; Mapp, Fiona ; MacNeil, Alyson ; Panca, Monica ; Holmes, Alison ; Machin, Nicholas ; Shin, Gee Yen ; Mahungu, Tabitha ; Saeed, Kordo ; Saluja, Tranprit ; Taha, Yusri ; Mahida, Nikunj ; Pope, Cassie ; Chawla, Anu ; Cutino-Moguel, Maria-Teresa ; Tamuri, Asif ; Williams, Rachel ; Darby, Alistair ; Robertson, David L ; Flaviani, Flavia ; Nastouli, Eleni ; Robson, Samuel ; Smith, Darren ; Loose, Matthew ; Laing, Kenneth ; Monahan, Irene ; Kele, Beatrix ; Haldenby, Sam ; George, Ryan ; Bashton, Matthew ; Witney, Adam A ; Byott, Matthew ; Coll, Francesc ; Chapman, Michael ; Peacock, Sharon J ; Hughes, Joseph ; Nebbia, Gaia ; Partridge, David G ; Parker, Matthew ; Price, James Richard ; Peters, Christine ; Roy, Sunando ; Snell, Luke B ; de Silva, Thushan I ; Thomson, Emma ; Flowers, Paul ; Copas, Andrew ; Breuer, Judith
Publisher:England: eLife Sciences Publications Ltd
Journal title:eLife, 2022-09, Vol.11
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ArticlesPeer ReviewedFull Text
Publisher Correction: Characterising within-hospital SARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves
Author / Creator:Lindsey, Benjamin B. ; Villabona-Arenas, Ch. Julián ; Campbell, Finlay ; Keeley, Alexander J. ; Parker, Matthew D. ; Shah, Dhruv R. ; Parsons, Helena ; Zhang, Peijun ; Kakkar, Nishchay ; Gallis, Marta ; Foulkes, Benjamin H. ; Wolverson, Paige ; Louka, Stavroula F. ; Christou, Stella ; State, Amy ; Johnson, Katie ; Raza, Mohammad ; Hsu, Sharon ; Jombart, Thibaut ; Cori, Anne ; Evans, Cariad M. ; Partridge, David G. ; Atkins, Katherine E. ; Hué, Stéphane ; de Silva, Thushan I.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2022-02, Vol.13 (1), p.1013-1, Article 1013
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ArticlesPeer ReviewedFull Text
Altered subgenomic RNA abundance provides unique insight into SARS-CoV-2 B.1.1.7/Alpha variant infections
Author / Creator:Parker, Matthew D. ; Stewart, Hazel ; Shehata, Ola M. ; Lindsey, Benjamin B. ; Shah, Dhruv R. ; Hsu, Sharon ; Keeley, Alexander J. ; Partridge, David G. ; Leary, Shay ; Cope, Alison ; State, Amy ; Johnson, Katie ; Ali, Nasar ; Raghei, Rasha ; Heffer, Joe ; Smith, Nikki ; Zhang, Peijun ; Gallis, Marta ; Louka, Stavroula F. ; Hornsby, Hailey R. ; Alamri, Hatoon ; Whiteley, Max ; Foulkes, Benjamin H. ; Christou, Stella ; Wolverson, Paige ; Pohare, Manoj ; Hansford, Samantha E. ; Green, Luke R. ; Evans, Cariad ; Raza, Mohammad ; Wang, Dennis ; Firth, Andrew E. ; Edgar, James R. ; Gaudieri, Silvana ; Mallal, Simon ; Collins, Mark O. ; Peden, Andrew A. ; de Silva, Thushan I.
Publisher:London: Nature Publishing Group UK
Journal title:Communications biology, 2022-07, Vol.5 (1), p.666-10, Article 666
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ArticlesPeer ReviewedFull Text
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 / Creator: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 ; Modat, Marc ; Hammers, Alexander ; Spector, Tim D. ; Steves, Claire J. ; Sudre, Carole H. ; Ourselin, Sebastien ; Duncan, Emma L.
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2022-06, Vol.12 (1), p.10904-10904, Article 10904
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Viral burden is associated with age, vaccination, and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection-related sampling bias

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Tracking SARS-CoV-2 mutations and variants through the COG-UK-Mutation Explorer

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CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance

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Lineage frequency time series reveal elevated levels of genetic drift in SARS-CoV-2 transmission in England

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Characterising within-hospitalSARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves

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The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: A genomics-based retrospective cohort analysis

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Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data

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Combining viral genomics and clinical data to assess risk factors for severe COVID-19 (mortality, ICU admission, or intubation) amongst hospital patients in a large acute UK NHS hospital Trust

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Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, prospective study

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Publisher Correction: Characterising within-hospital SARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves

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Altered subgenomic RNA abundance provides unique insight into SARS-CoV-2 B.1.1.7/Alpha variant infections

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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

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