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Page 1
Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool.
O'Toole Á, Scher E, Underwood A, Jackson B, Hill V, McCrone JT, Colquhoun R, Ruis C, Abu-Dahab K, Taylor B, Yeats C, du Plessis L, Maloney D, Medd N, Attwood SW, Aanensen DM, Holmes EC, Pybus OG, Rambaut A. O'Toole Á, et al. Among authors: colquhoun r. Virus Evol. 2021 Jul 30;7(2):veab064. doi: 10.1093/ve/veab064. eCollection 2021. Virus Evol. 2021. PMID: 34527285 Free PMC article.
Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020.
Alm E, Broberg EK, Connor T, Hodcroft EB, Komissarov AB, Maurer-Stroh S, Melidou A, Neher RA, O'Toole Á, Pereyaslov D; WHO European Region sequencing laboratories and GISAID EpiCoV group; WHO European Region sequencing laboratories and GISAID EpiCoV group*. Alm E, et al. Euro Surveill. 2020 Aug;25(32):2001410. doi: 10.2807/1560-7917.ES.2020.25.32.2001410. Euro Surveill. 2020. PMID: 32794443 Free PMC article.
Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.
Volz E, Hill V, McCrone JT, Price A, Jorgensen D, O'Toole Á, Southgate J, Johnson R, Jackson B, Nascimento FF, Rey SM, Nicholls SM, Colquhoun RM, da Silva Filipe A, Shepherd J, Pascall DJ, Shah R, Jesudason N, Li K, Jarrett R, Pacchiarini N, Bull M, Geidelberg L, Siveroni I; COG-UK Consortium; Goodfellow I, Loman NJ, Pybus OG, Robertson DL, Thomson EC, Rambaut A, Connor TR. Volz E, et al. Among authors: colquhoun rm. Cell. 2021 Jan 7;184(1):64-75.e11. doi: 10.1016/j.cell.2020.11.020. Epub 2020 Nov 19. Cell. 2021. PMID: 33275900 Free PMC article.
Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK.
du Plessis L, McCrone JT, Zarebski AE, Hill V, Ruis C, Gutierrez B, Raghwani J, Ashworth J, Colquhoun R, Connor TR, Faria NR, Jackson B, Loman NJ, O'Toole Á, Nicholls SM, Parag KV, Scher E, Vasylyeva TI, Volz EM, Watts A, Bogoch II, Khan K; COVID-19 Genomics UK (COG-UK) Consortium; Aanensen DM, Kraemer MUG, Rambaut A, Pybus OG. du Plessis L, et al. Among authors: colquhoun r. Science. 2021 Feb 12;371(6530):708-712. doi: 10.1126/science.abf2946. Epub 2021 Jan 8. Science. 2021. PMID: 33419936 Free PMC article.
Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence.
Kraemer MUG, Hill V, Ruis C, Dellicour S, Bajaj S, McCrone JT, Baele G, Parag KV, Battle AL, Gutierrez B, Jackson B, Colquhoun R, O'Toole Á, Klein B, Vespignani A; COVID-19 Genomics UK (COG-UK) Consortium; Volz E, Faria NR, Aanensen DM, Loman NJ, du Plessis L, Cauchemez S, Rambaut A, Scarpino SV, Pybus OG. Kraemer MUG, et al. Among authors: colquhoun r. Science. 2021 Aug 20;373(6557):889-895. doi: 10.1126/science.abj0113. Epub 2021 Jul 22. Science. 2021. PMID: 34301854 Free PMC article.
Genomic reconstruction of the SARS-CoV-2 epidemic in England.
Vöhringer HS, Sanderson T, Sinnott M, De Maio N, Nguyen T, Goater R, Schwach F, Harrison I, Hellewell J, Ariani CV, Gonçalves S, Jackson DK, Johnston I, Jung AW, Saint C, Sillitoe J, Suciu M, Goldman N, Panovska-Griffiths J; Wellcome Sanger Institute COVID-19 Surveillance Team; COVID-19 Genomics UK (COG-UK) Consortium*; Birney E, Volz E, Funk S, Kwiatkowski D, Chand M, Martincorena I, Barrett JC, Gerstung M. Vöhringer HS, et al. Nature. 2021 Dec;600(7889):506-511. doi: 10.1038/s41586-021-04069-y. Epub 2021 Oct 14. Nature. 2021. PMID: 34649268 Free PMC article.
The impact of viral mutations on recognition by SARS-CoV-2 specific T cells.
de Silva TI, Liu G, Lindsey BB, Dong D, Moore SC, Hsu NS, Shah D, Wellington D, Mentzer AJ, Angyal A, Brown R, Parker MD, Ying Z, Yao X, Turtle L, Dunachie S; COVID-19 Genomics UK (COG-UK) Consortium; Maini MK, Ogg G, Knight JC; ISARIC4C Investigators; Peng Y, Rowland-Jones SL, Dong T. de Silva TI, et al. iScience. 2021 Nov 19;24(11):103353. doi: 10.1016/j.isci.2021.103353. Epub 2021 Oct 28. iScience. 2021. PMID: 34729465 Free PMC article.
Context-specific emergence and growth of the SARS-CoV-2 Delta variant.
McCrone JT, Hill V, Bajaj S, Pena RE, Lambert BC, Inward R, Bhatt S, Volz E, Ruis C, Dellicour S, Baele G, Zarebski AE, Sadilek A, Wu N, Schneider A, Ji X, Raghwani J, Jackson B, Colquhoun R, O'Toole Á, Peacock TP, Twohig K, Thelwall S, Dabrera G, Myers R; COVID-19 genomics UK (COG-UK) consortium; Faria NR, Huber C, Bogoch II, Khan K, du Plessis L, Barrett JC, Aanensen DM, Barclay WS, Chand M, Connor T, Loman NJ, Suchard MA, Pybus OG, Rambaut A, Kraemer MUG. McCrone JT, et al. Among authors: colquhoun r. Res Sq [Preprint]. 2021 Dec 20:rs.3.rs-1159614. doi: 10.21203/rs.3.rs-1159614/v1. Res Sq. 2021. Update in: Nature. 2022 Oct;610(7930):154-160. doi: 10.1038/s41586-022-05200-3. PMID: 34981043 Free PMC article. Updated. Preprint.
Context-specific emergence and growth of the SARS-CoV-2 Delta variant.
McCrone JT, Hill V, Bajaj S, Pena RE, Lambert BC, Inward R, Bhatt S, Volz E, Ruis C, Dellicour S, Baele G, Zarebski AE, Sadilek A, Wu N, Schneider A, Ji X, Raghwani J, Jackson B, Colquhoun R, O'Toole Á, Peacock TP, Twohig K, Thelwall S, Dabrera G, Myers R; COVID-19 genomics UK (COG-UK) consortium; Faria NR, Huber C, Bogoch II, Khan K, du Plessis L, Barrett JC, Aanensen DM, Barclay WS, Chand M, Connor T, Loman NJ, Suchard MA, Pybus OG, Rambaut A, Kraemer MUG. McCrone JT, et al. Among authors: colquhoun r. medRxiv [Preprint]. 2021 Dec 21:2021.12.14.21267606. doi: 10.1101/2021.12.14.21267606. medRxiv. 2021. Update in: Nature. 2022 Oct;610(7930):154-160. doi: 10.1038/s41586-022-05200-3. PMID: 34981069 Free PMC article. Updated. Preprint.
Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa.
Viana R, Moyo S, Amoako DG, Tegally H, Scheepers C, Althaus CL, Anyaneji UJ, Bester PA, Boni MF, Chand M, Choga WT, Colquhoun R, Davids M, Deforche K, Doolabh D, du Plessis L, Engelbrecht S, Everatt J, Giandhari J, Giovanetti M, Hardie D, Hill V, Hsiao NY, Iranzadeh A, Ismail A, Joseph C, Joseph R, Koopile L, Kosakovsky Pond SL, Kraemer MUG, Kuate-Lere L, Laguda-Akingba O, Lesetedi-Mafoko O, Lessells RJ, Lockman S, Lucaci AG, Maharaj A, Mahlangu B, Maponga T, Mahlakwane K, Makatini Z, Marais G, Maruapula D, Masupu K, Matshaba M, Mayaphi S, Mbhele N, Mbulawa MB, Mendes A, Mlisana K, Mnguni A, Mohale T, Moir M, Moruisi K, Mosepele M, Motsatsi G, Motswaledi MS, Mphoyakgosi T, Msomi N, Mwangi PN, Naidoo Y, Ntuli N, Nyaga M, Olubayo L, Pillay S, Radibe B, Ramphal Y, Ramphal U, San JE, Scott L, Shapiro R, Singh L, Smith-Lawrence P, Stevens W, Strydom A, Subramoney K, Tebeila N, Tshiabuila D, Tsui J, van Wyk S, Weaver S, Wibmer CK, Wilkinson E, Wolter N, Zarebski AE, Zuze B, Goedhals D, Preiser W, Treurnicht F, Venter M, Williamson C, Pybus OG, Bhiman J, Glass A, Martin DP, Rambaut A, Gaseitsiwe S, von Gottberg A, de Oliveira T. Viana R, et al. Among authors: colquhoun r. Nature. 2022 Mar;603(7902):679-686. doi: 10.1038/s41586-022-04411-y. Epub 2022 Jan 7. Nature. 2022. PMID: 35042229 Free PMC article.
68 results