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Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey.
Lythgoe KA, Golubchik T, Hall M, House T, Cahuantzi R, MacIntyre-Cockett G, Fryer H, Thomson L, Nurtay A, Ghafani M, Buck D, Green A, Trebes A, Piazza P, Lonie LJ, Studley R, Rourke E, Smith D, Bashton M, Nelson A, Crown M, McCann C, Young GR, Andre Nunes Dos Santos R, Richards Z, Tariq A; Wellcome Sanger Institute COVID-19 Surveillance Team; COVID-19 Infection Survey Group, The COVID-19 Genomics UK (COG-UK) Consortium; Fraser C, Diamond I, Barrett J, Walker AS, Bonsall D. Lythgoe KA, et al. Among authors: hall m. Proc Biol Sci. 2023 Oct 25;290(2009):20231284. doi: 10.1098/rspb.2023.1284. Epub 2023 Oct 18. Proc Biol Sci. 2023. PMID: 37848057 Free PMC article.
PHYLOSCANNER: Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity.
Wymant C, Hall M, Ratmann O, Bonsall D, Golubchik T, de Cesare M, Gall A, Cornelissen M, Fraser C; STOP-HCV Consortium, The Maela Pneumococcal Collaboration, and The BEEHIVE Collaboration. Wymant C, et al. Among authors: hall m. Mol Biol Evol. 2018 Mar 1;35(3):719-733. doi: 10.1093/molbev/msx304. Mol Biol Evol. 2018. PMID: 29186559 Free PMC article.
A Comprehensive Genomics Solution for HIV Surveillance and Clinical Monitoring in Low-Income Settings.
Bonsall D, Golubchik T, de Cesare M, Limbada M, Kosloff B, MacIntyre-Cockett G, Hall M, Wymant C, Ansari MA, Abeler-Dörner L, Schaap A, Brown A, Barnes E, Piwowar-Manning E, Eshleman S, Wilson E, Emel L, Hayes R, Fidler S, Ayles H, Bowden R, Fraser C; HPTN 071 (PopART) Team. Bonsall D, et al. Among authors: hall m. J Clin Microbiol. 2020 Sep 22;58(10):e00382-20. doi: 10.1128/JCM.00382-20. Print 2020 Sep 22. J Clin Microbiol. 2020. PMID: 32669382 Free PMC article.
SARS-CoV-2 within-host diversity and transmission.
Lythgoe KA, Hall M, Ferretti L, de Cesare M, MacIntyre-Cockett G, Trebes A, Andersson M, Otecko N, Wise EL, Moore N, Lynch J, Kidd S, Cortes N, Mori M, Williams R, Vernet G, Justice A, Green A, Nicholls SM, Ansari MA, Abeler-Dörner L, Moore CE, Peto TEA, Eyre DW, Shaw R, Simmonds P, Buck D, Todd JA; Oxford Virus Sequencing Analysis Group (OVSG); Connor TR, Ashraf S, da Silva Filipe A, Shepherd J, Thomson EC; COVID-19 Genomics UK (COG-UK) Consortium; Bonsall D, Fraser C, Golubchik T. Lythgoe KA, et al. Among authors: hall m. Science. 2021 Apr 16;372(6539):eabg0821. doi: 10.1126/science.abg0821. Epub 2021 Mar 9. Science. 2021. PMID: 33688063 Free PMC article.
OpenABM-Covid19-An agent-based model for non-pharmaceutical interventions against COVID-19 including contact tracing.
Hinch R, Probert WJM, Nurtay A, Kendall M, Wymant C, Hall M, Lythgoe K, Bulas Cruz A, Zhao L, Stewart A, Ferretti L, Montero D, Warren J, Mather N, Abueg M, Wu N, Legat O, Bentley K, Mead T, Van-Vuuren K, Feldner-Busztin D, Ristori T, Finkelstein A, Bonsall DG, Abeler-Dörner L, Fraser C. Hinch R, et al. Among authors: hall m. PLoS Comput Biol. 2021 Jul 12;17(7):e1009146. doi: 10.1371/journal.pcbi.1009146. eCollection 2021 Jul. PLoS Comput Biol. 2021. PMID: 34252083 Free PMC article.
Viral infection and transmission in a large, well-traced outbreak caused by the SARS-CoV-2 Delta variant.
Li B, Deng A, Li K, Hu Y, Li Z, Shi Y, Xiong Q, Liu Z, Guo Q, Zou L, Zhang H, Zhang M, Ouyang F, Su J, Su W, Xu J, Lin H, Sun J, Peng J, Jiang H, Zhou P, Hu T, Luo M, Zhang Y, Zheng H, Xiao J, Liu T, Tan M, Che R, Zeng H, Zheng Z, Huang Y, Yu J, Yi L, Wu J, Chen J, Zhong H, Deng X, Kang M, Pybus OG, Hall M, Lythgoe KA, Li Y, Yuan J, He J, Lu J. Li B, et al. Among authors: hall m. Nat Commun. 2022 Jan 24;13(1):460. doi: 10.1038/s41467-022-28089-y. Nat Commun. 2022. PMID: 35075154 Free PMC article.
Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load.
Zhao L, Wymant C, Blanquart F, Golubchik T, Gall A, Bakker M, Bezemer D, Hall M, Ong SH, Albert J, Bannert N, Fellay J, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos RD, Laeyendecker O, Meyer L, Porter K, van Sighem A, van der Valk M, Berkhout B, Kellam P, Cornelissen M, Reiss P, Fraser C, Ferretti L. Zhao L, et al. Among authors: hall m. Virus Evol. 2022 Mar 16;8(1):veac022. doi: 10.1093/ve/veac022. eCollection 2022. Virus Evol. 2022. PMID: 35402002 Free PMC article.
The mutational spectrum of SARS-CoV-2 genomic and antigenomic RNA.
Zhao L, Hall M, de Cesare M, MacIntyre-Cockett G, Lythgoe K, Fraser C, Bonsall D, Golubchik T; COVID-19 Genomics UK (COG-UK) Consortium; Ferretti L. Zhao L, et al. Among authors: hall m. Proc Biol Sci. 2022 Nov 30;289(1987):20221747. doi: 10.1098/rspb.2022.1747. Epub 2022 Nov 16. Proc Biol Sci. 2022. PMID: 36382519 Free PMC article.
6,854 results