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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.
Fryer HR, Golubchik T, Hall M, Fraser C, Hinch R, Ferretti L, Thomson L, Nurtay A, Pellis L, House T, MacIntyre-Cockett G, Trebes A, Buck D, Piazza P, Green A, Lonie LJ, Smith D, Bashton M, Crown M, Nelson A, McCann CM, Adnan Tariq M, Elstob CJ, Nunes Dos Santos R, Richards Z, Xhang X, Hawley J, Lee MR, Carrillo-Barragan P, Chapman I, Harthern-Flint S; COVID-19 Genomics UK (COG-UK) consortium; Bonsall D, Lythgoe KA. Fryer HR, et al. Among authors: hall m. PLoS Pathog. 2023 Aug 14;19(8):e1011461. doi: 10.1371/journal.ppat.1011461. eCollection 2023 Aug. PLoS Pathog. 2023. PMID: 37578971 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.
Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver.
Wymant C, Blanquart F, Golubchik T, Gall A, Bakker M, Bezemer D, Croucher NJ, Hall M, Hillebregt M, Ong SH, Ratmann O, Albert J, Bannert N, Fellay J, Fransen K, Gourlay A, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos R, Laeyendecker O, Liitsola K, Meyer L, Porter K, Ristola M, van Sighem A, Berkhout B, Cornelissen M, Kellam P, Reiss P, Fraser C; BEEHIVE Collaboration. Wymant C, et al. Among authors: hall m. Virus Evol. 2018 May 18;4(1):vey007. doi: 10.1093/ve/vey007. eCollection 2018 Jan. Virus Evol. 2018. PMID: 29876136 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.
A highly virulent variant of HIV-1 circulating in the Netherlands.
Wymant C, Bezemer D, Blanquart F, Ferretti L, Gall A, Hall M, Golubchik T, Bakker M, Ong SH, Zhao L, Bonsall D, de Cesare M, MacIntyre-Cockett G, Abeler-Dörner L, Albert J, Bannert N, Fellay J, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos RD, Laeyendecker O, Meyer L, Porter K, Ristola M, van Sighem A, Berkhout B, Kellam P, Cornelissen M, Reiss P, Fraser C; Netherlands ATHENA HIV Observational Cohort†; BEEHIVE Collaboration†. Wymant C, et al. Among authors: hall m. Science. 2022 Feb 4;375(6580):540-545. doi: 10.1126/science.abk1688. Epub 2022 Feb 3. Science. 2022. PMID: 35113714 Free 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.
6,851 results