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The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape.
Martin DP, Weaver S, Tegally H, San EJ, Shank SD, Wilkinson E, Lucaci AG, Giandhari J, Naidoo S, Pillay Y, Singh L, Lessells RJ; NGS-SA; COVID-19 Genomics UK (COG-UK); Gupta RK, Wertheim JO, Nekturenko A, Murrell B, Harkins GW, Lemey P, MacLean OA, Robertson DL, de Oliveira T, Kosakovsky Pond SL. Martin DP, et al. Among authors: gupta rk. medRxiv [Preprint]. 2021 Jul 25:2021.02.23.21252268. doi: 10.1101/2021.02.23.21252268. medRxiv. 2021. Update in: Cell. 2021 Sep 30;184(20):5189-5200.e7. doi: 10.1016/j.cell.2021.09.003 PMID: 33688681 Free PMC article. Updated. Preprint.
The biological and clinical significance of emerging SARS-CoV-2 variants.
Tao K, Tzou PL, Nouhin J, Gupta RK, de Oliveira T, Kosakovsky Pond SL, Fera D, Shafer RW. Tao K, et al. Among authors: gupta rk. Nat Rev Genet. 2021 Dec;22(12):757-773. doi: 10.1038/s41576-021-00408-x. Epub 2021 Sep 17. Nat Rev Genet. 2021. PMID: 34535792 Free PMC article. Review.
The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages.
Martin DP, Weaver S, Tegally H, San JE, Shank SD, Wilkinson E, Lucaci AG, Giandhari J, Naidoo S, Pillay Y, Singh L, Lessells RJ; NGS-SA; COVID-19 Genomics UK (COG-UK); Gupta RK, Wertheim JO, Nekturenko A, Murrell B, Harkins GW, Lemey P, MacLean OA, Robertson DL, de Oliveira T, Kosakovsky Pond SL. Martin DP, et al. Among authors: gupta rk. Cell. 2021 Sep 30;184(20):5189-5200.e7. doi: 10.1016/j.cell.2021.09.003. Epub 2021 Sep 7. Cell. 2021. PMID: 34537136 Free PMC article.
Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function.
Martin DP, Lytras S, Lucaci AG, Maier W, Grüning B, Shank SD, Weaver S, MacLean OA, Orton RJ, Lemey P, Boni MF, Tegally H, Harkins GW, Scheepers C, Bhiman JN, Everatt J, Amoako DG, San JE, Giandhari J, Sigal A; NGS-SA; Williamson C, Hsiao NY, von Gottberg A, De Klerk A, Shafer RW, Robertson DL, Wilkinson RJ, Sewell BT, Lessells R, Nekrutenko A, Greaney AJ, Starr TN, Bloom JD, Murrell B, Wilkinson E, Gupta RK, de Oliveira T, Kosakovsky Pond SL. Martin DP, et al. Among authors: gupta rk. Mol Biol Evol. 2022 Apr 11;39(4):msac061. doi: 10.1093/molbev/msac061. Mol Biol Evol. 2022. PMID: 35325204 Free PMC article.
Population Effectiveness of Dolutegravir Implementation in Uganda: A Prospective Observational Cohort Study (DISCO), 48-Week Results.
McCluskey SM, Muyindike WR, Nanfuka V, Omoding D, Komukama N, Barigye IT, Kansiime L, Tumusiime J, Aung TN, Stuckwisch A, Hedt-Gauthier B, Marconi VC, Moosa MS, Pillay D, Giandhari J, Lessells R, Gupta RK, Siedner MJ. McCluskey SM, et al. Among authors: gupta rk. J Infect Dis. 2024 Sep 23;230(3):e622-e630. doi: 10.1093/infdis/jiae260. J Infect Dis. 2024. PMID: 38748986 Free PMC article.
Predicted antiviral activity of tenofovir versus abacavir in combination with a cytosine analogue and the integrase inhibitor dolutegravir in HIV-1-infected South African patients initiating or failing first-line ART.
Derache A, Iwuji CC, Danaviah S, Giandhari J, Marcelin AG, Calvez V, de Oliveira T, Dabis F, Pillay D, Gupta RK. Derache A, et al. Among authors: gupta rk. J Antimicrob Chemother. 2019 Feb 1;74(2):473-479. doi: 10.1093/jac/dky428. J Antimicrob Chemother. 2019. PMID: 30380053 Free PMC article. Clinical Trial.
Trends in Pretreatment HIV-1 Drug Resistance in Antiretroviral Therapy-naive Adults in South Africa, 2000-2016: A Pooled Sequence Analysis.
Chimukangara B, Lessells RJ, Rhee SY, Giandhari J, Kharsany ABM, Naidoo K, Lewis L, Cawood C, Khanyile D, Ayalew KA, Diallo K, Samuel R, Hunt G, Vandormael A, Stray-Pedersen B, Gordon M, Makadzange T, Kiepiela P, Ramjee G, Ledwaba J, Kalimashe M, Morris L, Parikh UM, Mellors JW, Shafer RW, Katzenstein D, Moodley P, Gupta RK, Pillay D, Abdool Karim SS, de Oliveira T. Chimukangara B, et al. Among authors: gupta rk. EClinicalMedicine. 2019 Mar 18;9:26-34. doi: 10.1016/j.eclinm.2019.03.006. eCollection 2019 Mar. EClinicalMedicine. 2019. PMID: 31143879 Free PMC article.
SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies.
Collier DA, De Marco A, Ferreira IATM, Meng B, Datir R, Walls AC, Kemp S SA, Bassi J, Pinto D, Fregni CS, Bianchi S, Tortorici MA, Bowen J, Culap K, Jaconi S, Cameroni E, Snell G, Pizzuto MS, Pellanda AF, Garzoni C, Riva A; CITIID-NIHR BioResource COVID-19 Collaboration; Elmer A, Kingston N, Graves B, McCoy LE, Smith KG, Bradley JR, Temperton N, Ceron-Gutierrez L L, Barcenas-Morales G; COVID-19 Genomics UK (COG-UK) consortium; Harvey W, Virgin HW, Lanzavecchia A, Piccoli L, Doffinger R, Wills M, Veesler D, Corti D, Gupta RK. Collier DA, et al. Among authors: gupta rk. medRxiv [Preprint]. 2021 Feb 15:2021.01.19.21249840. doi: 10.1101/2021.01.19.21249840. medRxiv. 2021. Update in: Nature. 2021 May;593(7857):136-141. doi: 10.1038/s41586-021-03412-7 PMID: 33619509 Free PMC article. Updated. Preprint.
2,816 results