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Tracking SARS-CoV-2 mutations and variants through the COG-UK-Mutation Explorer.
Wright DW, Harvey WT, Hughes J, Cox M, Peacock TP, Colquhoun R, Jackson B, Orton R, Nielsen M, Hsu NS; COVID-19 Genomics UK (COG-UK) consortium; Harrison EM, de Silva TI, Rambaut A, Peacock SJ, Robertson DL, Carabelli AM. Wright DW, et al. Among authors: de silva ti. Virus Evol. 2022 Mar 18;8(1):veac023. doi: 10.1093/ve/veac023. eCollection 2022. Virus Evol. 2022. PMID: 35502202 Free PMC article.
Co-infections, secondary infections, and antimicrobial use in patients hospitalised with COVID-19 during the first pandemic wave from the ISARIC WHO CCP-UK study: a multicentre, prospective cohort study.
Russell CD, Fairfield CJ, Drake TM, Turtle L, Seaton RA, Wootton DG, Sigfrid L, Harrison EM, Docherty AB, de Silva TI, Egan C, Pius R, Hardwick HE, Merson L, Girvan M, Dunning J, Nguyen-Van-Tam JS, Openshaw PJM, Baillie JK, Semple MG, Ho A; ISARIC4C investigators. Russell CD, et al. Among authors: de silva ti. Lancet Microbe. 2021 Aug;2(8):e354-e365. doi: 10.1016/S2666-5247(21)00090-2. Epub 2021 Jun 2. Lancet Microbe. 2021. PMID: 34100002 Free PMC article.
Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data.
Stirrup O, Hughes J, Parker M, Partridge DG, Shepherd JG, Blackstone J, Coll F, Keeley A, Lindsey BB, Marek A, Peters C, Singer JB; COVID-19 Genomics UK (COG-UK) consortium; Tamuri A, de Silva TI, Thomson EC, Breuer J. Stirrup O, et al. Among authors: de silva ti. Elife. 2021 Jun 29;10:e65828. doi: 10.7554/eLife.65828. Elife. 2021. PMID: 34184637 Free PMC article.
Characterisation of in-hospital complications associated with COVID-19 using the ISARIC WHO Clinical Characterisation Protocol UK: a prospective, multicentre cohort study.
Drake TM, Riad AM, Fairfield CJ, Egan C, Knight SR, Pius R, Hardwick HE, Norman L, Shaw CA, McLean KA, Thompson AAR, Ho A, Swann OV, Sullivan M, Soares F, Holden KA, Merson L, Plotkin D, Sigfrid L, de Silva TI, Girvan M, Jackson C, Russell CD, Dunning J, Solomon T, Carson G, Olliaro P, Nguyen-Van-Tam JS, Turtle L, Docherty AB, Openshaw PJ, Baillie JK, Harrison EM, Semple MG; ISARIC4C investigators. Drake TM, et al. Among authors: de silva ti. Lancet. 2021 Jul 17;398(10296):223-237. doi: 10.1016/S0140-6736(21)00799-6. Lancet. 2021. PMID: 34274064 Free PMC article.
Evolution of viral variants in remdesivir-treated and untreated SARS-CoV-2-infected pediatrics patients.
Boshier FAT, Pang J, Penner J, Parker M, Alders N, Bamford A, Grandjean L, Grunewald S, Hatcher J, Best T, Dalton C, Bynoe PD, Frauenfelder C, Köeglmeier J, Myerson P, Roy S, Williams R, de Silva TI, Goldstein RA, Breuer J; COVID-19 Genomics UK (COG-UK) consortium. Boshier FAT, et al. Among authors: de silva ti. J Med Virol. 2022 Jan;94(1):161-172. doi: 10.1002/jmv.27285. Epub 2021 Sep 4. J Med Virol. 2022. PMID: 34415583 Free PMC article.
Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level.
Leary S, Gaudieri S, Parker MD, Chopra A, James I, Pakala S, Alves E, John M, Lindsey BB, Keeley AJ, Rowland-Jones SL, Swanson MS, Ostrov DA, Bubenik JL, Das SR, Sidney J, Sette A; COVID-19 Genomics UK (COG-UK) consortium; de Silva TI, Phillips E, Mallal S. Leary S, et al. Among authors: de silva ti. Pathog Immun. 2021 Aug 20;6(2):27-49. doi: 10.20411/pai.v6i2.460. eCollection 2021. Pathog Immun. 2021. PMID: 34541432 Free PMC article.
Genomic and Epidemiological Analysis of SARS-CoV-2 Viruses in Sri Lanka.
Jeewandara C, Jayathilaka D, Ranasinghe D, Hsu NS, Ariyaratne D, Jayadas TT, Panambara Arachchige DM, Lindsey BB, Gomes L, Parker MD, Wijewickrama A, Karunaratne M, Ogg GS, de Silva TI, Malavige GN. Jeewandara C, et al. Among authors: de silva ti. Front Microbiol. 2021 Sep 16;12:722838. doi: 10.3389/fmicb.2021.722838. eCollection 2021. Front Microbiol. 2021. PMID: 34603246 Free PMC article.
The Alpha variant was not associated with excess nosocomial SARS-CoV-2 infection in a multi-centre UK hospital study.
Boshier FAT, Venturini C, Stirrup O, Guerra-Assunção JA, Alcolea-Medina A, Becket AH, Byott M, Charalampous T, Filipe ADS, Frampton D, Glaysher S, Khan T, Kulasegara-Shylini R, Kele B, Monahan IM, Mollett G, Parker M, Pelosi E, Randell P, Roy S, Taylor JF, Weller SJ, Wilson-Davies E, Wade P, Williams R, Copas AJ, Cutino-Moguel T, Freemantle N, Hayward AC, Holmes A, Hughes J, Mahungu TW, Nebbia G, Nastouli E, Partridge DG, Pope CF, Price JR, Robson SC, Saeed K, Shin GY, de Silva TI, Snell LB, Thomson EC, Witney AA, Breuer J; COG-UK HOCI Variant Substudy consortium*, The COVID-19 Genomics UK (COG-UK) consortium. Boshier FAT, et al. Among authors: de silva ti. J Infect. 2021 Dec;83(6):693-700. doi: 10.1016/j.jinf.2021.09.022. Epub 2021 Oct 2. J Infect. 2021. PMID: 34610391 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.
155 results