A phylogenetics and variant calling pipeline to support SARS-CoV-2 genomic epidemiology in the UK.

Autor:	Colquhoun R; Institute of Ecology and Evolution, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Rd, Edinburgh EH9 3FL, United Kingdom., O'Toole Á; Institute of Ecology and Evolution, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Rd, Edinburgh EH9 3FL, United Kingdom., Hill V; Institute of Ecology and Evolution, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Rd, Edinburgh EH9 3FL, United Kingdom.; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 60 College St, New Haven, CT 06510, United States., McCrone JT; Institute of Ecology and Evolution, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Rd, Edinburgh EH9 3FL, United Kingdom.; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave. N., Seattle, WA 98109-1024, United States., Yu X; Institute of Ecology and Evolution, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Rd, Edinburgh EH9 3FL, United Kingdom., Nicholls SM; Institute of Microbiology and Infection, University of Birmingham, School of Biosciences, Birmingham B15 2TT, United Kingdom., Poplawski R; Institute of Microbiology and Infection, University of Birmingham, School of Biosciences, Birmingham B15 2TT, United Kingdom., Whalley T; School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, Wales CF10 3AX, United Kingdom., Groves N; TARZET Division, UK Health Security Agency, 10 South Colonnade, Canary Wharf, London E14 4PU, United Kingdom., Ellaby N; TARZET Division, UK Health Security Agency, 10 South Colonnade, Canary Wharf, London E14 4PU, United Kingdom., Loman N; Institute of Microbiology and Infection, University of Birmingham, School of Biosciences, Birmingham B15 2TT, United Kingdom., Connor T; School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, Wales CF10 3AX, United Kingdom.; Pathogen Genomics Unit, Public Health Wales, Number 2 Capital Quarter, Tyndall St., Cardiff CF10 4BZ, United Kingdom., Rambaut A; Institute of Ecology and Evolution, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Rd, Edinburgh EH9 3FL, United Kingdom.
Jazyk:	angličtina
Zdroj:	Virus evolution [Virus Evol] 2024 Oct 17; Vol. 10 (1), pp. veae083. Date of Electronic Publication: 2024 Oct 17 (Print Publication: 2024).
DOI:	10.1093/ve/veae083
Abstrakt:	In response to the escalating SARS-CoV-2 pandemic, in March 2020 the COVID-19 Genomics UK (COG-UK) consortium was established to enable national-scale genomic surveillance in the UK. By the end of 2020, 49% of all SARS-CoV-2 genome sequences globally had been generated as part of the COG-UK programme, and to date, this system has generated >3 million SARS-CoV-2 genomes. Rapidly and reliably analysing this unprecedented number of genomes was an enormous challenge. To fulfil this need and to inform public health decision-making, we developed a centralized pipeline that performs quality control, alignment, and variant calling and provides the global phylogenetic context of sequences. We present this pipeline and describe how we tailored it as the pandemic progressed to scale with the increasing amounts of data and to provide the most relevant analyses on a daily basis. Competing Interests: None declared. (© The Author(s) 2024. Published by Oxford University Press.)
Databáze:	MEDLINE
Externí odkaz:	Zobrazit plný text záznamu