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.

Publikováno v: Virus evolution [Virus Evol] 2024 Oct 17; Vol. 10 (1), pp. veae083. Date of Electronic Publication: 2024 Oct 17 (Print Publication: 2024).

Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package.

Autor: Griffiths EJ; Faculty of Health Sciences, Simon Fraser University, Burnaby V5A 1S6, BC, Canada., Timme RE; Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD 20740, USA., Mendes CI; Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal., Page AJ; Microbes in the Food Chain, Quadram Institute Bioscience, Norwich, Norfolk NR4 7UQ, UK., Alikhan NF; Microbes in the Food Chain, Quadram Institute Bioscience, Norwich, Norfolk NR4 7UQ, UK., Fornika D; BC Centre for Disease Control Public Health Laboratory, Vancouver, BC V5Z 4R4, Canada., Maguire F; Faculty of Computer Science, Dalhousie University, Halifax, NS B3H 1W5, Canada., Campos J; INEI-ANLIS 'Dr Carlos G. Malbrán,' Buenos Aires C1282AFF, Argentina., Park D; Infectious Disease and Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA., Olawoye IB; African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State 232103, Nigeria.; Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State 232103, Nigeria., Oluniyi PE; African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State 232103, Nigeria.; Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State 232103, Nigeria., Anderson D; South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7530, South Africa., Christoffels A; South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7530, South Africa., da Silva AG; Microbiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC 3000, Australia., Cameron R; Faculty of Health Sciences, Simon Fraser University, Burnaby V5A 1S6, BC, Canada., Dooley D; Faculty of Health Sciences, Simon Fraser University, Burnaby V5A 1S6, BC, Canada., Katz LS; Center for Food Safety, University of Georgia, Atlanta, GA 30333, USA.; Office of Advanced Molecular Detection, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, GA 30333, USA., Black A; Department of Epidemiology, University of Washington, WA 98109, USA., Karsch-Mizrachi I; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA., Barrett T; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA., Johnston A; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA., Connor TR; Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK.; Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK., Nicholls SM; University of Birmingham, Birmingham B17 2TT, UK., Witney AA; Institute for Infection and Immunity, St George's, University of London, London SW17 0RE, UK., Tyson GH; Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD 20708, USA., Tausch SH; Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin 12277, Germany., Raphenya AR; Department of Biochemistry and Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada., Alcock B; Department of Biochemistry and Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada., Aanensen DM; Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Cambridge CB10 1SA, UK.; The Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK., Hodcroft E; Biozentrum, University of Basel, Basel 3012, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland., Hsiao WWL; Faculty of Health Sciences, Simon Fraser University, Burnaby V5A 1S6, BC, Canada.; BC Centre for Disease Control Public Health Laboratory, Vancouver, BC V5Z 4R4, Canada.; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z7 V6T 1Z7, Canada., Vasconcelos ATR; Bioinformatics Laboratory National Laboratory of Scientific Computation LNCC/MCTI, Petrópolis 25651-075, Brazil., MacCannell DR; Office of Advanced Molecular Detection, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, GA 30333, USA.

Publikováno v: GigaScience [Gigascience] 2022 Feb 16; Vol. 11.

CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance.

Autor: Nicholls SM; Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK., Poplawski R; Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK., Bull MJ; Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK., Underwood A; Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK.; Oxford Big Data Institute, Old Road Campus, Oxford, UK., Chapman M; Health Data Research UK Cambridge, Wellcome Genome Campus, Hinxton, UK., Abu-Dahab K; Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK.; Oxford Big Data Institute, Old Road Campus, Oxford, UK., Taylor B; Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK.; Oxford Big Data Institute, Old Road Campus, Oxford, UK., Colquhoun RM; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK., Rowe WPM; Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK., Jackson B; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK., Hill V; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK., O'Toole Á; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK., Rey S; Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK., Southgate J; School of Biosciences, The Sir Martin Evans Building, Cardiff University, Cardiff, UK., Amato R; Wellcome Sanger Institute, Hinxton, UK., Livett R; Wellcome Sanger Institute, Hinxton, UK., Gonçalves S; Wellcome Sanger Institute, Hinxton, UK., Harrison EM; Wellcome Sanger Institute, Hinxton, UK.; Department of Medicine, University of Cambridge, Cambridge, UK.; Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK., Peacock SJ; Department of Medicine, University of Cambridge, Cambridge, UK., Aanensen DM; Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK.; Oxford Big Data Institute, Old Road Campus, Oxford, UK., Rambaut A; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK., Connor TR; Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK.; School of Biosciences, The Sir Martin Evans Building, Cardiff University, Cardiff, UK.; Quadram Institute, Norwich, UK., Loman NJ; Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK. n.j.loman@bham.ac.uk.

Publikováno v: Genome biology [Genome Biol] 2021 Jul 01; Vol. 22 (1), pp. 196. Date of Electronic Publication: 2021 Jul 01.

SARS-CoV-2 within-host diversity and transmission.

Autor: Lythgoe KA; Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK. Tanya.Golubchik@bdi.ox.ac.uk Katrina.Lythgoe@bdi.ox.ac.uk Matthew.Hall@bdi.ox.ac.uk.; Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK., Hall M; Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK. Tanya.Golubchik@bdi.ox.ac.uk Katrina.Lythgoe@bdi.ox.ac.uk Matthew.Hall@bdi.ox.ac.uk., Ferretti L; Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK., de Cesare M; Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK.; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK., MacIntyre-Cockett G; Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK.; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK., Trebes A; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK., Andersson M; Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.; Division of Medical Virology, Stellenbosch University, Stellenbosch, South Africa., Otecko N; Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK., Wise EL; Hampshire Hospitals NHS Foundation Trust, Basingstoke and North Hampshire Hospital, Basingstoke RG24 9NA, UK.; School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, UK., Moore N; Hampshire Hospitals NHS Foundation Trust, Basingstoke and North Hampshire Hospital, Basingstoke RG24 9NA, UK., Lynch J; Hampshire Hospitals NHS Foundation Trust, Basingstoke and North Hampshire Hospital, Basingstoke RG24 9NA, UK., Kidd S; Hampshire Hospitals NHS Foundation Trust, Basingstoke and North Hampshire Hospital, Basingstoke RG24 9NA, UK., Cortes N; Hampshire Hospitals NHS Foundation Trust, Basingstoke and North Hampshire Hospital, Basingstoke RG24 9NA, UK.; Gibraltar Health Authority, Gibraltar, UK., Mori M; School of Medicine, University of Southampton, Southampton SO17 1BJ, UK., Williams R; Hampshire Hospitals NHS Foundation Trust, Basingstoke and North Hampshire Hospital, Basingstoke RG24 9NA, UK., Vernet G; Hampshire Hospitals NHS Foundation Trust, Basingstoke and North Hampshire Hospital, Basingstoke RG24 9NA, UK., Justice A; Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK., Green A; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK., Nicholls SM; Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK., Ansari MA; Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK., Abeler-Dörner L; Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK., Moore CE; Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK., Peto TEA; Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.; Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK., Eyre DW; Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.; Big Data Institute, Nuffield Department of Public Health, University of Oxford, Old Road Campus, Oxford OX3 7FL, UK., Shaw R; Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK., Simmonds P; Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK., Buck D; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK., Todd JA; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK., Connor TR; Pathogen Genomics Unit, Public Health Wales Microbiology, Cardiff CF10 4BZ, UK.; Cardiff University School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK., Ashraf S; MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK., da Silva Filipe A; MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK., Shepherd J; MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK., Thomson EC; MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK., Bonsall D; Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK.; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK.; Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK., Fraser C; Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK.; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Biomedical Research Centre, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK.; Wellcome Sanger Institute, Cambridge CB10 1SA, UK., Golubchik T; Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK. Tanya.Golubchik@bdi.ox.ac.uk Katrina.Lythgoe@bdi.ox.ac.uk Matthew.Hall@bdi.ox.ac.uk.; Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK.

Publikováno v: Science (New York, N.Y.) [Science] 2021 Apr 16; Vol. 372 (6539). Date of Electronic Publication: 2021 Mar 09.

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Autor: Volz E; MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK. Electronic address: e.volz@imperial.ac.uk., Hill V; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK., McCrone JT; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK., Price A; School of Biosciences, Cardiff University, Cardiff, UK., Jorgensen D; MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK., O'Toole Á; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK., Southgate J; School of Biosciences, Cardiff University, Cardiff, UK; Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK., Johnson R; MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK., Jackson B; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK., Nascimento FF; MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK., Rey SM; Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK., Nicholls SM; Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK., Colquhoun RM; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK., da Silva Filipe A; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK., Shepherd J; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK., Pascall DJ; Institute of Biodiversity, Animal Health and Comparative Medicine, Boyd Orr Centre for Population and Ecosystem Health, University of Glasgow, Glasgow, UK., Shah R; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK., Jesudason N; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK., Li K; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK., Jarrett R; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK., Pacchiarini N; Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK., Bull M; Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK., Geidelberg L; MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK., Siveroni I; MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK., Goodfellow I; Department of Pathology, University of Cambridge, Cambridge, UK., Loman NJ; Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK., Pybus OG; Department of Zoology, University of Oxford, Oxford, UK; Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, UK., Robertson DL; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK., Thomson EC; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK., Rambaut A; Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK. Electronic address: a.rambaut@ed.ac.uk., Connor TR; School of Biosciences, Cardiff University, Cardiff, UK; Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK; Quadram Institute Bioscience, Norwich, UK. Electronic address: connortr@cardiff.ac.uk.

Publikováno v: Cell [Cell] 2021 Jan 07; Vol. 184 (1), pp. 64-75.e11. Date of Electronic Publication: 2020 Nov 19.