Genomics-informed outbreak investigations of SARS-CoV-2 using civet

O’Toole, Áine, Hill, Verity, Jackson, Ben, Dewar, Rebecca, Sahadeo, Nikita, Colquhoun, Rachel, Rooke, Stefan, McCrone, J. T., Duggan, Kate, McHugh, Martin P., SamuNicholls, Samuel M, Poplawski, Radoslaw, The COVID-19 Genomics UK (COG-UK) Consortium, The COVID-19 Genomics UK (COG-UK) Consortium, COVID-19 Impact Project (Trinidad & Tobago Group), COVID-19 Impact Project (Trinidad & Tobago Group), Aanensen, David, Holden, Matt, Connor, Tom, Loman, Nick Loman, Goodfellow, Ian, Carrington, Christine V. F., Templeton, Kate, Rambaut, Andrew, Smith, Darren, Bashton, Matthew, Young, Greg, McCann, Clare, Nelson, Andrew, Crown, Matthew, Henderson, John, Hollis, Amy, Stanley, Wiliam and Yew, Wen Chyin (2022) Genomics-informed outbreak investigations of SARS-CoV-2 using civet. PLOS Global Public Health, 2 (12). e0000704. ISSN 2767-3375

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The scale of data produced during the SARS-CoV-2 pandemic has been unprecedented, with more than 13 million sequences shared publicly at the time of writing. This wealth of sequence data provides important context for interpreting local outbreaks. However, placing sequences of interest into national and international context is difficult given the size of the global dataset. Often outbreak investigations and genomic surveillance efforts require running similar analyses again and again on the latest dataset and producing reports. We developed civet (cluster investigation and virus epidemiology tool) to aid these routine analyses and facilitate virus outbreak investigation and surveillance. Civet can place sequences of interest in the local context of background diversity, resolving the query into different ’catchments’ and presenting the phylogenetic results alongside metadata in an interactive, distributable report. Civet can be used on a fine scale for clinical outbreak investigation, for local surveillance and cluster discovery, and to routinely summarise the virus diversity circulating on a national level. Civet reports have helped researchers and public health bodies feedback genomic information in the appropriate context within a timeframe that is useful for public health.

Item Type: Article
Additional Information: Funding: AOT is supported by the Wellcome Trust Hosts, Pathogens & Global Health Programme (grant number: grant.203783/Z/16/Z) and Fast Grants (award number: 2236). V.H. is supported by the Biotechnology and Biological Sciences Research Council (BBSRC) (grant number BB/ M010996/1). AR, RC, JTM acknowledge support from the Wellcome Trust (Collaborators Award 206298/Z/17/Z – ARTIC network). AR is supported by the European Research Council (grant agreement no. 725422 – ReservoirDOCS) and the Bill & Melinda Gates Foundation (OPP1175094 – HIV-PANGEA II). AOT, VH and BJ acknowledge funding from COVID-19 Genomics UK Consortium (COG-UK), which is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) grant code: MC_PC_19027. IG is a Wellcome Senior Fellow and is supported by funding from the Wellcome Trust (ref: 207498/Z/17/Z and 206298/B/17/Z). NS, CVFC and the COVID-19 Impact Project acknowledge funding from the Trinidad and Tobago - UWI Research Development Impact Fund. 'Darren L Smith, Matthew Bashton, Gregory R Young, Clare M McCann, Andrew Nelson, Matthew R Crown, John H Henderson, Amy Hollis, William Stanley, Wen C Yew are members of The COVID-19 Genomics UK (COG-UK) Consortium'.
Subjects: C400 Genetics
Department: Faculties > Health and Life Sciences > Applied Sciences
Depositing User: John Coen
Date Deposited: 22 Feb 2023 13:05
Last Modified: 22 Feb 2023 13:15

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