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

Published version
Peer-reviewed

Type

Article

Change log

Authors

Hill, Verity 
Dewar, Rebecca 
Sahadeo, Nikita 

Abstract

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.

Description

Funder: Trinidad and Tobago - UWI Research Development Impact Fund

Keywords

COVID-19 Genomics UK (COG-UK) Consortium, COVID-19 Impact Project (Trinidad & Tobago Group)

Journal Title

PLOS Glob Public Health

Conference Name

Journal ISSN

2767-3375
2767-3375

Volume Title

2

Publisher

Public Library of Science (PLoS)
Sponsorship
Wellcome Trust (206298/B/17/Z)
Wellcome Trust (207498/Z/17/Z)
Medical Research Council (MC_PC_19027)
MRC (MC_PC_19027)