ArticlePLOS global public health2022
Genomics-informed outbreak investigations of SARS-CoV-2 using civet.
Article in PLOS global public health, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
13 citing papers in PubMed, 16 citations in OpenAlex.
- 'Vivaldi': an amplicon-based whole-genome sequencing method for the four seasonal human coronaviruses, 229E, NL63, OC43 and HKU1, alongside SARS-CoV-2.Microbial genomics · 2025Article
- Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2.bioRxiv : the preprint server for biology · 2024Article
- Publication-ready single nucleotide polymorphism visualization with snipit.Bioinformatics (Oxford, England) · 2024Article
- Article
- Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2.Virus evolution · 2024Article
- A phylogenetics and variant calling pipeline to support SARS-CoV-2 genomic epidemiology in the UK.Virus evolution · 2024Article
- Toward a global virus genomic surveillance network.Cell host & microbe · 2023Review
- Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes.The Journal of hospital infection · 2023Article
- How public health authorities can use pathogen genomics in health protection practice: a consensus-building Delphi study conducted in the United Kingdom.Microbial genomics · 2023Article
- gofasta: command-line utilities for genomic epidemiology research.Bioinformatics (Oxford, England) · 2022Article
- Repeated transmission of SARS-CoV-2 in an overcrowded Irish emergency department elucidated by whole-genome sequencing.The Journal of hospital infection · 2022Article
- Recurrent SARS-CoV-2 mutations in immunodeficient patients.Virus evolution · 2022Article
- A large outbreak of COVID-19 in a UK prison, October 2020 to April 2021.Epidemiology and infection · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
22 authors at 9 institutions in 2 countries.
Funding
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.
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.