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Genomics-informed outbreak investigations of SARS-CoV-2 using civet
Áine O'Toole1, Verity Hill1, Ben Jackson1
1Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom.
PLOS Global Public Health
|March 24, 2023
Summary
The SARS-CoV-2 pandemic generated vast sequence data. Civet (cluster investigation and virus epidemiology tool) aids outbreak investigations by contextualizing viral sequences within local and global diversity for public health surveillance.
Area of Science:
- Genomic epidemiology
- Bioinformatics
- Public health surveillance
Background:
- The SARS-CoV-2 pandemic has resulted in an unprecedented volume of publicly shared viral sequence data.
- Interpreting local outbreaks requires placing viral sequences within broader national and international contexts, which is challenging due to dataset size.
- Routine genomic surveillance and outbreak investigations often involve repetitive analyses of updated datasets.
Purpose of the Study:
- To develop a tool, civet (cluster investigation and virus epidemiology tool), to streamline routine genomic analyses for virus outbreak investigation and surveillance.
- To enable researchers and public health bodies to place viral sequences of interest into local, national, and international contexts.
- To facilitate the timely feedback of genomic information for public health decision-making.
Main Methods:
- Civet analyzes viral sequences to place them within the context of background diversity, identifying distinct 'catchments'.
- It generates interactive, distributable reports that integrate phylogenetic results with relevant metadata.
- The tool supports analyses at various scales, from clinical outbreak investigations to national-level summaries of viral diversity.
Main Results:
- Civet effectively resolves query sequences into different catchments, providing local context.
- The tool facilitates the creation of interactive reports for visualizing phylogenetic data and metadata.
- Reports generated by Civet have been utilized by researchers and public health entities to provide contextualized genomic insights.
Conclusions:
- Civet is a valuable tool for routine genomic surveillance and outbreak investigation of viruses like SARS-CoV-2.
- The tool enhances the ability to interpret viral sequence data within relevant epidemiological contexts.
- Civet supports timely and effective public health responses by providing actionable genomic information.
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