Abstract
The unprecedented growth of publicly available SARS-CoV-2 genome sequence data has increased the demand for effective and accessible SARS-CoV-2 data analysis and visualization tools. The majority of the currently available tools either require computational expertise to deploy them or limit user input to preselected subsets of SARS-CoV-2 genomes. To address these limitations, we developed ViralVar, a publicly available, point-and-click webtool that gives users the freedom to investigate and visualize user-selected subsets of SARS-CoV-2 genomes obtained from the GISAID public database. ViralVar has two primary features that enable: (1) the visualization of the spatiotemporal dynamics of SARS-CoV-2 lineages and (2) a structural/functional analysis of genomic mutations. As proof-of-principle, ViralVar was used to explore the evolution of the SARS-CoV-2 pandemic in the USA in pediatric, adult, and elderly populations (n > 1.7 million genomes). Whereas the spatiotemporal dynamics of the variants did not differ between these age groups, several USA-specific sublineages arose relative to the rest of the world. Our development and utilization of ViralVar to provide insights on the evolution of SARS-CoV-2 in the USA demonstrates the importance of developing accessible tools to facilitate and accelerate the large-scale surveillance of circulating pathogens.
| Original language | English (US) |
|---|---|
| Article number | 2714 |
| Journal | Viruses |
| Volume | 14 |
| Issue number | 12 |
| DOIs | |
| State | Published - Dec 2022 |
Funding
We gratefully acknowledge the authors from the originating laboratories and the submitting laboratories, who generated and shared via the GISAID genetic sequence data on which this research is based, as well as the structural biology groups for contributing their structures to the PDB. This research is supported by grants (R21 AI163912 to Hultquist, U19 AI171110 to Hultquist, U19 AI135964 to Ozer) from the National Institutes of Health; a grant (to Lorenzo-Redondo) from the Northwestern University Havey Institute for Global Health; and a grant (to Ozer and Hultquist) from the Walder Foundation’s Chicago Coronavirus Assessment Network. This research was supported, in part, through the computational resources and staff contributions provided by the Quest high performance computing facility at Northwestern University, which is jointly supported by the Office of the Provost, the Office for Research, and Northwestern University Information Technology. The funding sources had no role in the study design, data collection, analysis, interpretation, or writing of the report.
Keywords
- COVID-19
- SARS-CoV-2
- ViralVar
- evolution
- genomic surveillance
- mutation
- webtool
ASJC Scopus subject areas
- Infectious Diseases
- Virology
