ViralVar: A Web Tool for Multilevel Visualization of SARS-CoV-2 Genomes

Arghavan Alisoltani*, Lukasz Jaroszewski, Adam Godzik, Arash Iranzadeh, Lacy M. Simons, Taylor J. Dean, Ramon Lorenzo-Redondo, Judd F. Hultquist, Egon A. Ozer*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

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 languageEnglish (US)
Article number2714
JournalViruses
Volume14
Issue number12
DOIs
StatePublished - Dec 2022

Keywords

  • COVID-19
  • SARS-CoV-2
  • ViralVar
  • evolution
  • genomic surveillance
  • mutation
  • webtool

ASJC Scopus subject areas

  • Infectious Diseases
  • Virology

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