Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

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

Version 1 : Received: 15 October 2022 / Approved: 17 October 2022 / Online: 17 October 2022 (12:59:07 CEST)

A peer-reviewed article of this Preprint also exists.

Alisoltani, A.; Jaroszewski, L.; Godzik, A.; Iranzadeh, A.; Simons, L.M.; Dean, T.J.; Lorenzo-Redondo, R.; Hultquist, J.F.; Ozer, E.A. ViralVar: A Web Tool for Multilevel Visualization of SARS-CoV-2 Genomes. Viruses 2022, 14, 2714. Alisoltani, A.; Jaroszewski, L.; Godzik, A.; Iranzadeh, A.; Simons, L.M.; Dean, T.J.; Lorenzo-Redondo, R.; Hultquist, J.F.; Ozer, E.A. ViralVar: A Web Tool for Multilevel Visualization of SARS-CoV-2 Genomes. Viruses 2022, 14, 2714.

Abstract

The unprecedented growth of publicly available SARS-CoV-2 genome sequence data has increased demand for effective and accessible SARS-CoV-2 data analysis and visualization tools. A majority of the currently available tools either require computational expertise to deploy or limit user input to pre-selected 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) visualization of spatiotemporal dynamics of SARS-CoV-2 lineages, and 2) 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 the pediatric, adult, and elderly population (n > 1.7 million genomes). While the spatiotemporal dynamics of 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 large-scale surveillance of circulating pathogens. The ViralVar webserver is freely available at http://viralvar.org/.

Keywords

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

Subject

Medicine and Pharmacology, Other

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