CoV Genome Tracker

CoV Genome Tracker tracks SARS-CoV-2 genomic variation in real time to elucidate viral origin, spread, and evolutionary dynamics.

Key Features:

• Haplotype Network Analysis: Employs a haplotype network approach to represent genomic changes and depict genetic relationships and mutation patterns among SARS-CoV-2 strains.
• Mutation Direction Resolution: Resolves mutation directionality using a bat-associated coronavirus genome as an outgroup to infer evolutionary pathways.
• Evolutionary Rate Analysis: Provides gene-by-gene and codon-by-codon evolutionary rate estimates to identify regions under selection and potential molecular targets.

Scientific Applications:

• Disease Control and Outbreak Forecasting: Supports monitoring of SARS-CoV-2 spread and inference of transmission events to inform public-health outbreak response.
• Development of Clinical Interventions: Informs vaccine and antiviral design by identifying conserved regions and critical mutations from gene- and codon-level analyses.

Methodology:

Integrates sequence data from GISAID, is updated weekly, and is implemented with custom JavaScript using jQuery and D3-force, with supporting scripts in JavaScript, Python, BASH, and PERL.