Abstract
Summary Genome sequences constitute the primary evidence on the origin and spread of the 2019-2020 Covid-19 pandemic. Rapid comparative analysis of coronavirus SARS-CoV-2 genomes is critical for disease control, outbreak forecasting, and developing clinical interventions. CoV Genome Tracker is a web portal dedicated to trace Covid-19 outbreaks in real time using a haplotype network, an accurate and scalable representation of genomic changes in a rapidly evolving population. We resolve the direction of mutations by using a bat-associated genome as outgroup. At a broader evolutionary time scale, a companion browser provides gene-by-gene and codon-by-codon evolutionary rates to facilitate the search for molecular targets of clinical interventions.
Availability and Implementation CoV Genome Tracker is publicly available at http://cov.genometracker.org and updated weekly with the data downloaded from GISAID (http://gisaid.org). The website is implemented with a custom JavaScript script based on jQuery (https://jquery.com) and D3-force (https://github.com/d3/d3-force).
Contact weigang{at}genectr.hunter.cuny.edu, City University of New York, Hunter College
Supplementary Information All supporting scripts developed in JavaScript, Python, BASH, and PERL programming languages are available as Open Source at the GitHub repository https://github.com/weigangq/cov-browser.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Emails: Saymon Akther < sakther{at}gradcenter.cuny.edu>; Edgaras Bezrucenkovas <edgaras993{at}gmail.com>; Brian Sulkow <drtwisto{at}gmail.com>; Christopher Panlasigui <christopher.panlasigui{at}gmail.com>; Li Li <lli4{at}gradcenter.cuny.edu>;