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bioRxiv · 10.1101/2020.04.10.036343

CoV Genome Tracker: tracing genomic footprints of Covid-19 pandemic

Akther, S.·Bezrucenkovas, E.·Sulkow, B.·Panlasigui, C.·Li, L.·Qiu, W.·Di, L.
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Abstract

SummaryGenome 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 ImplementationCoV 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). Contactweigang@genectr.hunter.cuny.edu, City University of New York, Hunter College Supplementary InformationAll 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.

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Akther, S., Bezrucenkovas, E., Sulkow, B., Panlasigui, C., Li, L., Qiu, W., Di, L.. 2020-04-14. CoV Genome Tracker: tracing genomic footprints of Covid-19 pandemic. https://doi.org/10.1101/2020.04.10.036343

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