CoVe-Tracker: An Interactive SARS-CoV-2 Pan Proteome Evolution Tracker

Abstract

SARS-CoV-2 has significantly mutated its genome during the past 3 years, leading to the periodic emergence of several variants. Some of the variants possess enhanced fitness advantage, transmissibility, and pathogenicity and can also reduce vaccine efficacy. Thus, it is important to track the viral evolution to prevent and protect the mankind from SARS-CoV-2 infection. To this end, an interactive web-GUI platform, namely, CoVe-tracker (SARS- CoV -2 e volution tracker ), is developed to track its pan proteome evolutionary dynamics ( ). CoVe-tracker provides an opportunity for the user to fetch the country-wise and protein-wise amino acid mutations (currently, 44139) of SARS-CoV-2 and their month-wise distribution. It also provides position-wise evolution observed in the SARS-CoV-2 proteome. Importantly, CoVe-tracker provides month- and country-wise distributions of 2065 phylogenetic assignment of named global outbreak (PANGO) lineages and their 177564 variants. It further provides periodic updates on SARS-CoV-2 variant(s) evolution. CoVe-tracker provides the results in a user-friendly interactive fashion by projecting the results onto the world map (for country-wise distribution) and protein 3D structure (for protein-wise mutation). The application of CoVe-tracker in tracking the closest cousin(s) of a variant is demonstrated by considering BA.4 and BA.5 PANGO lineages as test cases. Thus, CoVe-tracker would be useful in the quick surveillance of newly emerging mutations/variants/lineages to facilitate the understanding of viral evolution, transmission, and disease epidemiology.

Current Progress in Genomic and Genetic Research on Human Viral Diseases

“…Saldivar-Espinoza et al (2023) developed a SARS-CoV-2 Mutation Portal which provides access to a database of SARS-CoV-2 mutations. Sathyaseelan et al (2023) developed a CoVe-tracker (SARS-CoV-2 evolution tracker) 7 for quick surveillance of newly emerging mutations/variants/lineages to facilitate the understanding of viral evolution, transmission, and disease epidemiology. Huang et al (2023) developed a genomic surveillance framework and a dynamic community-based variant dictionary tree, which enables early detection and continuous investigation of SARS-CoV-2 variants.…”

The effects of amino acid substitution of spike protein and genomic recombination on the evolution of SARS-CoV-2

“… Saldivar-Espinoza et al (2023) developed a SARS-CoV-2 Mutation Portal which provides access to a database of SARS-CoV-2 mutations. Sathyaseelan et al (2023) developed a CoVe-tracker (SARS-CoV-2 evolution tracker) 7 for quick surveillance of newly emerging mutations/variants/lineages to facilitate the understanding of viral evolution, transmission, and disease epidemiology. Huang et al (2023) developed a genomic surveillance framework and a dynamic community-based variant dictionary tree, which enables early detection and continuous investigation of SARS-CoV-2 variants.…”

COVID Variants, Villain and Victory: A Bioinformatics Perspective

“…Besides this, numerous platforms and models were developed to study the fundamentals of evolutionary, epidemiology, and phylogenetic divergence of viruses. The phylodynamic models include BEAST 2 [ 51 ] for phylogeographic reconstruction; epidemic-mathematical models such as COPASI [ 52 ] and COVIDSIM [ 53 ]; and evolutionary tracking models like CoV-GLUE [ 54 ] and CoVe-Tracker are available [ 55 ]. The machine-learning model Covidex [ 56 ] is an open-source alignment tool based on Nextstrain and GISAID data used for the rapid classification of viral genomes in pre-defined clusters isolated from the population.…”