CorGAT and CorGAT-tracker : Functional annotation of SARS-CoV-2 genomes and tracking mutations and variants of concern

Novel variants of SARS-CoV-2 that represent a source of concern for international health authorities have been recently identified. Collectively these variants are known under the acronym VOC (variants of concern) and carry specific mutations in the spike glycoprotein (MOC, mutation of concern) that confer increased infectivity and/or an improved ability to escape recognition by some antibodies [1]. The rapid and timely tracking of VOCs and MOCs represents a priority in the fight against COVID-19. However, several factors limit the resolution of current strategies for tracking MOCs, including incomplete fixation, convergent evolution across different (non related) lineages and/or lack of regional data [2]. Here we present “CorGAT” [3] and “CorGAT-tracker”, a complete set of Galaxy tools designed to facilitate the functional annotation of SARS-CoV-2 genomes and the tracking in space and time of MOCs and VOCs. To demonstrate its application we applied our system to the complete collection of SARS-CoV-2 genomic sequences as available from January to April 2021. Our findings illustrate some recurrent patterns in the evolution of the virus and suggest the widespread and independent fixation of MOCs associated with “immune escape” in different lineages with a distinct geographic distribution. All in all, we believe that CorGAT and CorGAT-tracker will provide a useful addition to the currently available "arsenal" of bioinformatics methods for the genomic surveillance of SARS-CoV-2. Sources: [1] https://doi.org/10.1038/s41577-021-00556-5 [2] https://doi.org/10.1016/j.chom.2021.02.020 [3] https://doi.org/10.1093/bioinformatics/btaa1047 Availability: http://corgat.cloud.ba.infn.it/galaxy (CorGAT) https://github.com/matteo14c/CorGAT (CorGAT) https://github.com/F3rika/CorGAT-tracker (CorGAT-tracker)