Poulomi Sarkar: CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India; IICB-Translational Research Unit of Excellence, Salt Lake, WB 700091, India.
Sarthak Banerjee: CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India; IICB-Translational Research Unit of Excellence, Salt Lake, WB 700091, India.
Saikat Chakrabarti: CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India; IICB-Translational Research Unit of Excellence, Salt Lake, WB 700091, India.
Partha Chakrabarti: CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India.
Arun Bandyopadhyay: CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India; IICB-Translational Research Unit of Excellence, Salt Lake, WB 700091, India.
Arpita Ghosh Mitra: MEDICA Super-specialty Hospital, Kolkata, India.
Soumen Saha: MEDICA Super-specialty Hospital, Kolkata, India.
Aviral Roy: MEDICA Super-specialty Hospital, Kolkata, India.
Siddik Sarkar: CSIR-Indian Institute of Chemical Biology (IICB), Kolkata, WB 700032, India; IICB-Translational Research Unit of Excellence, Salt Lake, WB 700091, India. Electronic address: siddik.sarkar@iicb.res.in.
PURPOSE: The emergence of highly mutated and transmissible BA variants has caused an unprecedented surge in COVID-19 infections worldwide. Thorough analysis of its genome structure and phylogenomic evolutionary details will serve as scientific reference for future research. METHOD: Here, we have analyzed the BA variants from India using whole-genome sequencing, spike protein mutation study, spatio-temporal surveillance, phylogenomic assessment and epitope mapping. RESULTS: The predominance of BA.2/BA.2-like was observed in India during COVID-19 third wave. Genome analysis and mutation study highlighted the existence of 2128 amino acid changes within BA as compared to NC_045512.2. Presence of 23 unknown mutation sites (spanning region 61-831) were observed among the Indian BA variants as compared to the global BA strains. Unassigned probable Omicron showed the highest number of mutations (370) followed by BA.1 (104), BA.2.3 (56), and BA.2 (27). Presence of mutations 'Q493R + Q498R + N501Y', and 'K417 N + E484A + N501Y' remained exclusive to BA.2 as well as unassigned probable Omicron. The time-tree and phylogenomic network assessed the evolutionary relationship of the BA variants. Existence of 424 segregating sites and 113 parsimony informative sites within BA genomes were observed through haplotype network analysis. Epitope mapping depicted the presence of unique antigenic sites within the receptor binding domain of the BA variants that could be exploited for robust vaccine development. CONCLUSION: These findings provide important scientific insights about the nature, diversity, and evolution of Indian BA variants. The study further divulges in the avenues of therapeutic upgradation for better management and eventual eradication of COVID-19.
