Variant-specific deleterious mutations in the SARS-CoV-2 genome reveal immune responses and potentials for prophylactic vaccine development

• DOI: 10.3389/fphar.2023.1090717
• Publication Date: 2023-02-07T08:05:01Z
• Authors: Md. Aminul Islam; Shatila Shahi; Abdullah Al Marzan; Mohammad Ruhul Amin; Mohammad Nayeem H...; M. Nazmul Hoque; Ajit Ghosh; Abanti Barua; Abbas Khan; Kuldeep Dhama; Chiranjib Chakrab...; Prosun Bhattacharya; Dong-Qing Wei
• Keywords: SNP

Introduction: Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has had a disastrous effect worldwide during the previous three years due to widespread infections with SARS-CoV-2 and its emerging variations. More than 674 million confirmed cases over 6.7 deaths have been attributed successive waves of as 29th January 2023. Similar other RNA viruses, is more susceptible genetic evolution spontaneous mutations time, resulting in continual emergence variants distinct characteristics. Spontaneous increase transmissibility, virulence, severity diminish efficacy therapeutics vaccines, vaccine-breakthrough re-infection, leading high mortality morbidity rates. Materials methods: In this study, we evaluated 10,531 whole genome sequences all reported globally through computational approach assess spread genome. The available data sources NextCladeCLI 2.3.0 (https://clades.nextstrain.org/) NextStrain (https://nextstrain.org/) were searched for tracking mutations, analysed using PROVEAN, Polyphen-2, Predict SNP mutational analysis tools validated Machine Learning models. Result: Compared Wuhan-Hu-1 reference strain NC 045512.2, genome-wide annotations showed 16,954 We determined that Omicron variant 6,307 (retrieved sequence:1947), including 67.8% unique any study. spike protein harboured 876 443 deleterious mutations. Among these 187 common 256 non-synonymous contrast, after analysing 1,884 Delta variant, discovered 4,468 which 66% unique, not previously variants. Mutations affecting proteins are mostly found RBD regions Omicron, whereas most drawn focus on amino acid ranging from 911 924 context epitope prediction (B cell & T cell) stability impact protruding transmissible. Discussion: pathogenesis could be prevented if persistent immunosuppressive can targeted vaccination or small-molecule inhibitor designing. Thus, our findings will help researchers monitor track continuously evolving nature strains, associated variants, their implications developing effective control prophylaxis strategies.