Phylogenetics and Comparative Mutational Analysis of the Whole Genome of the Identified Variants of the SARS-COV-2 Virus Isolates in Bangladesh

A significant percentage of COVID-survived patients are suffering from post-COVID-19 conditions. For this reason, a comprehensive analysis of the genomic mutations of the variants of SARS-CoV-2 virus, and the interaction of the viral and host proteins and other biological components is necessary. In this study, after the collection of the sample specimen, RNA extraction, genome sequencing, and data analysis were performed. The study identified that within the time frame of March 2021 to February 2022, among the 96 virus isolates, 24 (25%) were from the Delta variants (clade 21A (n=21) and 21J (n=3)) and 72 (75%) were from the Omicron variants (clade 20A (n=6), and 20B (n=66)). In both of the variants, the percentages of substitution mutations were higher than the percentages of deletion and insertion mutations. Nucleotide base change patterns were similar (for C>T, and A>G) in both of the variants, but differed in some (i.e., G>T, G>A). Preferences for wild-type and mutant amino acid substitution and amino acid deletion were also observed to vary in different proteins of the Delta and Omicron variants. Phylogenetic analysis showed that the most ancestral viral isolates were from clade 21A of Delta and then the other variants emerged. The findings of the study add some information to the mutational pattern of SARS-CoV-2 variants and it might help in understanding the SARS-CoV-2 viral strategy and mutational preferences. Further analysis potentially can aid in understanding the interaction of the variants of the SARS-CoV-2 virus and the human body system for addressing and treating post-COVID-19 conditions.