Evaluation of the Mutational Preferences throughout the Whole Genome of the Identified Variants of the SARS-COV-2 Virus Isolates in Bangladesh

We aimed to identify the variants of SARS-CoV-2 virus isolates within the window of March 2021 to February 2022 in Bangladesh and investigate their comparative mutational preferences and phylogenetics. After the collection of the sample specimen and RNA extraction, the genome was sequenced using Illumina COVID Seq, and NGS data analysis was performed in DRAGEN COVID Lineage software. Among the 96 virus isolates, 24 (25%) were from Delta (clade 21A (n=21) and 21J (n=3)) and 72 (75%) were from Omicron (clade 20A (n=6), and 20B (n=66)). In Omicron and Delta, substitutions were much higher than deletions and insertion mutations. High-frequency nucleotide 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 amino acid substitutions and deletions were observed to vary in different proteins of these variants. Phylogenetic analysis showed that the most ancestral viral isolates were from clade 21A of Delta and then the other variants emerged. The study demonstrates noteworthy variations of Omicron and Delta in mutational pattern and preferences for amino acids and protein, further study with them might aid in understanding the interaction of these variants’ proteins with the human body systems in long-COVID.