# Evaluation of the Mutational Preferences Throughout the Whole Genome of the Identified Variants of the SARS-CoV-2 Virus Isolates in Bangladesh

## TL;DR

This study analyzed SARS-CoV-2 variants in Bangladesh from March 2021 to February 2022, comparing their mutation patterns and phylogenetics.

## Contribution

The paper provides new insights into the mutational preferences of SARS-CoV-2 Delta and Omicron variants in Bangladesh.

## Key findings

- Delta and Omicron variants showed higher substitution rates than deletions or insertions.
- Mutation patterns showed similar C > T and A > G changes but differed in G > T and G > A.
- Phylogenetic analysis revealed clade 21A and 20A as the most ancestral variants.

## Abstract

The study aimed to identify the variants of SARS-CoV-2 (Severe Acute Respiratory Syndrome related coronavirus-2) virus isolates within the window of March 2021 to February 2022 in Bangladesh and investigate their comparative mutational profiles, 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 (version 3.5.9). 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 insertions. High-frequency nucleotide change patterns were similar (for C > T, and A > G) in both of the variants, but different in some (i.e., G > T, G > A). Preferences for specific amino acids over the other amino acids in substitutions and deletions were observed to vary in different proteins of these variants. Phylogenetic analysis showed that the most ancestral variants were from clade 21A and clade 20A, 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, and further study on their biological functional impact might unveil the reason behind their mutational strategies and behavioral changes.