Evaluation of Genomic Surveillance of SARS-CoV-2 Virus Isolates and Comparison of Mutational Spectrum of Variants in Bangladesh

The SARS-CoV-2 induced disease, COVID-19 is a worldwide public health concern with a rapid transmission, pathogenicity, and mortality rate. To elucidate the viral mutational changes and screening the emergence of new variants of concern, we conducted this study in Bangladesh. The viral RNA genome was sequenced using Illumina COVID Seq protocol and genomic data processing and evaluation was performed in DRAGEN COVID Lineage software. Variant analysis revealed that the number of Delta, Omicron and Mauritius variants identified were 88%, 8%, and 4%, respectively. All of the 25 samples had 23403A>G (D614G, S gene), 3037 C>T (nsp3) and 14408 C>T (nsp12) mutations, where 23403 A>G was responsible for increased transmission. Omicron had the highest number of unique mutations in spike protein (i.e., substitutions, deletions and insertions) which may explain its more transmissibility and immune evading ability than Delta. A total of 799 mutations were identified where 691 substitution, 85 deletion and 3 insertion mutations were observed. To sum up, our study will enrich the genomic database of SARS-CoV-2, aiding treatment strategy along with understanding the virus’s preferences in both mutation type and site for predicting newly emerged virus’s survival strategy and thus for being prepared to counteract them.