Novel mutations identified from whole-genome sequencing of SARS-CoV-2 isolated from Noakhali, Bangladesh

Abstract

\n Whole-genome sequencing is increasingly being used to investigate the spatial and temporal distribution of viral pathogens including the Severe Acute Respiratory Syndrome Coronavirus Variant 2 (SARS-CoV-2) which is responsible for the ongoing COVID-19 pandemic. In this study, we determined 55 complete genome sequences of SARS-CoV-2 strains isolated from patients from Noakhali, a South-Eastern district in Bangladesh. Variant analysis of our sequenced genomes identified sixteen rare variations in S, six in N, two in M, one in E protein and the S protein variation, Y204F, identified in two of our sequenced strains, has not been reported from any other countries in the GISAID database. Comparison of the prevalence pattern across the country showed GH clade lineages B.1.36 and B.1.36.16 to be abundant in Noakhali and the South-Eastern region of Chittagong when compared to the rest of the country. Phylodynamic analysis of our sequenced genomes revealed that the virus was estimated to be evolving at the rate of 1.065 X 10−\u20094 subs/site/year. The study results demonstrated the necessity of initiating a concerted, country-wide genomics surveillance effort to determine any novel mutation of functional significance, understanding virus evolution, transmission, and spread in Bangladesh. Short running title: Genome sequencing of Noakhali isolates SARS-Cov-2 in Bangladesh