Spatial distribution of novel mutations identified from whole-genome sequencing of SARS-CoV-2 isolated from Noakhali, a South-Eastern District in Bangladesh. SARS-CoV-2 Genome Sequencing from Noakhali, Bangladesh

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) 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, with an aim to provide genomics insights on the isolates circulating in that specific geographic location and better understand spatial differences in mutational and lineage distribution of SARS-CoV-2 in Bangladesh. Variant analysis of our sequenced genomes identified sixteen rare variations in spike (S), six in nucleocapsid (N), two in the membrane (M), and one in envelope (E) protein. 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 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 10-4 subs/site/year. Identifying unique mutations pertinent to specific geographic locations demonstrated the necessity of initiating concerted, country-wide genomics surveillance efforts to determine any novel mutation of functional significance and understand virus evolution, transmission, and spread in Bangladesh.