Genomic surveillance unfolds the SARS-CoV-2 transmission and divergence dynamics in Bangladesh

• DOI: 10.3389/fgene.2022.966939
• Publication Date: 2022-09-26T04:45:47Z
• Authors: Tushar Ahmed Shishir; Taslimun Jannat; Iftekhar Bin Naser
• Keywords: 0301 basic medicine; Evolutionary biology; Plant Science; Infectious disease (medical specialty); QH426-470; Coronavirus Disease 2019 Research; FOS: Health sciences; Gene; Agricultural and Biological Sciences; Computational biology; Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated proteins; 03 medical and health sciences; Biochemistry, Genetics and Molecular Biology; Virology; evolution; Health Sciences; Genetics; Pathology; Missense mutation; Disease; Molecular Biology; Biology; Genome; Pandemic; SARS-CoV-2; pandemic; Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); COVID-19; Life Sciences; genetic diversity; molecular surveillance; Transmission (telecommunications); Computer science; Virus; 3. Good health; Coronavirus disease 2019 (COVID-19); Infectious Diseases; FOS: Biological sciences; Viral RNA Silencing and Plant Immunity; Viral Transmission; Mutation; Telecommunications; Medicine; Phylogenetic tree

The highly pathogenic virus SARS-CoV-2 has shattered the healthcare system of the world causing the COVID-19 pandemic since first detected in Wuhan, China. Therefore, scrutinizing the genome structure and tracing the transmission of the virus has gained enormous interest in designing appropriate intervention strategies to control the pandemic. In this report, we examined 4,622 sequences from Bangladesh and found that they belonged to thirty-five major PANGO lineages, while Delta alone accounted for 39%, and 78% were from just four primary lineages. Our research has also shown Dhaka to be the hub of viral transmission and observed the virus spreading back and forth across the country at different times by building a transmission network. The analysis resulted in 7,659 unique mutations, with an average of 24.61 missense mutations per sequence. Moreover, our analysis of genetic diversity and mutation patterns revealed that eight genes were under negative selection pressure to purify deleterious mutations, while three genes were under positive selection pressure. Together with an ongoing genomic surveillance program, these data will contribute to a better understanding of SARS-CoV-2, as well as its evolution pattern and pandemic characteristics in Bangladesh.