The genetic variants analysis of circulating SARS-CoV-2 in Bangladesh.

Genomic mutation of the virus may impact the viral adaptation to the local environment, their transmission, disease manifestation, and the effectiveness of existing treatment and vaccination. The objectives of this study were to characterize genomic variations, non-synonymous amino acid substitutions especially in target proteins, mutation events per samples, rate, and overall scenario of coronaviruses across the country. To investigate the genetic diversity, a total of 184 genomes of virus strains sampled from different divisions of Bangladesh with sampling dates between 10 May 2019 and 27 June 2020 were analyzed. To date, a total of 634 mutations located along the entire genome resulting in nonsynonymous 274 amino acid substitutions in 22 different proteins were detected. The mutation rate estimated to be 23.715 substitutions per year. The highest non-synonymous amino acid substitutions were observed at 48 different positions of the papain-like protease (nsp3). Although no mutations were observed in nsp7, nsp9, nsp10, and nsp11, yet orf1ab accounts for 56% of total mutations. Among the structural proteins, the highest mutations at 36 different positions have identified in spike proteins. A total of 9 mutations at spike proteins were found unique in relative to the global mutations including mutations at position 516 in the boundary of the ACE2 binding region of the spike protein. The most dominated variant G614 (95%) based in spike protein is circulating across the country followed by coevolving other variants including L323 (94%) in RNA dependent RNA polymerase (RdRp), K203 (82%) and R204 (82%) in nucleocapsid, and F120 (78%) in NSP2. These variants are mostly seen as linked mutations and are part of a haplotype observed high in Europe. Data suggest effective containment of clade G strains (4.8%) with sub-clusters GR covered by 82.4%, and GH clade 6.4%. Whereas 2.7 and 3.2 % of variants belonged to clade S and O clade, respectively.