Genetic analysis of SARS-CoV-2 isolates collected from Bangladesh: insights into the origin, mutation spectrum, and possible pathomechanism

Abstract

As the coronavirus disease 2019 , caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), rages across the world, killing hundreds of thousands and infecting millions, researchers are racing against time to elucidate the viral genome. Some Bangladeshi institutes are also in this race, sequenced a few isolates of the virus collected from Bangladesh. Here, we present a genomic analysis of 14 isolates. The analysis revealed that SARS-CoV-2 isolates sequenced from Dhaka and Chittagong were the lineage of Europe and the Middle East, respectively. Our analysis identified a total of 42 mutations, including three large deletions, half of which were synonymous. Most of the missense mutations in Bangladeshi isolates found to have weak effects on the pathogenesis. Some mutations may lead the virus to be less pathogenic than the other countries. Molecular docking analysis to evaluate the effect of the mutations on the interaction between the viral spike proteins and the human ACE2 receptor, though no significant interaction was observed. This study provides some preliminary insights into the origin of Bangladeshi SARS-CoV-2 isolates, mutation spectrum and its possible pathomechanism, which may give an essential clue for designing therapeutics and management of COVID-19 in Bangladesh.

Temporal landscape of mutation accumulation in SARS-CoV-2 genomes from Bangladesh: possible implications from the ongoing outbreak in Bangladesh

“…Although their direct evolution from that reference Wuhan virus was not found. So, it can be suggested that viruses from different regions other than China might also contribute to the SARS-CoV-2 outbreak in Bangladesh, which was also previously reported by Parvez et al 2020;Hasan et al 2020. Besides, that majority of the Bangladeshi isolates were found to fall within the clade B belonging to L type (Supplementary Table ST2).…”

“…To infer the evolutionary relationships among the examined sequences, the sequences were aligned with relevant reference sequences retrieved from NCBI database using the neighborjoining approach (Rahman et al, 2020). The Molecular Evolutionary Genetics Analysis across…”

Global and local mutations in Bangladeshi SARS-CoV-2 genomes

“…As for instance, one study reported analyses of 60 SARS-CoV-2 genome sequences from Bangladesh and compared them with 6 Southeast Asian countries ( Islam et al, 2020 ). Another group analyzed only 14 isolates and found 42 mutations ( Parvez et al, 2020 ). A separate study identified only 9 variants where unique mutations (UMs) were found prevalent mostly in ORF1ab ( Hasan et al, 2020 ).…”

Sequence Analysis of Hot Spot Regions of Spike and Rna‑dependent‑rna Polymerase (Rdrp) Genes of Sars-Cov-2 in Kerman, Iran

“… 47 Parvez and colleagues' molecular docking analysis revealed no significant interactions between the putative RNA binding site and the genome. 48 Doga Eskier et al reported that the third most common RdRp, 15324C>T, decreased the mutation rate created by RdRp, while the 14408C>T mutation had the opposite effect. They also suggested that the 14408C>T mutation contributed to co-mutations' dominance in Europe and elsewhere.…”