Abstract
Virus evolution and mutation analyses are crucial for tracing virus transmission, the potential variants, and other pathogenic determinants. Despite continuing circulation of the SARS-CoV-2, very limited studies have been conducted on genetic evolutionary analysis of the virus in Bangladesh. In this study, a total of 791 complete genome sequences of SARS-CoV-2 from Bangladesh deposited in the GISAID database during March 2020 to January 2021 were analyzed. Phylogenetic analysis revealed circulation of seven GISAID clades G, GH, GR, GRY, L, O, and S or five Nextstrain clades 20A, 20B, 20C, 19A, and 19B in the country during the study period. The GISAID clade GR or the Nextstrain clade 20B or lineage B.1.1.25 is predominant in Bangladesh and closely related to the sequences from India, USA, Canada, UK, and Italy. The GR clade or B.1.1.25 lineage is likely to be responsible for the widespread community transmission of SARS-CoV-2 in the country during the first wave of infection. Significant amino acid diversity was observed among Bangladeshi SARS-CoV-2 isolates, where a total of 1023 mutations were detected. In particular, the D614G mutation in the spike protein (S_D614G) was found in 97% of the sequences. However, the introduction of lineage B.1.1.7 (UK variant/S_N501Y) and S_E484K mutation in lineage B.1.1.25 in a few sequences reported in late December 2020 is of particular concern. The wide genomic diversity indicated multiple introductions of SARS-CoV-2 into Bangladesh through various routes. Therefore, a continuous and extensive genome sequence analysis would be necessary to understand the genomic epidemiology of SARS-CoV-2 in Bangladesh.
Highlights
During the year 2020, the corona virus disease-19 (COVID-19) pandemic spread quickly across the world, and it is still circulating in waves
The evolutionary fitness of SARS-CoV-2 was investigated by comparing the distance matrix (Supplementary Figure S2) among Bangladeshi strains of different clades or lineages and with the reference strain (Wuhan-Hu-1/NC_045512)
Among SARS-CoV-2 sequences reported from Bangladesh, 241C > T, 3037C > T, 14408C > T, 23403A > G, 28881G > A, and 28883G > C mutations were the six most abundant nucleotide mutations that occurred in 98% sequences
Summary
During the year 2020, the corona virus disease-19 (COVID-19) pandemic spread quickly across the world, and it is still circulating in waves. The disease is caused by the newly discovered coronavirus-2, which causes severe acute respiratory syndrome (SARSCoV-2) [1,2]. Despite the fact that many countermeasures against SARS-CoV-2 transmission have been implemented around the world, there are no indications that the pandemic will be over anytime soon. SARS-CoV-2 is an enveloped, positive-sense, single-stranded RNA virus that belongs to the family Coronaviridae. There are four genera of coronaviruses (CoVs), namely, Alphacoronavirus (αCoV), Betacoronavirus (βCoV), Deltacoronavirus (δCoV), and Gammacoronavirus (γCoV) [3]. CoVs have repeatedly crossed species barriers, and a few have emerged as important human pathogens such as severe acute respiratory syndrome.
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