Molecular Analysis of SARS-CoV-2 Circulating in Bangladesh during 2020 Revealed Lineage Diversity and Potential Mutations

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.

Whole-genome sequence analysis reveals the circulation of multiple SARS-CoV-2 variants of concern in Nairobi and neighboring counties, Kenya between March and July 2021

“…Surveillance of the SARS-CoV-2 by whole genome sequencing is crucial in providing insights into its transmission and evolutionary dynamics [4,22]. It's equally valuable in identifying potential variants and virulence determinants [4,41,42].…”

“…*Correspondence: Wbulimo@kemri.org many countries, causing multiple waves of COVID-19 epidemics [4]. Indeed, as of 21st July 2022, > 564 million people have been infected worldwide, with > 6 million deaths reported, with Kenya registering 336,904 cases and 5668 deaths [5].…”

“…Indeed, as of 21st July 2022, > 564 million people have been infected worldwide, with > 6 million deaths reported, with Kenya registering 336,904 cases and 5668 deaths [5]. Since its first appearance, the SARS-CoV-2 has undergone significant numbers of mutations over time, giving rise to multiple genetic variants, some of which have beneficial host adaptive fitness [4,[6][7][8][9][10][11]. The emerging SARS-CoV-2 variants have been described as variants of interest (VOI) and variants of concern (VOC) [10,12].…”

“…The emerging SARS-CoV-2 variants have been described as variants of interest (VOI) and variants of concern (VOC) [10,12]. Certainly, considerable attention has been focused on the latter as they harbor genetic attributes associated with increased transmissibility, increased virulence, and reduced effectiveness of public health countermeasures [4,[8][9][10].…”

“…Five major SARS-CoV-2 lineages, Alpha (B.1.1.7), first reported in the United Kingdom; Beta (B.1.351), first reported in South Africa; Delta (B.1.617.2) first seen in India; Gamma (P.1) first seen in Japan/Brazil; and Omicron (B.1.1.529) first reported in South Africa have been identified as variants of concern [4,[8][9][10][13][14][15][16]. They possess point mutations in the receptor-binding domain (RBD) of the spike protein, which enhances binding affinity to the human angiotensin-converting enzyme 2 (ACE2) receptor.…”