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.

Keywords: Bangladesh; SARS-CoV-2; clade; evolution; lineage B.1.1.7; mutation.

Figure 1

Nextstrain phylogeny tree showing evolutionary relationships of SARS-CoV-2 viruses. The tree was built using 791 Bangladeshi strains and 1902 global reference strains (Africa = 256, Asia = 431, Europe = 719, North America = 210, Oceania = 131, South America = 155). The red node suggests Bangladeshi strains.

Figure 2

RAxML phylogenetic tree of 791 complete sequences of Bangladeshi SARS-CoV-2 showing the branch separating clades and lineages. The tree is rooted on Wuhan-Hu-1 (NC045512) reference strain. Seven different clades (GISAID) are highlighted as G = blue, GH = pink, GR = black, GRY = red, O = cyan, S = green, and L = orange. Five Nextstrain clades (20A, 20B, 20C, 19A, and 19B), as well as lineages A and B, are outlined in the left two-color columns. Compressed sub-tree indicates taxon names from similar clade branch/clusters. The full tree is available as Supplementary Figure S1.

Figure 3

A time-scaled MCC tree indicating multiple clusters with many subdivisions (color separated). Viruses from March–September 2020 were incorporated in Cluster I, Cluster II, and Cluster III, whereas the viruses from October–December 2020 and January 2021 were assimilated into Cluster IV. All generated clusters belong to lineage B. Branch lengths were noted at the root of the tree. A and B indicate the origin of lineages A and B. The tree is rooted on Wuhan-Hu-1 (NC045512) reference strain. The full tree is available as Supplementary Figure S2.

Figure 4

Distribution of SARS-CoV-2 genomes in Bangladesh. (a) The graph represents the number of sequences submitted in the GISAID database and the monthly confirmed new cases in Bangladesh. (b) The proportionate prevalence of the seven clades of SARS-CoV-2 detected in Bangladesh. (c) The proportionate distribution of seven clades of SARS-CoV-2 in eight administrative divisions of Bangladesh.

Figure 5

Mutational profile of Bangladeshi SARS-CoV-2. (a) Graph showing the total number of mutations detected by each encoded protein. (b) Nextstrain generated amino acid (AA) diversity graph of respective proteins; the spike protein had the most diversity (red circled). Diversity scale ranges from 0.0 to 0.8 are shown on the left side of the graph. (c) Illustration of selected amino acid substitutions in the S protein that are responsible for increased infectivity. The reddish substitutions are globally established, naturally occurring variants that increase infectivity, whereas the gray substitutions are found to be infective in experimental infection [8].