Dynamics of SARS-CoV-2 variants of concern (VOC) in Bangladesh during the first half of 2021

Abstract

Bangladesh is the second-worst-affected country in South Asia by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The aim of this study is to examine genome sequences from Bangladesh from January 2021 to June 2021 in order to monitor the SARS-CoV-2 VOC and the clades or lineages that are prevalent in the country. Within the study timeframe, at least eight Nextstrain clades were found: 20A, 20B, 20C, 20H (Beta, V2), 20I (Alpha, V1), 20 J (Gamma, V3), 21A (Delta), 21D (Eta), and six GISAID clades: four main (G, GH, GR, GRY) and two minors (GV, O) with an introduction of VOC B.1.1.7/Alpha, B.1.351/Beta and B.1.617.2/Delta. The introduction and recent occurrence of VOCs with substantial alterations in the receptor binding site of spike protein (K417 N, K417T, L452R, T478K, E484K, S494P, N501Y) are of particular importance. Specifically, VOC B.1.617.2/Delta has surpassed all prior VOCs in Bangladesh, posing a challenge to the existing disease management.

Keywords: Bangladesh; Mutation; Phylogeny; SARS-CoV-2; Sequence; Variant.

Fig. 1

Phylogenetic relationship of SARS-CoV-2 viruses from the ongoing novel coronavirus COVID-19 pandemic. a) Phylogenetic clusters and clades as generated by Nextstrain for the dataset of 820 high-quality Bangladeshi SARS CoV-2 genomes in comparison with the 1794 global reference sequences. The different color nodes (circles) indicated the designated clades (20H, 20I, 20 J, 21A, 21D, 20A, 20B and 20C) identified within the Bangladeshi strains. The global reference sequences are showing in ash color lines without any node circles. b) The circular representation of a phylogenetic tree constructed using the ML method with 820 Bangladeshi strains (BD) revealed separate clusters for different VOCs and lineages circulating in the country (Alpha: pink; Beta: red; Gamma: green; Delta: blue, and Others: brown). GISAID clades (G, GH, GR, GRY, GV, O) distribution were also depicted within each cluster. Taxa with similar node matrices within each branch were collapsed.

Fig. 2

Scatter plot showing evolutionary relationship and divergence limit based on Nextstrain phylogeny. The plot was generated in online Auspice platform (https://auspice.us/) by given input from Nextclade generated “JSON_Auspice” data. The branches showed the prototype strain from where the divergence start and pillared on the root strain (clade 19A) found at December 2019 in Wuhan (Wuhan-Hu-1/NC_045512). Bangladeshi strains were indicated by a red node. Until June 2021, the highest divergence was observed in clade 20H (Beta, V2).

Fig. 3

Distribution of circulating clades and lineages and SARS CoV-2 surge within January to June 2021 in Bangladesh based on GISAID EpiCoV database. a) Stacked area plot shows the month-wise clade prevalence b) Stacked area plot shows the month-wise prevalence of various lineages c) The map showing the division-wise proportion of lineages within the given time frame. The proportion was estimated taking the total number of sequences accessible in each division as denominator.

Fig. 4

Mutational profile of SARC-CoV-2 observed in Bangladesh from January to June 2021. a) Month-by-month distribution of amino acid alterations in the relevant proteins of Bangladeshi SARS-CoV-2. b) SARS-CoV-2 genomic structure with cartoon structural conformation of RBS (aa 336–518) of S protein. Differently colored level atoms indicated major mutations at the given position, which is also seen in Bangladeshi sequences and is required for VOC formulation.