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. 2024 Oct;18(10):e70019.
doi: 10.1111/irv.70019.

A Strategic Framework of SARS-CoV-2 Genomic Surveillance in Bangladesh

Mohammad Jubair  1 , Md Mobarok Hossain  1 , Mst Noorjahan Begum  2 , Shovan Basak Moon  1 , Shahriar Islam  1 , Md Yeasir Karim  2 , Sezanur Rahman  2 , Manjur H Khan  3 , Mohammad Tanbir Habib  4 , Tahmina Shirin  3 , Firdausi Qadri  2   4 , Mustafizur Rahman  1   2
Affiliations

A Strategic Framework of SARS-CoV-2 Genomic Surveillance in Bangladesh

Mohammad Jubair et al. Influenza Other Respir Viruses. 2024 Oct.

Abstract

Background: The global pandemic caused by SARS-CoV-2 has underlined the significance of strict genomic surveillance to track virus evolution and the possible emergence of new variants, particularly in densely populated countries like Bangladesh. This study outlines a strategic framework of genomic surveillance to track the evolution of the virus in Bangladesh between June 2021 and December 2022 through the National SARS-CoV-2 Variant Surveillance (NSVS) program involving collaboration across 4 major institutes and 13 hospitals nationwide.

Methods: We aimed to capture the variants of SARS-CoV-2 throughout the country utilizing standardized procedures, modern sequencing technology, and stringent quality control, promoting data accuracy and the timely detection of new variants of concern. We sequenced over 2200 genomes, documenting the prevalence of the Delta variant initially, followed by the emergence of Omicron variants BA.1, BA.2, BA.5, and XBB, each affecting transmission rates and vaccine efficacy differently.

Results: The clinical manifestations of the variants differed, with some symptoms occurring more frequently in Delta cases and vice versa. Vaccinated individuals were more affected by Omicron cases compared to Delta cases. These variants were responsible for two major COVID-19 waves in the country, each with significant clinical effects. Phylogenetic analyses placed the local SARS-CoV-2 variants within a global context, indicating the Delta variant likely entered from India and Omicron from Europe.

Conclusion: This research highlights the significance of collaborative surveillance strategies for guiding public health choices and the critical role of genomic analysis in monitoring virus evolution, shaping targeted pandemic responses. Bangladesh's contributions significantly enhance global insight into COVID-19's genomic evolution.

Keywords: Bangladesh; COVID‐19; Delta; Omicron; SARS‐CoV‐2; surveillance.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

FIGURE 1
FIGURE 1
A strategic framework of National SARS‐CoV‐2 Variant Surveillance in Bangladesh.
FIGURE 2
FIGURE 2
Improving turnover time throughout the project.
FIGURE 3
FIGURE 3
Genomic Epidemiology of SARS‐CoV‐2 in Bangladesh throughout the study period. (A) Timeline distribution of confirmed case and death; (B) geographical and temporal distribution of Delta sequences (top 5 lineages); and (C) geographical and temporal distribution of Omicron sequences (top 5 lineages), with the Y axis representing the divisions of Bangladesh. Each dot in (B) and (C) represents a genome.
FIGURE 4
FIGURE 4
Phylogenetic evolution of SARS‐CoV‐2 in Bangladesh over the course of the study, conducted by nextstrain.org. (A) Maximum‐likelihood tree representing Nextclade variants; (B) maximum‐likelihood trees depicting the distribution of Nextclade variants across the eight divisions in Bangladesh.
FIGURE 5
FIGURE 5
Transmission dynamics of SARS‐CoV‐2 in Bangladesh in the Context of Global Sequences. A wider line indicates the higher transmission rates. (A) Based on clades classified according to Nextclade and (B) based on the selected countries (n = 20).
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