International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases · 2026
Epidemiological and genomic surveillance of influenza virus A, RSV B and SARS-CoV-2 in Bangladesh (2022-2024).
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Jubair Mohammad, Begum Mst Noorjahan, Samia Nure Sharaf Nower, Alam Md Shaheen, Karim Yeasir, Ahmed Tazkia, Cella Eleonora, Rahman Saikt, Habib Mohammad Tanbir, Khan Manjur H, Shirin Tahmina, Chowdhury Fahmida, Qadri Firdausi, Rahman Mustafizur
Аннотация
BACKGROUND: The establishment of integrated genomic surveillance for respiratory pathogens in low- and middle-income countries (LMICs) is critical for pandemic preparedness. This study aims to describe the implementation of an integrated multi-pathogen genomic surveillance system in Bangladesh and to present key genomic and epidemiological insights generated from this platform, rather than to provide a comprehensive epidemiological analysis.
METHODS: From October 2022 to March 2024, surveillance was conducted across nine sentinel hospitals. Samples from over 23,000 patients meeting WHO SARI/ILI case definitions were tested by multiplex RT-PCR. Positive samples with high viral load (Ct ≤ 27) underwent whole-genome sequencing using Oxford Nanopore and Illumina platforms.
RESULTS: RSV was the leading cause of pediatric SARI (34.3% in children under five), exhibiting a biphasic seasonal pattern. Influenza resurged July-August 2023 with monsoon-season peaks, while SARS-CoV-2 showed persistent, low-level transmission. Genomic analysis of 544 isolates revealed localized evolution: RSV B formed a monophyletic B.D.E.1 clade with conserved glycoprotein mutations; influenza A viruses identified belonged to two subtypes, H1N1 and H3N2, which segregated into two phylogenetically distinct clades; and SARS-CoV-2 followed global Omicron lineage progression.
CONCLUSION: This study demonstrates the feasibility and utility of an integrated genomic surveillance platform in a resource-limited setting, generating evidence that may support public health planning and preparedness.
METHODS: From October 2022 to March 2024, surveillance was conducted across nine sentinel hospitals. Samples from over 23,000 patients meeting WHO SARI/ILI case definitions were tested by multiplex RT-PCR. Positive samples with high viral load (Ct ≤ 27) underwent whole-genome sequencing using Oxford Nanopore and Illumina platforms.
RESULTS: RSV was the leading cause of pediatric SARI (34.3% in children under five), exhibiting a biphasic seasonal pattern. Influenza resurged July-August 2023 with monsoon-season peaks, while SARS-CoV-2 showed persistent, low-level transmission. Genomic analysis of 544 isolates revealed localized evolution: RSV B formed a monophyletic B.D.E.1 clade with conserved glycoprotein mutations; influenza A viruses identified belonged to two subtypes, H1N1 and H3N2, which segregated into two phylogenetically distinct clades; and SARS-CoV-2 followed global Omicron lineage progression.
CONCLUSION: This study demonstrates the feasibility and utility of an integrated genomic surveillance platform in a resource-limited setting, generating evidence that may support public health planning and preparedness.