Epidemiological and genomic surveillance of influenza virus A, RSV B and SARS-CoV-2 in Bangladesh (2022-2024)

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.