Clinical Report: Epidemiological and genomic surveillance of influenza virus A, RSV B, and SARS-CoV-2 in Bangladesh, 2022-2024
Background
Integrated genomic surveillance of respiratory pathogens is important for pandemic preparedness, particularly in low- and middle-income countries with limited surveillance capacity. In 2022, Bangladesh established the National Respiratory Pathogen Genomic Surveillance consortium to integrate epidemiological and genomic monitoring of influenza viruses, respiratory syncytial virus (RSV), and SARS-CoV-2. This study primarily described the surveillance platform’s implementation and selected findings rather than providing a comprehensive epidemiological analysis.
Data highlights
From October 2022 through March 2024, investigators collected 23,087 respiratory specimens from patients meeting World Health Organization criteria for severe acute respiratory infection (SARI) or influenza-like illness (ILI). Influenza viruses were detected in 1,329 specimens (5.8%), and SARS-CoV-2 was detected in 428 (1.9%). RSV testing was limited to 7,356 specimens from children younger than 5 years, of which 2,277 (31.0%) were positive.
Key findings
Surveillance was conducted at 9 predominantly urban and peri-urban sentinel hospitals across 7 divisions of Bangladesh.
Among children younger than 5 years, RSV was detected in 34.3% of SARI specimens and 19.1% of ILI specimens. SARI positivity was highest among infants younger than 6 months.
RSV exhibited a biphasic seasonal pattern. Influenza activity peaked during the 2023 monsoon season, while SARS-CoV-2 circulated at persistently low levels with intermittent increases.
Bangladeshi RSV B genomes formed a monophyletic cluster within the B.D.E.1 clade, although global-sequence downsampling may have accentuated this clustering.
Influenza A(H1N1) and A(H3N2) viruses co-circulated and formed distinct phylogenetic clades. SARS-CoV-2 genomes reflected the progression of Omicron lineages, including XBB- and JN.1-related lineages.
Sequencing used pathogen-specific Oxford Nanopore protocols, with selected samples also sequenced on Illumina platforms for benchmarking and cross-platform validation.
Public health implications
The findings demonstrate the feasibility of integrated, multipathogen genomic surveillance in a resource-limited setting. The platform generated data that may support respiratory-virus surveillance, public health planning, antiviral preparedness, and vaccine-strain monitoring. The findings also illustrate how infrastructure developed during the COVID-19 pandemic can be adapted to monitor multiple respiratory pathogens.
Conclusion
Bangladesh successfully used pandemic-era infrastructure to establish an integrated respiratory-pathogen surveillance platform. Interpretation is limited by the predominance of urban and peri-urban sentinel sites, exclusion of immunocompromised patients, and restriction of sequencing to specimens with high viral loads. Global-sequence downsampling may also have affected phylogenetic clustering, so the genomic findings may not fully represent all infections or broader transmission patterns.
Related resources and content
Original study: Epidemiological and genomic surveillance of influenza virus A, RSV B and SARS-CoV-2 in Bangladesh (2022-2024)
World Health Organization global epidemiological surveillance standards for influenza
World Health Organization Global Influenza Surveillance and Response System
GISAID genomic sequence database
Study data-analysis code on GitHub
RSV-associated hospitalizations in Bangladeshi children under five: Unveiling the disease burden
