To describe the implementation and evaluate the feasibility and public health value of integrated, multipathogen genomic surveillance in a low- and middle-income country.
Approach:
Surveillance and sequencing: From October 2022 through March 2024, respiratory specimens were collected from patients meeting World Health Organization criteria for severe acute respiratory infection or influenza-like illness at 9 sentinel hospitals. Positive specimens with cycle-threshold values of 27 or lower underwent pathogen-specific sequencing using Oxford Nanopore, with selected specimens sequenced using Illumina for validation.
Key Findings:
Integrated surveillance of influenza viruses, respiratory syncytial virus (RSV), and SARS-CoV-2 was feasible.
RSV was detected in 34.3% of children younger than 5 years with severe acute respiratory infection. Influenza peaked during the 2023 monsoon, whereas SARS-CoV-2 circulation remained low.
Genomic analyses identified localized RSV B evolution, co-circulating influenza A(H1N1) and A(H3N2), and progression of SARS-CoV-2 Omicron lineages.
Limitations:
Predominantly urban sentinel sites may underrepresent rural transmission.
Excluding immunocompromised patients and those with significant comorbidities may limit generalizability. Sequencing only specimens with cycle-threshold values of 27 or lower may introduce selection bias.
Conclusion:
The National Respiratory Pathogen Genomic Surveillance platform demonstrated the feasibility and utility of sustainable, integrated respiratory virus surveillance in Bangladesh.
