Epidemiology and Molecular Characterization of Human Metapneumovirus in Influenza-Like Illness: A Decade of Surveillance in Dibrugarh, Assam (2014-2025).

Background

Human metapneumovirus (hMPV) is a globally recognized cause of influenza-like illness (ILI), especially among children, but data from Northeast India are limited. This study analyzed epidemiological and molecular features of hMPV detected in Dibrugarh, Assam, over a decade-long surveillance period.

Methods

Between May 2014 and November 2025, 3,597 ILI patients were screened for hMPV at a tertiary hospital in Dibrugarh, Assam. Clinical samples (nasopharyngeal/throat swabs) were tested using multiplex respiratory panels and TaqMan-based real-time RT-PCR. Partial sequencing of the G gene was performed by Sanger sequencing, followed by phylogenetic and glycosylation analyses using MEGA 11, NetNGlyc, and NetOGlyc tools. Statistical analysis was done using SPSS v26.

Results

Overall, hMPV prevalence was 3.1% (112/3597), significantly higher among children aged <5 years than older individuals (3.9% vs. 1.3%; p = 0.003). hMPV activity exhibited marked winter seasonality, with significantly higher positivity during the colder months (5.6% vs. 0.8%; p < 0.001). Phylogenetic analysis demonstrated the circulation of A2.2.1 (A2b1), A2.2.2 (A2b2), and B2 lineages in Assam. The two 2025 A2.2.2 strains harbored the characteristic 111-nucleotide G-gene duplication, while comparative glycosylation analysis revealed lineage-specific variation in predicted N- and O-linked glycosylation profiles.

Conclusion

hMPV remains an important cause of pediatric influenza-like illness in Northeast India, with marked winter seasonality. The detection of A2.2.1, A2.2.2, and B2 lineages, including A2.2.2 strains with the characteristic 111-nucleotide G-gene duplication, underscores the importance of continued molecular surveillance.