Molecular characterization of circulating mumps virus in Kerala, 2024-2025.

The mumps virus (MuV) remains a significant public health issue in India, with recurrent outbreaks reported in different regions. There has been a notable increase in cases in Kerala since 2024. From March 2024 to March 2025, the state-level Viral Diagnostic and Research Laboratory (SL-VRDL) at the ICMR-National Institute of Virology (NIV) in Kerala evaluated a total of 197 suspected cases. Of these, 58 cases (29.4%) were confirmed through quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis. Most confirmed cases were found in children aged 5-9 years and adolescents aged 10-19 years. Ten low-Ct clinical samples were selected for whole-genome sequencing, of which four successfully generated high-quality near-complete genomes. Phylogenetic analysis identified all four genomes as genotype C. Comparative genomic analysis revealed divergence from the L-Zagreb vaccine strain (genotype N). Several amino acid changes were identified in the hemagglutinin-neuraminidase (HN) and fusion (F) glycoproteins, including alterations in antigenic and functional regions. However, the biological impact of these mutations needs more testing. These findings provide genomic evidence for the presence of MuV genotype C in Kerala and highlight the need for continued molecular surveillance to monitor viral evolution and its potential implications for vaccine effectiveness, while emphasizing the need to evaluate the inclusion of mumps-containing vaccines in the National Immunization Programme.