Molecular characterization of mumps viruses from the 2022–2023 outbreak reveals circulation of multiple genotypes in Uganda

Mumps is a highly contagious viral disease caused by the mumps virus (MuV), a member of the genus Orthorubulavirus in the family Paramyxoviridae. Although effective vaccines exist, mumps vaccination is not yet part of Uganda's routine immunization program. In 2022 and 2023, Uganda experienced a notable outbreak of mumps, underscoring the need for molecular characterization of the circulating virus strains. This study aimed to identify and genetically characterize the mumps virus strains responsible for the outbreak. Buccal or oropharyngeal swabs were collected from clinically confirmed cases from five districts. The mumps virus was isolated using the WHO Vero cell line. RNA was extracted from the isolates and clinical samples using the Qiagen kit. Real-time PCR testing was conducted and positive samples subjected to Sanger sequencing of the SH gene, a key target for genotypic classification. Phylogenetic analysis was performed using MEGA v12 software, with genotypes assigned based on phylogenetic clustering of study sequences with the 24 WHO mumps reference sequences. The study obtained ten virus isolates and fourteen sequences belonging to three genotypes: D, H and G. This genotypic variation, observed within a relatively small sample size, underscores the potential complexity of mumps virus transmission and evolution within the country. This study presents the first genetic characterization of mumps viruses from Uganda and the findings provide critical genomic baseline data for future mumps virus surveillance in Uganda, contributing to the understanding of mumps virus evolution, transmission dynamics, and potential vaccine introduction strategies.