Circulation of Mumps virus genotype G in Pakistan during 2023 outbreak

Abstract

Aim: Despite recurring mumps outbreaks in Pakistan, the virus's genomic diversity remains unavailable. This study explores the mumps genomic diversity in the 2023 Islamabad outbreak. Methods: During January and February 2023, 32 buccal/throat swabs were collected from suspected mumps cases. 15 tested mumps virus (MuV)-positive via RT-PCR. Positive samples underwent partial SH gene sequencing; a subset (n = 10) was whole-genome sequenced using Illumina MiSeq. Results: Phylogenetic analysis identified genotype-G, sharing 95.57–98.73% homology with Japanese/Canadian isolates. Whole-genome-sequencing (n = 2) confirmed genotype-G, 99% similar to Sheffield/Iowa strain. HN region displayed 95.01–95.36% identity with Jeryl Lynn, with genotype G-specific mutations, except T265I. Conclusion: This is the first report of partial and whole-genome sequencing of MuV from Pakistan, highlighting the necessity for genomic surveillance and vaccine integration.