Abstract / Summary
Human metapneumovirus (HMPV) is a major cause of acute respiratory infections in children, yet its genomic epidemiology remains understudied in Nepal. Previous studies have relied either on PCR or partial sequencing, providing limited insight into the viral genome. This study aimed to characterize HMPV genomes from pediatric respiratory infections using whole-genome sequencing (WGS) and understand their phylogenomics. Four archived HMPV-positive nasopharyngeal swab samples collected in 2024, from children aged 15–48 months, were sequenced in Illumina iSeq100. The consensus genomes were generated using Chan Zuckerberg ID, lineage assignment was performed using Nextclade, and maximum likelihood phylogenomic analysis was conducted with representative regional HMPV genomes. Complete or near-complete HMPV genomes were successfully generated from all four samples, with average sequencing depths ranging from 9.4x to 103.1x and genome coverage from 96.6% to 98.7%. Two genomes were of sublineage A2.2.2, while one each belonged to lineages B1 and B2, demonstrating the co-circulation of multiple lineages. Phylogenetic analysis showed that all genomes clustered within known regional lineages, with no evidence of novel lineage emergence. All children presented with lower respiratory tract infections, predominantly bronchopneumonia, while laboratory parameters varied across subjects. This study reports one of the first whole-genome sequencing of HMPV from Nepal and demonstrates the co-circulation of A2.2.2, B1, and B2 lineages among pediatric respiratory infections. These findings provide a baseline for genomic surveillance of respiratory viruses in Nepal and support the integration of next-generation sequencing to monitor viral evolution and transmission.