Molecular epidemiology and genetic diversity of human metapneumovirus among hospitalized children in Saudi Arabia during the COVID-19 era.

INTRODUCTION: Human metapneumovirus (HMPV) is a major viral cause of acute respiratory tract infections, especially in young children and older adults. However, data on its molecular epidemiology in the Middle East remain scarce. As the COVID-19 pandemic may have altered the circulation and molecular epidemiology of respiratory viruses, this study represents one of the first efforts to assess the genetic diversity and circulation patterns of HMPV in Saudi Arabia during the COVID-19 era. METHODS: A total of 216 nasopharyngeal aspirates were collected from hospitalized children with suspected respiratory infections in Riyadh during the COVID-19 pandemic. Samples were screened for HMPV by RT-PCR, and the full-length G gene of positive isolates was amplified, sequenced, and analyzed for phylogeny, mutations, and glycosylation profiles. RESULTS: HMPV was detected in 10 (4.63%) of screened samples, with the highest prevalence among children aged 2-5 months and a predominance in males. Co-infections with other respiratory viruses were observed in 5 (50%) positive cases. Phylogenetic analysis identified five distinct genotypes (A2.1, A2.2, A2.2.2, B1, B2). Notably, genotype A2.2.2 was identified for the first time in Saudi Arabia and the Middle East region. Comparative sequence analysis revealed 43.75% nucleotide mutations and 25.83% amino acid substitutions, many of which were genotype-specific, along with distinct glycosylation patterns unique to the study isolates. CONCLUSION: This study provides the first molecular characterization of HMPV in Saudi Arabia during the COVID-19 pandemic. The results demonstrate notable genetic diversity, including the circulation of five genotypes and the first detection of the A2.2.2 genotype in the country. These findings highlight the importance of continuous genomic surveillance to monitor viral evolution and guide regional public-health strategies. CLINICAL TRIAL NUMBER: Not applicable.