Abstract
Molecular Epidemiology of Human Metapneumovirus in Kilifi, Coastal Kenya, 2016-2017 and 2021-2024
Okanda, D.
O. Odoyo S
Kiprono, H.
Katama, E.
Maina, G.
Mutunga, M.
Nyiro, J.
Agoti, C. N.
Githinji, G.
Wellcome Open Res. 2026; 11106
Permanent descriptor
https://doi.org/10.12688/wellcomeopenres.25865.2BACKGROUND: Human metapneumovirus (hMPV) is a major contributor of acute respiratory infections (ARI) in childhood and vulnerable adults. It comprises two antigenically distinct lineages (A and B), with multiple sub-lineages. Genomic analyses of hMPV strains enable monitoring of viral evolution and transmission to inform future interventions but remain underutilized in Africa. METHODS: We generated 52 near-complete hMPV genomes from respiratory samples collected in Kilifi, Coastal Kenya, using a tiled-amplicon approach and Oxford Nanopore Technologies sequencing. These samples had been identified as hMPV positive by quantitative PCR during (a) a multi-facility outpatient ARI surveillance in nine health facilities in Kilifi between 2016 and 2017, and 2021 to 2023 and (b) a community-based respiratory infection cohort surveillance study between 2023-2024 that sampled enrolled participants irrespective of symptom status. RESULTS: Of the 192 positive samples analyzed from the two studies, children under 5 years accounted for most hMPV cases (134/186, 72%). 52 samples were sequenced (>70% genome coverage), and hMPV-A (27/52, 53.8%) and hMPV-B (25/52, 46.2%) lineages were identified. The recovered sequences mapped into sub-lineages A2c (27/52, 53.8%), B1 (12/52, 21.2%), and B2b (13/52, 25%). A shift in the predominant sub-lineage was observed from B2b (2016) to B1 (2021), and finally to A2c-wild type (2023). In February 2021, for the first time, we detected a single A2c strain with a 111-nucleotide duplication in the G gene among Kenyan samples. CONCLUSION: Our study expands the global nucleotide sequence database for hMPV by adding new whole-genome sequences from Kenya collected over the last decade. It highlights the ongoing replacement of locally predominant hMPV lineages and the importation and local transmission of globally circulating strains. These findings underscore the importance of sustained hMPV genomic surveillance to detect emerging variants and monitor lineage circulation patterns that may impact viral transmission, molecular detection, and future control measures. Human metapneumovirus (hMPV) infection can result in mild-to-severe acute respiratory illness, especially in young children, the elderly and individuals with weakened body defenses. Analyzing the genetic code of hMPV can enhance understanding on how this virus spreads and adapts to host populations over time. However, such investigations are scarce in Africa. Here, we generated and analyzed the genome sequences from 52 hMPV-positive samples, collected from individuals enrolled in our outpatient clinics/community surveillance studies in Kilifi, Coastal Kenya, between 2016-2017 and 2021-2024. Using the Oxford Nanopore Technologies (ONT) sequencing approach, we recovered hMPV sequences belonging to both known viral lineages, hMPV-A and hMPV-B, which were further classified into three distinct genetic sub-lineages (A2c, B1 and B2b). Over the years, the predominant hMPV sub-lineage in the region changed from B2b in 2016, to B1 in 2021, and then to A2c in 2023. Notably, for the first time in Kenya, we detected a sequence belonging to a newly characterized variant of hMPV, A2c-111nt-dup, that has a 111-nucleotide duplication in the G (glycoprotein) gene. Our findings demonstrate the sub-lineage dynamics of hMPV in Coastal Kenya. We recommend continuous monitoring of hMPV sequence characteristics to track its spread and inform the design of future interventions. eng