Eight coding-complete genomes of human metapneumovirus recovered by virus metagenomics in coastal Kenya, 2021-2024

Samuel K Mwasya; Dorcas Okanda; Samuel Odoyo; Esther Nyadzua Katama; Clement Lewa; Arnold W Lambisia; George Githinji; Charles N Agoti

doi:10.1128/mra.00065-26

Eight coding-complete genomes of human metapneumovirus recovered by virus metagenomics in coastal Kenya, 2021-2024

Microbiol Resour Announc. 2026 Apr 9;15(4):e0006526. doi: 10.1128/mra.00065-26. Epub 2026 Mar 16.

Authors

Samuel K Mwasya¹, Dorcas Okanda¹, Samuel Odoyo¹, Esther Nyadzua Katama¹, Clement Lewa¹, Arnold W Lambisia¹, George Githinji^{1

2}, Charles N Agoti^{1

3}

Affiliations

¹ Kenya Medical Research Institute, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.
² Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya.
³ School of Public Health, Pwani University, Kilifi, Kenya.

Abstract

Few human metapneumovirus coding-complete genomes are available from Africa despite significance in optimizing local molecular diagnostics and global phylogeographic analysis. We report eight genomes recovered following nanopore metagenomic sequencing of samples collected in coastal Kenya (2021-2024). These fell into sub-lineages A2b/A2.2.1 (n = 3), A2c-wt/A2.2.2 (n = 4), and B1 (n = 1).

Keywords: Kenya; Kilifi; genomic surveillance; hMPV; human metapneumovirus; lineages; metagenomics.