This dataset contains metadata for HMPV and RSV positive samples by country collected between August 2011 and January 2014 from Kenya, Mali, Gambia, South Africa and Zambia. GenBank accession numbers for HMPV and RSV successfully sequenced samples plus the Genbank accession numbers of the contemporenous sequences analysed in this study. Metadata file linking each GenBank Id for samples sequenced in this study to their genotypes for both HMPV and RSV.