COMPARISON OF THE PATTERNS OF SPREAD OF HUMAN METAPNEUMOVIRUS (HMPV) AND RESPIRATORY SYNCYTIAL VIRUS (RSV) IN AFRICA USING VIRUS SEQUENCE DATA

Abstract

Background: Human metapneumovirus (HMPV) and respiratory syncytial virus (RSV) are the leading causes of viral severe acute respiratory disease in childhood. They are related viruses from the Pneumoviridae family and show overlapping clinical, epidemiological and transmission features. Whether the two viruses also share similar patterns of geographic spread remains unknown; this may provide insight on common modalities of control. Materials and Methods: Using 232 HMPV and 842 RSV attachment (G) glycoprotein gene sequences obtained from Gambia, Zambia, Mali, South Africa, and Kenya, between August 2011 and January 2014, we conducted a comparative phylogenetic and phylogeographic analyses to explore the spatial-temporal patterns of HMPV and RSV across Africa using Bayesian discrete phylogeography. Results: HMPV and RSV epidemics are characterised by co-circulation of multiple genetic variants. Similar genotype dominance patterns were observed between neighbouring countries. Phylogeographic analyses indicate sequences largely cluster by geographical region i.e., West Africa (Mali, Gambia), East Africa (Kenya) and Southern Africa (Zambia, South Africa), with strong regional links between neighbouring locations. African sequences were well-mixed with global sequences. Sequences from different African subregions fell into separate clusters interspersed with sequences from other countries globally. Conclusion: HMPV and RSV share similar patterns of geographic spread across Africa, characterised by co-circulation of multiple genetic variants within epidemics, geographic clustering of sequences and strong regional links between neighbouring locations. Geographical clustering of sequences suggests independent introduction of HMPV and RSV variants in Africa from the global pool, and further local diversification. The genotype dominance patterns observed further supports strong epidemiological linkage between neighbouring countries. Globally, African strains are not different from globally circulating strains.