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 diseasein childhood. They are related viruses from the Pneumoviridaefamily andshow 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 2011andJanuary 2014,we conducted acomparative phylogenetic and phylogeographic analysesto 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 observedbetween neighbouring countries.Phylogeographicanalyses indicate sequences largely cluster by geographical region i.e.,West Africa (Mali, Gambia), East Africa (Kenya) and Southern Africa (Zambia, South Africa), with strongregionallinksbetween neighbouring locations. African sequences were well-mixed with global sequences. Sequences from different African subregions fell into separate clusters interspersed with sequences fromother countriesglobally. Conclusion:HMPV and RSV share similar patterns of geographic spread across Africa, characterised by co-circulation of multiple genetic variantswithin epidemics, geographic clustering of sequences and strong regional linksbetween neighbouring locations. Geographicalclustering of sequences suggests independent introduction of HMPVand RSVvariants inAfrica from the global pool, and further local diversification. The Vgenotype dominance patterns observedfurther supports strong epidemiological linkage between neighbouring countries.Globally, African strains are not different from globally circulating strains