Spatiotemporal evolutionary epidemiology of H5N1 highly pathogenic avian influenza in West Africa and Nigeria, 2006-2015

Abstract

SummaryH5N1 highly pathogenic avian influenza virus (HPAIV) was first observed in Nigeria in early 2006 and has now spread to more than 17 African countries having severe economic and public health implications. Here, we explore the spatiotemporal patterns of viral dispersal both among West African countries and within Nigeria using sequence data from hemagglutinin (HA) gene region of the virus. Analyses were performed within a statistical Bayesian framework using phylodynamic models on data sets comprising of all publically available HA sequence data collected from seven West African countries and Egypt between 2006 and 2015. Our regional-level analyses indicated that H5N1 in West Africa originated in Nigeria in three geopolitical regions, specifically north central and north-east, where backyard poultry and wild birds are in frequent contact, as well as south-west, a major commercial poultry area, then dispersed to West African countries. We inferred significant virus dispersal routes between Niger and Nigeria on one side and Burkina Faso, Ivory Coast, Ghana and Egypt on the other. Furthermore, south-west Nigeria identified as a primary source for virus dispersal within Nigeria as well as to Niger in 2006 and2008. Niger was an important epicentre for the virus spread into other West African countries in 2015. Egyptian introductions from West Africa were sporadic and resulted most likely from poultry trade with Nigeria rather than contact with infected wild birds. Our inferred viral dispersal routes reflected the large-scale unrestricted movements of infected poultry in the region. Our study illustrates the ability of phylodynamic models to trace important HPAIV dispersal routes at a regional and national level. Our results have clear implications for the control and prevention of this pathogen across scales and will help improve molecular surveillance of transboundary HPAIVs. K E Y W O R D Savian influenza, Bayesian phylodynamics, dispersal routes, Phylogeography, poultry | INTRODUCTIONThe continuous spread of H5N1 highly pathogenic avian influenza (HPAI) in West and Central Africa has caused large-scale economic losses and threatens farmer's livelihoods, poultry production and trade. Furthermore, there is added concern of the disease becoming endemic in the region which also threatens public health Tables S1 and S2).The IRD data do not always report all precise geographic coordinates, collection date and/or host species of accessions, so we consulted the metadata field of each sequence isolate to identify the approximate location and collection dates. Furthermore, when possible, we identified metadata for each sequence by cross-referencing information with the corresponding publication Chen & Holmes, 2006; Ducatez et al., 2006 Ducatez et al., , 2007Ekong et al., 2012; FAO Empress, 2015;Fusaro et al., 2009Fusaro et al., , 2010Joannis et al., 2006;Monne et al., 2008;Paul, Assam, & Ndang, 2013;Scotch et al., 2013;Shittu et al., 2017, Tassoni et al., 2016Williams, Fasina, & Peterson, 2008). We converted the ...

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“…2B , Table 1 ). Similar expansion events have been observed in other viruses with worldwide distribution, such as HIV and influenza, associated with the emergence of genetic variants ( Ekong et al 2017 ; Li et al 2017 ).…”

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