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

H5N1 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 and 2008. 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.

Spatio-temporal dynamics of African swine fever outbreaks in Nigeria, 2002-2007.

African swine fever (ASF) was first introduced into Nigeria through Lagos state in 1997. The disease rapidly spread to Ogun state in 1998 and extended to the Niger Delta (Delta, Rivers and Akwa Ibom states) in the same year. In 1998, Kaduna, Plateau and Benue states all north of the country experienced ASF for the first time. Poor farm biosecurity, bad abattoir practices and extensive/free range pig farming systems led to extensive spread of the diseases to about 16 Nigerian states excluding the far northwest and north east. A total of 1036 field samples collected over a 6-year period covering 19 Nigerian states were analysed during the period under review; 805 samples were PCR positive and 231 negative. Positive samples were detected in all three surveillance phases and from all agroecological zones across the country. For the first time since its incursion, ASF was identified in some states; Bauchi, Adamawa Taraba and Gombe with chances of control very slim and further spread of the virus northward envisaged. Outbreaks of the disease are now a perennial problem with an increasing disease burden in areas where high numbers of pigs are produced in the country. The National Veterinary Research Institute (NVRI), Vom, since 2002 investigated ASF based on tissue submissions and reports made by individuals, private & commercial farms and agricultural bodies. We present an analysis of geographical and temporal distribution of ASF in the country from 2002 to 2007 and a review of historic outbreaks since the first incursion. Risk factors and prospects for control are discussed.