Search

It is unclear whether West Nile virus (WNV) circulates between Africa and Europe, despite numerous studies supporting an African origin and high transmission in Europe. We integrated genomic data with geographic observations and phylogenetic and phylogeographic inferences to uncover the spatial and temporal viral dynamics of WNV between these two continents. We focused our analysis towards WNV lineages 1 (L1) and 2 (L2), the most spatially widespread and pathogenic WNV lineages. Our study shows a Northern-Western African origin of L1, with back-and-forth exchanges between West Africa and Southern-Western Europe; and a Southern African origin of L2, with one main introduction from South Africa to Europe, and no back introductions observed. We also noticed a potential overlap between L1 and L2 Eastern and Western phylogeography and two Afro-Palearctic bird migratory flyways. Future studies linking avian and mosquito species susceptibility, migratory connectivity patterns, and phylogeographic inference are suggested to elucidate the dynamics of emerging viruses., (© 2023. Springer Nature Limited.)

West Nile virus is a re-emerging arbovirus whose impact on public health is increasingly important as more and more epidemics and epizootics occur, particularly in America and Europe, with evidence of active circulation in Africa. Because birds constitute the main reservoirs, migratory movements allow the diffusion of various lineages in the world. It is therefore crucial to properly control the dispersion of these lineages, especially because some have a greater health impact on public health than others. This work describes the development and validation of a novel whole-genome amplicon-based sequencing approach to West Nile virus. This study was carried out on different strains from lineage 1 and 2 from Senegal and Italy. The presented protocol/approach showed good coverage using samples derived from several vertebrate hosts and may be valuable for West Nile genomic surveillance.

West Nile virus (WNV) is a virus of the Japanese encephalitis antigenic complex and belongs to the family Flaviviridae of the genus flavivirus. The virus can cause infection in humans which in most cases is asymptomatic, however symptomatic cases exist and the disease can be severe causing encephalitis and meningoencephalitis. The virus is maintained in an enzootic cycle involving mosquitoes and birds, humans and other mammals such as horses can be accidental hosts. A mosquito-based arbovirus surveillance system and the sentinel syndromic surveillance network (4S) have been in place since 1988 and 2015 respectively, to better understand the transmission dynamics of arboviruses including WNV in Senegal. Arthropod and human samples have been collected from the field and analysed at Institut Pasteur de Dakar using different methods including RT-PCR, ELISA, plaque reduction neutralization test and viral isolation. RT-PCR positive samples have been analysed by Next Generation Sequencing. From 2012 to 2021, 7912 samples have been analysed and WNV positive cases have been detected, 20 human cases (19 IgM and 1 RT-PCR positive cases) and 41 mosquito pools. Phylogenetic analyzes of the sequences of complete genomes obtained showed the circulation of lineage 1a, with all these recent strains from Senegal identical to each other and very close to strains isolated from horse in France in 2015, Italy and Spain. Our data showed lineage 1a endemicity in Senegal as previously described, with circulation of WNV in humans and mosquitoes. Phylogenetic analyzes carried out with the genome sequences obtained also revealed exchanges of WNV strains between Europe and Senegal which could be possible via migratory birds. The surveillance systems that have enabled the detection of WNV in humans and arthropods should be extended to animals in a one-health approach to better prepare for global health threats.