Spatial and temporal dynamics of West Nile virus between Africa and Europe

Abstract

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.

Fig. 1. Phylogeographic reconstruction of West Nile virus lineage 1 (WNV L1) strains.

a Geographic diffusion pattern of 80 WNV L1 genomes and their ancestors was reconstructed. African and European countries from which the samples come from are coloured in dark orange and blue, respectively. Black areas correspond to the 80% HPDs of the inferred location. The time of each area or sample is indicated by different shades (black for areas and red for dots), with the oldest samples corresponding to the most intense shade. The main events of the diffusion of the virus are indicated on the map, with numbers from 1 to 6: 1) introductions to West and East of Africa, 2) first introduction in Morocco and then Spain, 3) movement towards France and Italy, 4) back reintroductions from Spain to Morocco and from Italy to Senegal, 5) introduction from Senegal to France in 2015, and 6) back introduction from Italy to Senegal. The direction of the spread of the virus is indicated by arrows, while colours indicate movements happened only in Africa or involving Africa and Europe (in green) and routes that took place entirely in Europe (in yellow). Dotted arcs indicate back reintroductions from Europe to Africa. b A molecular clock shows the phylogenetic relationships between the same 80 WNV L1 genomes. Light orange dots indicate nodes with a posterior probability <0.9, while 95% HPDs of the median ages are indicated by blue bars. African and European sequences are coloured by continent. The time of the most recent common ancestor (tMRCA) for Clade 1A was estimated to be around 1919. On the right, inside Clade 1A, three groups of interest are highlighted: cluster 2, Western Mediterranean clade 1 (WMed-1), and Western Mediterranean clade 2 (WMed-2). The map in Fig. 1 has been produced using free vector and raster map data from Natural Earth (naturalearthdata.com), downloaded from a web platform freely available at https://geojson-maps.ash.ms/.

Fig. 2. Phylogenetic inference of West Nile virus lineage 2 (WNV L2) strains.

a Geographic diffusion pattern of 80 WNV L2 genomes and their ancestors was reconstructed. African and European countries from which the samples come from are coloured in dark orange and blue, respectively. Black areas correspond to the 80%HPDs of the inferred location. The time of each area or sample is indicated by different shades (black for areas and red for dots), with the oldest samples corresponding to the most intense shade. The main events of the diffusion of the virus are indicated on the map, with numbers from 1 to 4: 1) two introductions from South Africa to Hungary in 2001 and 2005, 2) introductions from Hungary to Austria around 2006, 3) introduction from Hungary to Greece around 2007, and 4) introduction from Austria to Italy around 2009. The direction of the spread of the virus is indicated by arrows, while colours indicate movements happened only in Africa or involving Africa and Europe (in green) and routes that took place entirely in Europe (in yellow). Dotted arcs indicate back reintroductions from Europe to Africa. b A molecular clock shows the phylogenetic relationships between the same 80 WNV L2 genomes. Light orange dots indicate nodes with a posterior probability <0.9, while 95% HPDs of the median ages are indicated with blue bars. African and European sequences are coloured by continent. The time of the most recent common ancestor (tMRCA) for all WNV L2 sequences included in the analysis was estimated to be around 1733. On the right, 6 groups of interest, which are considered relevant to our discussion are highlighted: clusters 1-5 all part of Clade 2d, are indicated by C1-5 codes. The map in Fig. 2 has been produced using free vector and raster map data from Natural Earth (naturalearthdata.com), downloaded from a web platform freely available at https://geojson-maps.ash.ms/.