Biological and phylogenetic characteristics of West African lineages of West Nile virus

Abstract

The West Nile virus (WNV), isolated in 1937, is an arbovirus (arthropod-borne virus) that infects thousands of people each year. Despite its burden on global health, little is known about the virus' biological and evolutionary dynamics. As several lineages are endemic in West Africa, we obtained the complete polyprotein sequence from three isolates from the early 1990s, each representing a different lineage. We then investigated differences in growth behavior and pathogenicity for four distinct West African lineages in arthropod (Ap61) and primate (Vero) cell lines, and in mice. We found that genetic differences, as well as viral-host interactions, could play a role in the biological properties in different WNV isolates in vitro, such as: (i) genome replication, (ii) protein translation, (iii) particle release, and (iv) virulence. Our findings demonstrate the endemic diversity of West African WNV strains and support future investigations into (i) the nature of WNV emergence, (ii) neurological tropism, and (iii) host adaptation.

Fig 1. The genetic diversity of the West Nile virus lineages.

A) Pairwise percent identity between nucleotide (blue) and amino acid (orange) sequences of the polyprotein. Sequences are labeled in the following format: accession number, 2-letter country code, and year of isolation. B) Genomic structure of West Nile virus with genes labeled. Alignments of known virulence motifs are shown. Codons of special interest are labeled by their position at each individual protein sequence and not by their position in the polyprotein. Sequences are labeled by country, year of isolation and phylogenetic lineage.

Fig 2. Bayesian maximum clade credibility tree estimating the phylogenetic relationships of West Nile virus.

Tree nodes with a posterior probability greater than 0.7 are displayed. Tree tip nodes are colored by proposed lineage and for visual clarity. For each sequence, the two-letter code representing a country of isolation is included in the sequence label. Branches are scaled in years before 2015. ^# NY99 strain.

Fig 3. Growth kinetics of West African West Nile virus strains.

The strain lineage label is in reference to the strains in Table 1. Figs A-D show the amount of viral RNA equivalents isolated from cells (A and B) and supernatant (C and D) (log₁₀ of RNA copy number), the percent (% immunofluorescence) of cells infected (E and F) and the number of infectious viral particles (G and H) (log₁₀PFU/ml) over a 146-hour post-infection time period. The experiments were performed with Ap61 cells (left column) and Vero cells (right column). The error bars indicate the range in values of two independent experiments.

Fig 4. Replication Efficiency of West Nile virus in vitro.

Replication efficiency of West African strains in Ap61 and Vero cell lines over 146 hour post-infection period. The error bars indicate the range in values of two independent experiments.

Fig 5

Survival curves of 5- to 6-week-old mice following intraperitoneal infection with (A) 10,000, (B) 1,000 and (C) 100 PFU. Mice were monitored daily for 21 days. Except in (C) when comparing lineage 8 and lineage 1, all survival curves were significantly different (Wilcoxon rank sum test, p-values < 0.05).