Summary auto-generated
This study analyzed envelope protein gene sequences from 21 West Nile (WN) virus strains isolated across Africa, Madagascar, and France to characterize genetic diversity. Researchers extracted viral RNA from infected cells and amplified a 327-nucleotide envelope gene fragment using RT-PCR, then sequenced and compared the samples. The analysis revealed two distinct viral lineages with up to 29% nucleotide divergence between groups. Four strains contained a 12-nucleotide in-frame deletion that removed amino acids at positions 154-157, eliminating a potential glycosylation site present in other strains. Importantly, the distribution of virus subtypes into these two lineages did not correlate with geographic origin, host preference, or isolation time. Different subtypes were found circulating simultaneously in the same country (Senegal, Madagascar), and closely related strains appeared in distant locations. The Kunjin virus, previously considered distinct, was reclassified as a West Nile subtype based on sequence similarity. These findings support the hypothesis that wild birds migrating between continents disseminate West Nile virus strains with little apparent selection pressure.
Key findings
- West Nile virus strains cluster into two genetically distinct lineages with up to 29% nucleotide sequence divergence in the envelope gene
- Four viral strains harbor a 12-nucleotide deletion that eliminates an N-glycosylation site, resulting in variable glycosylation status among naturally occurring strains
- Virus subtype distribution does not correlate with geographic origin, time of isolation, or host/vector species, suggesting free circulation with bird migration
- Kunjin virus shares sufficient nucleotide identity (>80%) with West Nile lineage I strains to be classified as a West Nile subtype
- Multiple genetically distinct West Nile virus subtypes circulate simultaneously in the same geographic regions
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Abstract
We compared the sequence of an envelope protein gene fragment from 21 temporally distinct West Nile (WN) virus strains, isolated in nine African countries and in France. Alignment of nucleotide sequences defined two groups of viruses which diverged by up to 29%. The first group of subtypes is composed of nine WN strains from France and Africa. The Austral-Asian Kunjin virus was classified as a WN subtype in this first group. The second group includes 12 WN strains from Africa and Madagascar. Four strains harboured a 12 nucleotide in-frame deletion. The loss of the corresponding four amino acids resulted in the loss of the potential glycosylation site present in several WN strains. The distribution of virus subtypes into two lineages did not correlate with host preference or geographical origin. The isolation of closely related subtypes in distant countries is consistent with WN viruses being disseminated by migrating birds.