Viral recombination contributes to the genetic diversity found in viruses. Phylogenetic analysis has been used to determine evolutionary relationships of viruses, often assuming the absence of recombination. However, viral recombination results in mosaic genomes which cause conflicting phylogenetic signals in the data. Therefore, a unique, bifurcating tree topology cannot accurately describe the evolutionary relationships within a set of sequences. Quantifying viral recombination is an essential element in the study of evolutionary processes as well as any subsequent vaccine development.

West Nile virus (WNV) is a mosquito-borne, RNA virus and a member of the family Flaviviridae. Homologous recombination has been observed within this family in natural populations and under laboratory conditions. In this study, a dataset of WNV sequences was analyzed for intraspecies, homologous recombination. A NeighborNet analysis of the sequences revealed extensive networked evolution, indicative of recombination with additional evidence provided by nonparametric methods within the RDP2 software package. However, results from parametric methods within the RDP2 software package did not indicate recombination. A new parametric method based on the Jensen-Shannon divergence was developed to reconcile these different results as well as analyze all sequences in the dataset for recombination. The results of this analysis indicate WNV is not recombinant.