Recombination in West Nile Virus: minimal contribution to genomic diversity

Abstract

Recombination is known to play a role in the ability of various viruses to acquire sequence diversity. We consequently examined all available West Nile virus (WNV) whole genome sequences both phylogenetically and with a variety of computational recombination detection algorithms. We found that the number of distinct lineages present on a phylogenetic tree reconstruction to be identical to the 6 previously reported. Statistically-significant evidence for recombination was only observed in one whole genome sequence. This recombination event was within the NS5 polymerase coding region. All three viruses contributing to the recombination event were originally isolated in Africa at various times, with the major parent (SPU116_89_B), minor parent (KN3829), and recombinant sequence (AnMg798) belonging to WNV taxonomic lineages 2, 1a, and 2 respectively. This one isolated recombinant genome was out of a total of 154 sequences analyzed. It therefore does not seem likely that recombination contributes in any significant manner to the overall sequence variation within the WNV genome.

Figure 1

Whole Genome Phylogenetic Tree. Bayesian phylogenetic tree reconstruction of 154 whole genomic WNV (and Kunjin virus) sequences. The 6 distinct lineages are maintained and are delineated by red brackets. Branch lengths are proportional to distance (the number of nucleotide changes), and the distance scale for the number of changes is provided at the bottom of the figure.

Figure 2

Phylogenetic Trees Showing Recombination. Shows the Bayesian consensus trees for (A) the NS5 coding region lacking the recombinant region and (B) only the recombinant region. The labels for all non-recombinant taxa were removed for clarity. The translocation of the AnMg798 sequence from the lineage 2 clade in panel A to the lineage 1a clade in panel B indicates the presence of recombinant sequence within this region. Major parent, minor parent, and daughter sequences are shaded in blue, green, and red respectively. Lineages are indicated as in figure 1. Branch lengths are proportional to distance (the number of nucleotide changes), and the distance scale for the number of changes is provided at the top each panel.