Recombination in feline immunodeficiency virus genomes from naturally infected cougars

Abstract

Recombination contributes significantly to diversity within virus populations and ultimately to viral evolution. Here we use a recently developed statistical test to perform exploratory analysis of recombination in fourteen feline immunodeficiency virus (FIVpco) genomes derived from a wild population of cougars. We use both the global and local Phi statistical test as an overall guide to predict where recombination may have occurred. Further analyses, including similarity plots and phylogenetic incongruence tests, confirmed that three FIVpco lineages were derived from recombinant events. Interestingly, the regions of mosaic origin were clustered in the area encoding lentiviral accessory genes and largely spared the viral structural genes. Because some of the mosaic strains are currently geographically disparate, our data indicate that the dispersal of cougars infected with these strains was preceded by recombination events. These results suggest that recombination has played an important role in the evolution of FIVpco for this wild population of cougars.

Figure 1

Statistically significant regions (peaks that contain at least one breakpoint) containing a recombinant signal of fourteen FIVpco genomes determined by Phi statistic. The window size was 500 bp and step size was 25 bp. p values are multiple test corrected using Hommel’s modified Bonferroni procedure (Hommel, 1988). Numbers on the x-axis indicate nucleotide position in the genome alignment. The position of open reading frames is indicated beneath the figure. The first exon of rev encompasses approximately the first 200 bp of the env ORF.

Figure 2

Maximum likelihood tree inferred for the first 4500 bp (before the first recombinant region or ‘peak’ in Figure 1) for fourteen FIVpco sequences. A substitution model of GTR+Γ was selected using ModelTest (Posada and Crandall, 1998) (with Γ equal to 0.26) and was used to infer the tree. The location of each infected cougar is listed next to the isolate name and is referenced to a schematic map of the area.

Figure 3

Exploratory neighbor-joining trees corresponding to the regions in between ‘peaks’ of Figure 1. Only major lineages are shown for readability. Because the width of the peaks differs in length, the midpoint of each peak was chosen to delineate the region. Lineages that have boxes around them (JM01, SR631 and JF6) appear to be recombinant. The trees suggest an initial estimate of which lineages are recombinant.

Figure 4

Similarity plots of suspected recombinant and parental sequences. All sequences are compared to putative parental sequence YF125 and YM29 except in b. a) JF6, b) JM01 with SR631 and YF125, c) SR631, and d) JM01. Window size was 200 bp and step size was 20 bp. The dashed lines correspond to maximum likelihood estimate of recombinant points. Note their correspondence to the areas of significant recombination (shaded regions) in Figure 1.

Figure 5

Maximum likelihood trees inferred for a) Partition_A and b) Partition_B. The trees differ in their placement of recombinant sequence JF6. Partitions (including nucleotide substitution models) are described in Table 1. Recombinant viruses are boxed.

Figure 6

Maximum likelihood trees (drawn to scale) for partition a) Partition_C, b) Partition_D and c) Partition_E with recombinant sequences JM01/YM137 and SR631/SR631B. Partitions (including nucleotide substitution models) described in Table 1. Recombinant viruses are boxed.