Epidemiology, genetic diversity, and evolution of endemic feline immunodeficiency virus in a population of wild cougars

Abstract

Within the large body of research on retroviruses, the distribution and evolution of endemic retroviruses in natural host populations have so far received little attention. In this study, the epidemiology, genetic diversity, and molecular evolution of feline immunodeficiency virus specific to cougars (FIVpco) was examined using blood samples collected over several years from a free-ranging cougar population in the western United States. The virus prevalence was 58% in this population (n = 52) and increased significantly with host age. Based on phylogenetic analysis of fragments of envelope (env) and polymerase (pol) genes, two genetically distinct lineages of FIVpco were found to cooccur in the population but not in the same individuals. Within each of the virus lineages, geographically nearby isolates formed monophyletic clusters of closely related viruses. Sequence diversity for env within a host rarely exceeded 1%, and the evolution of this gene was dominated by purifying selection. For both pol and env, our data indicate mean rates of molecular evolution of 1 to 3% per 10 years. These results support the premise that FIVpco is well adapted to its cougar host and provide a basis for comparing lentivirus evolution in endemic and epidemic infections in natural hosts.

FIG. 1.

Prevalence of FIVpco infection in a population of free-ranging cougars in southeast Wyoming by sex and age class. Prevalence was determined by serology using a flow cytometric assay and confirmed by PCR. The sample sizes are shown above the bars (n = 52 [total]). For individuals that were sampled repeatedly, only infection status for the most recent sample was considered.

FIG. 2.

ML tree of partial FIVpco pol sequences from free-ranging cougars in the Rocky Mountains (United States and Canada). Taxa designated SR represent animals from the study area. For each SR individual, one sequence was randomly selected from a larger data set. Taxa designated Pco represent previously described FIV pol sequences from other cougar populations in western North America. The state or province where the animal was captured is indicated in boldface letters (YNP, Yellowstone National Park). Branch lengths of >0.02 are shown below the branches. The FIVpco sequence from a Vancouver Island cougar (PLV1695) was used as an outgroup. The values next to tree nodes represent bootstrap values of >70 based on 500 replicates using an NJ tree algorithm and the same model of substitution used for the ML tree.

FIG. 3.

ML tree of 292 partial FIV env sequences from 28 infected cougars in a population in southeast Wyoming. Mother-kitten groups are indicated by open boxes, and animals with related viruses and confirmed overlap in home ranges are indicated by shaded boxes. Where identical sequences were identified, their number is indicated in parentheses next to the taxon symbol. Branch lengths of .0.01 are shown below the branches. The ML search was terminated after 100,000 iterations (see the text). See Fig. 2 for further descriptions.

FIG. 4.

Partitioning of genetic diversity in FIV env sequences from 28 naturally infected cougars based on p distances observed in pairwise comparisons. For each category of comparison (e.g., within individuals, same time point), frequencies sum up to 1.

FIG. 5.

Plots of nucleotide diversity for FIV env (A) and pol (B) gene fragments. Diversity is expressed as the average number of character states found per sliding window of 10 nucleotides.