Evolution of Puma Lentivirus in Bobcats (Lynx rufus) and Mountain Lions (Puma concolor) in North America

Abstract

Mountain lions (Puma concolor) throughout North and South America are infected with puma lentivirus clade B (PLVB).A second, highly divergent lentiviral clade, PLVA, infects mountain lions in southern California and Florida. Bobcats (Lynx rufus) in these two geographic regions are also infected with PLVA, and to date, this is the only strain of lentivirus identified in bobcats. We sequenced full-length PLV genomes in order to characterize the molecular evolution of PLV in bobcats and mountain lions. Low sequence homology (88% average pairwise identity) and frequent recombination (1 recombination breakpoint per 3 isolates analyzed) were observed in both clades. Viral proteins have markedly different patterns of evolution; sequence homology and negative selection were highest in Gag and Pol and lowest in Vif and Env. A total of 1.7% of sites across the PLV genome evolve under positive selection, indicating that host-imposed selection pressure is an important force shaping PLV evolution. PLVA strains are highly spatially structured, reflecting the population dynamics of their primary host, the bobcat. In contrast, the phylogeography of PLVB reflects the highly mobile mountain lion, with diverse PLVB isolates cocirculating in some areas and genetically related viruses being present in populations separated by thousands of kilometers. We conclude that PLVA and PLVB are two different viral species with distinct feline hosts and evolutionary histories. IMPORTANCEAn understanding of viral evolution in natural host populations is a fundamental goal of virology, molecular biology, and disease ecology. Here we provide a detailed analysis of puma lentivirus (PLV) evolution in two natural carnivore hosts, the bobcat and mountain lion. Our results illustrate that PLV evolution is a dynamic process that results from high rates of viral mutation/ recombination and host-imposed selection pressure.

Feline Immunodeficiency Virus Cross-Species Transmission: Implications for Emergence of New Lentiviral Infections

“…Previously described nested PCR protocols (11) were used to amplify PLVA proviral DNA from additional bobcats (n ϭ 12) and mountain lions (n ϭ 6). This represented approximately 20% of bobcat samples tested and 10% of available mountain lion samples, consistent with previously reported prevalences in the sampled regions (23,30,31). Reaction mixtures contained 100 to 1,000 ng of genomic DNA.…”

“…We previously evaluated PLV phylogenetic relationships in the context of broad-scale geographic patterns and gene-by-gene evolution (30). In the present analysis, we report on as yet uncharacterized traits of PLV diversity that provide insight into the evolutionary dynamics of this two-host, two-virus system.…”

“…To compare selection pressures across host species, separate PLVA (n ϭ 26) and PLVB (n ϭ 33) translation alignments were generated using the Muscle plug-in, with default parameters, in Geneious (72,73). Each alignment was split into multiple nonrecombinant sections based on the recombination breakpoints identified previously (30) and was screened using branch-site random-effects likelihood analysis (branch-site REL) in Datamonkey (74). Branch-site REL does not use a priori assumptions about which viruses may be diversifying, but rather selection is allowed to vary among all lineages and across all sites.…”

“…Previous analyses of PLVA and PLVB genomic characterizations were performed using the Datamonkey tools MEME and FEL, and results were reported on a gene-by-gene basis independent of the host of origin (30). To compare selection pressures across host species, separate PLVA (n ϭ 26) and PLVB (n ϭ 33) translation alignments were generated using the Muscle plug-in, with default parameters, in Geneious (72,73).…”

“…We previously described several aspects of PLV evolution, including the roles of mutation, recombination, and natural selection in generating genetic diversity over time and space (30). Specifically, both PLVA and -B evolve under predominantly purifying selection, with high rates of synonymous mutations occurring at the nucleotide level but relatively infrequent nonsynonymous substitutions resulting in diversity in the corresponding proteins.…”