Evolution of endogenous retroviruses in the Suidae: Evidence for different viral subpopulations in African and Eurasian host species

Abstract

Background: Porcine endogenous retroviruses (PERVs) represent remnants of an exogenous form that have become integrated in the domestic pig (Sus scrofa) genome. Although they are usually inactive, the capacity of 1 ERVs to infect human cells in vitro has raised concerns about xenotransplantation because the viruses could cross the species barrier to humans. Here we have analyzed the evolution of 1 ERVs in ten species of Suidae (suids, pigs and hogs) from Eurasia and Africa using DNA sequences for their coding domains (gag, pro/pol and env genes). For comparison with 1 PERVs, we have also analysed 2 ERVs which in domestic pigs are known to be inactive and do not pose a risk to xenotransplantation. Results: Phylogenetic analysis using Bayesian inference showed that 1 and 2 ERVs have distinctive evolutionary histories. Firstly, two different viral lineages of 1 ERVs were found and a coevolutionary analysis demonstrated that they correspond broadly to their host phylogeny, one of Eurasian and another of African species, and show no evidence of horizontal transmission. 2 ERVs, however, show a bush-like evolution, suggesting a rapid viral radiation from a single common ancestor with no correspondence between host and viral evolutionary trees. Furthermore, though 1 ERV env genes do not possess frequent stop codons, 2 env genes do. To understand whether 1 suid ERVs may be still replicating, we have also evaluated their likely mechanism of proliferation by statistically testing internal to terminal branches using nonsynonymous versus synonymous substitution ratios. Our results suggest that 1 ERVs are increasing in copy number by reinfection, which requires the translocation of the virus from one cell to another. Conclusions: Evidence of at least two viral subpopulations was observed in 1 ERVs from Eurasian and African host species. These results should be taken into account in xenotransplantation since 1 ERVs appear to be codiverging with their host and maintaining ongoing capacity to infect somatic and germ cells. © 2011 Nascimento et al; licensee BioMed Central Ltd.