Endogenous viral sequences from the Cape golden mole (Chrysochloris asiatica) reveal the presence of foamy viruses in all major placental mammal clades

Abstract

Endogenous retroviruses provide important insights into the deep history of this viral lineage. Endogenous foamy viruses are thought to be very rare and only a few cases have been identified to date. Here we report a novel endogenous foamy virus (CaEFV) within the genome of the Cape golden mole (Chrysochloris asiatica). The identification of CaEFV reveals the presence of foamy virus in the placental mammal superorder Afrotheria. Phylogenetic analyses place CaEFV basal to other foamy viruses of Eutherian origin, suggesting an ancient codivergence between foamy virus and placental mammals. These findings have implications for understanding the long-term evolution, diversity, and biology of retroviruses.

Figure 1. Phylogenetic analysis of CaEFV and other retroviruses.

The phylogenetic tree was reconstructed based on conserved regions of CaEFV and other representative retrovirus Pol proteins using the neighbor-joining method with 1,000 bootstrap replicates. The node labels are bootstrap values. Only selected bootstrap values are shown. The foamy virus clade is highlighted in red.

Figure 2. Phylogenetic analysis of CaEFV and other endogenous and exogenous foamy viruses.

The phylogenetic tree is 50% majority-rule consensus tree reconstructed based on conserved regions of foamy virus Env proteins using MrBayes 3. The node labels are posterior probabilities. Branch lengths are in expected changes per site. The viruses are colored according to the superorder their hosts belong to. BFV, bovine foamy virus; EFV, equine foamy virus; FFV, feline foamy virus; RaFV, Rhinolophus affinis foamy virus; SFVspm, spider monkey simian foamy virus; SFVgor, gorilla simian foamy virus; SFVcpz, chimpanzee simian foamy virus; SFVmac, macaque simian foamy virus; SFVagm, African green monkey simian foamy virus; SloEFV, sloth endogenous foamy virus; PSFV, aye-aye prosimian foamy virus; CoeEFV, coelacanth endogenous foamy-like virus. This consensus tree is depicted with the CoeEFV sequence as the outgroup, but it is an unrooted phylogeny and there is thus no posterior probablity associated with the node connecting the CaEFV sequence with the other mammalian ones.