Identification of diverse groups of endogenous gammaretroviruses in mega- and microbats

Abstract

A previous phylogenetic study suggested that mammalian gammaretroviruses may have originated in bats. Here we report the discovery of RNA transcripts from two putative endogenous gammaretroviruses in frugivorous (Rousettus leschenaultii retrovirus, RlRV) and insectivorous (Megaderma lyra retrovirus, MlRV) bat species. Both genomes possess a large deletion in pol, indicating that they are defective retroviruses. Phylogenetic analysis places RlRV and MlRV within the diversity of mammalian gammaretroviruses, with the former falling closer to porcine endogenous retroviruses and the latter to Mus dunni endogenous virus, koala retrovirus and gibbon ape leukemia virus. Additional genomic mining suggests that both microbat (Myotis lucifugus) and megabat (Pteropus vampyrus) genomes harbour many copies of endogenous retroviral forms related to RlRV and MlRV. Furthermore, phylogenetic analysis reveals the presence of three genetically diverse groups of endogenous gammaretroviruses in bat genomes, with M. lucifugus possessing members of all three groups. Taken together, this study indicates that bats harbour distinct gammaretroviruses and may have played an important role as reservoir hosts during the diversification of mammalian gammaretroviruses.

Fig. 1.

ML tree of the Gag gene (amino acids) of gammaretroviruses. The viral sequences detected in this study are underlined. RlRV was isolated from R. leschenaultii, MlRV was isolated from M. lyra and RfRV was taken from R. ferrumequinum. Bat icons are shown to indicate bat gammaretroviruses. Bar, 0.2 amino acid substitutions per site and the tree is midpoint rooted for clarity only. Only bootstrap values >70 % are shown. GenBank nos are shown in Table 3.

Fig. 2.

ML tree of the Pol gene (amino acids) of gammaretroviruses. The viral sequence underlined was detected in this study. RfRV, RpuRV, RpeRV, RmRV, RaRV, MrRV and PaRV represent gammaretroviruses isolated from R. ferrumequinum, R. pusillus, R. pearsoni, R. megaphyllus, R. affinis, M. ricketti and P. alecto, respectively (Cui et al., 2012). Bat icons are shown to indicate bat gammaretroviruses. Bar, 0.2 amino acid substitutions per site and the tree is midpoint rooted for clarity only. Only bootstrap values >70 % are shown. GenBank nos are shown in Table 3.

Fig. 3.

Phylogenetic diversity of bat gammaretroviruses. The viral sequence detected in this study is underlined. ERVs are shown using scaffold names, with (M) denoting M. lucifugus and (P) P. vampyrus. The three major groups of ERVs are marked A, B and C. Bat icons are shown to indicate bat viruses. Bar, 0.2 amino acid substitutions per site and the tree is midpoint rooted for clarity only. Only bootstrap values >70 % are shown. GenBank nos are shown in Table 3.