Complete nucleotide sequence of simian endogenous type D retrovirus with intact genome organization: evidence for ancestry to simian retrovirus and baboon endogenous virus

Abstract

A complete endogenous type D viral genome has been isolated from a baboon genomic library. The provirus, simian endogenous retrovirus (SERV), is 8,393 nucleotides long and contains two long terminal repeats and complete genes for gag, pro, pol, and env. The primer binding site is complementary to tRNA 3 Lys , like in lentiviruses. The env GP70 protein is highly homologous to that of baboon endogenous virus (BaEV). PCR analysis of primate DNA showed that related proviral sequences are present in Old World monkeys of the subfamily Cercopithecinae but not in apes and humans. Analysis of virus and host sequences indicated that the proviral genomes were inherited from a common ancestor. Comparison of the evolution of BaEV, exogenous simian retrovirus types 1 to 3 (SRV1 to SRV3), and SERV suggests that SERV is ancestral to both BaEV and the SRVs.

Comprehensive phylogenomic analysis reveals a novel cluster of simian endogenous retroviral sequences in Colobinae monkeys

“…Studies on col‐SERVs lag far behind those on cer‐SERVs (particularly macaque SERVs), although a few studies have identified SERVs in Colobinae monkeys (Sommerfelt et al, ; Todaro et al, ). One reason for the apparent lack of interest in col‐SERVs is that an early hybridization‐based screening failed to identify SERVs in Colobus guereza (van der Kuyl, Mang, Dekker, & Goudsmit, ), which suggested that SERVs were integrated after the divergence between Cercopithecinae and Colobinae monkeys. Another reason is that the genomic resources of Cercopithecinae monkeys including draft genome sequences are better established than those of Colobinae monkeys, partly because Cercopithecinae monkeys have been preferentially used for biomedical research.…”

“…Genomic sequences highly homologous to SRV genes were first identified in a baboon ( Papio cynocephalus ) (van der Kuyl et al, ) and termed as simian endogenous retroviruses (SERVs). Although the sequences isolated in this study contained frameshift mutations, the basic genomic architecture of SRVs was preserved in SERVs, suggesting that SERVs are fossils of ancient SRVs.…”

Discovery of a New Endogenous Type C Retrovirus (FcEV) in Cats: Evidence for RD-114 Being an FcEV Gag-Pol /Baboon Endogenous Virus BaEV Env Recombinant

“…In simian immunodeficiency virus, the virus harbored by sabaeus monkeys is a recombinant between African green monkey and sooty mangabey simian immunodeficiency viruses (12). Also, BaEV itself is a recombinant between C-type (PcEV) and D-type (SERV) primate retroviruses (17,27).…”

“…The last common ancestor of the Cercopithicinae supposedly lived at least 9 million years ago, indicating that exogenous BaEV was spreading in Africa after that time. BaEV is a recombinant retrovirus, containing type C gag and pol genes and a type D env gene, which probably arose by recombination of two primate viruses (simian endogenous retrovirus [SERV] and Papio cynocephalus endogenous virus [PcEV]), whose genomes are also present in monkey genomic DNA (17,27). RD-114 has the same mosaic genomic structure as BaEV.…”

Novel Endogenous Type C Retrovirus in Baboons: Complete Sequence, Providing Evidence for Baboon Endogenous Virus gag-pol Ancestry

“…Two complete endogenous retroviral sequences, those of baboon endogenous virus (BaEV) (15) and simian endogenous retrovirus (SERV) (39), have been isolated from the genome of the baboon (Papio cynocephalus). Originally, BaEV was isolated from baboon tissue by cocultivation with permissive cell lines (3,34).…”