The structure and phylogeny of a new family of human endogenous retroviruses

A novel endogenous retrovirus (ERV) designated XA34 was isolated from a human glioma cDNA library using low stringency hybridization with an ERV-9 env probe. Southern blot hybridizations with human genomic DNA revealed the presence of approximately 16 genomic copies closely related to XA34. Sequencing of a 2303 bp cDNA clone of XA34 showed that it belongs to a new ERV family. The XA34 ERV has recombined with an ERV-9-like retrovirus resulting in a truncated ERV-9-like env region that ends with an Alul-like 3' LTR. By using PCR, we isolated approximately 940 bp pol fragments from three additional members of this family, XA35, XA36 and XA37. A fifth member, XA38, was isolated and sequenced as a 4729 bp genomic clone. The genomic XA38 clone spans from pol towards the 3' flanking region. The XA38 virus contains a more cryptic env region. The XA38 env is truncated in the transmembrane region and the virus then ends with three Alu repeats. Southern blot studies with human, chimpanzee, orangutan and squirrel monkey DNA show the presence of the XA34 family in all these species. That both the New and Old World monkeys have this ERV family means that the integration and/or amplification in the primate germ-line of XA34 probably took place about 40-45 million years ago. The phylogeny and the closet relatives to ERV XA34 are discussed.