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 relat ed 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 e nds with an Alul-like 3' LTR, By using PCR, we isolated approximate to 940 bp pol fragments from three additional members of this family, XA 35, XA36 and XA37, A fifth member, XA38, was isolated and sequenced as a 4729 bp genomic clone, The genomic XA38 clone spans from pol toward s the 3' Ranking region, The XA38 virus contains a more cryptic env re gion, The XA38 env is truncated in the transmembrane region and the vi rus then ends with three Alu repeats, Southern blot studies with human , chimpanzee, orangutan and squirrel monkey DNA show the presence of t he XA34 family in all these species. That both the New and Old World m onkeys have this ERV family means that the integration and/or amplific ation in the primate germ-line of XA34 probably took place about 40-45 million years ago. The phylogeny and the closest relatives to ERV XA3 4 are discussed.