Identification, phylogeny, and evolution of retroviral elements based on their envelope genes

Phylogenetic analyses of retroviral elements, including endogenous retrovir uses, have relied essentially on the retroviral pol gene expressing the hig hly conserved reverse transcriptase. This enzyme is essential for the life cycle of all retroid elements, but other genes are also endowed with conser ved essential functions. Among them, the transmembrane (TM) subunit of the envelope gene is involved in virus entry through membrane fusion. It has al so been reported to contain a domain, named the immunosuppressive domain, t hat has immunosuppressive properties most probably essential for virus spre ad within the host. This domain is conserved among a large series of retrov iral elements, and we have therefore attempted to generate phylogenetic lin ks between retroviral elements identified from databases following tentativ e alignments of the immunosuppressive domain and adjacent sequences. This a llowed us to unravel a conserved organization among TM domains, also found in the Ebola and Marburg filoviruses, and to identify a large number of hum an endogenous retroviruses (HERVs) from sequence databases. The latter elem ents are part of previously identified families of HERVs, and some of them define new families. A general phylogenetic analysis based on the TM protei ns of retroelements, and including those with no clearly identified immunos uppressive domain, could then be derived and compared with pol-based phylog enetic trees, providing a comprehensive survey of retroelements and definit ive evidence for recombination events in the generation of both the endogen ous and the present-day infectious retroviruses.