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Journal of Virology, December 2001, p. 11709-11719, Vol. 75, No. 23
0022-538X/01/$04.00+0   DOI: 10.1128/JVI.75.23.11709-11719.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.

Identification, Phylogeny, and Evolution of Retroviral Elements Based on Their Envelope Genes

Laurence Bénit,1 Philippe Dessen,2 and Thierry Heidmann1,*

Unité des Rétrovirus Endogènes et Éléments Rétroïdes des Eucaryotes Supérieurs, CNRS UMR 1573, Institut Gustave Roussy, 94805 Villejuif Cedex,1 and INFOBIOGEN, Service de Bioinformatique, UMS825 CNRS/SC13 INSERM, 94801 Villejuif Cedex,2 France

Received 14 June 2001/Accepted 23 August 2001

Phylogenetic analyses of retroviral elements, including endogenous retroviruses, have relied essentially on the retroviral pol gene expressing the highly conserved reverse transcriptase. This enzyme is essential for the life cycle of all retroid elements, but other genes are also endowed with conserved essential functions. Among them, the transmembrane (TM) subunit of the envelope gene is involved in virus entry through membrane fusion. It has also been reported to contain a domain, named the immunosuppressive domain, that has immunosuppressive properties most probably essential for virus spread within the host. This domain is conserved among a large series of retroviral elements, and we have therefore attempted to generate phylogenetic links between retroviral elements identified from databases following tentative alignments of the immunosuppressive domain and adjacent sequences. This allowed us to unravel a conserved organization among TM domains, also found in the Ebola and Marburg filoviruses, and to identify a large number of human endogenous retroviruses (HERVs) from sequence databases. The latter elements are part of previously identified families of HERVs, and some of them define new families. A general phylogenetic analysis based on the TM proteins of retroelements, and including those with no clearly identified immunosuppressive domain, could then be derived and compared with pol-based phylogenetic trees, providing a comprehensive survey of retroelements and definitive evidence for recombination events in the generation of both the endogenous and the present-day infectious retroviruses.

* Corresponding author. Mailing address: Unité des Rétrovirus Endogènes et Éléments Rétroïdes des Eucaryotes Supérieurs, CNRS UMR 1573, Institut Gustave Roussy, 94805 Villejuif Cedex, France. Phone: 33-1.42.11.49.70. Fax: 33-1.42.11.53.42. E-mail: heidmann{at}igr.fr.

Journal of Virology, December 2001, p. 11709-11719, Vol. 75, No. 23
0022-538X/01/$04.00+0   DOI: 10.1128/JVI.75.23.11709-11719.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.


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