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Journal of Virology, May 2005, p. 6478-6486, Vol. 79, No. 10
0022-538X/05/$08.00+0     doi:10.1128/JVI.79.10.6478-6486.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Evolution and Distribution of Class II-Related Endogenous Retroviruses

Robert Gifford,^* Peter Kabat, Joanne Martin, Clare Lynch, and Michael Tristem

Department of Biological Sciences, Imperial College, Silwood Park, Buckhurst Rd., Ascot, Berkshire SL5 7PY, United Kingdom

Received 22 July 2004/ Accepted 28 November 2004

Endogenous retroviruses (ERVs) are widespread in vertebrate genomes and have been loosely grouped into "classes" on the basis of their phylogenetic relatedness to the established genera of exogenous retroviruses. Four of these genera—the lentiviruses, alpharetroviruses, betaretroviruses, and deltaretroviruses—form a well-supported clade in retroviral phylogenies, and ERVs that group with these genera have been termed class II ERVs. We used PCR amplification and sequencing of retroviral fragments from more than 130 vertebrate taxa to investigate the evolution of the class II retroviruses in detail. We confirm that class II retroviruses are largely confined to mammalian and avian hosts and provide evidence for a major novel group of avian retroviruses, and we identify additional members of both the alpha- and the betaretrovirus genera. Phylogenetic analyses demonstrated that the avian and mammalian viruses form distinct monophyletic groups, implying that interclass transmission has occurred only rarely during the evolution of the class II retroviruses. In contrast to previous reports, the lentiviruses clustered as sister taxa to several endogenous retroviruses derived from rodents and insectivores. This topology was further supported by the shared loss of both the class II PR-Pol frameshift site and the class II retrovirus G-patch domain.

Supplemental material for this article may be found at http://jvi.asm.org/.

Present address: Division of Virology, The National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom.

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