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Journal of Virology, July 2003, p. 7202-7213, Vol. 77, No. 13
0022-538X/03/$08.00+0     DOI: 10.1128/JVI.77.13.7202-7213.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.

Mosaic Genomes of the Six Major Primate Lentivirus Lineages Revealed by Phylogenetic Analyses

Marco Salemi,1* Tulio De Oliveira,2 Valerie Courgnaud,3 Vincent Moulton,4 Barbara Holland,5 Sharon Cassol,2 William M. Switzer,6 and Anne-Mieke Vandamme1

Rega Institute for Medical Research, KULeuven, Leuven, Belgium,1 Molecular Virology and Bioinformatics Unit, Africa Centre, Nelson Mandela School of Medicine, Durban, South Africa,2 Laboratoire Retrovirus, IRD, Montpellier, France,3 Linnaeus Center for Bioinformatics, Uppsala University, Uppsala, Sweden,4 Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand,5 Human Immunodeficiency Virus and Retrovirology Branch, Division of AIDS, Sexually Transmitted Diseases, and Tuberculosis, Centers for Disease Control and Prevention, Atlanta, Georgia6

Received 23 October 2002/ Accepted 3 April 2003

To clarify the origin and evolution of the primate lentiviruses (PLVs), which include human immunodeficiency virus types 1 and 2 as well as their simian relatives, simian immunodeficiency viruses (SIVs), isolated from several host species, we investigated the phylogenetic relationships among the six supposedly nonrecombinant PLV lineages for which the full genome sequences are available. Employing bootscanning as an exploratory tool, we located several regions in the PLV genome that seem to have uncertain or conflicting phylogenetic histories. Phylogeny reconstruction based on distance and maximum-likelihood algorithms followed by a number of statistical tests confirms the existence of at least five putative recombinant fragments in the PLV genome with different clustering patterns. Split decomposition analysis also shows that phylogenetic relationships among PLVs may be better represented by network-based graphs, such as the ones produced by SplitsTree. Our findings not only imply that the six so-called pure PLV lineages have in fact mosaic genomes but also make more unlikely the hypothesis of cospeciation of SIVs and their simian hosts.

* Corresponding author. Present address: Department of Ecology and Evolutionary Biology, 383 Steinhaus Hall, University of California at Irvine, Irvine, CA 92697. Phone: (949) 824-1056. Fax: (949) 824-2181. E-mail: msalemi68{at}hotmail.com.

Journal of Virology, July 2003, p. 7202-7213, Vol. 77, No. 13
0022-538X/03/$08.00+0     DOI: 10.1128/JVI.77.13.7202-7213.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.



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