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Journal of Virology, September 2005, p. 11343-11352, Vol. 79, No. 17
0022-538X/05/$08.00+0     doi:10.1128/JVI.79.17.11343-11352.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Phylodynamic Analysis of Human Immunodeficiency Virus Type 1 in Distinct Brain Compartments Provides a Model for the Neuropathogenesis of AIDS

Marco Salemi,1,2* Susanna L. Lamers,3,4 Stephanie Yu,4 T. de Oliveira,5 Walter M. Fitch,1 and Michael S. McGrath4*

Department of Ecology and Evolutionary Biology, University of California at Irvine, Irvine, California,1 Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida,2 Gene Johnson Inc., St. Augustine, Florida,3 Department of Laboratory Medicine, Positive Health Program, University of California at San Francisco, San Francisco, California,4 Evolutionary Biology Group, Zoology Department, University of Oxford, Oxford, United Kingdom5

Received 17 December 2004/ Accepted 20 May 2005

"Phylodynamic" analysis combines various statistical procedures that can be used to correlate the epidemiological and evolutionary behavior of viral pathogens with the immune system of the host. We utilized this approach to examine human immunodeficiency virus type 1 (HIV-1) gp120 envelope DNA sequences (V1, V2, and V3) isolated from different brain compartments of a T-cell-depleted patient diagnosed with severe HIV-associated dementia at the time of death. In agreement with previous reports, phylogenetic analysis showed distinct virodemes but also revealed a significant amount of viral gene flow among different brain compartments. Local-molecular-clock analysis showed that HIV-1 meninges and temporal lobe subpopulations evolve about 30 and 100 times faster, respectively, than the other viral populations in the brain. However, maximum likelihood codon-based substitution models did not detect any site under significant positive selective pressure, and the main cause of HIV-1 genetic variation appeared to be random genetic drift. Therefore, the higher evolutionary rate in the meninges and temporal lobe could be due to an enhanced infection/expansion rate of macrophages as a consequence of the immune system failure. In conclusion, in this case study, viral infection in the brain progressed with a nonspecific genetic evolution, recurrent migration events, and an expansion of macrophage-tropic sequences. The data suggest that after immune failure newly produced viral variants, which would be rapidly cleared under normal conditions, begin to productively infect macrophages in a "self-amplifying" cycle of infection/inflammatory response that could be at the origin of HIV-associated dementia.

* Corresponding author. Mailing address for M. Salemi: Dept. of Pathology Immunology and Laboratory Medicine, 1600 S.W. Archer Road, University of Florida, Gainesville, FL 32610. Phone: (352) 392-3749. Fax: (352) 392-3053. E-mail: msalemi68{at}yahoo.com. Mailing address for M. S. McGrath: Dept. of Laboratory Medicine UCSF 0874, SFGH Bldg. 80, Wd 84, 1001 Potrero Ave., San Francisco, CA 94110. Phone: (415) 476-4082 ext. 415. Fax: (415) 476-6017. E-mail: mmcgrath{at}php.ucsf.edu.

Journal of Virology, September 2005, p. 11343-11352, Vol. 79, No. 17
0022-538X/05/$08.00+0     doi:10.1128/JVI.79.17.11343-11352.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



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