Background:  HIV-1 infection of the central nervous system (CNS) can lead to neurological complications, including the development of HIV-associated dementia (HAD). A subset of infected individuals develop HAD, but it is not known to what extent independent replication and evolution of HIV-1 in the CNS is a factor in CNS pathogenesis. 

Methods:  Viral genetic compartmentalization was examined by conducting single genome amplification on the env gene from cross-sectional and longitudinal plasma and cerebrospinal fluid (CSF) samples from human subjects with varying degrees of neurological disease. The polymerase chain reaction (PCR) amplicons were sequenced, aligned, and maximum-likelihood phylogenetic trees were generated using PHYML. 

Results:  Phylogenetic analysis of virus obtained from subjects with HAD (n = 7) and MCMD (n = 1) revealed trees with large bifurcations and deep branch points separating virus from the plasma and the CSF. In addition, clonal amplification of viral variants was detected in the CSF of subjects with neurological disease, including one primary infection subject. In subjects with neurological disease that were analyzed longitudinally (n = 3), the virus population that was selectively amplified changed over time. Asymptomatic subjects (n = 4) did not show a prominent division between plasma and CSF virus. We did not detect a correlation between neurological disease state and the presence of the N283 envelope variant or the loss of a glycosylation site at position 386. 

Conclusions:  Deep bifurcations in the phylogenetic trees from subjects with HAD and MCMD indicate that sustained HIV-1 replication is occurring in the CNS of subjects with neurological disease, which is not seen in asymptomatic subjects. In addition, we detected 2 distinct stages of clonal amplification of virus in the CSF of subjects with neurological disease. Prior to late stage disease, clonal amplification is detected for CSF HIV-1 variants that are similar to plasma virus. This represents CNS virus that is newly seeded from the plasma, and indicates the first stage of immunodeficiency when there is a sporadic loss of immune control. During late stage disease, clonal amplification occurs in CSF variants that are separated phylogenetically from plasma virus, indicating viral growth and increased HIV-1 replication in the CNS, possibly due to virus seeding a previously uninfected anatomical location.