Background:  Envelope glycoprotein (gp160) sequences from the brain of SIV-infected macaques often encode envelopes with mutations that impart macrophage-tropism and CD4-independent usage of CCR5 suggesting that these phenotypes are important for the evolution of a neurotropic or neuropathogenic virus. To determine the extent of compartmentalization in the central nervous system (CNS) and to study the phenotypic consequences of mutations found in different CNS sites, we analyzed gp160 sequences from different CNS regions of SIV_mac239-infected macaques with varying disease progressions.

Methods:  Full-length gp160 was cloned from genomic DNA from different CNS and non-CNS tissues of 2 long-term progressing (1 with and 1 without encephalitis) and 1 rapidly progressing macaque (without encephalitis). Phylogenetic analysis was performed using PAUP4.0b10 and Modeltest3.06 to determine the extent of compartmentalization. Sequences were examined for conserved mutations in the variable loops and CD4-binding domains. Functional envelopes were tested in cell–cell fusion assays for CD4 independence and neutralization sensitivity.

Results:  Phylogenetic analysis demonstrated clustering of sequences into clades defined by their CNS tissue source indicating that gp160 compartmentalizes in long-term progressing macaques. These regional clades were supported by high bootstrap values (> 50). In contrast, sequences from the rapidly progressing macaque failed to cluster by region or clustered with only low bootstrap support. Regional clades from the CNS shared most recent common ancestors with clades from non-CNS tissues indicating multiple neuroinvasion events into different CNS sites. Region-specific mutations in V1, V3, V4, and in a CD4-binding domain suggested altered phenotypes in CD4-dependent entry and neutralization sensitivity to antibodies. Envelopes from the brain of the encephalitic macaque with a mutation in a CD4-binding domain mediated cell–cell fusion in a CD4-independent manner and were neutralized by pooled serum from SIV-infected macaques.

Conclusions:  Phylogenetic analysis of gp160 demonstrates CNS compartmentalization initiated by independent neuroinvasion events in anatomically distinct CNS sites in long-term but not rapid progression of immunodeficiency. Mutations found in CNS envelopes indicate that evolution of key regions, such as variable loops and CD4-binding domains, may be important for the development of viruses that acquire neuropathogenic potential.

Keywords: SIV encephalitis; gp160; viral compartmentalization