Correlation between CD4 T cell counts and virus compartmentalization in genital and systemic compartments of HIV-infected females

Abstract

The majority of infection by the human immunodeficiency virus (HIV-1) across the world occurs by heterosexual transmission and is likely mediated by virus present in genital secretions. In spite of this, infection is followed by clinical markers of the virus present in blood, which may not be representative of the virus involved in transmission. In fact, several studies have demonstrated that the genital tract represents a unique compartment for the virus. We assessed the relationship between immune system integrity, represented by CD4+ T cell counts, and the maintenance of viral compartmentalization between plasma and vaginal fluid virus in treatment naïve women from the Dominican Republic infected by the heterosexual transmission route. We cloned and sequenced cell free virus from plasma and genital fluid samples from six women to assess viral evolution, phylogenetic relatedness, and calculated co-receptor use for the C2V3 region of the envelope. Our analyses demonstrated plasma and vaginal fluid virus compartments remained intact only in samples from women with CD4+ T cell counts over 350 cells/μl. The majority of viral forms were predicted to use the CCR5 co-receptor, although several dual tropic forms were also identified. None of the clones were found to use the CXCR4 co-receptor even though many of the patients showed severe disease. Our findings lend further support to the role of an intact immune system in maintaining compartmentalization across blood and genital quasispecies and provide a compelling rationale to specifically consider genital tract viral forms in therapeutic and vaccine research.

Figure 1. Maximum Likelihood Model Phylogenetic Analysis shows compartmentalization in patients with higher CD4+ T cell counts

Maximum likelihood model was employed to infer evolutionary history. Trees indicate phylogenetic relationship of clones isolated from vaginal fluid (closed circles) or plasma (open circles) from simultaneous samples. Patients 001M and 007M trees indicate separation of clones from plasma and vaginal fluid (leftmost tree). The phylogenetic arrangements of clones from 005M, 003M (middle tree) and 027M, 006M (rightmost tree) fail to show separate clusters of plasma and vaginal fluid clones. Scale bars indicate 2 nucleotide changes per 1000 positions. Bootstrap values greater than 70 are shown to indicate strength of clustering patterns.

Figure 2. Inferred amino acid alignment of C2V3 HIV-1 env sequences from plasma and vaginal fluid derived clones in therapy naïve females

Amino acid changes are indicated relative to the C2V3 sequence as a reference sequence generated by the Bio Edit. Identical clones within each patient are not shown, but clones appearing multiple times are indicated in parentheses after clone names. Dots indicate identical amino acid sequences, dashes indicate deletions.