Genetic and phenotypic features of blood and genital viral populations of clinically asymptomatic and antiretroviral-treatment-naive clade a human immunodeficiency virus type 1-infected women

Abstract

In the present study, we assessed whether human immunodeficiency virus type 1 (HIV-1) genetic compartmentalization was associated with phenotypic CCR5 (R5) or CXCR4 (X4) coreceptor usage differences between the systemic and the genital viral populations. Four clinically asymptomatic and treatment-naïve clade A HIV-1-infected patients were selected from a cohort of 274 African women, because they were free of all the biological cofactors known to modify the kinetics of viral production in the genital tract. HIV RNA envelope sequences (V1 to V3) derived from plasma and cervicovaginal secretions (CVS) were amplified, subcloned, and sequenced. CCR5 or CXCR4 coreceptor usage was determined by production of recombinant viral particles, followed by single-cycle infection assays of indicator cell lines, using the tropism recombinant test. In these four selected patients, CVS-derived sequences appeared to be genetically distinct from blood-derived sequences (P < or = 0.001). Two patients were found to harbor virus populations with only the R5 phenotype in both compartments, whereas viruses using CXCR4 in addition to CCR5 were detected in two other patients. In particular, one woman harbored genital virus populations with mixed R5 and X4 phenotypes associated with peripheral blood populations with only the R5 phenotype. These results demonstrate genetic compartmentalization of HIV between the plasma and genital secretions of clinically asymptomatic, treatment-naïve, clade A-infected women. Also, for one patient, we report phenotypic coreceptor usage differences between the systemic (R5) and genital (R5/X4) viral populations. These features may be critical for the development of further mucosal vaccines, therapies, or new preventive strategies to block heterosexual transmission.

FIG. 1.

Phylogenetic trees were built with PAUP*4.0b10 software (Sinauer Associates, Inc., Sunderland, MA). Maximum likelihood trees were constructed by using the HKY85 model of nucleotide substitution, with the transition/transversion ratio and alpha shape parameter for a gamma distribution estimated on a neighbor-joining tree. The resulting model was used in a heuristic search using subtree pruning regrafting (SPR) branch swapping to find the best maximum likelihood tree. Branch length distances calculated by PAUP* were used to calculate diversity by using the HKY85+G+I model of evolution in PAUP*. Sequences issued from the plasma (filled circles) and from the genital tract (open squares) of each patient are shown. Numbers at each branch point indicate the bootstrap values derived from 1,000 bootstrap resamplings. Bootstrap values greater than 95% are indicated.