An Examination of Subtype B HIV-1 Genetic Infection Tropism Prediction

HIV usually makes use of either the CCR5 or CXCR4 co-receptors to gain entry into cells. Which coreceptor the virus uses (the tropism) determines the efficacy of different cell entry-inhibiting antiretroviral drugs, and is therefore important medical information. HIV tropism may be accurately assessed with sensitive recombinant virus phenotyping tests such as the Trofile assay, but these tests are often prohibitively expensive. Viral genome sequencing and interpretation of genotype using free online software programs such as Web PSSM and Geno2Pheno offer a low-cost alternative by predicting tropism from the V3 loop sequence in the HIV env gene. However, these programs' predictions are insensitive to minority viral variants and may be less accurate than the commercial recombinant virus phenotypic assays.

We sequenced proviral subtype B HIV-1 DNA from peripheral blood mononuclear cell (PBMC) samples obtained from patients under drug-induced viral suppression and viral RNA from plasma samples obtained from the same patients after viral re-emergence. Predictions of re-emergent viral tropism were made by Geno2Pheno and Web PSSM assessment of the proviral DNA V3 loop sequences. Trofile tests were performed on plasma samples to provide a gold-standard re-emergent virus phenotype. Through statistical and qualitative analysis of these paired prediction and tropism data, we tested the hypothesis that the tropism of virus re-emerging into the blood following drug interruption can be accurately predicted by Geno2Pheno and Web PSSM analysis of proviral DNA.

We show here that proviral DNA sequence analysis was able to predict re-emergent plasma virus tropism with 83.3% success, and exclusive R5 tropism with 87.0% success. Generalized linear modeling showed a highly significant relationship between prediction-tropism discordance and lower DNA-RNA sequence similarity. Qualitative analysis of clone env sequences demonstrated sequence interpretation accuracy by both Geno2Pheno and Web PSSM. Together, these results suggest that proviral PBMC DNA consensus sequences may fail to predict the re-emergent plasma virus tropism in more than 10% of cases. Differences between proviral DNA-based tropism predictions and re-emergent plasma virus phenotype may result from the selection of minority variants and the evolution of plasma virus.