Utilization of HIV-1 envelope V3 to identify X4- and R5-specific Tat and LTR sequence signatures. Human immunodeficiency virus 1 strain:Subtype B

Background: HIV-1 entry is a receptor-mediated process directed by the interaction of the viral envelope with the host cell CD4 molecule and one of two co-receptors, CCR5 or CXCR4. The amino acid sequence of the third variable (V3) loop of the HIV-1 envelope is highly predictive of co-receptor utilization preference during entry, and machine learning predictive algorithms have been developed to characterize sequences as CCR5-utilizing (R5) or CXCR4-utilizing (X4). It was hypothesized that while the V3 loop is predominantly responsible for determining co-receptor binding, additional components of the HIV-1 genome may contribute to overall viral tropism and display sequence signatures associated with co-receptor utilization.Methods: The accessory protein Tat and the HlV-1 long terminal repeat (LTR) were analyzed with respect to genetic diversity and compared by Jensen-Shannon divergence to identify R5- and X4-genome specific trends. We further analyzed LTR sequences for putative transcription factor binding sites using the JASPAR transcription factor binding profile database. Sequences containing a full-length V3 loop in addition to a co-linear Tat or LTR were obtained from the Los Alamos National Laboratory HIV Sequence Database and supplemented with additional sequences from the Drexel University College of Medicine (Drexel Medicine) CNS AIDS Research and Eradication Study (CARES) Cohort.Results: It was determined that Jensen-Shannon divergence was correlated with both mean genetic diversity as well as the absolute difference in genetic diversity. As expected, the V3 domain of the gp120 protein was enriched with statistically divergent positions. Statistically divergent positions were identified in Tat amino acid sequences within the transactivation and TAR-binding domains, and in nucleotide positions throughout the LTR. We found several putative differences in transcription factor binding sites between R5 and X4 HIV-1 genomes, specifically identifying the C/EBP sites I and II, and Sp site III to differ with respect to sequence configuration for R5 and X4 LTRs.Conclusion: These observations support the hypothesis that co-receptor utilization coincides with specific genetic signatures in HIV-1 Tat and the LTR, likely due to differing transcriptional regulatory mechanisms and selective pressures applied within specific cellular targets during the course of productive HIV-1 infection.