Official websites use. Share sensitive information only on official, secure websites. HIV Gag polyprotein is central to assembly, budding, and maturation of HIV virions, and there is substantial interest in Gag as a therapeutic target. Previously, maturation inhibitors have been limited by natural polymorphisms in gag. A more comprehensive analysis of intra-patient gag genetic variation, including linkage analysis is essential to inform novel approaches to therapeutics.
As a first step, we developed a new single genome sequencing SGS assay to analyze full length HIV gag to investigate intra-patient genetic variation, localize regions of variability, and determine linkage patterns. Full length gag sequences were genetically diverse average pairwise difference range 0.
Although diversity was present throughout gag , most of the variation was attributed to p6. On the protein level, translated p6 sequences had significantly higher average pairwise difference APD compared to translated full length gag 1. Indels were common in p6, including PTAP duplications and contribute additional variability. Intra-patient gag genetic diversity is substantial but overall variability is largely limited to p6. No significant linkage between polymorphic positions was detected, indicating that populations were in linkage equilibrium.
Next generation sequencing approaches focusing on specific regions in gag will be useful in characterizing intra-patient diversity. As defects may persist in patients receiving antiretroviral therapy ART , it is important to understand their cause so that antibody responses to vaccines, including therapeutic HIV vaccines, might be enhanced in ART-treated patients. We have investigated the role of interferon IFN -alpha. Plasma markers of monocyte activation sCD14 were also examined for comparison.
There was no relationship between any of these parameters and sCD Increased IFN-alpha activity may contribute to defects of B cells and antibody production in patients with HIV-1 infection, including persistent defects of antibody isotype diversification in patients receiving ART. Generation of optimal antibody responses by vaccines in ART-treated patients may require therapeutic modulation of IFN-alpha activity. However this immune recovery is variable and difficult to predict.
