Genotypic and phenotypic characterization of HIV-1 transmitted/founder viruses and their effect on cytokine profiles and disease progression among acutely infected Ugandans
Virus-host interaction early after transmission elicit changes that are known to impact the course of the infection and clinical outcome. The nature of the virus that initiates the infection seems to play a key role. For example, rates of disease progression among people living with HIV-1 have been reported to vary based on the infecting subtype (genotype) and the efficiency of the virus to replicate (replicative capacity) (phenotype). The early immune response to HIV-1 infection is another significant determinant of HIV-1 clinical path. Among the repertoire of diverse viral variants that typically exist in an infecting individual, the unique features of the transmitted virus that establishes successful infection (transmitted founder (T/F) virus) has not been well characterized yet. Therefore, a thorough understanding of the genotypic and phenotypic characteristics of T/F HIV-1 viruses and their effect on disease progression is important. Understanding the relevant differences among all infecting subtypes will aid in designing of novel prevention strategies such as development of vaccines for the East African region. However, there is still limited understanding of the properties of these T/F viruses especially among HIV-1 subtype A, D and recombinants which predominate in Uganda. Plasma samples from Ugandan Protocol C participants with acute/early infection enrolled between December 2006 and June 2011 in Uganda, were selected based on documented seroconversion and availability of plasma samples taken within 90 days of infection. Single genome amplification assays were used to characterize T/F near full genome viruses in samples previously classified as subtype D by pol sequencing. A panel of T/F gag-pol sequences were also cloned into a common HIV-1 NL4-3 backbone and the influence of gag-pol changes on viral replication capacity was monitored. Using a novel protein domain approach, diversity in the functional protein domains across the gag-pol region was documented. Additionally, 37 plasma cytokines were quantitated using V-Plex kits on Meso Scale Discovery platform in 65 recent seroconverters to study host responses in early infection. Subtype analysis of near full-length genome sequences from inferred T/F viruses showed a high proportion (69%) of intersubtype recombinants involving mainly A1/D. The signal peptide-C1 region and gp41 transmembrane domain (Tat2/Rev2 flanking region) were hotspots for A1/D recombination events. Gag-pol NL4-3 chimeric viruses showed that recombinants exhibited highest mean replication scores followed by subtype D, and subtype A had the lowest mean score. Diversity analysis of functional protein domains across the gag-pol region identified differences in the Gag-p6 domain as well as the adjacent protease cleavage sites that were frequently associated with higher in vitro replication. Additionally, the study revealed that subtype D (pol) infections exhibit significantly higher median plasma concentrations of IL-5, IL-16, IL-1, IL-7, IL-17A, Eotaxin-1, IP10, MCP-4 and VEGF-D when compared to subtype A1 (pol) infections. IL-12/23p40 and IL-1 were associated with faster CD4+ T cell count decline, while high bFGF levels were associated with maintenance of CD4+ T counts above 350 cells/microliter. High levels of bFGF and VEGF-C were significantly elevated in plasma of participants with HIV-1 of low in vitro replicative capacity of HIV-1 pol chimeric viruses. The high transmission rate of unique intersubtype recombinants observed here is striking and emphasizes the extraordinary challenge for vaccine design and in particular for the highly variable and recombinogenic envelope gene, which is targeted by rational vaccine designs aimed to elicit broadly neutralizing antibodies. The current study has also revealed crucial features of the HIV-1 gag-pol region, especially the Gag-p6 domain that seems to influence viral replicative capacity and may play a role in establishing new HIV-1 infections. The results also suggested that overproduction of cytokines in early HIV infection may trigger an early disruption of the immune environment and contribute to pathogenic mechanisms underlying the accelerated disease progression seen in individuals infected with some viral strains in Uganda.