Computational comparison of availability in CTL/gag epitopes among patients with acute and chronic HIV-1 infection
Date
2016
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Abstract
Background
Recent studies indicate that there is selection bias for transmission of viral polymorphisms associated with higher viral fitness. Furthermore, after transmission and before a specific immune response is mounted in the recipient, the virus undergoes a number of reversions which allow an increase in their replicative capacity. These aspects, and others, affect the viral population characteristic of early acute infection.
Methods
160 single gag-gene amplifications were obtained by limiting-dilution RT-PCR from plasma samples of 8 ARV-naïve patients with early acute infection (<30 days, 22 days average) and 8 ARV-naive patients with approximately a year of infection (10 amplicons per patient). Sanger sequencing and NGS SMRT technology (Pacific Biosciences) were implemented to sequence the amplicons. Phylogenetic analysis was performed by using MEGA 6.06. HLA-I (A and B) typing was performed by SSOP-PCR method. The chromatograms were analyzed with Sequencher 4.10. Epitopes and immune-proteosomal cleavages prediction was performed with CBS prediction server for the 30 HLA-A and -B alleles most prevalent in our population with peptide lengths from 8 to 14 mer. Cytotoxic response prediction was performed by using IEDB Analysis Resource.
Results
After implementing epitope prediction analysis, we identified a total number of 325 possible viral epitopes present in two or more acute or chronic patients. 60.3% (n = 196) of them were present only in acute infection (prevalent acute epitopes) while 39.7% (n = 129) were present only in chronic infection (prevalent chronic epitopes). Within p24, the difference was equally dramatic with 59.4% (79/133) being acute epitopes (p < 0.05). This is consistent with progressive viral adaptation to immune response in time and further supported by the fact that cytotoxic responses prediction showed that acute epitopes are more likely to generate immune response than chronic epitopes. Interestingly, only 27.5% of acute epitopes match the population-level consensus sequence of the virus.
Conclusions
Our results indicate that certain non-consensus viral residues might be transmitted more frequently than consensus-residues when located in immunological relevant positions (epitopes). This observation might be relevant to the rationale behind development of an effective vaccine to reduce viral reservoir and induce functional cure of HIV infection based in prevalent acute epitopes.
Introduction
Following transmission, Cytotoxic CD8+T lymphocytes (CTLs) mount a powerful response to transmitted HIV in the acute phase of infection [1]. However, the vast majority of cases is an inefficient response and directed to a limited number of epitopes [2]. This response is manifested producing a viral set point generally after first month of infection [3], [4], [5] with great specificity on the gag protein, which is strongly associated with control of viral replication [6], [7], [8], [9]. At this point, just after the peak of viremia, the first viral populations with HLA/CTL escape mutations are generated [2], which will increase over time and will have an impact on viral diversity during the chronic phase [10], [11], [12]. Therefore, it is interesting to investigate if these HLA-dependent reversions that occur during the acute phase are associated with a greater availability of epitopes in this stage.
Reversions are another important aspect to be considered among viral factors shaping the viral diversity during the acute stage of infection [13], [14]. While their impact on viral fitness on transmitted/founder virus has not yet been elucidated, it is believes reversal mutations make the virus more fit [13], [15], [16].These post-transmission reversions may range from those associated with HLA alleles present on the donor [17], to the CD8 T-cell TCR receptor [13], [18], [19], to the proteasome [20], [21], or reversions that arise at random and increase the viral fitness that end up being established in the major viral population [22], [24]. Also, these reversions could occur prior to transmission, in a process of viral compartmentalization in mucosal associated tissues [25], [26], [27].
In this research, our objective was to determine, in patients under study, whether the viral sequences approach phylogenetically in acute patients compared with chronic patients. In turn, we evaluated whether possible reversions in acute viral sequences could significantly influence to decrease viral phylogenetic distance in these patients. Also, using computational prediction analysis, we evaluated the relationship of phylogenetically relevant amino acid positions (possibly reversions), with epitopes associated with cytotoxic immune response mediated by HLA I. Finally, we evaluated the distribution and characteristics of CTL epitopes, in conserved viral segments. We did an availability and frequency analysis of possible CTL epitopes found in the early acute phase compared to those found in the chronic phase.
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Citation
Damilano GD et al. Computational comparison of availability in CTL/gag epitopes among patients with acute and chronic
HIV-1 infection. Vaccine (2018), https://doi.org/10.1016/j.vaccine.2018.04.086