Increased Sequence Coverage through Combined Targeting of Variant and Conserved Epitopes Correlates with Control of HIV Replication

Abstract

A major challenge in the development of an HIV vaccine is that of contending with the extensive sequence variability found in circulating viruses. Induction of HIV-specific T-cell responses targeting conserved regions and induction of HIV-specific T-cell responses recognizing a high number of epitope variants have both been proposed as strategies to overcome this challenge. We addressed the ability of cytotoxic T lymphocytes from 30 untreated HIV-infected subjects with and without control of virus replication to recognize all clade B Gag sequence variants encoded by at least 5% of the sequences in the Los Alamos National Laboratory HIV database (1,300 peptides) using gamma interferon and interleukin-2 (IFN-␥/IL-2) FluoroSpot analysis. While targeting of conserved regions was similar in the two groups (P ‫؍‬ 0.47), we found that subjects with control of virus replication demonstrated marginally lower recognition of Gag epitope variants than subjects with normal progression (P ‫؍‬ 0.05). In viremic controllers and progressors, we found variant recognition to be associated with viral load (r ‫؍‬ 0.62, P ‫؍‬ 0.001). Interestingly, we show that increased overall sequence coverage, defined as the overall proportion of HIV database sequences targeted through the Gag-specific repertoire, is inversely associated with viral load (r ‫؍‬ ؊0.38, P ‫؍‬ 0.03). Furthermore, we found that sequence coverage, but not variant recognition, correlated with increased recognition of a panel of clade B HIV founder viruses (r ‫؍‬ 0.50, P ‫؍‬ 0.004). We propose sequence coverage by HIV Gag-specific immune responses as a possible correlate of protection that may contribute to control of virus replication. Additionally, sequence coverage serves as a valuable measure by which to evaluate the protective potential of future vaccination strategies.

HIV Control Is Mediated in Part by CD8 + T-Cell Targeting of Specific Epitopes

“…The latter observation is further supported by our observation that individuals with higher viral load target more epitopes and at higher intensity (see Fig. S2 in the supplemental material), consistent with a model in which a higher viral load leads to a high cell surface viral peptide concentration that stimulates further responses (similar observations with respect to variant recognition within Gag have been reported previously [62]). Note that these results suggest but do not prove cause and effect, as the models we examined were by no means exhaustive.…”

“…One explanation of the predictive ability of targeting beyond HLA alleles is that targeting is a cause of viral control. Another explanation is that increased virus load resulting from lack of control leads to the targeting of additional epitopes (62). To explore the relative likelihood of these two explanations, we considered how well alternative statistical models uniquely consistent with each explanation predicted the data.…”

“…Limitations of this approach include the reduction of specificity, as each OLP may contain more than one epitope, and an increase in false-negative rates due to the oversize peptides and required processing (23,62), requiring additional follow-up to identify the protective epitopes. Two advantages of the OLP approach are that it provides an unbiased scan of HIV peptides and covers the entire proteome.…”

Fitness-Balanced Escape Determines Resolution of Dynamic Founder Virus Escape Processes in HIV-1 Infection

“…Therefore, escape processes during primary HIV infection have the potential to increase the breadth and depth of Gag-specific CTL responses. We recently reported that during chronic HIV infection, progressors maintain higher levels of epitope variant recognition than viremic controllers (36). Our current results demonstrate that cross-reactivity and induction of de novo responses to epitope variants over time may lead to the high levels of variant recognition observed during chronic progressive infection.…”

“…The IFN-␥/IL-2 FluoroSpot assay was used for detection of Gag-specific T-cell responses in all SPs and TPs as previously described (36). Briefly, cryopreserved peripheral blood mononuclear cells (PBMC) were thawed and incubated in R10 medium overnight before stimulation.…”