Antisense-Derived HIV-1 Cryptic Epitopes Are Not Major Drivers of Viral Evolution during the Acute Phase of Infection

Abstract

While prior studies have demonstrated that CD8 T cell responses to cryptic epitopes (CE) are readily detectable during HIV-1 infection, their ability to drive escape mutations following acute infection is unknown. We predicted 66 CE in a Zambian acute infection cohort based on escape mutations occurring within or near the putatively predicted HLA-I-restricted epitopes. The CE were evaluated for CD8 T cell responses for patients with chronic and acute HIV infections. Of the 66 predicted CE, 10 were recognized in 8/32 and 4/11 patients with chronic and acute infections, respectively. The immunogenic CE were all derived from a single antisense reading frame within However, when these CE were tested using longitudinal study samples, CE-specific T cell responses were detected but did not consistently select for viral escape mutations. Thus, while we demonstrated that CE are immunogenic in acute infection, the immune responses to CE are not major drivers of viral escape in the initial stages of HIV infection. The latter finding may be due to either the subdominant nature of CE-specific responses, the low antigen sensitivity, or the magnitude of CE responses during acute infections. Although prior studies demonstrated that cryptic epitopes of HIV-1 induce CD8 T cell responses, evidence that targeting these epitopes drives HIV escape mutations has been substantially limited, and no studies have addressed this question following acute infection. In this comprehensive study, we utilized longitudinal viral sequencing data obtained from three separate acute infection cohorts to predict potential cryptic epitopes based on HLA-I-associated viral escape. Our data show that cryptic epitopes are immunogenic during acute infection and that many of the responses they elicit are toward translation products of HIV-1 antisense reading frames. However, despite cryptic epitope targeting, our study did not find any evidence of early CD8-mediated immune escape. Nevertheless, improving cryptic epitope-specific CD8 T cell responses may still be beneficial in both preventative and therapeutic HIV-1 vaccines.

Defective HIV-1 genomes and their potential impact on HIV pathogenesis

“…The use of alternative and cryptic splice sites is suspected to enable translation of chimeric and non-canonical HIV-1 fusion proteins [79]. Antisense transcription from the 3ʹ LTR is another mechanism for generating HIV-1 transcripts; however, whether antisense transcription is regulated by the same signaling cascades as transcription from the 5ʹ LTR, and its functional relevance, is unclear [80][81][82][83].…”

HIV T-cell immunogen design and delivery

“…Indeed, T-cell responses against these epitopes are able to inhibit viral replication in vivo and leave a specific HLA footprint on the viral sequence [37]. However, they do not seem to contribute in a major manner to viral evolution in the early stages of acute infection [39]. Clearly, similarly to the glycosylated epitopes, the potential of such responses in vaccine design has not been sufficiently explored.…”

Unconventional viral gene expression mechanisms as therapeutic targets

“…The use of ARF as epitopes has been proposed for HIV 108,[111][112][113] , influenza virus 110 and in some cancers 109 and has several major advantages. First, ARFs in simian immunodeficiency virus and HIV contribute greatly to CD8 + T cell responses in infected individuals and trigger a stronger Review cytotoxic T lymphocyte response compared to epitopes that target the canonical proteins 108,114 .…”

“…The potential of ARFs as epitopes is further substantiated by the observation that codon-optimized recombinant HIV vaccines (in which ARFs are disrupted or skewed) trigger a reduced cytotoxic T lymphocyte response compared to non-codon optimized vaccines 112 . Second, cytotoxic T lymphocyte responses to at least some ARF epitopes do not drive viral escape 113 and presentation of ARF epitopes has been associated with favourable clinical outcomes 111 . Finally, overprinting ORFs tend to be highly conserved among strains of the same virus, as in IAV 98 .…”