P16-41. Evidence for in vivo immune selection pressure exerted by HLA class I restricted CTL responses to anti-sense encoded HIV sequences
Bibliographic record
Abstract
Past studies have suggested that certain portions of the integrated HIV-1 proviral genome can be transcribed in the anti-sense direction, resulting in novel viral protein products that may provide alternative targets for the host anti-viral immune response. Little is known whether immune responses exist against antisense HIV peptides, whether they can recognize HIV infected cells and whether CTL-driven escape mutations within antisense peptides may be detectable on a population level. Anti-sense sequences with potential start codons (Methionine) that preceded well-conserved genome sequences of at least 50 nucleotide triplets without stop codon were identified in 261 aligned HIV whole-genome sequences. Plasma HIV gag, pol and nef sequences from >500 treatment-naive, chronic infected patients were analyzed for HLA class I allele-specific viral polymorphisms in all three possible reading frames in the anti-sense direction. A maximal false-discovery rate of 20% (q value < 0.2) was applied to correct for multiple tests. Polymorphisms in the anti-sense direction that affected the original coding sequence were excluded from study. Five potential anti-sense encoded proteins, including the previously described HIV anti-sense protein (ASP) were identified. Each putative protein sequence was synthesized as overlapping peptide set and was targeted by at least 2 individuals (range 2–22) of 40 HIV infected subjects tested. HLA-footprint analyses revealed 67 HLA-associated imprints (37 gag, 6 nef, 34 pol). For each imprint, the predicted epitopes were tested in individuals expressing the appropriate HLA allele. Several frequently-targeted antisense epitopes were identified. CTL responses targeting anti-sense derived epitopes in HIV may be relatively common and may have an impact on viral evolution at the population level. Thus, T cell specificities to anti-sense encoded epitopes may be a biologically relevant mechanism contributing to immune control of HIV and may represent interesting vaccine immunogen candidates.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.004 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".