{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,27]],"date-time":"2025-09-27T16:32:09Z","timestamp":1758990729903,"version":"3.41.2"},"reference-count":36,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2022,1,14]],"date-time":"2022-01-14T00:00:00Z","timestamp":1642118400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Immunol."],"abstract":"<jats:p>A series of HIV-1 CRF01_AE\/CRF07_BC recombinants were previously found to have emerged gradually in a superinfected patient (patient LNA819). However, the extent to which T-cell responses influenced the development of these recombinants after superinfection is unclear. In this study, we undertook a recombination structure analysis of the <jats:italic>gag<\/jats:italic>, <jats:italic>pol<\/jats:italic>, and <jats:italic>nef<\/jats:italic> genes from longitudinal samples of patient LNA819. A total of 9 <jats:italic>pol<\/jats:italic> and 5 <jats:italic>nef<\/jats:italic> CRF01_AE\/CRF07_BC recombinants were detected. The quasispecies makeup and the composition of the <jats:italic>pol<\/jats:italic> and <jats:italic>nef<\/jats:italic> gene recombinants changed continuously, suggestive of continuous evolution <jats:italic>in vivo<\/jats:italic>. T-cell responses targeting peptides of the primary strain and the recombination regions were screened. The results showed that Pol-LY10, Pol-RY9, and Nef-GL9 were the immunodominant epitopes. Pol-LY10 overlapped with the recombination breakpoints in multiple recombinants. For the LY10 epitope, escape from T-cell responses was mediated by both recombination with a CRF07_BC insertion carrying the T467E\/T472V variants and T467N\/T472V mutations originating in the CRF01_AE strain. In <jats:italic>pol<\/jats:italic> recombinants R8 and R9, the recombination breakpoints were located ~23 amino acids upstream of the RY9 epitope. The appearance of new recombination breakpoints harboring a CRF07_BC insertion carrying a R984K variant was associated with escape from RY9-specific T-cell responses. Although the Nef-GL9 epitope was located either within or 10~11 amino acids downstream of the recombination breakpoints, no variant of this epitope was observed in the <jats:italic>nef<\/jats:italic> recombinants. Instead, a F85V mutation originating in the CRF01_AE strain was the main immune escape mechanism. Understanding the cellular immune pressure on recombination is critical for monitoring the new circulating recombinant forms of HIV and designing epitope-based vaccines. Vaccines targeting antigens that are less likely to escape immune pressure by recombination and\/or mutation are likely to be of benefit to patients with HIV-1.<\/jats:p>","DOI":"10.3389\/fimmu.2021.820628","type":"journal-article","created":{"date-parts":[[2022,1,14]],"date-time":"2022-01-14T04:23:40Z","timestamp":1642134220000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":3,"title":["HIV-1\u2013Specific Immunodominant T-Cell Responses Drive the Dynamics of HIV-1 Recombination Following 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