# Duration of Initial Viremia Modulates Functional Properties of HIV-specific T Cell Receptors

**Authors:** Funsho J. Ogunshola, Nishant K. Singh, Vincent Butty, Anurag R. Mishra, Zacharia Habte, Liza Vecchiarello, Ahmed Fahad, Kate B. Juergens, Sophia Cheever, Marius Allombert, Anabelle Webber, Alicja Piechocka-Trocha, Nasreen Ismail, Anusha Nathan, Xiaolong Li, Kavidha Reddy, Kamini Gounder, Omolara O. Baiyegunhi, David R. Collins, Musie Ghebremichael, Gaurav Gaiha, Krista Dong, Brandon J. Dekosky, Thumbi Ndung’u, Michael E. Birnbaum, Bruce D. Walker

PMC · DOI: 10.21203/rs.3.rs-6668459/v1 · Research Square · 2026-02-18

## TL;DR

The study shows that starting HIV treatment early helps preserve better T cell responses, which could improve future HIV treatments.

## Contribution

The study reveals that early ART preserves higher-avidity TCRs and memory T cell profiles in HIV-specific repertoires.

## Key findings

- Early ART initiation preserves higher-avidity TCRs and transitional memory CD8+ T cell subsets.
- Prolonged antigen exposure enriches cross-reactive TCR clonotypes in HIV-specific repertoires.
- Functional differences in TCR repertoires are not linked to TRBV gene sharing patterns.

## Abstract

Virus-specific CD8+ T cells are crucial in controlling chronic human viral infections such as HIV-1, but the effect of persistent antigen exposure on T cell repertoire formation is not well understood. In this study, we examined epitope-specific CD8+ T cell repertoires in people living with HIV-1, where duration of viremia following hyperacute infection was modulated by the time of initiation of continuous suppressive antiretroviral therapy (ART). After ART-induced suppression of viremia in persons expressing the same HLA class I allele, we analyzed the impact of early (n=6) versus delayed (n=6) ART initiation on the clonotypic composition, cross-reactivity, functional avidity and memory differentiation profile of the HIV-specific T cell repertoire restricted by HLA-B*58:01. Using a panel of barcoded tetramers, we mapped T cell receptor (TCR) clonotypes specific for three dominant epitopes and their variants. Both groups exhibited polyclonal TCR repertoires with evidence of cross-reactivity, which was significantly enriched in donors with prolonged antigen exposure. Within this cohort, broadly cross-reactive clonotypes capable of recognizing all autologous variants were identified, but these were rare (<1%). Early ART initiation preserved repertoires characterized by higher-avidity TCRs and a relative enrichment of transitional memory CD8+ T cell subsets. These functional differences were not associated with differences in TRBV gene sharing, indicating that ART timing shapes repertoire quality and memory differentiation without altering TRBV gene bias. These findings demonstrate how antigen suppression dynamics differentially shape the breadth, functional sensitivity, and memory composition of the HIV-specific TCR repertoire, with implications for T cell-directed immunotherapies and HIV cure strategies.

## Linked entities

- **Proteins:** CD8A (CD8 subunit alpha)

## Full-text entities

- **Genes:** IFNG (interferon gamma) [NCBI Gene 3458] {aka IFG, IFI, IMD69}, Cat [NCBI Gene 2847485], HLA-A (major histocompatibility complex, class I, A) [NCBI Gene 3105] {aka HLAA}, CD4 (CD4 molecule) [NCBI Gene 920] {aka CD4mut, IMD79, Leu-3, OKT4D, T4}, HLA-G (major histocompatibility complex, class I, G) [NCBI Gene 3135] {aka MHC-G}, SELL (selectin L) [NCBI Gene 6402] {aka CD62L, LAM1, LECAM1, LEU8, LNHR, LSEL}, FLNB (filamin B) [NCBI Gene 2317] {aka ABP-278, ABP-280, FH1, FLN-B, FLN1L, LRS1}, CD8A (CD8 subunit alpha) [NCBI Gene 925] {aka CD8, CD8alpha, IMD116, Leu2, p32}, CD69 (CD69 molecule) [NCBI Gene 969] {aka AIM, BL-AC/P26, CLEC2C, EA1, GP32/28, MLR-3}, CD28 (CD28 molecule) [NCBI Gene 940] {aka IMD123, Tp44}, Env [NCBI Gene 155971], gag (Pr55(Gag)) [NCBI Gene 155030], CCL5 (C-C motif chemokine ligand 5) [NCBI Gene 6352] {aka D17S136E, RANTES, SCYA5, SIS-delta, SISd, TCP228}, TRBV20OR9-2 (T cell receptor beta variable 20/OR9-2 (non-functional)) [NCBI Gene 6962] {aka CDR3, TCRBV20S2, TCRBV2O, TCRBV2S2O}, HLA-C (major histocompatibility complex, class I, C) [NCBI Gene 3107] {aka D6S204, HLA-JY3, HLAC, HLC-C, MHC, PSORS1}, gag-pol (Gag-Pol) [NCBI Gene 155348], APC (APC regulator of Wnt signaling pathway) [NCBI Gene 324] {aka BTPS2, DESMD, DP2, DP2.5, DP3, GS}, LEF1 (lymphoid enhancer binding factor 1) [NCBI Gene 51176] {aka ECTD1, ECTD17, LEF-1, TCF10, TCF1ALPHA, TCF7L3}, Nef [NCBI Gene 156110], B2M (beta-2-microglobulin) [NCBI Gene 567] {aka AMYLD6, IMD43, MHC1D4}, CCR7 (C-C motif chemokine receptor 7) [NCBI Gene 1236] {aka BLR2, CC-CKR-7, CCR-7, CD197, CDw197, CMKBR7}, TLR2 (toll like receptor 2) [NCBI Gene 7097] {aka CD282, TIL4}, TRAJ60 (T cell receptor alpha joining 60 (pseudogene)) [NCBI Gene 28695] {aka TCRA}, TCF7 (transcription factor 7) [NCBI Gene 6932] {aka TCF-1}, EEF1A2 (eukaryotic translation elongation factor 1 alpha 2) [NCBI Gene 1917] {aka DEE33, EEF1AL, EF-1-alpha-2, EF1A, EIEE33, HS1}
- **Diseases:** HIV (MESH:D015658), hyperacute infection (MESH:D007239), HIV-1 infection (MESH:D015490), viral infection (MESH:D014777), acute infection (MESH:D000208), AIDS (MESH:D000163), CMV infection (MESH:D003586), Viremia (MESH:D014766), Cancer (MESH:D009369)
- **Chemicals:** PBS (MESH:D007854), DMSO (MESH:D004121), polyA (MESH:D011061), dextran sulfate (MESH:D016264), IPTG (MESH:D007544), L-Glutamine (MESH:D005973), CO2 (MESH:D002245), glutathione (MESH:D005978), polybrene (MESH:D006583), dasatinib (MESH:D000069439), urea (MESH:D014508), oxidized glutathione (MESH:D019803), dT (MESH:D013936), arginine (MESH:D001120), A5131 (-), HEPES (MESH:D006531), penicillin (MESH:D010406), HCl (MESH:D006851), EDTA (MESH:D004492), Triton X-100 (MESH:D017830), NaCl (MESH:D012965)
- **Species:** Simian immunodeficiency virus (no rank) [taxon 11723], human gammaherpesvirus 4 (Epstein Barr virus, no rank) [taxon 10376], Homo sapiens (human, species) [taxon 9606], Macaca mulatta (rhesus macaque, species) [taxon 9544], Human immunodeficiency virus 1 (no rank) [taxon 11676], Qubevirus faecium (species) [taxon 39804], Lentivirus (genus) [taxon 11646], Mus musculus (house mouse, species) [taxon 10090], Escherichia coli (E. coli, species) [taxon 562]
- **Mutations:** R0146S, R0111S, T3-T
- **Cell lines:** Hi5 — Trichoplusia ni (Cabbage looper), Spontaneously immortalized cell line (CVCL_C190), Jurkat — Homo sapiens (Human), Childhood T acute lymphoblastic leukemia, Cancer cell line (CVCL_0065), SF9 — Spodoptera frugiperda (Fall armyworm), Spontaneously immortalized cell line (CVCL_0549), 721.221 — Homo sapiens (Human), Transformed cell line (CVCL_6263), 293FT — Homo sapiens (Human), Transformed cell line (CVCL_6911)

## Full text

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## Figures

6 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12934977/full.md

## References

103 references — full list in the complete paper: https://tomesphere.com/paper/PMC12934977/full.md

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Source: https://tomesphere.com/paper/PMC12934977