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Broad and persistent Gag-specific CD8+ T-cell responses are associated with viral control but rarely drive viral escape during primary HIV-1 infection

Radebe, Mopoa,b; Gounder, Kaminia,b; Mokgoro, Mammekwaa; Ndhlovu, Zaza M.a,c; Mncube, Zenelea; Mkhize, Lungilea; van der Stok, Marya; Jaggernath, Manjeethaa; Walker, Bruce D.a,b,c,d; Ndung’u, Thumbia,b,c,e

doi: 10.1097/QAD.0000000000000508
Basic Science

Objective: We characterized protein-specific CD8+ T-cell immunodominance patterns during the first year of HIV-1 infection, and their impact on viral evolution and immune control.

Methods: We analyzed CD8+ T-cell responses to the full HIV-1 proteome during the first year of infection in 18 antiretroviral-naïve individuals with acute HIV-1 subtype C infection, all identified prior to seroconversion. Ex-vivo and cultured interferon-γ ELISPOT assays were performed and viruses from plasma were sequenced within defined CTL Gag epitopes.

Results: Nef-specific CD8+ T-cell responses were dominant during the first 4 weeks after infection and made up 40% of the total responses at this time; yet, by 1 year, responses against this region had declined and Gag responses made up to 47% of all T-cell responses measured. An inverse correlation between the breadth of Gag-specific responses and viral load set point was evident at 26 weeks after infection (P = 0.0081, r = −0.60) and beyond. An inverse correlation between the number of persistent responses targeting Gag and viral set point was also identified (P = 0.01, r = −0.58). Gag-specific responses detectable by the cultured ELISPOT assay correlated negatively with viral load set point (P = 0.0013, r = −0.91). Sequence evolution in targeted and nontargeted Gag epitopes in this cohort was infrequent.

Conclusions: These data underscore the importance of HIV-specific CD8+ T-cell responses, particularly to the Gag protein, in the maintenance of low viral load levels during primary infection, and show that these responses are initially poorly elicited by natural infection. These data have implications for vaccine design strategies.

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aHIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal

bKwaZulu-Natal Research Institute for Tuberculosis and HIV, Nelson R. Mandela School of Medicine, Durban, South Africa

cRagon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts

dHoward Hughes Medical Institute, Maryland, USA

eMax Planck Institute for Infection Biology, Charitestraße 1, Berlin, Germany.

Correspondence to Thumbi Ndung’u, HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, 719 Umbilo Road, Durban, South Africa. E-mail:

Received 22 July, 2014

Revised 29 September, 2014

Accepted 7 October, 2014

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© 2015 Lippincott Williams & Wilkins, Inc.