An unanticipated lack of consensus cytotoxic T lymphocyte epitopes in HIV-1 databases: the contribution of prediction programs

Schellens, Ingrid MMa; Keşmir, Canb; Miedema, Franka; van Baarle, Debbiea; Borghans, José AMa,b

doi: 10.1097/QAD.0b013e3282f15622
Basic Science

Background: Most consensus HIV-1-specific cytotoxic T lymphocytes epitopes presented via intensively studied HLA molecules are thought to be known

Objective: To identify possible novel HIV-1 epitopes for HLA-B27 and HLA-B57; two HLA types which are abundantly studied because of their correlation with slow HIV disease progression.

Methods: HIV-1 consensus subtype B sequences were analysed using peptide prediction programs based on major histocompatibility complex binding, proteasomal cleavage and TAP (transporter associated with antigen processing) transport. Recognition of the novel identified epitopes by cytotoxic T lymphocytes was tested using interferon-γ ELISpot assay.

Results: In total, 22 novel epitopes predicted to be presented by either HLA-B27 or HLA-B57 were selected. Of these, 86% elicited significant immune responses in HIV-1-infected individuals.

Conclusions: These data show that numerous HIV-1 epitopes remain to be identified, and that prediction programs are powerful tools for this purpose.

Author Information

From the aDepartment of Immunology, University Medical Center, the Netherlands

bTheoretical Biology/Bioinformatics, Utrecht University, Utrecht, the Netherlands.

Received 24 July, 2007

Revised 13 August, 2007

Accepted 17 August, 2007

Correspondence to Dr J.A.M. Borghans, University Medical Center Utrecht, KC02.085.2, Lundlaan 6, 3584 EA Utrecht, the Netherlands. E-mail:

© 2008 Lippincott Williams & Wilkins, Inc.