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HLA-B molecules target more conserved regions of the HIV-1 proteome.

Fontaine Costa, Ana Ia,*; Rao, Xiangyub,*; LeChenadec, Emmanuelleb; van Baarle, Debbiea,d; Keşmir, Canb,c

doi: 10.1097/QAD.0b013e328334442e
Basic Science: Concise Communications

Background: HLA-B alleles of HIV-infected individuals have been shown to have a major impact on their rate of progression toward AIDS, and the T-cell responses they restrict are immunodominant.

Objective: We sought to identify whether the association of HLA-B alleles with rate of progression toward AIDS is due to targeting of more restricted and thus more conserved regions of the HIV-1 proteome.

Methods: Each residue of the HIV-1 consensus subtype B sequence was coded according to the presence/absence of an epitope, using the compiled epitope data available in the HIV-LANL immunology database. The Shannon entropy for each HXB2 position was calculated using pre-aligned HIV-1 clade B sequences as a measure of its degree of conservation. We then compared the entropy of empty versus epitope-containing positions and HLA-B-restricted versus HLA-A-restricted positions.

Results: Positions containing CD8+ epitopes were significantly more conserved than corresponding empty positions. Moreover, residues targeted by HLA-B alleles in the HIV-1 proteome were significantly more conserved than the ones targeted by HLA-A alleles. Analysing a recent dataset, we found that B epitope regions contain significantly more escape mutations and reversions, which might be the reason why we find them to be more conserved.

Conclusion: Our results suggest that epitopes in HIV-1 targeted by HLA-B alleles lie in more constrained regions of its proteins, in which mutations might have a higher fitness cost and tend to revert. Consequently, HLA-B-restricted cytotoxic T-lymphocyte (CTL) responses may persist longer. This may be one of the factors contributing to the immunodominance and impact of HLA-B-restricted CTL responses on disease progression.

aDepartment of Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, The Netherlands

bDepartment of Theoretical Biology/Bioinformatics, Utrecht University, The Netherlands

cAcademic Biomedical Centre, Utrecht University, Utrecht, The Netherlands

dDepartment of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, Heidelberglaan, The Netherlands.

*A.I.F.C. and X.R. contributed equally to this work.

Received 17 July, 2009

Revised 7 October, 2009

Accepted 15 October, 2009

Correspondence to Dr Can Keşmir, Department of Theoretical Biology/Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands. Tel: +31 30 2534212; fax: +31 30 2513655; e-mail:

© 2010 Lippincott Williams & Wilkins, Inc.