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Human leukocyte antigen-specific polymorphisms in HIV-1 Gag and their association with viral load in chronic untreated infection

Brumme, Zabrina La; Tao, Irisb,*; Szeto, Sharonb,*; Brumme, Chanson Ja; Carlson, Jonathan Mc,d; Chan, Dennisonb; Kadie, Carlc; Frahm, Nicolea; Brander, Christiana; Walker, Brucea,e; Heckerman, Davidc; Harrigan, P Richardb,f

doi: 10.1097/QAD.0b013e3283021a8c
Basic Science

Objective: Selection of specific human leukocyte antigen (HLA)-restricted cytotoxic T-lymphocyte (CTL) escape mutations in key Gag epitopes has been associated with loss of HIV immune control on an individual basis. Here we undertake a population-based identification of HLA-associated polymorphisms in Gag and investigate their relationship with plasma viral load.

Design: Cross-sectional analysis of 567 chronically HIV subtype B-infected, treatment-naive individuals.

Methods: HLA class I-associated Gag substitutions were identified using phylogenetically corrected analysis methods featuring a multivariate adjustment for HLA linkage disequilibrium and a q-value correction for multiple tests. Presence of HLA-associated substitutions and markers of HIV disease status were correlated using Spearman's rank test.

Results: We have created a gene-wide map of HLA class I-associated substitutions in HIV-1 subtype B Gag. This features 111 HLA-associated substitutions occurring at 51 of 500 Gag codons, more than 50% of which occur within published and/or putative HLA-restricted CTL epitopes. A modest inverse correlation was observed between the total number of HLA-associated Gag polymorphic sites within each individual and plasma viral load in chronic untreated infection (R = −0.17, P < 0.0001), supporting the hypothesis that a broad ability to target Gag in vivo contributes to viral control. A modest positive correlation was observed between the proportion of these sites exhibiting HLA-associated substitutions and plasma viral load (R = 0.09, P = 0.03), consistent with a loss of viremia control with the accumulation of CTL escape mutations.

Conclusion: Results contribute to our understanding of immune-driven viral adaptation and suggest that the accumulation of CTL escape mutations in Gag results in clinically detectable consequences at the population level. These data have implications for HIV vaccines.

From the aPartners AIDS Research Center, Massachusetts General Hospital, Boston, Harvard Medical School, Massachusetts, USA

bBC Centre for Excellence in HIV/AIDS, Vancouver, Canada

cMicrosoft Research, Redmond, Washington, USA

dDepartment of Computer Science, University of Washington, Seattle, Washington, USA

eHoward Hughes Medical Institute, Chevy Chase, Maryland, USA

fDivision of AIDS, University of British Columbia, Vancouver, British Columbia, Canada.

* These authors contributed equally to this work.

Received 24 January, 2008

Revised 12 March, 2008

Accepted 18 March, 2008

Correspondence to Zabrina L. Brumme, PhD, Partners AIDS Research Center, Massachusetts General Hospital, 149 13th Street, Charlestown, MA 02129, USA.

© 2008 Lippincott Williams & Wilkins, Inc.