14th Conference on Retroviruses and Opportunistic Infections Los Angeles, California - February 25-28, 2007

Conf Retrovir Opportunistic Infect 2007 Feb 25-28;14: (abstract no. 23)

Zabrina Brumme^1,2, C Brumme^1,2, C Kadie³, J Carlson³, C Chui², T Mo², J Montaner², B Walker¹, D Heckerman³, and P Harrigan^2
1Partners AIDS Res Ctr, Massachusetts Gen Hosp, Boston, US; ²BC Ctr for Excellence in HIV/AIDS, Vancouver, Canada; and ³Microsoft Res, Redmond, WA, US

BACKGROUND: Selection of cytotoxic T lymphocyte (CTL) escape mutations in response to HLA class I selective pressure has been documented on an individual and a population basis, however, the clinical impact of escape is not well quantified. We identified HLA allele-associated sequence changes across protease (PR), reverse transcriptase (RT), and Nef in a cross-sectional analysis of 765 chronically infected, ART-naïve individuals, and investigated associations between presence of escape mutations and clinical markers of HIV disease progression.

METHODS: HLA-A, B, and C sequence-based typing was performed on DNA extracted from archived blood (n = 765 subjects) and alleles summarized to 2-digit resolution. Genotyping of extracted plasma HIV RNA of Nef, PR, and RT was performed by real time polymerase chain reaction (RT-PCR) followed by DNA sequencing (97% subtype B sequences). Significant HLA/HIV sequence associations were identified in a codon-by-codon analysis using a novel, likelihood-ratio-test approach featuring phylogenetic correction. Multiple comparisons were addressed by applying a q-value statistic and results limited to q <0.2 (corresponding to a ~20% false-positive rate).

RESULTS: After removing associations attributable to HLA linkage disequilibrium (n = 46), a total of 176 significant (q <0.2, corresponding to p <0.004) HLA/HIV sequence associations were identified, including 9, 31, and 136 associations occurring at 8, 22, and 63 unique codons in PR, RT, and Nef, respectively. Of 176, 74 (42.0%) mapped inside (n = 59) or within 3 amino acids (n = 15) of a published, HLA-restricted CTL epitope, and thus likely represent escape mutationns. Overall, possession of an escape mutation in a published epitope in Nef, RT, or PR was significantly associated with higher pVL (median [IQR] 5.1 [4.7 to 5.5] vs 4.3 [3.9 to 4.7] log₁₀ copies HIV RNA/mL in subjects with and without escape; p = 0.002) and lower CD4 counts (median [IQR] 280 [130 to 430] vs 460 [290 to 550] cells/mm³, p = 0.04). Analysis of escape among individual genes suggested a dose-response relationship between the presence of multiple (vs single or no) escape mutations in RT and Nef and markers of more severe HIV disease.

CONCLUSIONS: Selected in vivo CTL escape mutations occurring in response to HLA-mediated selection pressure are common and reproducible enough to be detected on a population level, and are observed with exceptional density in Nef compared with PR/RT. Presence of escape mutations in Nef and PR/RT is associated with more severe HIV disease progression.

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2007-02-25
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