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- Open Access
Ethnic differences in the adaptation rate of HIV gp120 from a vaccine trial
© Pérez-Losada et al; licensee BioMed Central Ltd. 2009
Received: 03 May 2009
Accepted: 15 July 2009
Published: 15 July 2009
Differences in HIV-1 gp120 sequence variation were examined in North American volunteers who became infected during a phase III vaccine trial using the rgp120 vaccine. Molecular adaptation of the virus in vaccine and placebo recipients from different ethnic subgroups was compared by estimating the dN/dS ratios in viruses sampled from each individual using three different methods. ANOVA analyses detected significant differences in dN/dS ratios among races (P < 0.02). gp120 sequences from the black individuals showed higher mean dN/dS ratios for all estimators (1.24–1.45) than in other races (0.66–1.35), and several pairwise comparisons involving blacks remained significant (P < 0.05) after correction for multiple tests. In addition, black-placebo individuals showed significantly (P < 0.02) higher mean dN/dS ratios (1.3–1.66) than placebo individuals from the other races (0.65–1.56). These results suggest intrinsic differences among races in immune response and highlight the need for including multiple ethnicities in the design of future HIV-1 vaccine studies and trials.
More than 33 million people are currently infected with HIV-1, resulting in 2–3 million deaths every year. Natural immunity to the virus is virtually nonexistent; hence, the creation of a vaccine to combat this global pandemic is an international public-health priority [1, 2]. In 2003, the results were released for a phase III HIV-1 vaccine efficacy trial conducted in North America and The Netherlands (VAX004) . This study tested the efficacy of bivalent vaccines containing recombinant HIV-1 envelope glycoprotein 120 (rgp120) antigens, the major antigen on the surface of the virus . Overall, the vaccine candidate did not seem to reduce the incidence of HIV-1 infection, but an interesting trend was noted in the analysis of the different self-described ethnic groups [white (non-Hispanic), blacks, Hispanic, Asian, and "others"]. When only the non-white volunteers (17% of the total study population) were considered, the vaccine seemed to confer a slight benefit (P = 0.012). After adjustment for multiple tests, this difference was not significant (P = 0.13) . Despite a lack of statistical support, this is not a trivial result. If this trend was to be confirmed, it would imply that non-whites developed protective immunity to HIV-1 or, even more important, that rgp120 immunogens could protect against HIV infection under certain circumstances. Here we explored this possibility further.
HIV-1 evolution is driven, to a significant extent, by the immune response. If viruses isolated from non-white patients are in fact under a stronger selection pressure either because of genetic differences in the magnitude, specificity, or potency of the natural immune response, or because of differences in factors affecting virus replication, we should expect higher ratios of nonsynonymous (amino acid changing) to synonymous nucleotide substitutions (dN/dS) [5–8] than in viral samples isolated from vaccinated and placebo (non-vaccinated) white individuals.
Mean dN/dSestimates across patients in PAML, SNAP and HYPHY.
Mean dN/dS ratios across races and treatments were compared using ANOVA, linear models (lm) and pairwise t-tests. Because treating all non-whites as a single unit is unrealistic considering their own genetic differences , we tested for differences in selection pressure on a race-by-race basis. Multiple significance in the pairwise t-tests was corrected using the Benjamini and Hochberg's procedure .
Statistically significant comparisons of dN/dSestimates among races and race-treatments.
Race by treatment
Corrected pairwise t-tests
black vs hispanic (0.020)
black vs other (0.013)
black vs white (0.004)
black placebo (0.001)
black vs hispanic (0.047)
black vs other (0.047)
black vs white (0.033)
black placebo (0.016)
black placebo (0.015)
Does the greater virus adaptive variation presumed in black participants reflect genetic differences in the intrinsic (no-preconditioned) immune response to HIV-1, or is it a consequence of the conditioned immune response induced by vaccination with rgp120? Comparison of vaccine and placebo recipients showed different results based on the dN/dS estimators used. No significant differences were observed among vaccinees, but significant differences (ANOVA; P = 0.025) in SNAP dN/dS ratios were detected among placebo individuals. Moreover, black-placebo patients showed significantly (lm coefficients; P < 0.02) higher mean dN/dS ratios (1.3, 1.38 and 1.66, for SNAP, PAML and HYPHY, respectively) than the other races (0.65–1.01, 0.84–1.14 and 0.73–1.56, respectively). These results might indicate that natural differences in the immune response may have increased viral rgp120 adaptation in blacks.
In North America, blacks correspond to 42% of all newly diagnosed HIV/AIDS cases, while white (non-Hispanic) and Hispanic individuals represent approximately 40% and 17%, respectively . If more data including both placebo and vaccinated recipients confirm that selection pressure differs between viruses infecting these three races, deciphering the genetic determinants of these differences should become a public-health priority. Indeed, our results highlight the need for selecting a broader representation of volunteers, based on ethnicity, in the design of future HIV-1 vaccine studies and trials .
This study was supported by a Bill & Melinda Gates Foundation grant to Global Solutions for Infectious Diseases. It was also supported by the Spanish Ministry of Science and Education [grant number BIO2007-61411 to DP, FPI fellowship BES-2005-9151 to MA]. We also want to thank the reviewers for their excellent suggestions.
- Esparza J, Bhamarapravati N: Accelerating the development and future availability of HIV-1 vaccines: why, when, where, and how?. Lancet. 2000, 355: 2061-2066. 10.1016/S0140-6736(00)02360-6.View ArticlePubMedGoogle Scholar
- Spearman P: HIV vaccine development: lessons from the past and promise for the future. Curr HIV Res. 2003, 1: 101-120. 10.2174/1570162033352093.View ArticlePubMedGoogle Scholar
- rgp120 HIV Vaccine Study Group: Placebo controlled phase 3 trial of a recombinant glycoprotein 120 vaccine to prevent HIV-1 infection. rgp120 HIV Vaccine Study Group. J Infect Dis. 2005, 191: 654-665. 10.1086/428404.View ArticleGoogle Scholar
- Eggink D, Melchers M, Sanders RW: Antibodies to HIV-1: aiming at the right target. Trends Microbiol. 2007, 15: 291-294. 10.1016/j.tim.2007.05.006.View ArticlePubMedGoogle Scholar
- Sharp PM: In search of molecular Darwinism. Nature. 1997, 385: 111-112. 10.1038/385111a0.View ArticlePubMedGoogle Scholar
- Nei M, Gojobori T: Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol. 1986, 3: 418-426.PubMedGoogle Scholar
- Ross HA, Rodrigo AG: Immune-mediated positive selection drives human immunodeficiency virus type 1 molecular variation and predicts disease duration. J Virol. 2002, 76: 11715-11720. 10.1128/JVI.76.22.11715-11720.2002.PubMed CentralView ArticlePubMedGoogle Scholar
- Williamson S: Adaptation in the env gene of HIV-1 and evolutionary theories of disease progression. Mol Biol Evol. 2003, 20: 1318-1325. 10.1093/molbev/msg144.View ArticlePubMedGoogle Scholar
- Gilbert PB, Peterson ML, Follmann D, Hudgens MG, Francis DP, Gurwith M, Heyward WL, Jobes DV, Popovic V, Self SG, et al: Correlation between immunologic responses to a recombinant glycoprotein 120 vaccine and incidence of HIV-1 infection in a phase 3 HIV-1 preventive vaccine trial. J Infect Dis. 2005, 191: 666-677. 10.1086/428405.View ArticlePubMedGoogle Scholar
- Pérez-Losada M, Jobes DV, Sinangil F, Crandall KA, Posada D, Berman PW: Phylodynamics of gp120 sequences from a Phase 3 HIV-1 vaccine trial in North America. Mol Biol Evol. 2009, in reviewGoogle Scholar
- Katoh K, Kuma K, Toh H, Miyata T: MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 2005, 33: 511-518. 10.1093/nar/gki198.PubMed CentralView ArticlePubMedGoogle Scholar
- Korber B: HIV signature and sequence variation analysis. Computational and evolutionary analysis of HIV molecular sequences. Edited by: Rodrigo AG, Learn GH. 2000, Dordrecht, Netherlands: Kluwer Academic Publishers, 4: 55-72.Google Scholar
- Yang Z: PAML: Phylogenetic Analysis by Maximum Likelihood. 2001, London: University College London, 3.1Google Scholar
- Kosakovsky Pond SL, Frost SDW, Muse SV: HyPhy: hypothesis testing using phylogenies. Bioinformatics. 2005, 21: 676-679. 10.1093/bioinformatics/bti079.View ArticleGoogle Scholar
- Kosakovsky Pond SL, Posada D, Gravenor MB, Woelk CH, Frost SD: GARD: a genetic algorithm for recombination detection. Bioinformatics. 2006, 22: 3096-3098. 10.1093/bioinformatics/btl474.View ArticlePubMedGoogle Scholar
- Benjamini Y, Hochberg Y: Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Statist Soc B. 1995, 57: 289-300.Google Scholar
- Sugimoto K, Stadanlick J, Ikeda F, Brensinger C, Furth EE, Alter HJ, Chang KM: Influence of ethnicity in the outcome of hepatitis C virus infection and cellular immune response. Hepatology. 2003, 37: 590-599. 10.1053/jhep.2003.50103.View ArticlePubMedGoogle Scholar
- CDC: HIV/AIDS Surveillance Report. 2007, Atlanta: Centers for Disease Control and Prevention (CDC), 19:Google Scholar
- Graham BS, Mascola JR: Lessons from failure – preparing for future HIV-1 vaccine efficacy trials. J Infect Dis. 2005, 191: 647-649. 10.1086/428406.View ArticlePubMedGoogle Scholar
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