An introduction to a novel population genetic approach for HIV characterization

Perez‐Sweeney, Beatriz; DeSalle, Rob; Ho, John L.

doi:10.1016/j.meegid.2010.07.010

Cited by 4 publications

(4 citation statements)

References 63 publications

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“…To assess the performance of our new approach in identifying bnMAb epitopes, we compared its predictions to those of a standard classification approach that has been previously used, for example, to identify positions in gp120 subject to differential selection pressure between two distinct HIV cohorts [61] . Specifically, we compared the distribution of amino acid residues occupying a particular position over those strains in the panel that are neutralized by the bnMAb, to the distribution over those strains that are not.…”

Section: Resultsmentioning

confidence: 99%

Computational Prediction of Broadly Neutralizing HIV-1 Antibody Epitopes from Neutralization Activity Data

et al. 2013

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Broadly neutralizing monoclonal antibodies effective against the majority of circulating isolates of HIV-1 have been isolated from a small number of infected individuals. Definition of the conformational epitopes on the HIV spike to which these antibodies bind is of great value in defining targets for vaccine and drug design. Drawing on techniques from compressed sensing and information theory, we developed a computational methodology to predict key residues constituting the conformational epitopes on the viral spike from cross-clade neutralization activity data. Our approach does not require the availability of structural information for either the antibody or antigen. Predictions of the conformational epitopes of ten broadly neutralizing HIV-1 antibodies are shown to be in good agreement with new and existing experimental data. Our findings suggest that our approach offers a means to accelerate epitope identification for diverse pathogenic antigens.

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Section: Resultsmentioning

confidence: 99%

Computational Prediction of Broadly Neutralizing HIV-1 Antibody Epitopes from Neutralization Activity Data

et al. 2013

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“…Eight codons were both divergent between groups, and inferred to be under positive selection: PR35, PR93, RT135, RT162, RT245, RT277, RT293 and RT297 (Figure S2). According to the definition put forward by Perez-Sweeney et al [18], these sites can be considered putatively adaptive divergent sites, i.e. selective pressure may differ at these codons between the groups studied.…”

Section: Resultsmentioning

confidence: 99%

“…In order to examine the differences in selective pressure within different ethnic groups, we compared site-specific frequencies of amino acids in HIV pol sequences classified according to ethnicity. This method offers the additional advantage of not requiring phylogenetic separation of sequences for the populations studied [18]. We found divergent HIV sequence patterns among ethnic groups at 8 sites under positive selection that have been shown to mutate under HLA-associated immune pressure.…”

Section: Introductionmentioning

confidence: 92%

“…Since HLA allele frequency data are currently not available for association studies in the Canadian population we studied, we used a recently developed method to compare host selection pressure between populations in the absence of HLA allele frequency data [18]. In order to examine the differences in selective pressure within different ethnic groups, we compared site-specific frequencies of amino acids in HIV pol sequences classified according to ethnicity.…”

Section: Introductionmentioning

confidence: 99%

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Adaptive Evolution of HIV at HLA Epitopes Is Associated with Ethnicity in Canada

et al. 2012

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Host immune selection pressure influences the development of mutations that allow for HIV escape. Mutation patterns induced in HIV by the human leukocyte antigen (HLA) are HLA-allele specific. As ethnic groups have distinct and characteristic HLA allele frequencies, we can expect divergent viral evolution within ethnicities. Here, we have sequenced and analyzed the HIV pol gene from 1248 subtype B infected, treatment-naïve individuals in Canada. Phylogenetic analysis showed no separation between pol sequences from five self-identified ethnic groups, yet fixation index (FST) values showed significant divergence between ethnicities. A total of 17 amino acid sites showed an ethnic-specific fixation pattern (0.015

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Pulmonary-Respiratory Medicine

2001

JAMA

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An introduction to a novel population genetic approach for HIV characterization

Cited by 4 publications

References 63 publications

Computational Prediction of Broadly Neutralizing HIV-1 Antibody Epitopes from Neutralization Activity Data

Computational Prediction of Broadly Neutralizing HIV-1 Antibody Epitopes from Neutralization Activity Data

Adaptive Evolution of HIV at HLA Epitopes Is Associated with Ethnicity in Canada

Pulmonary-Respiratory Medicine

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