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      Plasma IgG to Linear Epitopes in the V2 and V3 Regions of HIV-1 gp120 Correlate with a Reduced Risk of Infection in the RV144 Vaccine Efficacy Trial

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          Abstract

          Neutralizing and non-neutralizing antibodies to linear epitopes on HIV-1 envelope glycoproteins have potential to mediate antiviral effector functions that could be beneficial to vaccine-induced protection. Here, plasma IgG responses were assessed in three HIV-1 gp120 vaccine efficacy trials (RV144, Vax003, Vax004) and in HIV-1-infected individuals by using arrays of overlapping peptides spanning the entire consensus gp160 of all major genetic subtypes and circulating recombinant forms (CRFs) of the virus. In RV144, where 31.2% efficacy against HIV-1 infection was seen, dominant responses targeted the C1, V2, V3 and C5 regions of gp120. An analysis of RV144 case-control samples showed that IgG to V2 CRF01_AE significantly inversely correlated with infection risk (OR= 0.54, p=0.0042), as did the response to other V2 subtypes (OR=0.60-0.63, p=0.016-0.025). The response to V3 CRF01_AE also inversely correlated with infection risk but only in vaccine recipients who had lower levels of other antibodies, especially Env-specific plasma IgA (OR=0.49, p=0.007) and neutralizing antibodies (OR=0.5, p=0.008). Responses to C1 and C5 showed no significant correlation with infection risk. In Vax003 and Vax004, where no significant protection was seen, serum IgG responses targeted the same epitopes as in RV144 with the exception of an additional C1 reactivity in Vax003 and infrequent V2 reactivity in Vax004. In HIV-1 infected subjects, dominant responses targeted the V3 and C5 regions of gp120, as well as the immunodominant domain, heptad repeat 1 (HR-1) and membrane proximal external region (MPER) of gp41. These results highlight the presence of several dominant linear B cell epitopes on the HIV-1 envelope glycoproteins. They also generate the hypothesis that IgG to linear epitopes in the V2 and V3 regions of gp120 are part of a complex interplay of immune responses that contributed to protection in RV144.

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          Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing.

          Accurate identification of the transmitted virus and sequences evolving from it could be instrumental in elucidating the transmission of human immunodeficiency virus type 1 (HIV-1) and in developing vaccines, drugs, or microbicides to prevent infection. Here we describe an experimental approach to analyze HIV-1 env genes as intact genetic units amplified from plasma virion RNA by single-genome amplification (SGA), followed by direct sequencing of uncloned DNA amplicons. We show that this strategy precludes in vitro artifacts caused by Taq-induced nucleotide substitutions and template switching, provides an accurate representation of the env quasispecies in vivo, and has an overall error rate (including nucleotide misincorporation, insertion, and deletion) of less than 8 x 10(-5). Applying this method to the analysis of virus in plasma from 12 Zambian subjects from whom samples were obtained within 3 months of seroconversion, we show that transmitted or early founder viruses can be identified and that molecular pathways and rates of early env diversification can be defined. Specifically, we show that 8 of the 12 subjects were each infected by a single virus, while 4 others acquired more than one virus; that the rate of virus evolution in one subject during an 80-day period spanning seroconversion was 1.7 x 10(-5) substitutions per site per day; and that evidence of strong immunologic selection can be seen in Env and overlapping Rev sequences based on nonrandom accumulation of nonsynonymous mutations. We also compared the results of the SGA approach with those of more-conventional bulk PCR amplification methods performed on the same patient samples and found that the latter is associated with excessive rates of Taq-induced recombination, nucleotide misincorporation, template resampling, and cloning bias. These findings indicate that HIV-1 env genes, other viral genes, and even full-length viral genomes responsible for productive clinical infection can be identified by SGA analysis of plasma virus sampled at intervals typical in large-scale vaccine trials and that pathways of viral diversification and immune escape can be determined accurately.
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            Structural definition of a conserved neutralization epitope on HIV-1 gp120

            The remarkable diversity, glycosylation and conformational flexibility of the human immunodeficiency virus type 1 (HIV-1) envelope (Env), including substantial rearrangement of the gp120 glycoprotein upon binding the CD4 receptor, allow it to evade antibody-mediated neutralization. Despite this complexity, the HIV-1 Env must retain conserved determinants that mediate CD4 binding. To evaluate how these determinants might provide opportunities for antibody recognition, we created variants of gp120 stabilized in the CD4-bound state, assessed binding of CD4 and of receptor-binding-site antibodies, and determined the structure at 2.3 Å resolution of the broadly neutralizing antibody b12 in complex with gp120. b12 binds to a conformationally invariant surface that overlaps a distinct subset of the CD4-binding site. This surface is involved in the metastable attachment of CD4, before the gp120 rearrangement required for stable engagement. A site of vulnerability, related to a functional requirement for efficient association with CD4, can therefore be targeted by antibody to neutralize HIV-1. Supplementary information The online version of this article (doi:10.1038/nature05580) contains supplementary material, which is available to authorized users.
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              Structure of a V3-containing HIV-1 gp120 core.

              The third variable region (V3) of the HIV-1 gp120 envelope glycoprotein is immunodominant and contains features essential for coreceptor binding. We determined the structure of V3 in the context of an HIV-1 gp120 core complexed to the CD4 receptor and to the X5 antibody at 3.5 angstrom resolution. Binding of gp120 to cell-surface CD4 would position V3 so that its coreceptor-binding tip protrudes 30 angstroms from the core toward the target cell membrane. The extended nature and antibody accessibility of V3 explain its immunodominance. Together, the results provide a structural rationale for the role of V3 in HIV entry and neutralization.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2013
                26 September 2013
                : 8
                : 9
                : e75665
                Affiliations
                [1 ] Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
                [2 ]Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
                [3 ]Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Álamos, New Mexico, United States of America
                [4 ]Duke University Medical Center, Durham, North Carolina, United States of America
                [5 ]JPT Peptide Technologies GmbH, Berlin, Germany
                [6 ] Baskin School of Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
                [7 ]Global Solutions for Infectious Diseases, South San Francisco, California, United States of America
                [8 ]Department of Retrovirology, US Army Medical Component, AFRIMS, Bangkok, Thailand
                [9 ]Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand
                [10 ]Center of Excellence for Biomedical and Public Health Informatics BIOPHICS, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
                [11 ]Vaccine Trial Center and Department of Clinical Tropical Medicine, Mahidol University, Bangkok, Thailand
                [12 ]Department of Research and Development, Sanofi Pasteur, Swiftwater, Pennsylvania, United States of America
                [13 ]US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
                [14 ]Veterans Affairs New York Harbor Healthcare System, New York, New York, United States of America
                [15 ]New York University School of Medicine, New York, New York, United States of America
                The University of Hong Kong, Hong Kong
                Author notes

                Competing Interests: Larry Eckler, Holger Wenschuh and Johannes Zerweck are employed by JPT Peptide Technologies and James Tartaglia by Sanofi Pasteur. JPT Peptide Technologies provided the peptide array slides for this work. There are no further patents, products in development or marketed products to declare. This does not alter the authors' adherence to all the PLOS ONE policies on sharing data and materials, as detailed online in the guide for authors.

                Conceived and designed the experiments: DCM BTK JRM. Performed the experiments: RTB ET XS GDT. Analyzed the data: RG BTK SG JP GI SZP BFH SS PG. Contributed reagents/materials/analysis tools: LE HW JZ KG HG PWB DF FS CL SN SRN JK PP JT MLR NLM JHK. Wrote the manuscript: DCM RG SG BTK.

                Article
                PONE-D-13-29733
                10.1371/journal.pone.0075665
                3784573
                24086607
                90cdf81a-32fc-4b8d-b473-7e606af65653
                Copyright @ 2013

                This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

                History
                : 18 July 2013
                : 19 August 2013
                Funding
                This study was funded in part by a grant from the Bill & Melinda Gates Foundation (#38619) to DCM as part of the Collaboration for AIDS Vaccine Discovery ( www.cavd.org), and by an Interagency Agreement Y1-AI-2642-12 between U.S. Army Medical Research and Material Command (USAMRMC), the National Institutes of Allergy and Infectious Diseases, and by the Department of Veterans Affairs, Veterans Health Administration, Office of Research and Development. This work was also supported by a cooperative agreement (W81XWH-07-2-0067) between the Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., and the U.S. Department of Defense (DOD) and New York University School of Medicine (Contract No. 692526). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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