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Schorcht A, van den Kerkhof TLGM, Cottrell CA, Allen JD, Torres JL, Behrens AJ, Schermer EE, Burger JA, de Taeye SW, Torrents de la Peña A, Bontjer I, Gumbs S, Ozorowski G, LaBranche CC, de Val N, Yasmeen A, Klasse PJ, Montefiori DC, Moore JP, Schuitemaker H, Crispin M, van Gils MJ, Ward AB, Sanders RW. Neutralizing Antibody Responses Induced by HIV-1 Envelope Glycoprotein SOSIP Trimers Derived from Elite Neutralizers. J Virol 2020; 94:e01214-20. [PMID: 32999024 PMCID: PMC7925178 DOI: 10.1128/jvi.01214-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/08/2020] [Indexed: 12/12/2022] Open
Abstract
The induction of broadly neutralizing antibodies (bNAbs) is a major goal in vaccine research. HIV-1-infected individuals that develop exceptionally strong bNAb responses, termed elite neutralizers, can inform vaccine design by providing blueprints for the induction of similar bNAb responses. We describe a new recombinant native-like envelope glycoprotein (Env) SOSIP trimer, termed AMC009, based on the viral founder sequences of an elite neutralizer. The subtype B AMC009 SOSIP protein formed stable native-like trimers that displayed multiple bNAb epitopes. Overall, its structure at 4.3-Å resolution was similar to that of BG505 SOSIP.664. The AMC009 trimer resembled one from a second elite neutralizer, AMC011, in having a dense and complete glycan shield. When tested as immunogens in rabbits, the AMC009 trimers did not induce autologous neutralizing antibody (NAb) responses efficiently while the AMC011 trimers did so very weakly, outcomes that may reflect the completeness of their glycan shields. The AMC011 trimer induced antibodies that occasionally cross-neutralized heterologous tier 2 viruses, sometimes at high titer. Cross-neutralizing antibodies were more frequently elicited by a trivalent combination of AMC008, AMC009, and AMC011 trimers, all derived from subtype B viruses. Each of these three individual trimers could deplete the NAb activity from the rabbit sera. Mapping the polyclonal sera by electron microscopy revealed that antibodies of multiple specificities could bind to sites on both autologous and heterologous trimers. These results advance our understanding of how to use Env trimers in multivalent vaccination regimens and the immunogenicity of trimers derived from elite neutralizers.IMPORTANCE Elite neutralizers, i.e., individuals who developed unusually broad and potent neutralizing antibody responses, might serve as blueprints for HIV-1 vaccine design. Here, we studied the immunogenicity of native-like recombinant envelope glycoprotein (Env) trimers based on viral sequences from elite neutralizers. While immunization with single trimers from elite neutralization did not recapitulate the breadth and potency of neutralization observed in these infected individuals, a combination of three subtype B Env trimers from elite neutralizers resulted in some neutralization breadth within subtype B viruses. These results should guide future efforts to design vaccines to induce broadly neutralizing antibodies.
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Affiliation(s)
- Anna Schorcht
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Tom L G M van den Kerkhof
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Department of Experimental Immunology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Christopher A Cottrell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Joel D Allen
- School of Biological Science, University of Southampton, Southampton, United Kingdom
| | - Jonathan L Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Anna-Janina Behrens
- School of Biological Science, University of Southampton, Southampton, United Kingdom
| | - Edith E Schermer
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Judith A Burger
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Steven W de Taeye
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Alba Torrents de la Peña
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Ilja Bontjer
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Stephanie Gumbs
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Celia C LaBranche
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Natalia de Val
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick National Laboratory, Leidos Biomedical Research Inc., Frederick, Maryland, USA
| | - Anila Yasmeen
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, USA
| | - Per Johan Klasse
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, USA
| | - David C Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - John P Moore
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, USA
| | | | - Max Crispin
- School of Biological Science, University of Southampton, Southampton, United Kingdom
| | - Marit J van Gils
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, USA
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Profiling the neutralizing antibody response in chronically HIV-1 CRF07_BC-infected intravenous drug users naïve to antiretroviral therapy. Sci Rep 2017; 7:46308. [PMID: 28387330 PMCID: PMC5384219 DOI: 10.1038/srep46308] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 03/15/2017] [Indexed: 11/23/2022] Open
Abstract
Characterizing neutralizing antibody (NAb) responses in individuals infected with diverse HIV-1 strains is necessary to reveal the novel targets for regional preventive and therapeutic strategies development. We evaluated the prevalence, breadth, and potency of NAb responses in 98 CRF07_BC-infected individuals using a large, multi-subtype panel of 30 tier 2-3 Env-pseudotyped viruses. Furthermore, we compared the neutralization pattern of CRF07_BC-infected people with that of subtype B’-infected individuals in China. Of the 98 plasma samples tested, 18% neutralized more than 80% of viruses in the panel, and 53% neutralized more than 50%, suggesting the presence of broadly NAbs in these individuals. A preferential intra-subtype neutralization of CRF07_BC was found. Notably, CRF07_BC-infected individuals generated higher neutralization titers against intra-subtype viruses than subtype B’-infected individuals with longer infection length. However, subtype B’-infected individuals mounted broader neutralization responses against inter-subtype viruses than CRF07_BC infection with shorter infection time, indicating the transition from narrow autologous to broad heterologous neutralization over time. Neutralization activity of the top six plasmas from each cohort was attributable to IgG fraction, and half of them developed CD4 binding site antibody reactivity. Heatmap analysis identified three statistically robust clusters of plasmas that offer valuable resources for further in-depth virological and immunological study.
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Anti-V3/Glycan and Anti-MPER Neutralizing Antibodies, but Not Anti-V2/Glycan Site Antibodies, Are Strongly Associated with Greater Anti-HIV-1 Neutralization Breadth and Potency. J Virol 2015; 89:5264-75. [PMID: 25673728 DOI: 10.1128/jvi.00129-15] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 02/05/2015] [Indexed: 02/02/2023] Open
Abstract
UNLABELLED The membrane-proximal external region (MPER), the V2/glycan site (initially defined by PG9 and PG16 antibodies), and the V3/glycans (initially defined by PGT121-128 antibodies) are targets of broadly neutralizing antibodies and potential targets for anti-HIV-1 antibody-based vaccines. Recent evidence shows that antibodies with moderate neutralization breadth are frequently attainable, with 50% of sera from chronically infected individuals neutralizing ≥ 50% of a large, diverse set of viruses. Nonetheless, there is little systematic information addressing which specificities are preferentially targeted among such commonly found, moderately broadly neutralizing sera. We explored associations between neutralization breadth and potency and the presence of neutralizing antibodies targeting the MPER, V2/glycan site, and V3/glycans in sera from 177 antiretroviral-naive HIV-1-infected (>1 year) individuals. Recognition of both MPER and V3/glycans was associated with increased breadth and potency. MPER-recognizing sera neutralized 4.62 more panel viruses than MPER-negative sera (95% prediction interval [95% PI], 4.41 to 5.20), and V3/glycan-recognizing sera neutralized 3.24 more panel viruses than V3/glycan-negative sera (95% PI, 3.15 to 3.52). In contrast, V2/glycan site-recognizing sera neutralized only 0.38 more panel viruses (95% PI, 0.20 to 0.45) than V2/glycan site-negative sera and no association between V2/glycan site recognition and breadth or potency was observed. Despite autoreactivity of many neutralizing antibodies recognizing MPER and V3/glycans, antibodies to these sites are major contributors to neutralization breadth and potency in this cohort. It may therefore be appropriate to focus on developing immunogens based upon the MPER and V3/glycans. IMPORTANCE Previous candidate HIV vaccines have failed either to induce wide-coverage neutralizing antibodies or to substantially protect vaccinees. Therefore, current efforts focus on novel approaches never before successfully used in vaccine design, including modeling epitopes. Candidate immunogen models identified by broadly neutralizing antibodies include the membrane-proximal external region (MPER), V3/glycans, and the V2/glycan site. Autoreactivity and polyreactivity of anti-MPER and anti-V3/glycan antibodies are thought to pose both direct and indirect barriers to achieving neutralization breadth. We found that antibodies to the MPER and the V3/glycans contribute substantially to neutralization breadth and potency. In contrast, antibodies to the V2/glycan site were not associated with neutralization breadth/potency. This suggests that the autoreactivity effect is not critical and that the MPER and the V3/glycans should remain high-priority vaccine candidates. The V2/glycan site result is surprising because broadly neutralizing antibodies to this site have been repeatedly observed. Vaccine design priorities should shift toward the MPER and V3/glycans.
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Manhas S, Chau D, Rempel C, Clark BE, Auyeung K, Pantophlet R. The presence of glutamine at position 315 but not epitope masking predominantly hinders HIV subtype C neutralization by the anti-V3 antibody B4e8. Virology 2014; 462-463:98-106. [PMID: 24971702 PMCID: PMC4125615 DOI: 10.1016/j.virol.2014.05.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Revised: 04/14/2014] [Accepted: 05/19/2014] [Indexed: 11/19/2022]
Abstract
Antibody B4e8 exhibits modest cross-neutralizing activity, with preference for HIV subtype B. This preference might be explained by B4e8׳s extensive interaction with Arg315, which occurs at the center of most subtype B V3 sequences but is replaced by Gln in subtype C. The extent to which B4e8׳s ability to neutralize subtype C strains is hindered by Gln315 and/or other factors, e.g. epitope masking, is unclear. We confirmed here that an Arg315-to-Gln substitution in a subtype B virus abrogates B4e8 neutralizing activity. Conversely, B4e8-resistant subtype C viruses were rendered sensitive upon Gln 315-to-Arg substitution. V2 region swapping between B4e8-sensitive and- resistant subtype C strains revealed a role for V2 in limiting B4e8 access, but this was less significant than the absence of Arg315. Our findings, while illustrating the importance of Arg315 for B4e8, suggest that some subtype C strains may be vulnerable to B4e8 derivatives capable of binding stronger to Gln315-containing sequences.
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Affiliation(s)
- Savrina Manhas
- Faculty of Health Sciences, Simon Fraser University, British Columbia, Burnaby, Canada V5A 1S6
| | - Dennis Chau
- Faculty of Health Sciences, Simon Fraser University, British Columbia, Burnaby, Canada V5A 1S6
| | - Caitlin Rempel
- Faculty of Health Sciences, Simon Fraser University, British Columbia, Burnaby, Canada V5A 1S6
| | - Brenda E Clark
- Faculty of Health Sciences, Simon Fraser University, British Columbia, Burnaby, Canada V5A 1S6
| | - Kate Auyeung
- Faculty of Health Sciences, Simon Fraser University, British Columbia, Burnaby, Canada V5A 1S6
| | - Ralph Pantophlet
- Faculty of Health Sciences, Simon Fraser University, British Columbia, Burnaby, Canada V5A 1S6; Department of Molecular Biology and Biochemistry, Simon Fraser University, British Columbia, Burnaby, Canada V5A 1S6.
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Abstract
Viral diseases are leading cause of deaths worldwide as WHO report suggests that hepatitis A virus (HAV) infects more than 80 % of the population of many developing countries. Viral hepatitis B (HBV) affects an estimated 360 million people, whereas hepatitis C affects 123 million people worldwide, and last but not least, at current, India has an HIV/AIDS population of approximately 2.4 million people and more than 30 million in whole world and now it has become a reason for 1.8 million death globally; thus, millions of people still struggle for their lives. The progress in medical science has made it possible in overcoming the various fatal diseases such as small pox, chicken pox, dengue, etc., but human immunodeficiency viruses, influenza, and hepatitis virus have renewed challenge surprisingly. The obstacles and challenges in therapy include existence of antibiotic resistance strains of common organisms due to overuse of antibiotics, lack of vaccines, adverse drug reaction, and last but not least the susceptibility concerns. Emergence of pharmacogenomics and pharmacogenetics has shown some promises to take challenges. The discovery of human genome project has opened new vistas to understand the behaviors of genetic makeup in development and progression of diseases and treatment in various viral diseases. Current and previous decade have been engaged in making repositories of polymorphisms (SNPs) of various genes including drug-metabolizing enzymes, receptors, inflammatory cells related with immunity, and antigen-presenting cells, along with the prediction of risks. The genetic makeup alone is most likely an adequate way to handle the therapeutic decision-making process for previous regimen failure. With the introduction of new antiviral therapeutic agents, a significant improvement in progression and overall survival has been achieved, but these drugs have shown several adverse responses in some individuals, so the success is not up to the expectations. Research and acquisition of new knowledge of pharmacogenomics may help in overcoming the prevailing burden of viral diseases. So it will definitely help in selecting the most effective therapeutic agents, effective doses, and drug response for the individuals. Thus, it will be able to transform the laboratory research into the clinical bench side and will also help in understanding the pathogenesis of viral diseases with drug action, so the patients will be managed more properly and finally become able to fulfill the promise of the future.
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Affiliation(s)
- Debmalya Barh
- Centre for Genomics & Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Purba Medinipur, West Bengal India
| | - Dipali Dhawan
- Institute of Life Sciences, B.V. Patel Pharmaceutical Education and Research Development Centre, Ahmedabad University, Ahmedabad, Gujarat India
| | - Nirmal Kumar Ganguly
- Policy Centre for Biomedical Research, Translational Health Science and Technology Institute (Department of Biotechnology Institute, Government of India), Office @ National Institute of Immunology, New Delhi, India
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Resistance to antibody neutralization in HIV-2 infection occurs in late stage disease and is associated with X4 tropism. AIDS 2012; 26:2275-84. [PMID: 23151495 DOI: 10.1097/qad.0b013e328359a89d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
OBJECTIVES To characterize the nature and dynamics of the neutralizing antibody (NAb) response and escape in chronically HIV-2 infected patients. METHODS Twenty-eight chronically infected adults were studied over a period of 1-4 years. The neutralizing activity of plasma immunoglobulin G (IgG) antibodies against autologous and heterologous primary isolates was analyzed using a standard assay in TZM-bl cells. Coreceptor usage was determined in ghost cells. The sequence and predicted three-dimensional structure of the C2V3C3 Env region were determined for all isolates. RESULTS Only 50% of the patients consistently produced IgG NAbs to autologous and contemporaneous virus isolates. In contrast, 96% of the patients produced IgG antibodies that neutralized at least two isolates of a panel of six heterologous R5 isolates. Breadth and potency of the neutralizing antibodies were positively associated with the number of CD4(+) T cells and with the titer and avidity of C2V3C3-specific binding IgG antibodies. X4 isolates were obtained only from late stage disease patients and were fully resistant to neutralization. The V3 loop of X4 viruses was longer, had a higher net charge, and differed markedly in secondary structure compared to R5 viruses. CONCLUSION Most HIV-2 patients infected with R5 isolates produce C2V3C3-specific neutralizing antibodies whose potency and breadth decreases as the disease progresses. Resistance to antibody neutralization occurs in late stage disease and is usually associated with X4 viral tropism and major changes in V3 sequence and conformation. Our studies support a model of HIV-2 pathogenesis in which the neutralizing antibodies play a central role and have clear implications for the vaccine field.
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Hu X, Hong K, Zhao C, Zheng Y, Ma L, Ruan Y, Gao H, Greene K, Sarzotti-Kelsoe M, Montefiori DC, Shao Y. Profiles of neutralizing antibody response in chronically human immunodeficiency virus type 1 clade B'-infected former plasma donors from China naive to antiretroviral therapy. J Gen Virol 2012; 93:2267-2278. [PMID: 22791603 DOI: 10.1099/vir.0.043802-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Broadly neutralizing antibodies (NAbs) such as those generated in chronic human immunodeficiency virus type 1 (HIV-1) infection are considered a key component for an effective HIV-1 vaccine. Here, we measured NAb responses using a panel of 25 Env-pseudotyped viruses, including clade B, C, A, CRF07_BC and CRF01_AE strains, against plasma samples from 103 subjects in a former plasma donor cohort in central China, who were infected with HIV-1 clade B' for at least 10 years and naïve to antiretroviral therapy at the time of sampling. We found that 64 % of samples (n = 66) neutralized at least half of the viruses tested and 2 % (n = 2) neutralized all of the viruses, while 5 % (n = 5) neutralized none of the viruses tested. Strikingly, 29 % of plasma samples (n = 30) neutralized >80 % of the viral strains tested, indicating the presence of broadly reactive NAbs in these patients. When the magnitude (geometric mean ID(50) titres, GMTs) or breadth of neutralization was assessed for correlation with CD4 count or plasma viral load, the only significant positive correlations were observed between viral load and neutralization magnitude (r = 0.2189, P = 0.0263) and between viral load and neutralization breadth (r = 0.1970, P = 0.0461). A moderate difference between progressors and long-term non-progressors was observed in both the breadth (P = 0.0316) and the potency (P = 0.0300). A significant difference was found in the GMTs between intra-clade and inter-clade strains (P<0.001). Heat-map analysis based on k-means clustering of plasma determined a statistically stable cluster of plasma with cross-reactive and potent neutralizing reactivity. These samples could provide physical biomaterials for further virological and serological studies from which useful insights into rational HIV-1 vaccine development and therapeutic design might be derived.
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Affiliation(s)
- Xintao Hu
- State Key Laboratory for Infectious Disease Control and Prevention, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Kunxue Hong
- State Key Laboratory for Infectious Disease Control and Prevention, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Chunhong Zhao
- State Key Laboratory for Infectious Disease Control and Prevention, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Yang Zheng
- State Key Laboratory for Infectious Disease Control and Prevention, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Liying Ma
- State Key Laboratory for Infectious Disease Control and Prevention, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Yuhua Ruan
- State Key Laboratory for Infectious Disease Control and Prevention, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Hongmei Gao
- Department of Experimental Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Kelli Greene
- Department of Experimental Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Marcella Sarzotti-Kelsoe
- Department of Immunology, Duke University Medical Center, Durham, NC 27710, USA.,Department of Experimental Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - David C Montefiori
- Department of Experimental Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Yiming Shao
- State Key Laboratory for Infectious Disease Control and Prevention, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
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Chhatbar C, Mishra R, Kumar A, Singh SK. HIV vaccine: hopes and hurdles. Drug Discov Today 2011; 16:948-56. [DOI: 10.1016/j.drudis.2011.08.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Revised: 07/16/2011] [Accepted: 08/22/2011] [Indexed: 10/17/2022]
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Revilla A, Delgado E, Christian EC, Dalrymple J, Vega Y, Carrera C, González-Galeano M, Ocampo A, de Castro RO, Lezaún MJ, Rodríguez R, Mariño A, Ordóñez P, Cilla G, Cisterna R, Santamaría JM, Prieto S, Rakhmanova A, Vinogradova A, Ríos M, Pérez-Álvarez L, Nájera R, Montefiori DC, Seaman MS, Thomson MM. Construction and phenotypic characterization of HIV type 1 functional envelope clones of subtypes G and F. AIDS Res Hum Retroviruses 2011; 27:889-901. [PMID: 21226626 DOI: 10.1089/aid.2010.0177] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Subtype G has been estimated to represent the fourth most prevalent clade in the HIV-1 pandemic and subtype F is widely circulating in parts of South America (frequently within BF recombinant forms) and in Romania. However, functional envelope clones of these subtypes are lacking, which are needed for studies on antibody-mediated neutralization, coreceptor usage, and efficiency of viral entry inhibitor drugs. Here we report the construction, neutralization properties, and coreceptor usage of HIV-1 functional envelope clones of subtypes G (n = 15) and F (n = 7). These clones were obtained through RT-PCR amplification of HIV-1 gp160 from plasma RNA, and were used for pseudovirus production. All 15 subtype G-enveloped pseudoviruses were resistant to neutralization by gp120-targeted broadly neutralizing monoclonal antibodies (MAbs) b12 and 2G12, while a majority were neutralized by gp41-targeted MAbs 2F5 and 4E10. With regard to the subtype F envelopes, all seven pseudoviruses were resistant to 2F5 and b12, six were resistant to G12, and six were neutralized by 4E10. Coreceptor usage testing revealed that 21 of 22 envelopes were CCR5-tropic, including all 15 subtype G envelopes, seven of which were from patients with CD4(+) T cell counts <200/ml. These results confirm the broadly neutralizing activity of 4E10 on envelope clones across all tested group M clades, including subtypes G and F, reveal the resistance of most subtype F-enveloped pseudoviruses to broadly neutralizing MAbs b12, 2G12, and 2F5, and suggest that, similarly to subtype C, CXCR4 tropism is uncommon in subtype G, even at advanced stages of infection.
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Affiliation(s)
- Ana Revilla
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Elena Delgado
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Elizabeth C. Christian
- Division of Viral Pathogenesis, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Justin Dalrymple
- Division of Viral Pathogenesis, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Yolanda Vega
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Cristina Carrera
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - María González-Galeano
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Antonio Ocampo
- Complejo Hospitalario Xeral-Cíes, Vigo, Pontevedra, Spain
| | | | | | | | - Ana Mariño
- Hospital Arquitecto Marcide, Ferrol, A Coruña, Spain
| | | | | | | | | | | | - Aza Rakhmanova
- Botkin's Infectious Diseases Hospital, St. Petersburg, Russia
| | | | - Maritza Ríos
- National Reference Center of HIV/AIDS, Public Health Institute of Chile, Santiago, Chile
| | - Lucía Pérez-Álvarez
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Rafael Nájera
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - David C. Montefiori
- Department of Surgery, Laboratory for AIDS Vaccine Research and Development, Duke University Medical Center, Durham, North Carolina
| | - Michael S. Seaman
- Division of Viral Pathogenesis, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Michael M. Thomson
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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Gray ES, Madiga MC, Hermanus T, Moore PL, Wibmer CK, Tumba NL, Werner L, Mlisana K, Sibeko S, Williamson C, Abdool Karim SS, Morris L. The neutralization breadth of HIV-1 develops incrementally over four years and is associated with CD4+ T cell decline and high viral load during acute infection. J Virol 2011; 85:4828-40. [PMID: 21389135 PMCID: PMC3126191 DOI: 10.1128/jvi.00198-11] [Citation(s) in RCA: 370] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 02/24/2011] [Indexed: 11/20/2022] Open
Abstract
An understanding of how broadly neutralizing activity develops in HIV-1-infected individuals is needed to guide vaccine design and immunization strategies. Here we used a large panel of 44 HIV-1 envelope variants (subtypes A, B, and C) to evaluate the presence of broadly neutralizing antibodies in serum samples obtained 3 years after seroconversion from 40 women enrolled in the CAPRISA 002 acute infection cohort. Seven of 40 participants had serum antibodies that neutralized more than 40% of viruses tested and were considered to have neutralization breadth. Among the samples with breadth, CAP257 serum neutralized 82% (36/44 variants) of the panel, while CAP256 serum neutralized 77% (33/43 variants) of the panel. Analysis of longitudinal samples showed that breadth developed gradually starting from year 2, with the number of viruses neutralized as well as the antibody titer increasing over time. Interestingly, neutralization breadth peaked at 4 years postinfection, with no increase thereafter. The extent of cross-neutralizing activity correlated with CD4(+) T cell decline, viral load, and CD4(+) T cell count at 6 months postinfection but not at later time points, suggesting that early events set the stage for the development of breadth. However, in a multivariate analysis, CD4 decline was the major driver of this association, as viral load was not an independent predictor of breadth. Mapping of the epitopes targeted by cross-neutralizing antibodies revealed that in one individual these antibodies recognized the membrane-proximal external region (MPER), while in two other individuals, cross-neutralizing activity was adsorbed by monomeric gp120 and targeted epitopes that involved the N-linked glycan at position 332 in the C3 region. Serum antibodies from the other four participants targeted quaternary epitopes, at least 2 of which were PG9/16-like and depended on the N160 and/or L165 residue in the V2 region. These data indicate that fewer than 20% of HIV-1 subtype C-infected individuals develop antibodies with cross-neutralizing activity after 3 years of infection and that these antibodies target different regions of the HIV-1 envelope, including as yet uncharacterized epitopes.
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Affiliation(s)
- Elin S. Gray
- AIDS Virus Research Unit, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Maphuti C. Madiga
- AIDS Virus Research Unit, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Tandile Hermanus
- AIDS Virus Research Unit, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Penny L. Moore
- AIDS Virus Research Unit, National Institute for Communicable Diseases, Johannesburg, South Africa
- University of Witwatersrand, Johannesburg, South Africa
| | - Constantinos Kurt Wibmer
- AIDS Virus Research Unit, National Institute for Communicable Diseases, Johannesburg, South Africa
- University of Witwatersrand, Johannesburg, South Africa
| | - Nancy L. Tumba
- AIDS Virus Research Unit, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Lise Werner
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Koleka Mlisana
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Sengeziwe Sibeko
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Carolyn Williamson
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Salim S. Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Lynn Morris
- AIDS Virus Research Unit, National Institute for Communicable Diseases, Johannesburg, South Africa
- University of Witwatersrand, Johannesburg, South Africa
| | - and the CAPRISA002 Study Team
- AIDS Virus Research Unit, National Institute for Communicable Diseases, Johannesburg, South Africa
- University of Witwatersrand, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
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11
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Thomson MM, Fernández-García A. Phylogenetic structure in African HIV-1 subtype C revealed by selective sequential pruning. Virology 2011; 415:30-8. [PMID: 21507449 DOI: 10.1016/j.virol.2011.03.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Revised: 03/11/2011] [Accepted: 03/17/2011] [Indexed: 10/18/2022]
Abstract
Subtype C is the most prevalent clade in the HIV-1 pandemic. Previous studies suggested that African HIV-1 subtype C lacks a well-defined phylogenetic structure. Here we show that, by sequential pruning of ambiguously positioned taxa, a well-defined intrasubtype C phylogenetic structure becomes apparent, with 52% African HIV-1 subtype C isolates analyzed in envelope sequences branching within 11 clusters, also supported in a tree of full-length genomes, and all with geographical associations. Among 46 viruses recently transmitted in South Africa, 70% branched within 7 clusters (41% in the largest one) and 15% additional isolates were intercluster recombinants. Choice of the outgroup sequence and inclusion of intrasubtype recombinant viruses in the analyses could greatly affect support of clusters. The identification of clusters comprising a large proportion of African HIV-1 subtype C viruses may have implications for the design of vaccines intended for use in areas where subtype C is prevalent.
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Affiliation(s)
- Michael M Thomson
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo Km. 2, Majadahonda, Madrid, Spain.
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12
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Potent and broad neutralization of HIV-1 subtype C by plasma antibodies targeting a quaternary epitope including residues in the V2 loop. J Virol 2011; 85:3128-41. [PMID: 21270156 DOI: 10.1128/jvi.02658-10] [Citation(s) in RCA: 135] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The targets of broadly cross-neutralizing (BCN) antibodies are of great interest in the HIV vaccine field. We have identified a subtype C HIV-1-superinfected individual, CAP256, with high-level BCN activity, and characterized the antibody specificity mediating breadth. CAP256 developed potent BCN activity peaking at 3 years postinfection, neutralizing 32 (76%) of 42 heterologous viruses, with titers of antibodies against some viruses exceeding 1:10,000. CAP256 showed a subtype bias, preferentially neutralizing subtype C and A viruses over subtype B viruses. CAP256 BCN serum targeted a quaternary epitope which included the V1V2 region. Further mapping identified residues F159, N160, L165, R166, D167, K169, and K171 (forming the FN/LRD-K-K motif) in the V2 region as crucial to the CAP256 epitope. However, the fine specificity of the BCN response varied over time and, while consistently dependent on R166 and K169, became gradually less dependent on D167 and K171, possibly contributing to the incremental increase in breadth over 4 years. The presence of an intact FN/LRD-K-K motif in heterologous viruses was associated with sensitivity, although the length of the adjacent V1 loop modulated the degree of sensitivity, with a shorter V1 region significantly associated with higher titers. Repair of the FN/LRD-K-K motif in resistant heterologous viruses conferred sensitivity, with titers sometimes exceeding 1:10,000. Comparison of the CAP256 epitope with that of the PG9/PG16 monoclonal antibodies suggested that these epitopes overlapped, adding to the mounting evidence that this may represent a common neutralization target that should be further investigated as a potential vaccine candidate.
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13
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Delgado E, Ríos M, Fernández J, Pérez-Álvarez L, Nájera R, Thomson MM. Identification of a new HIV type 1 BF intersubtype circulating recombinant form (CRF44_BF) in Chile. AIDS Res Hum Retroviruses 2010; 26:821-6. [PMID: 20618101 DOI: 10.1089/aid.2010.0006] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
HIV-1 BF intersubtype recombinants are frequent in Argentina, Uruguay, and Brazil, where among a high diversity of BF unique recombinant forms (URFs), eight circulating recombinant forms (CRFs) have been characterized. Here, we describe a new one, designated CRF44_BF, identified in HIV-1 samples from Chile. In a previous report, where partial pol sequences of 136 HIV-1 infections of Chilean subjects were analyzed, a phylogenetic cluster of HIV-1 recombinant BF viruses from 10 individuals, with coincident intersubtype recombination points, was detected. One virus of this cluster had been characterized along its near full-length genome. A second one, from an epidemiologically unlinked HIV-1-infected subject, is described here. Both genomes share identical mosaic structures, consisting of a predominantly subtype F1 genome with three fragments of subtype B. Coincident breakpoints and phylogenetic clustering of the newly identified CRF44_BF with CRF12_BF, CRF17_BF, and CRF38_BF support a common origin of different CRF_BFs identified in Argentina, Uruguay, and Chile.
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Affiliation(s)
- Elena Delgado
- Unit of Biology and Variability of HIV, Spanish National Center of Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Maritza Ríos
- National Reference Center of HIV/AIDS, Public Health Institute of Chile, Santiago, Chile
| | - Jorge Fernández
- Laboratory of Molecular Genetics, Public Health Institute of Chile, Santiago, Chile
| | - Lucía Pérez-Álvarez
- Unit of Biology and Variability of HIV, Spanish National Center of Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Rafael Nájera
- Unit of Biology and Variability of HIV, Spanish National Center of Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Michael M. Thomson
- Unit of Biology and Variability of HIV, Spanish National Center of Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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