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Rahim MN, Wee EG, He S, Audet J, Tierney K, Moyo N, Hannoun Z, Crook A, Baines A, Korber B, Qiu X, Hanke T. Complete protection of the BALB/c and C57BL/6J mice against Ebola and Marburg virus lethal challenges by pan-filovirus T-cell epigraph vaccine. PLoS Pathog 2019; 15:e1007564. [PMID: 30817809 PMCID: PMC6394903 DOI: 10.1371/journal.ppat.1007564] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/04/2019] [Indexed: 01/31/2023] Open
Abstract
There are a number of vaccine candidates under development against a small number of the most common outbreak filoviruses all employing the virus glycoprotein (GP) as the vaccine immunogen. However, antibodies induced by such GP vaccines are typically autologous and limited to the other members of the same species. In contrast, T-cell vaccines offer a possibility to design a single pan-filovirus vaccine protecting against all known and even likely existing, but as yet unencountered members of the family. Here, we used a cross-filovirus immunogen based on conserved regions of the filovirus nucleoprotein, matrix and polymerase to construct simian adenovirus- and poxvirus MVA-vectored vaccines, and in a proof-of-concept study demonstrated a protection of the BALB/c and C57BL/6J mice against high, lethal challenges with Ebola and Marburg viruses, two distant members of the family, by vaccine-elicited T cells in the absence of GP antibodies.
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Affiliation(s)
- Md Niaz Rahim
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Edmund G. Wee
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Shihua He
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Jonathan Audet
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Kevin Tierney
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Nathifa Moyo
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Zara Hannoun
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Alison Crook
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Andrea Baines
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Bette Korber
- Los Alamo National Laboratory, Theoretical Biology and Biophysics, Los Alamos, New Mexico, United States of America
- The New Mexico Consortium, Los Alamos, New Mexico, United States of America
| | - Xiangguo Qiu
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Tomáš Hanke
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
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Saphire EO, Schendel SL, Fusco ML, Gangavarapu K, Gunn BM, Wec AZ, Halfmann PJ, Brannan JM, Herbert AS, Qiu X, Wagh K, He S, Giorgi EE, Theiler J, Pommert KBJ, Krause TB, Turner HL, Murin CD, Pallesen J, Davidson E, Ahmed R, Aman MJ, Bukreyev A, Burton DR, Crowe JE, Davis CW, Georgiou G, Krammer F, Kyratsous CA, Lai JR, Nykiforuk C, Pauly MH, Rijal P, Takada A, Townsend AR, Volchkov V, Walker LM, Wang CI, Zeitlin L, Doranz BJ, Ward AB, Korber B, Kobinger GP, Andersen KG, Kawaoka Y, Alter G, Chandran K, Dye JM. Systematic Analysis of Monoclonal Antibodies against Ebola Virus GP Defines Features that Contribute to Protection. Cell 2018; 174:938-952.e13. [PMID: 30096313 PMCID: PMC6102396 DOI: 10.1016/j.cell.2018.07.033] [Citation(s) in RCA: 146] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 05/22/2018] [Accepted: 07/24/2018] [Indexed: 12/24/2022]
Abstract
Antibodies are promising post-exposure therapies against emerging viruses, but which antibody features and in vitro assays best forecast protection are unclear. Our international consortium systematically evaluated antibodies against Ebola virus (EBOV) using multidisciplinary assays. For each antibody, we evaluated epitopes recognized on the viral surface glycoprotein (GP) and secreted glycoprotein (sGP), readouts of multiple neutralization assays, fraction of virions left un-neutralized, glycan structures, phagocytic and natural killer cell functions elicited, and in vivo protection in a mouse challenge model. Neutralization and induction of multiple immune effector functions (IEFs) correlated most strongly with protection. Neutralization predominantly occurred via epitopes maintained on endosomally cleaved GP, whereas maximal IEF mapped to epitopes farthest from the viral membrane. Unexpectedly, sGP cross-reactivity did not significantly influence in vivo protection. This comprehensive dataset provides a rubric to evaluate novel antibodies and vaccine responses and a roadmap for therapeutic development for EBOV and related viruses.
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Affiliation(s)
- Erica Ollmann Saphire
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Sharon L Schendel
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Marnie L Fusco
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Karthik Gangavarapu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | | | - Anna Z Wec
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Peter J Halfmann
- Division of Pathobiological Sciences, University of Wisconsin, Madison, WI 53706, USA
| | - Jennifer M Brannan
- Division of Virology, United States Army Research Institute for Infectious Diseases, Ft. Detrick, MD 21702, USA
| | - Andrew S Herbert
- Division of Virology, United States Army Research Institute for Infectious Diseases, Ft. Detrick, MD 21702, USA
| | - Xiangguo Qiu
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg R3E 3R2, Canada
| | - Kshitij Wagh
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Shihua He
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg R3E 3R2, Canada
| | - Elena E Giorgi
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - James Theiler
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Kathleen B J Pommert
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tyler B Krause
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Hannah L Turner
- Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Charles D Murin
- Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jesper Pallesen
- Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | | | - Rafi Ahmed
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - M Javad Aman
- Integrated BioTherapeutics, Rockville, MD 20850, USA
| | - Alexander Bukreyev
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James E Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Carl W Davis
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - George Georgiou
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Jonathan R Lai
- Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Cory Nykiforuk
- Emergent BioSolutions, Winnipeg, Manitoba, R3T 5Y3, Canada
| | | | - Pramila Rijal
- Human Immunology Unit, University of Oxford, Oxford OX3 9DS, UK
| | - Ayato Takada
- Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan
| | | | | | | | - Cheng-I Wang
- Singapore Immunology Network, Agency for Science, Technology and Research (A(∗)STAR), Biopolis 138648, Singapore
| | | | | | - Andrew B Ward
- Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bette Korber
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Gary P Kobinger
- Département de Microbiologie-Infectiologie et d'Immunologie, Médecine, Université Laval Quebec, G1V 046 Canada.
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Yoshihiro Kawaoka
- Division of Pathobiological Sciences, University of Wisconsin, Madison, WI 53706, USA.
| | | | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - John M Dye
- Division of Virology, United States Army Research Institute for Infectious Diseases, Ft. Detrick, MD 21702, USA.
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53
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Barouch DH, Tomaka FL, Wegmann F, Stieh DJ, Alter G, Robb ML, Michael NL, Peter L, Nkolola JP, Borducchi EN, Chandrashekar A, Jetton D, Stephenson KE, Li W, Korber B, Tomaras GD, Montefiori DC, Gray G, Frahm N, McElrath MJ, Baden L, Johnson J, Hutter J, Swann E, Karita E, Kibuuka H, Mpendo J, Garrett N, Mngadi K, Chinyenze K, Priddy F, Lazarus E, Laher F, Nitayapan S, Pitisuttithum P, Bart S, Campbell T, Feldman R, Lucksinger G, Borremans C, Callewaert K, Roten R, Sadoff J, Scheppler L, Weijtens M, Feddes-de Boer K, van Manen D, Vreugdenhil J, Zahn R, Lavreys L, Nijs S, Tolboom J, Hendriks J, Euler Z, Pau MG, Schuitemaker H. Evaluation of a mosaic HIV-1 vaccine in a multicentre, randomised, double-blind, placebo-controlled, phase 1/2a clinical trial (APPROACH) and in rhesus monkeys (NHP 13-19). Lancet 2018; 392:232-243. [PMID: 30047376 PMCID: PMC6192527 DOI: 10.1016/s0140-6736(18)31364-3] [Citation(s) in RCA: 225] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/07/2018] [Accepted: 06/08/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND More than 1·8 million new cases of HIV-1 infection were diagnosed worldwide in 2016. No licensed prophylactic HIV-1 vaccine exists. A major limitation to date has been the lack of direct comparability between clinical trials and preclinical studies. We aimed to evaluate mosaic adenovirus serotype 26 (Ad26)-based HIV-1 vaccine candidates in parallel studies in humans and rhesus monkeys to define the optimal vaccine regimen to advance into clinical efficacy trials. METHODS We conducted a multicentre, randomised, double-blind, placebo-controlled phase 1/2a trial (APPROACH). Participants were recruited from 12 clinics in east Africa, South Africa, Thailand, and the USA. We included healthy, HIV-1-uninfected participants (aged 18-50 years) who were considered at low risk for HIV-1 infection. We randomly assigned participants to one of eight study groups, stratified by region. Participants and investigators were blinded to the treatment allocation throughout the study. We primed participants at weeks 0 and 12 with Ad26.Mos.HIV (5 × 1010 viral particles per 0·5 mL) expressing mosaic HIV-1 envelope (Env)/Gag/Pol antigens and gave boosters at weeks 24 and 48 with Ad26.Mos.HIV or modified vaccinia Ankara (MVA; 108 plaque-forming units per 0·5 mL) vectors with or without high-dose (250 μg) or low-dose (50 μg) aluminium adjuvanted clade C Env gp140 protein. Those in the control group received 0·9% saline. All study interventions were administered intramuscularly. Primary endpoints were safety and tolerability of the vaccine regimens and Env-specific binding antibody responses at week 28. Safety and immunogenicity were also assessed at week 52. All participants who received at least one vaccine dose or placebo were included in the safety analysis; immunogenicity was analysed using the per-protocol population. We also did a parallel study in rhesus monkeys (NHP 13-19) to assess the immunogenicity and protective efficacy of these vaccine regimens against a series of six repetitive, heterologous, intrarectal challenges with a rhesus peripheral blood mononuclear cell-derived challenge stock of simian-human immunodeficiency virus (SHIV-SF162P3). The APPROACH trial is registered with ClinicalTrials.gov, number NCT02315703. FINDINGS Between Feb 24, 2015, and Oct 16, 2015, we randomly assigned 393 participants to receive at least one dose of study vaccine or placebo in the APPROACH trial. All vaccine regimens demonstrated favourable safety and tolerability. The most commonly reported solicited local adverse event was mild-to-moderate pain at the injection site (varying from 69% to 88% between the different active groups vs 49% in the placebo group). Five (1%) of 393 participants reported at least one grade 3 adverse event considered related to the vaccines: abdominal pain and diarrhoea (in the same participant), increased aspartate aminotransferase, postural dizziness, back pain, and malaise. The mosaic Ad26/Ad26 plus high-dose gp140 boost vaccine was the most immunogenic in humans; it elicited Env-specific binding antibody responses (100%) and antibody-dependent cellular phagocytosis responses (80%) at week 52, and T-cell responses at week 50 (83%). We also randomly assigned 72 rhesus monkeys to receive one of five different vaccine regimens or placebo in the NHP 13-19 study. Ad26/Ad26 plus gp140 boost induced similar magnitude, durability, and phenotype of immune responses in rhesus monkeys as compared with humans and afforded 67% protection against acquisition of SHIV-SF162P3 infection (two-sided Fisher's exact test p=0·007). Env-specific ELISA and enzyme-linked immunospot assay responses were the principal immune correlates of protection against SHIV challenge in monkeys. INTERPRETATION The mosaic Ad26/Ad26 plus gp140 HIV-1 vaccine induced comparable and robust immune responses in humans and rhesus monkeys, and it provided significant protection against repetitive heterologous SHIV challenges in rhesus monkeys. This vaccine concept is currently being evaluated in a phase 2b clinical efficacy study in sub-Saharan Africa (NCT03060629). FUNDING Janssen Vaccines & Prevention BV, National Institutes of Health, Ragon Institute of MGH, MIT and Harvard, Henry M Jackson Foundation for the Advancement of Military Medicine, US Department of Defense, and International AIDS Vaccine Initiative.
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Affiliation(s)
- Dan H Barouch
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
| | | | - Frank Wegmann
- Janssen Vaccines & Prevention BV, Leiden, Netherlands
| | | | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Merlin L Robb
- Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Nelson L Michael
- Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Lauren Peter
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Joseph P Nkolola
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Erica N Borducchi
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | | | - David Jetton
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Kathryn E Stephenson
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Wenjun Li
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Georgia D Tomaras
- Department of Surgery and Duke Human Vaccine Institute, Duke University, Durham, NC, USA
| | - David C Montefiori
- Department of Surgery and Duke Human Vaccine Institute, Duke University, Durham, NC, USA
| | - Glenda Gray
- Perinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole Frahm
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Lindsey Baden
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jennifer Johnson
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Julia Hutter
- Vaccine Clinical Research Branch, Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Edith Swann
- Vaccine Clinical Research Branch, Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Etienne Karita
- Project San Francisco, Rwanda-Zambia HIV Research Group, Kigali, Rwanda
| | - Hannah Kibuuka
- Makerere University Walter Reed Project, Kampala, Uganda
| | - Juliet Mpendo
- Uganda Virus Research Institute, International AIDS Vaccine Initiative HIV Vaccine Program, Entebbe, Uganda
| | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Kathy Mngadi
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | | | - Frances Priddy
- International AIDS Vaccine Initiative, New York City, NY, USA
| | - Erica Lazarus
- Department of Surgery and Duke Human Vaccine Institute, Duke University, Durham, NC, USA
| | - Fatima Laher
- Department of Surgery and Duke Human Vaccine Institute, Duke University, Durham, NC, USA
| | - Sorachai Nitayapan
- Royal Thai Army, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Punnee Pitisuttithum
- The Vaccine Trial Center, Faculty of Tropical Medicine, Mahidol University, Bangkok
| | | | | | | | | | | | | | | | - Jerald Sadoff
- Janssen Vaccines & Prevention BV, Leiden, Netherlands
| | - Lorenz Scheppler
- Janssen Vaccines & Prevention BV, Leiden, Netherlands; Janssen Infectious Diseases BV, Beerse, Belgium
| | - Mo Weijtens
- Janssen Vaccines & Prevention BV, Leiden, Netherlands
| | | | | | | | - Roland Zahn
- Janssen Vaccines & Prevention BV, Leiden, Netherlands
| | | | - Steven Nijs
- Janssen Infectious Diseases BV, Beerse, Belgium
| | | | | | - Zelda Euler
- Janssen Vaccines & Prevention BV, Leiden, Netherlands
| | - Maria G Pau
- Janssen Vaccines & Prevention BV, Leiden, Netherlands
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54
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Song H, Giorgi EE, Ganusov VV, Cai F, Athreya G, Yoon H, Carja O, Hora B, Hraber P, Romero-Severson E, Jiang C, Li X, Wang S, Li H, Salazar-Gonzalez JF, Salazar MG, Goonetilleke N, Keele BF, Montefiori DC, Cohen MS, Shaw GM, Hahn BH, McMichael AJ, Haynes BF, Korber B, Bhattacharya T, Gao F. Tracking HIV-1 recombination to resolve its contribution to HIV-1 evolution in natural infection. Nat Commun 2018; 9:1928. [PMID: 29765018 PMCID: PMC5954121 DOI: 10.1038/s41467-018-04217-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 04/10/2018] [Indexed: 11/29/2022] Open
Abstract
Recombination in HIV-1 is well documented, but its importance in the low-diversity setting of within-host diversification is less understood. Here we develop a novel computational tool (RAPR (Recombination Analysis PRogram)) to enable a detailed view of in vivo viral recombination during early infection, and we apply it to near-full-length HIV-1 genome sequences from longitudinal samples. Recombinant genomes rapidly replace transmitted/founder (T/F) lineages, with a median half-time of 27 days, increasing the genetic complexity of the viral population. We identify recombination hot and cold spots that differ from those observed in inter-subtype recombinants. Furthermore, RAPR analysis of longitudinal samples from an individual with well-characterized neutralizing antibody responses shows that recombination helps carry forward resistance-conferring mutations in the diversifying quasispecies. These findings provide insight into molecular mechanisms by which viral recombination contributes to HIV-1 persistence and immunopathogenesis and have implications for studies of HIV transmission and evolution in vivo. Recombination contributes to HIV evolution in patients, but its identification can be difficult. Here, the authors develop a computational tool called RAPR to track recombination in patients, identify recombination hot spots, and show contribution of recombination to antibody escape.
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Affiliation(s)
- Hongshuo Song
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA.,United States Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Elena E Giorgi
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87544, USA
| | - Vitaly V Ganusov
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Fangping Cai
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
| | - Gayathri Athreya
- Office for Research & Discovery, University of Arizona, Tucson, AZ, 85721, USA
| | - Hyejin Yoon
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87544, USA
| | - Oana Carja
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Bhavna Hora
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
| | - Peter Hraber
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87544, USA
| | | | - Chunlai Jiang
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA.,National Engineering Laboratory For AIDS Vaccine, College of Life Science, Jilin University, Changchun, Jilin, 130012, China
| | - Xiaojun Li
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
| | - Shuyi Wang
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Hui Li
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jesus F Salazar-Gonzalez
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.,MRC/UVRI and LSHTM Uganda Research Unit, Plot 51-57, Nakiwogo Road, Entebbe, Uganda
| | - Maria G Salazar
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Nilu Goonetilleke
- Departments of Microbiology and Immunology & Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - David C Montefiori
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
| | - Myron S Cohen
- Departments of Microbiology and Immunology & Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - George M Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Andrew J McMichael
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Barton F Haynes
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
| | - Bette Korber
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87544, USA
| | - Tanmoy Bhattacharya
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87544, USA.,Santa Fe Institute, Santa Fe, NM, 87501, USA
| | - Feng Gao
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA. .,National Engineering Laboratory For AIDS Vaccine, College of Life Science, Jilin University, Changchun, Jilin, 130012, China.
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55
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Julg B, Tartaglia LJ, Keele BF, Wagh K, Pegu A, Sok D, Abbink P, Schmidt SD, Wang K, Chen X, Joyce MG, Georgiev IS, Choe M, Kwong PD, Doria-Rose NA, Le K, Louder MK, Bailer RT, Moore PL, Korber B, Seaman MS, Abdool Karim SS, Morris L, Koup RA, Mascola JR, Burton DR, Barouch DH. Broadly neutralizing antibodies targeting the HIV-1 envelope V2 apex confer protection against a clade C SHIV challenge. Sci Transl Med 2018; 9:9/406/eaal1321. [PMID: 28878010 DOI: 10.1126/scitranslmed.aal1321] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 03/15/2017] [Accepted: 08/14/2017] [Indexed: 12/18/2022]
Abstract
Neutralizing antibodies to the V2 apex antigenic region of the HIV-1 envelope (Env) trimer are among the most prevalent cross-reactive antibodies elicited by natural infection. Two recently described V2-specific antibodies, PGDM1400 and CAP256-VRC26.25, have demonstrated exquisite potency and neutralization breadth against HIV-1. However, little data exist on the protective efficacy of V2-specific neutralizing antibodies. We created a novel SHIV-325c viral stock that included a clade C HIV-1 envelope and was susceptible to neutralization by both of these antibodies. Rhesus macaques received a single infusion of either antibody at three different concentrations (2, 0.4, and 0.08 mg/kg) before challenge with SHIV-325c. PGDM1400 was fully protective at the 0.4 mg/kg dose, whereas CAP256-VRC26.25-LS was fully protective even at the 0.08 mg/kg dose, which correlated with its greater in vitro neutralization potency against the challenge virus. Serum antibody concentrations required for protection were <0.75 μg/ml for CAP256-VRC26.25-LS. These data demonstrate unprecedented potency and protective efficacy of V2-specific neutralizing antibodies in nonhuman primates and validate V2 as a potential target for the prevention of HIV-1 infection in passive immunization strategies in humans.
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Affiliation(s)
- Boris Julg
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA.,Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Lawrence J Tartaglia
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Kshitij Wagh
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Amarendra Pegu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Devin Sok
- The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Peter Abbink
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Stephen D Schmidt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Keyun Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Xuejun Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - M G Joyce
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Ivelin S Georgiev
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Misook Choe
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Khoa Le
- The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mark K Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Robert T Bailer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Penny L Moore
- National Institute for Communicable Diseases of the National Health Laboratory Service and the University of the Witwatersrand, 2131 Johannesburg, South Africa.,Centre for the AIDS Programme of Research in South Africa, 4013 Durban, South Africa
| | - Bette Korber
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, 4013 Durban, South Africa.,Columbia University, New York, NY 10032, USA
| | - Lynn Morris
- National Institute for Communicable Diseases of the National Health Laboratory Service and the University of the Witwatersrand, 2131 Johannesburg, South Africa.,Centre for the AIDS Programme of Research in South Africa, 4013 Durban, South Africa
| | - Richard A Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Dennis R Burton
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA.,The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dan H Barouch
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA. .,Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
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56
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Wagh K, Seaman MS, Zingg M, Fitzsimons T, Barouch DH, Burton DR, Connors M, Ho DD, Mascola JR, Nussenzweig MC, Ravetch J, Gautam R, Martin MA, Montefiori DC, Korber B. Potential of conventional & bispecific broadly neutralizing antibodies for prevention of HIV-1 subtype A, C & D infections. PLoS Pathog 2018; 14:e1006860. [PMID: 29505593 PMCID: PMC5854441 DOI: 10.1371/journal.ppat.1006860] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 03/15/2018] [Accepted: 01/08/2018] [Indexed: 12/18/2022] Open
Abstract
There is great interest in passive transfer of broadly neutralizing antibodies (bnAbs) and engineered bispecific antibodies (Abs) for prevention of HIV-1 infections due to their in vitro neutralization breadth and potency against global isolates and long in vivo half-lives. We compared the potential of eight bnAbs and two bispecific Abs currently under clinical development, and their 2 Ab combinations, to prevent infection by dominant HIV-1 subtypes in sub-Saharan Africa. Using in vitro neutralization data for Abs against 25 subtype A, 100 C, and 20 D pseudoviruses, we modeled neutralization by single Abs and 2 Ab combinations assuming realistic target concentrations of 10μg/ml total for bnAbs and combinations, and 5μg/ml for bispecifics. We used IC80 breadth-potency, completeness of neutralization, and simultaneous coverage by both Abs in the combination as metrics to characterize prevention potential. Additionally, we predicted in vivo protection by Abs and combinations by modeling protection as a function of in vitro neutralization based on data from a macaque simian-human immunodeficiency virus (SHIV) challenge study. Our model suggests that nearly complete neutralization of a given virus is needed for in vivo protection (~98% neutralization for 50% relative protection). Using the above metrics, we found that bnAb combinations should outperform single bnAbs, as expected; however, different combinations are optimal for different subtypes. Remarkably, a single bispecific 10E8-iMAb, which targets HIV Env and host-cell CD4, outperformed all combinations of two conventional bnAbs, with 95-97% predicted relative protection across subtypes. Combinations that included 10E8-iMAb substantially improved protection over use of 10E8-iMAb alone. Our results highlight the promise of 10E8-iMAb and its combinations to prevent HIV-1 infections in sub-Saharan Africa.
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Affiliation(s)
- Kshitij Wagh
- Theoretical Biology & Biophysics, Los Alamos National Laboratory, Los Alamos, United States of America
- New Mexico Consortium, Los Alamos, United States of America
- * E-mail: (BK); (KW)
| | - Michael S. Seaman
- Center for Virology & Vaccine Research, Beth Israel Deaconness Medical Center, Boston, United States of America
| | - Marshall Zingg
- Center for Virology & Vaccine Research, Beth Israel Deaconness Medical Center, Boston, United States of America
| | - Tomas Fitzsimons
- Center for Virology & Vaccine Research, Beth Israel Deaconness Medical Center, Boston, United States of America
| | - Dan H. Barouch
- Center for Virology & Vaccine Research, Beth Israel Deaconness Medical Center, Boston, United States of America
| | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, United States of America
| | - Mark Connors
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda,United States of America
| | - David D. Ho
- Aaron Diamond AIDS Research Center, The Rockefeller University, New York, United States of America
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Insitutes of Health, Bethesda, United States of America
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, United States of America
| | - Jeffrey Ravetch
- Laboratory of Molecular Genetics and Immunology, The Rockefeller University, New York, United States of America
| | - Rajeev Gautam
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States of America
| | - Malcolm A. Martin
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States of America
| | - David C. Montefiori
- Department of Surgery, Duke University Medical Center, Durham, United States of America
| | - Bette Korber
- Theoretical Biology & Biophysics, Los Alamos National Laboratory, Los Alamos, United States of America
- New Mexico Consortium, Los Alamos, United States of America
- * E-mail: (BK); (KW)
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57
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Abstract
Epigraph is a recently developed algorithm that enables the computationally efficient design of single or multi-antigen vaccines to maximize the potential epitope coverage for a diverse pathogen population. Potential epitopes are defined as short contiguous stretches of proteins, comparable in length to T-cell epitopes. This optimal coverage problem can be formulated in terms of a directed graph, with candidate antigens represented as paths that traverse this graph. Epigraph protein sequences can also be used as the basis for designing peptides for experimental evaluation of immune responses in natural infections to highly variable proteins. The epigraph tool suite also enables rapid characterization of populations of diverse sequences from an immunological perspective. Fundamental distance measures are based on immunologically relevant shared potential epitope frequencies, rather than simple Hamming or phylogenetic distances. Here, we provide a mathematical description of the epigraph algorithm, include a comparison of different heuristics that can be used when graphs are not acyclic, and we describe an additional tool we have added to the web-based epigraph tool suite that provides frequency summaries of all distinct potential epitopes in a population. We also show examples of the graphical output and summary tables that can be generated using the epigraph tool suite and explain their content and applications. Published 2017. This article is a U.S. Government work and is in the public domain in the USA. Statistics in Medicine published by John Wiley & Sons Ltd.
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Affiliation(s)
- James Theiler
- Los Alamos National LaboratoryLos Alamos87545NMU.S.A
- New Mexico ConsortiumLos Alamos87545NMU.S.A
| | - Bette Korber
- Los Alamos National LaboratoryLos Alamos87545NMU.S.A
- New Mexico ConsortiumLos Alamos87545NMU.S.A
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58
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Hraber P, Korber B, Wagh K, Montefiori D, Roederer M. A single, continuous metric to define tiered serum neutralization potency against HIV. eLife 2018; 7:31805. [PMID: 29350181 PMCID: PMC5788501 DOI: 10.7554/elife.31805] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 01/16/2018] [Indexed: 01/01/2023] Open
Abstract
HIV-1 Envelope (Env) variants are grouped into tiers by their neutralization-sensitivity phenotype. This helped to recognize that tier 1 neutralization responses can be elicited readily, but do not protect against new infections. Tier 3 viruses are the least sensitive to neutralization. Because most circulating viruses are tier 2, vaccines that elicit neutralization responses against them are needed. While tier classification is widely used for viruses, a way to rate serum or antibody neutralization responses in comparable terms is needed. Logistic regression of neutralization outcomes summarizes serum or antibody potency on a continuous, tier-like scale. It also tests significance of the neutralization score, to indicate cases where serum response does not depend on virus tiers. The method can standardize results from different virus panels, and could lead to high-throughput assays, which evaluate a single serum dilution, rather than a dilution series, for more efficient use of limited resources to screen samples from vaccinees.
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Affiliation(s)
- Peter Hraber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, United States
| | - Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, United States.,New Mexico Consortium, Los Alamos, United States
| | - Kshitij Wagh
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, United States
| | - David Montefiori
- Department of Surgery, Duke University Medical Center, Durham, United States
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
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59
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Saunders KO, Nicely NI, Wiehe K, Bonsignori M, Meyerhoff RR, Parks R, Walkowicz WE, Aussedat B, Wu NR, Cai F, Vohra Y, Park PK, Eaton A, Go EP, Sutherland LL, Scearce RM, Barouch DH, Zhang R, Von Holle T, Overman RG, Anasti K, Sanders RW, Moody MA, Kepler TB, Korber B, Desaire H, Santra S, Letvin NL, Nabel GJ, Montefiori DC, Tomaras GD, Liao HX, Alam SM, Danishefsky SJ, Haynes BF. Vaccine Elicitation of High Mannose-Dependent Neutralizing Antibodies against the V3-Glycan Broadly Neutralizing Epitope in Nonhuman Primates. Cell Rep 2017; 18:2175-2188. [PMID: 28249163 DOI: 10.1016/j.celrep.2017.02.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 12/19/2016] [Accepted: 01/30/2017] [Indexed: 12/26/2022] Open
Abstract
Induction of broadly neutralizing antibodies (bnAbs) that target HIV-1 envelope (Env) is a goal of HIV-1 vaccine development. A bnAb target is the Env third variable loop (V3)-glycan site. To determine whether immunization could induce antibodies to the V3-glycan bnAb binding site, we repetitively immunized macaques over a 4-year period with an Env expressing V3-high mannose glycans. Env immunizations elicited plasma antibodies that neutralized HIV-1 expressing only high-mannose glycans-a characteristic shared by early bnAb B cell lineage members. A rhesus recombinant monoclonal antibody from a vaccinated macaque bound to the V3-glycan site at the same amino acids as broadly neutralizing antibodies. A structure of the antibody bound to glycan revealed that the three variable heavy-chain complementarity-determining regions formed a cavity into which glycan could insert and neutralized multiple HIV-1 isolates with high-mannose glycans. Thus, HIV-1 Env vaccination induced mannose-dependent antibodies with characteristics of V3-glycan bnAb precursors.
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Affiliation(s)
- Kevin O Saunders
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Nathan I Nicely
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kevin Wiehe
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mattia Bonsignori
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - R Ryan Meyerhoff
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert Parks
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | | | - Baptiste Aussedat
- Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Nelson R Wu
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Fangping Cai
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yusuf Vohra
- Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Peter K Park
- Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Amanda Eaton
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Eden P Go
- University of Kansas, Lawrence, KS 66045, USA
| | - Laura L Sutherland
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Richard M Scearce
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Ruijun Zhang
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Tarra Von Holle
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - R Glenn Overman
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kara Anasti
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Rogier W Sanders
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - M Anthony Moody
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | | | | | | | | | | | | | - David C Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Georgia D Tomaras
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA; Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hua-Xin Liao
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - S Munir Alam
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | | | - Barton F Haynes
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.
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60
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Rademeyer C, Korber B, Seaman MS, Giorgi EE, Thebus R, Robles A, Sheward DJ, Wagh K, Garrity J, Carey BR, Gao H, Greene KM, Tang H, Bandawe GP, Marais JC, Diphoko TE, Hraber P, Tumba N, Moore PL, Gray GE, Kublin J, McElrath MJ, Vermeulen M, Middelkoop K, Bekker LG, Hoelscher M, Maboko L, Makhema J, Robb ML, Karim SA, Karim QA, Kim JH, Hahn BH, Gao F, Swanstrom R, Morris L, Montefiori DC, Williamson C. Correction: Features of Recently Transmitted HIV-1 Clade C Viruses that Impact Antibody Recognition: Implications for Active and Passive Immunization. PLoS Pathog 2017; 13:e1006641. [PMID: 28945784 PMCID: PMC5612725 DOI: 10.1371/journal.ppat.1006641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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61
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Abstract
A key unresolved challenge for developing an effective HIV‐1 vaccine is the discovery of strategies to elicit immune responses that are able to cross‐protect against a significant fraction of the diverse viruses that are circulating worldwide. Here, we summarize some of the immunological implications of HIV‐1 diversity, and outline the rationale behind several polyvalent vaccine design strategies that are currently under evaluation. Vaccine‐elicited T‐cell responses, which contribute to the control of HIV‐1 in natural infections, are currently being considered in both prevention and treatment settings. Approaches now in preclinical and human trials include full proteins in novel vectors, concatenated conserved protein regions, and polyvalent strategies that improve coverage of epitope diversity and enhance the cross‐reactivity of responses. While many barriers to vaccine induction of broadly neutralizing antibody (bNAb) responses remain, epitope diversification has emerged as both a challenge and an opportunity. Recent longitudinal studies have traced the emergence of bNAbs in HIV‐1 infection, inspiring novel approaches to recapitulate and accelerate the events that give rise to potent bNAb in vivo. In this review, we have selected two such lineage‐based design strategies to illustrate how such in‐depth analysis can offer conceptual improvements that may bring us closer to an effective vaccine.
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Affiliation(s)
- Bette Korber
- Theoretical Biology and Biophysics, T6, Los Alamos National Laboratory, Los Alamos, NM, USA.,New Mexico Consortium, Los Alamos, NM, USA
| | - Peter Hraber
- Theoretical Biology and Biophysics, T6, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Kshitij Wagh
- Theoretical Biology and Biophysics, T6, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
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62
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Meyerhoff RR, Scearce RM, Ogburn DF, Lockwood B, Pickeral J, Kuraoka M, Anasti K, Eudailey J, Eaton A, Cooper M, Wiehe K, Montefiori DC, Tomaras G, Ferrari G, Alam SM, Liao HX, Korber B, Gao F, Haynes BF. HIV-1 Consensus Envelope-Induced Broadly Binding Antibodies. AIDS Res Hum Retroviruses 2017; 33:859-868. [PMID: 28314374 PMCID: PMC5564029 DOI: 10.1089/aid.2016.0294] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Antibodies that cross-react with multiple HIV-1 envelopes (Envs) are useful reagents for characterizing Env proteins and for soluble Env capture and purification assays. We previously reported 10 murine monoclonal antibodies induced by group M consensus Env, CON-6 immunization. Each demonstrated broad cross-reactivity to recombinant Envs. Here we characterized the Env epitopes to which they bind. Seven mapped to linear epitopes in gp120, five at the Env N-terminus, and two at the Env C-terminus. One antibody, 13D7, bound at the gp120 N-terminus (aa 30-42), reacted with HIV-1-infected CD4+ T cells, and when expressed in a human IgG1 backbone, mediated antibody-dependent cellular cytotoxicity. Antibody 18F11 bound at the gp120 C-terminus (aa 445-459) and reactivity was glycan dependent. Antibodies 13D7, 3B3, and 16H3 bound to 100 percent of HIV-1 Envs tested in ELISA and sodium dodecyl sulfate/polyacrylamide gel electrophoresis/western blot analysis. These data define the epitopes of monoclonal antibody reagents for characterization of recombinant Envs, one epitope of which is also expressed on the surface of HIV-1-infected CD4+ T cells.
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Affiliation(s)
- R. Ryan Meyerhoff
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina
| | - Richard M. Scearce
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina
| | - Damon F. Ogburn
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina
| | - Brad Lockwood
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina
| | - Joy Pickeral
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina
| | - Masa Kuraoka
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina
| | - Kara Anasti
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina
| | - Joshua Eudailey
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina
| | - Amanda Eaton
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina
| | - Melissa Cooper
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina
| | - David C. Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina
| | - Georgia Tomaras
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina
| | - Guido Ferrari
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina
| | - S. Munir Alam
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina
| | - Hua-Xin Liao
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina
- College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Bette Korber
- Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Feng Gao
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina
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63
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Williams LD, Ofek G, Schätzle S, McDaniel JR, Lu X, Nicely NI, Wu L, Lougheed CS, Bradley T, Louder MK, McKee K, Bailer RT, O'Dell S, Georgiev IS, Seaman MS, Parks RJ, Marshall DJ, Anasti K, Yang G, Nie X, Tumba NL, Wiehe K, Wagh K, Korber B, Kepler TB, Munir Alam S, Morris L, Kamanga G, Cohen MS, Bonsignori M, Xia SM, Montefiori DC, Kelsoe G, Gao F, Mascola JR, Moody MA, Saunders KO, Liao HX, Tomaras GD, Georgiou G, Haynes BF. Potent and broad HIV-neutralizing antibodies in memory B cells and plasma. Sci Immunol 2017; 2:2/7/eaal2200. [PMID: 28783671 DOI: 10.1126/sciimmunol.aal2200] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 12/20/2016] [Indexed: 12/13/2022]
Abstract
Induction of broadly neutralizing antibodies (bnAbs) is a goal of HIV-1 vaccine development. Antibody 10E8, reactive with the distal portion of the membrane-proximal external region (MPER) of HIV-1 gp41, is broadly neutralizing. However, the ontogeny of distal MPER antibodies and the relationship of memory B cell to plasma bnAbs are poorly understood. HIV-1-specific memory B cell flow sorting and proteomic identification of anti-MPER plasma antibodies from an HIV-1-infected individual were used to isolate broadly neutralizing distal MPER bnAbs of the same B cell clonal lineage. Structural analysis demonstrated that antibodies from memory B cells and plasma recognized the envelope gp41 bnAb epitope in a distinct orientation compared with other distal MPER bnAbs. The unmutated common ancestor of this distal MPER bnAb was autoreactive, suggesting lineage immune tolerance control. Construction of chimeric antibodies of memory B cell and plasma antibodies yielded a bnAb that potently neutralized most HIV-1 strains.
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Affiliation(s)
- LaTonya D Williams
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Gilad Ofek
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
| | - Sebastian Schätzle
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Jonathan R McDaniel
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Xiaozhi Lu
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nathan I Nicely
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Liming Wu
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
| | - Caleb S Lougheed
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
| | - Todd Bradley
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mark K Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Krisha McKee
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Robert T Bailer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Sijy O'Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Ivelin S Georgiev
- Vanderbilt Vaccine Center and Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Michael S Seaman
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Robert J Parks
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Dawn J Marshall
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kara Anasti
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Guang Yang
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xiaoyan Nie
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nancy L Tumba
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg 2131, South Africa.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Congella 4013, South Africa
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kshitij Wagh
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Thomas B Kepler
- Departments of Microbiology and Mathematics & Statistics, Boston University School of Medicine, Boston, MA 02118, USA
| | - S Munir Alam
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Lynn Morris
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg 2131, South Africa.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Congella 4013, South Africa
| | - Gift Kamanga
- University of North Carolina Project-Malawi, Kamuzu Central Hospital, Lilongwe, Malawi
| | - Myron S Cohen
- Departments of Medicine, Epidemiology, and Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Mattia Bonsignori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Shi-Mao Xia
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - David C Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Garnett Kelsoe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Feng Gao
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - M Anthony Moody
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hua-Xin Liao
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - George Georgiou
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA. .,Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA. .,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
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Tian J, López CA, Derdeyn CA, Jones MS, Pinter A, Korber B, Gnanakaran S. Effect of Glycosylation on an Immunodominant Region in the V1V2 Variable Domain of the HIV-1 Envelope gp120 Protein. PLoS Comput Biol 2016; 12:e1005094. [PMID: 27716795 PMCID: PMC5055340 DOI: 10.1371/journal.pcbi.1005094] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 08/01/2016] [Indexed: 12/14/2022] Open
Abstract
Heavy glycosylation of the envelope (Env) surface subunit, gp120, is a key adaptation of HIV-1; however, the precise effects of glycosylation on the folding, conformation and dynamics of this protein are poorly understood. Here we explore the patterns of HIV-1 Env gp120 glycosylation, and particularly the enrichment in glycosylation sites proximal to the disulfide linkages at the base of the surface-exposed variable domains. To dissect the influence of glycans on the conformation these regions, we focused on an antigenic peptide fragment from a disulfide bridge-bounded region spanning the V1 and V2 hyper-variable domains of HIV-1 gp120. We used replica exchange molecular dynamics (MD) simulations to investigate how glycosylation influences its conformation and stability. Simulations were performed with and without N-linked glycosylation at two sites that are highly conserved across HIV-1 isolates (N156 and N160); both are contacts for recognition by V1V2-targeted broadly neutralizing antibodies against HIV-1. Glycosylation stabilized the pre-existing conformations of this peptide construct, reduced its propensity to adopt other secondary structures, and provided resistance against thermal unfolding. Simulations performed in the context of the Env trimer also indicated that glycosylation reduces flexibility of the V1V2 region, and provided insight into glycan-glycan interactions in this region. These stabilizing effects were influenced by a combination of factors, including the presence of a disulfide bond between the Cysteines at 131 and 157, which increased the formation of beta-strands. Together, these results provide a mechanism for conservation of disulfide linkage proximal glycosylation adjacent to the variable domains of gp120 and begin to explain how this could be exploited to enhance the immunogenicity of those regions. These studies suggest that glycopeptide immunogens can be designed to stabilize the most relevant Env conformations to focus the immune response on key neutralizing epitopes. Heavy glycosylation of the envelope surface subunit, gp120, is a key adaptation of HIV-1, however, the precise effects of glycosylation on the folding, conformation and dynamics of this protein are poorly understood. The network of glycans on gp120 is of particular interest with regards to vaccine design, because the glycans both serve as targets for many classes of broadly neutralizing antibodies, and contribute to patterns of immune evasion and escape during HIV-1 infection. In this manuscript, we report on how glycosylation influences an immunogenic but disordered region of gp120. Glycosylation stabilizes the pre-existing conformation, and reduces its propensity to form other secondary structures. It also stabilizes preformed conformation against thermal unfolding. These complementary effects originate from a combination of multiple factors, including the observation that having a glycosylation site adjacent to the disulfide bond further promotes the formation of beta-strand structure in this peptide.
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Affiliation(s)
- Jianhui Tian
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Center for Biomolecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Cesar A. López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Cynthia A. Derdeyn
- Department of Pathology and Laboratory Medicine and Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Morris S. Jones
- University of California Berkeley, School of Public Health, Berkeley, California, United States of America
| | - Abraham Pinter
- New Jersey Medical School, Rutgers University, Newark, New Jersey, United States of America
| | - Bette Korber
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - S. Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- * E-mail:
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65
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Theiler J, Yoon H, Yusim K, Picker LJ, Fruh K, Korber B. Epigraph: A Vaccine Design Tool Applied to an HIV Therapeutic Vaccine and a Pan-Filovirus Vaccine. Sci Rep 2016; 6:33987. [PMID: 27703185 PMCID: PMC5050445 DOI: 10.1038/srep33987] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 09/01/2016] [Indexed: 11/09/2022] Open
Abstract
Epigraph is an efficient graph-based algorithm for designing vaccine antigens to optimize potential T-cell epitope (PTE) coverage. Epigraph vaccine antigens are functionally similar to Mosaic vaccines, which have demonstrated effectiveness in preliminary HIV non-human primate studies. In contrast to the Mosaic algorithm, Epigraph is substantially faster, and in restricted cases, provides a mathematically optimal solution. Epigraph furthermore has new features that enable enhanced vaccine design flexibility. These features include the ability to exclude rare epitopes from a design, to optimize population coverage based on inexact epitope matches, and to apply the code to both aligned and unaligned input sequences. Epigraph was developed to provide practical design solutions for two outstanding vaccine problems. The first of these is a personalized approach to a therapeutic T-cell HIV vaccine that would provide antigens with an excellent match to an individual’s infecting strain, intended to contain or clear a chronic infection. The second is a pan-filovirus vaccine, with the potential to protect against all known viruses in the Filoviradae family, including ebolaviruses. A web-based interface to run the Epigraph tool suite is available (http://www.hiv.lanl.gov/content/sequence/EPIGRAPH/epigraph.html).
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Affiliation(s)
- James Theiler
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA.,New Mexico Consortium, Los Alamos, NM 87544, USA
| | - Hyejin Yoon
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Karina Yusim
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA.,New Mexico Consortium, Los Alamos, NM 87544, USA
| | - Louis J Picker
- Oregon Health and Science University, Portland, OR 97239, USA
| | - Klaus Fruh
- Oregon Health and Science University, Portland, OR 97239, USA
| | - Bette Korber
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA.,New Mexico Consortium, Los Alamos, NM 87544, USA
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66
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Rademeyer C, Korber B, Seaman MS, Giorgi EE, Thebus R, Robles A, Sheward DJ, Wagh K, Garrity J, Carey BR, Gao H, Greene KM, Tang H, Bandawe GP, Marais JC, Diphoko TE, Hraber P, Tumba N, Moore PL, Gray GE, Kublin J, McElrath MJ, Vermeulen M, Middelkoop K, Bekker LG, Hoelscher M, Maboko L, Makhema J, Robb ML, Abdool Karim S, Abdool Karim Q, Kim JH, Hahn BH, Gao F, Swanstrom R, Morris L, Montefiori DC, Williamson C. Features of Recently Transmitted HIV-1 Clade C Viruses that Impact Antibody Recognition: Implications for Active and Passive Immunization. PLoS Pathog 2016; 12:e1005742. [PMID: 27434311 PMCID: PMC4951126 DOI: 10.1371/journal.ppat.1005742] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 06/14/2016] [Indexed: 11/18/2022] Open
Abstract
The development of biomedical interventions to reduce acquisition of HIV-1 infection remains a global priority, however their potential effectiveness is challenged by very high HIV-1 envelope diversity. Two large prophylactic trials in high incidence, clade C epidemic regions in southern Africa are imminent; passive administration of the monoclonal antibody VRC01, and active immunization with a clade C modified RV144-like vaccines. We have created a large representative panel of C clade viruses to enable assessment of antibody responses to vaccines and natural infection in Southern Africa, and we investigated the genotypic and neutralization properties of recently transmitted clade C viruses to determine how viral diversity impacted antibody recognition. We further explore the implications of these findings for the potential effectiveness of these trials. A panel of 200 HIV-1 Envelope pseudoviruses was constructed from clade C viruses collected within the first 100 days following infection. Viruses collected pre-seroconversion were significantly more resistant to serum neutralization compared to post-seroconversion viruses (p = 0.001). Over 13 years of the study as the epidemic matured, HIV-1 diversified (p = 0.0009) and became more neutralization resistant to monoclonal antibodies VRC01, PG9 and 4E10. When tested at therapeutic levels (10ug/ml), VRC01 only neutralized 80% of viruses in the panel, although it did exhibit potent neutralization activity against sensitive viruses (IC50 titres of 0.42 μg/ml). The Gp120 amino acid similarity between the clade C panel and candidate C-clade vaccine protein boosts (Ce1086 and TV1) was 77%, which is 8% more distant than between CRF01_AE viruses and the RV144 CRF01_AE immunogen. Furthermore, two vaccine signature sites, K169 in V2 and I307 in V3, associated with reduced infection risk in RV144, occurred less frequently in clade C panel viruses than in CRF01_AE viruses from Thailand. Increased resistance of pre-seroconversion viruses and evidence of antigenic drift highlights the value of using panels of very recently transmitted viruses and suggests that interventions may need to be modified over time to track the changing epidemic. Furthermore, high divergence such as that observed in the older clade C epidemic in southern Africa may impact vaccine efficacy, although the correlates of infection risk are yet to be defined in the clade C setting. Findings from this study of acute/early clade C viruses will aid vaccine development, and enable identification of new broad and potent antibodies to combat the HIV-1 C-clade epidemic in southern Africa.
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Affiliation(s)
- Cecilia Rademeyer
- Division of Medical Virology & Institute of Infectious Diseases and Molecular Medicine, University of Cape Town and National Health Laboratory Service (NHLS), Cape Town South Africa
| | - Bette Korber
- Los Alamos National Laboratory and New Mexico Consortium, Los Alamos, New Mexico, United States of America
| | - Michael S. Seaman
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Elena E. Giorgi
- Los Alamos National Laboratory and New Mexico Consortium, Los Alamos, New Mexico, United States of America
| | - Ruwayhida Thebus
- Division of Medical Virology & Institute of Infectious Diseases and Molecular Medicine, University of Cape Town and National Health Laboratory Service (NHLS), Cape Town South Africa
| | - Alexander Robles
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Daniel J. Sheward
- Division of Medical Virology & Institute of Infectious Diseases and Molecular Medicine, University of Cape Town and National Health Laboratory Service (NHLS), Cape Town South Africa
| | - Kshitij Wagh
- Los Alamos National Laboratory and New Mexico Consortium, Los Alamos, New Mexico, United States of America
| | - Jetta Garrity
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Brittany R. Carey
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Hongmei Gao
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Kelli M. Greene
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Haili Tang
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Gama P. Bandawe
- Division of Medical Virology & Institute of Infectious Diseases and Molecular Medicine, University of Cape Town and National Health Laboratory Service (NHLS), Cape Town South Africa
| | - Jinny C. Marais
- Division of Medical Virology & Institute of Infectious Diseases and Molecular Medicine, University of Cape Town and National Health Laboratory Service (NHLS), Cape Town South Africa
| | | | - Peter Hraber
- Los Alamos National Laboratory and New Mexico Consortium, Los Alamos, New Mexico, United States of America
| | - Nancy Tumba
- National Institute for Communicable Diseases (NICD), NHLS & University of the Witwatersrand, Johannesburg, South Africa
| | - Penny L. Moore
- National Institute for Communicable Diseases (NICD), NHLS & University of the Witwatersrand, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Glenda E. Gray
- Perinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg and South African Medical Research Council, Cape Town, South Africa
| | - James Kublin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - M. Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Marion Vermeulen
- South African National Blood Service, Weltevreden Park, South Africa
| | - Keren Middelkoop
- Desmond Tutu HIV Centre, Department of Medicine and Institute of Infectious Disease and Molecular Medicine, University of Cape Town (UCT), Cape Town, South Africa
| | - Linda-Gail Bekker
- Desmond Tutu HIV Centre, Department of Medicine and Institute of Infectious Disease and Molecular Medicine, University of Cape Town (UCT), Cape Town, South Africa
| | - Michael Hoelscher
- Department for Infectious Diseases & Tropical Medicine, Klinikum University of Munich, LMU and German Center for Infection Research (DZIF) partner site Munich, Munich, Germany
| | | | - Joseph Makhema
- Botswana-Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Merlin L. Robb
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Salim Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Quarraisha Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Jerome H. Kim
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- International Vaccine Institute, Seoul, Republic of Korea
| | - Beatrice H. Hahn
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Feng Gao
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Ronald Swanstrom
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Lynn Morris
- National Institute for Communicable Diseases (NICD), NHLS & University of the Witwatersrand, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - David C. Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Carolyn Williamson
- Division of Medical Virology & Institute of Infectious Diseases and Molecular Medicine, University of Cape Town and National Health Laboratory Service (NHLS), Cape Town South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- * E-mail:
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67
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Yusim K, Yoon H, Foley B, Feng S, Macke J, Dimitrijevic M, Abfalterer W, Szinger J, Fischer W, Kuiken C, Korber B. Integrated sequence and immunology filovirus database at Los Alamos. Database (Oxford) 2016; 2016:baw047. [PMID: 27103629 PMCID: PMC4839628 DOI: 10.1093/database/baw047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 03/14/2016] [Indexed: 12/11/2022]
Abstract
The Ebola outbreak of 2013–15 infected more than 28 000 people and claimed more lives than all previous filovirus outbreaks combined. Governmental agencies, clinical teams, and the world scientific community pulled together in a multifaceted response ranging from prevention and disease control, to evaluating vaccines and therapeutics in human trials. As this epidemic is finally coming to a close, refocusing on long-term prevention strategies becomes paramount. Given the very real threat of future filovirus outbreaks, and the inherent uncertainty of the next outbreak virus and geographic location, it is prudent to consider the extent and implications of known natural diversity in advancing vaccines and therapeutic approaches. To facilitate such consideration, we have updated and enhanced the content of the filovirus portion of Los Alamos Hemorrhagic Fever Viruses Database. We have integrated and performed baseline analysis of all family Filoviridae sequences deposited into GenBank, with associated immune response data, and metadata, and we have added new computational tools with web-interfaces to assist users with analysis. Here, we (i) describe the main features of updated database, (ii) provide integrated views and some basic analyses summarizing evolutionary patterns as they relate to geo-temporal data captured in the database and (iii) highlight the most conserved regions in the proteome that may be useful for a T cell vaccine strategy. Database URL: www.hfv.lanl.gov
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Affiliation(s)
- Karina Yusim
- Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Hyejin Yoon
- Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Brian Foley
- Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Shihai Feng
- Los Alamos National Laboratory, Los Alamos, NM, USA
| | | | | | | | | | - Will Fischer
- Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Carla Kuiken
- Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Bette Korber
- Los Alamos National Laboratory, Los Alamos, NM, USA
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68
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Ondondo B, Murakoshi H, Clutton G, Abdul-Jawad S, Wee EGT, Gatanaga H, Oka S, McMichael AJ, Takiguchi M, Korber B, Hanke T. Novel Conserved-region T-cell Mosaic Vaccine With High Global HIV-1 Coverage Is Recognized by Protective Responses in Untreated Infection. Mol Ther 2016; 24:832-42. [PMID: 26743582 PMCID: PMC4886941 DOI: 10.1038/mt.2016.3] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 12/31/2015] [Indexed: 12/12/2022] Open
Abstract
An effective human immunodeficiency virus type 1 (HIV-1) vaccine is the best solution for halting the acquired immune deficiency syndrome epidemic. Here, we describe the design and preclinical immunogenicity of T-cell vaccine expressing novel immunogens tHIVconsvX, vectored by DNA, simian (chimpanzee) adenovirus, and poxvirus modified vaccinia virus Ankara (MVA), a combination highly immunogenic in humans. The tHIVconsvX immunogens combine the three leading strategies for elicitation of effective CD8(+) T cells: use of regions of HIV-1 proteins functionally conserved across all M group viruses (to make HIV-1 escape costly on viral fitness), inclusion of bivalent complementary mosaic immunogens (to maximize global epitope matching and breadth of responses, and block common escape paths), and inclusion of epitopes known to be associated with low viral load in infected untreated people (to induce field-proven protective responses). tHIVconsvX was highly immunogenic in two strains of mice. Furthermore, the magnitude and breadth of CD8(+) T-cell responses to tHIVconsvX-derived peptides in treatment-naive HIV-1(+) patients significantly correlated with high CD4(+) T-cell count and low viral load. Overall, the tHIVconsvX design, combining the mosaic and conserved-region approaches, provides an indisputably better coverage of global HIV-1 variants than previous T-cell vaccines. These immunogens delivered in a highly immunogenic framework of adenovirus prime and MVA boost are ready for clinical development.
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Affiliation(s)
- Beatrice Ondondo
- The Jenner Institute, University of Oxford, Roosevelt Drive, Oxford, UK
| | | | - Genevieve Clutton
- The Jenner Institute, University of Oxford, Roosevelt Drive, Oxford, UK
- Current address: Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Edmund G-T Wee
- The Jenner Institute, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Hiroyuki Gatanaga
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Shinichi Oka
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | | | - Masafumi Takiguchi
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Bette Korber
- Los Alamo National Laboratory, Theoretical Biology and Biophysics, Los Alamos, New Mexico, USA
- The New Mexico Consortium, Los Alamos, New Mexico, USA
| | - Tomáš Hanke
- The Jenner Institute, University of Oxford, Roosevelt Drive, Oxford, UK
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
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69
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Wagh K, Bhattacharya T, Williamson C, Robles A, Bayne M, Garrity J, Rist M, Rademeyer C, Yoon H, Lapedes A, Gao H, Greene K, Louder MK, Kong R, Karim SA, Burton DR, Barouch DH, Nussenzweig MC, Mascola JR, Morris L, Montefiori DC, Korber B, Seaman MS. Optimal Combinations of Broadly Neutralizing Antibodies for Prevention and Treatment of HIV-1 Clade C Infection. PLoS Pathog 2016; 12:e1005520. [PMID: 27028935 PMCID: PMC4814126 DOI: 10.1371/journal.ppat.1005520] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 03/01/2016] [Indexed: 01/03/2023] Open
Abstract
The identification of a new generation of potent broadly neutralizing HIV-1 antibodies (bnAbs) has generated substantial interest in their potential use for the prevention and/or treatment of HIV-1 infection. While combinations of bnAbs targeting distinct epitopes on the viral envelope (Env) will likely be required to overcome the extraordinary diversity of HIV-1, a key outstanding question is which bnAbs, and how many, will be needed to achieve optimal clinical benefit. We assessed the neutralizing activity of 15 bnAbs targeting four distinct epitopes of Env, including the CD4-binding site (CD4bs), the V1/V2-glycan region, the V3-glycan region, and the gp41 membrane proximal external region (MPER), against a panel of 200 acute/early clade C HIV-1 Env pseudoviruses. A mathematical model was developed that predicted neutralization by a subset of experimentally evaluated bnAb combinations with high accuracy. Using this model, we performed a comprehensive and systematic comparison of the predicted neutralizing activity of over 1,600 possible double, triple, and quadruple bnAb combinations. The most promising bnAb combinations were identified based not only on breadth and potency of neutralization, but also other relevant measures, such as the extent of complete neutralization and instantaneous inhibitory potential (IIP). By this set of criteria, triple and quadruple combinations of bnAbs were identified that were significantly more effective than the best double combinations, and further improved the probability of having multiple bnAbs simultaneously active against a given virus, a requirement that may be critical for countering escape in vivo. These results provide a rationale for advancing bnAb combinations with the best in vitro predictors of success into clinical trials for both the prevention and treatment of HIV-1 infection. In recent years, a new generation of monoclonal antibodies has been isolated from HIV-1 infected individuals that exhibit broad and potent neutralizing activity when tested against diverse strains of virus. There is a high level of interest in the field in determining if these antibodies can be used to prevent or treat HIV-1 infection. Because HIV-1 is adept at escaping from immune recognition, it is generally thought that combinations of multiple antibodies targeting different sites will be required for efficacy, much the same as seen for conventional antiretroviral drugs. How many and which antibodies to include in such combinations is not known. In this study, a new mathematical model was developed and used to accurately predict various measures of neutralizing activity for all possible combinations having a total of 2, 3, or 4 of the most promising antibodies. Through a systematic and comprehensive comparison, we identified optimal combinations of antibodies that best complement one another for enhanced anti-viral activity, and therefore may be most effective for the prevention or treatment of HIV-1 infection. These results provide important parameters that inform the selection of antibodies to develop for clinical use.
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Affiliation(s)
- Kshitij Wagh
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Tanmoy Bhattacharya
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Carolyn Williamson
- Division of Medical Virology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town and NHLS, Cape Town, South Africa
| | - Alex Robles
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Madeleine Bayne
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Jetta Garrity
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Michael Rist
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Cecilia Rademeyer
- Division of Medical Virology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town and NHLS, Cape Town, South Africa
| | - Hyejin Yoon
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Alan Lapedes
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Hongmei Gao
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Kelli Greene
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Mark K. Louder
- Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Rui Kong
- Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Salim Abdool Karim
- University of KwaZulu-Natal, Durban Department of Immunology and Microbial Science, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Dennis R. Burton
- The Scripps Research Institute, La Jolla, California, United States of America
| | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, United States of America
| | - John R. Mascola
- Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Lynn Morris
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- National Institute for Communicable Diseases (NICD), NHLS, University of the Witwatersrand, Johannesburg, South Africa
| | - David C. Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Bette Korber
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Michael S. Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
- * E-mail:
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Haynes BF, Shaw GM, Korber B, Kelsoe G, Sodroski J, Hahn BH, Borrow P, McMichael AJ. HIV-Host Interactions: Implications for Vaccine Design. Cell Host Microbe 2016; 19:292-303. [PMID: 26922989 DOI: 10.1016/j.chom.2016.02.002] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Development of an effective AIDS vaccine is a global priority. However, the extreme diversity of HIV type 1 (HIV-1), which is a consequence of its propensity to mutate to escape immune responses, along with host factors that prevent the elicitation of protective immune responses, continue to hinder vaccine development. Breakthroughs in understanding of the biology of the transmitted virus, the structure and nature of its envelope trimer, vaccine-induced CD8 T cell control in primates, and host control of broadly neutralizing antibody elicitation have given rise to new vaccine strategies. Despite this promise, emerging data from preclinical trials reinforce the need for additional insight into virus-host biology in order to facilitate the development of a successful vaccine.
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Affiliation(s)
- Barton F Haynes
- Department of Medicine, Duke University, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA; Duke University Human Vaccine Institute, Duke University, Durham, NC 27710, USA.
| | - George M Shaw
- Departments of Medicine and Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Bette Korber
- Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Garnett Kelsoe
- Department of Immunology, Duke University, Durham, NC 27710, USA; Duke University Human Vaccine Institute, Duke University, Durham, NC 27710, USA
| | - Joseph Sodroski
- Dana Farber-Cancer Institute, Harvard Medical School, Harvard University, Boston, MA 02215, USA
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Andrew J McMichael
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7FZ, UK
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71
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Abdul-Jawad S, Ondondo B, van Hateren A, Gardner A, Elliott T, Korber B, Hanke T. Increased Valency of Conserved-mosaic Vaccines Enhances the Breadth and Depth of Epitope Recognition. Mol Ther 2016; 24:375-384. [PMID: 26581160 PMCID: PMC4817818 DOI: 10.1038/mt.2015.210] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 11/09/2015] [Indexed: 12/19/2022] Open
Abstract
The biggest roadblock in development of effective vaccines against human immunodeficiency virus type 1 (HIV-1) is the virus genetic diversity. For T-cell vaccine, this can be tackled by focusing the vaccine-elicited T-cells on the highly functionally conserved regions of HIV-1 proteins, mutations in which typically cause a replicative fitness loss, and by computing multivalent mosaic proteins, which maximize the coverage of potential 9-mer T-cell epitopes of the input viral sequences. Our first conserved region vaccines HIVconsv employed clade alternating consensus sequences and showed promise in the initial clinical trials in terms of magnitude and breadth of elicited CD8(+) T-cells. Here, monitoring T-cells restricted by HLA-A*02:01 in transgenic mice, we assessed whether or not the tHIVconsv design (HIVconsv with a tissue plasminogen activator leader sequence) benefits from combining with a complementing conserved mosaic immunogen tHIVcmo, and compared the bivalent immunization to that with trivalent conserved mosaic vaccines. A hierarchy of tHIVconsv ≤ tHIVconsv+tHIVcmo < tCmo1+tCmo2+tCmo3 vaccinations for induction of CD8(+) T-cell responses was observed in terms of recognition of tested peptide variants. Thus, our HLA-A*02:01-restricted epitope data concur with previously published mouse and macaque observations and suggest that even conserved region vaccines benefit from oligovalent mosaic design.
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Affiliation(s)
| | | | - Andy van Hateren
- Faculty of Medicine and Institute for Life Science, University of Southampton, Southampton, UK
| | | | - Tim Elliott
- Faculty of Medicine and Institute for Life Science, University of Southampton, Southampton, UK
| | - Bette Korber
- Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, New Mexico, USA; The New Mexico Consortium, Los Alamos, New Mexico, USA
| | - Tomáš Hanke
- The Jenner Institute, University of Oxford, Oxford, UK; International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan.
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72
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Yusim K, Richardson R, Tao N, Dalwani A, Agrawal A, Szinger J, Funkhouser R, Korber B, Kuiken C. Los alamos hepatitis C immunology database. ACTA ACUST UNITED AC 2015; 4:217-25. [PMID: 16309340 DOI: 10.2165/00822942-200504040-00002] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The Los Alamos Hepatitis C Virus (HCV) Sequence Database (http://hcv.lanl.gov or http://hcv-db.org) was officially launched in September 2003. The sister HCV Immunology Database was made public in September 2004. The HCV Immunology Database is based on the Human Immunodeficiency Virus (HIV) Immunology Database. The HCV Immunology Database contains a curated inventory of immunological epitopes in HCV and their interaction with the immune system, with associated retrieval and analysis tools. This article describes in detail the types of data and services that the new database offers, the tools provided and the database framework. The data and some of the HCV database tools are available for download for non-commercial use.
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Affiliation(s)
- Karina Yusim
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
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73
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Yoon H, Macke J, West AP, Foley B, Bjorkman PJ, Korber B, Yusim K. CATNAP: a tool to compile, analyze and tally neutralizing antibody panels. Nucleic Acids Res 2015; 43:W213-9. [PMID: 26044712 PMCID: PMC4489231 DOI: 10.1093/nar/gkv404] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 04/15/2015] [Indexed: 02/01/2023] Open
Abstract
CATNAP (Compile, Analyze and Tally NAb Panels) is a new web server at Los Alamos HIV Database, created to respond to the newest advances in HIV neutralizing antibody research. It is a comprehensive platform focusing on neutralizing antibody potencies in conjunction with viral sequences. CATNAP integrates neutralization and sequence data from published studies, and allows users to analyze that data for each HIV Envelope protein sequence position and each antibody. The tool has multiple data retrieval and analysis options. As input, the user can pick specific antibodies and viruses, choose a panel from a published study, or supply their own data. The output superimposes neutralization panel data, virus epidemiological data, and viral protein sequence alignments on one page, and provides further information and analyses. The user can highlight alignment positions, or select antibody contact residues and view position-specific information from the HIV databases. The tool calculates tallies of amino acids and N-linked glycosylation motifs, counts of antibody-sensitive and -resistant viruses in conjunction with each amino acid or N-glycosylation motif, and performs Fisher's exact test to detect potential positive or negative amino acid associations for the selected antibody. Website name: CATNAP (Compile, Analyze and Tally NAb Panels). Website address: http://hiv.lanl.gov/catnap.
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Affiliation(s)
- Hyejin Yoon
- Los Alamos National Laboratory, Los Alamos, NM, USA
| | | | | | - Brian Foley
- Los Alamos National Laboratory, Los Alamos, NM, USA
| | | | - Bette Korber
- Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Karina Yusim
- Los Alamos National Laboratory, Los Alamos, NM, USA
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74
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Castro A, Stephenson K, Neubauer G, Korber B, Barouch D, Pawlowski N, Zerweck J, Reimer U. Peptide microarrays for coverage of sequence diversity in monitoring the B cell immune response (TECH2P.911). The Journal of Immunology 2015. [DOI: 10.4049/jimmunol.194.supp.206.21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Pathogens such as HIV or other viruses exhibit considerable sequence diversity as a strategy to escape the host immune system. However, sequence diversity is not limited to infectious agents. The increasing application of DNA sequencing indicates diversity between individuals (germ line mutations) and within individuals (somatic mutations) for many proteins. Such mutations can be connected to diseases such as cancer or autoimmune disease. The knowledge of antibody reactivities within individuals against self and foreign antigens is important for diagnosis, patient stratification, prevention and treatment of disease. Here we describe the application of high content peptide microarrays presenting thousands of peptides to be assayed with ~1µl serum sample of a donor to asses the reactivity pattern of antibodies towards a number of given antigens under consideration of sequence diversity using HIV as an example. A library of 6564 overlapping peptides represents the immunogenic fraction of the HIV proteome and covers the majority of the available sequences from the LANL global HIV-1 database. This high content library enables the assessment of antibody reactivity within different individuals independent on the serotype of the infecting HIV-viruses as well as the breadth and depth of antibody binding after boosting the immune system by vaccination. This concept can be easily adapted to other pathogens as well as self antigens such as tumor-associated antigens.
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Affiliation(s)
| | - Kathryn Stephenson
- 2Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - George Neubauer
- 2Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Bette Korber
- 3Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM
| | - Dan Barouch
- 2Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | | | | | - Ulf Reimer
- 1JPT Innovative Peptide Solutions, Acton, MA
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Kijak GH, Sanders-Buell E, Chenine AL, Eller M, Goonetilleke N, Thomas R, Leviyang S, Harbolick E, Bose M, Pham P, Oropeza C, Poltavee K, O'Sullivan AM, Merbah M, Costanzo M, Li H, Fischer W, Gao F, Eller LA, O'Connell RJ, Sinei S, Maganga L, Kibuuka H, Nitayaphan S, Rolland M, Korber B, McCutchan F, Shaw G, Michael N, Robb M, Tovanabutra S, Kim J. Cryptic Multiple HIV-1 Infection Revealed by Early, Frequent, and Deep Sampling during Acute Infection. AIDS Res Hum Retroviruses 2014. [DOI: 10.1089/aid.2014.5102a.abstract] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Gustavo Hernan Kijak
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD, United States
- U.S. Military HIV Research Program (MHRP)/ Henry M. Jackson Foundation, Silver Spring, MD, United States
| | - Eric Sanders-Buell
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD, United States
- U.S. Military HIV Research Program (MHRP)/ Henry M. Jackson Foundation, Silver Spring, MD, United States
| | - Agnes-Laurance Chenine
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD, United States
- U.S. Military HIV Research Program (MHRP)/ Henry M. Jackson Foundation, Silver Spring, MD, United States
| | - Michael Eller
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD, United States
- U.S. Military HIV Research Program (MHRP)/ Henry M. Jackson Foundation, Silver Spring, MD, United States
| | - Nilu Goonetilleke
- School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Rasmi Thomas
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD, United States
- U.S. Military HIV Research Program (MHRP)/ Henry M. Jackson Foundation, Silver Spring, MD, United States
| | - Sivan Leviyang
- Department of Mathematics and Statistics, Georgetown University, Washington, DC, United States
| | - Elizabeth Harbolick
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD, United States
- U.S. Military HIV Research Program (MHRP)/ Henry M. Jackson Foundation, Silver Spring, MD, United States
| | - Meera Bose
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD, United States
- U.S. Military HIV Research Program (MHRP)/ Henry M. Jackson Foundation, Silver Spring, MD, United States
| | - Phuc Pham
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD, United States
- U.S. Military HIV Research Program (MHRP)/ Henry M. Jackson Foundation, Silver Spring, MD, United States
| | - Celina Oropeza
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD, United States
- U.S. Military HIV Research Program (MHRP)/ Henry M. Jackson Foundation, Silver Spring, MD, United States
| | - Kultida Poltavee
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD, United States
- U.S. Military HIV Research Program (MHRP)/ Henry M. Jackson Foundation, Silver Spring, MD, United States
| | - Anne Marie O'Sullivan
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD, United States
- U.S. Military HIV Research Program (MHRP)/ Henry M. Jackson Foundation, Silver Spring, MD, United States
| | - Melanie Merbah
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD, United States
- U.S. Military HIV Research Program (MHRP)/ Henry M. Jackson Foundation, Silver Spring, MD, United States
| | - Margaret Costanzo
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD, United States
- U.S. Military HIV Research Program (MHRP)/ Henry M. Jackson Foundation, Silver Spring, MD, United States
| | - Hui Li
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Will Fischer
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Feng Gao
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, United States
| | - Leigh Anne Eller
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD, United States
- U.S. Military HIV Research Program (MHRP)/ Henry M. Jackson Foundation, Silver Spring, MD, United States
| | | | | | - Lucas Maganga
- Mbeya Medical Research Programme, Mbeya, Tanzania, United Republic of
| | - Hannah Kibuuka
- Makerere University-Walter Reed Project, Kampala, Uganda
| | | | - Morgane Rolland
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD, United States
- U.S. Military HIV Research Program (MHRP)/ Henry M. Jackson Foundation, Silver Spring, MD, United States
| | - Bette Korber
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, NM, United States
| | | | - George Shaw
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Nelson Michael
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Merlin Robb
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD, United States
- U.S. Military HIV Research Program (MHRP)/ Henry M. Jackson Foundation, Silver Spring, MD, United States
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD, United States
- U.S. Military HIV Research Program (MHRP)/ Henry M. Jackson Foundation, Silver Spring, MD, United States
| | - Jerome Kim
- U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD, United States
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Song T, Park Y, Shamputa IC, Seo S, Lee SY, Jeon HS, Choi H, Lee M, Glynne RJ, Barnes SW, Walker JR, Batalov S, Yusim K, Feng S, Tung CS, Theiler J, Via LE, Boshoff HIM, Murakami KS, Korber B, Barry CE, Cho SN. Fitness costs of rifampicin resistance in Mycobacterium tuberculosis are amplified under conditions of nutrient starvation and compensated by mutation in the β' subunit of RNA polymerase. Mol Microbiol 2014; 91:1106-19. [PMID: 24417450 DOI: 10.1111/mmi.12520] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2014] [Indexed: 12/31/2022]
Abstract
Rifampicin resistance, a defining attribute of multidrug-resistant tuberculosis, is conferred by mutations in the β subunit of RNA polymerase. Sequencing of rifampicin-resistant (RIF-R) clinical isolates of Mycobacterium tuberculosis revealed, in addition to RIF-R mutations, enrichment of potential compensatory mutations around the double-psi β-barrel domain of the β' subunit comprising the catalytic site and the exit tunnel for newly synthesized RNA. Sequential introduction of the resistance allele followed by the compensatory allele in isogenic Mycobacterium smegmatis showed that these mutations respectively caused and compensated a starvation enhanced growth defect by altering RNA polymerase activity. While specific combinations of resistance and compensatory alleles converged in divergent lineages, other combinations recurred among related isolates suggesting transmission of compensated RIF-R strains. These findings suggest nutrient poor growth conditions impose larger selective pressure on RIF-R organisms that results in the selection of compensatory mutations in a domain involved in catalysis and starvation control of RNA polymerase transcription.
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Affiliation(s)
- Taeksun Song
- International Tuberculosis Research Center, Changwon, South Korea
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77
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78
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Brodin J, Krishnamoorthy M, Athreya G, Fischer W, Hraber P, Gleasner C, Green L, Korber B, Leitner T. A multiple-alignment based primer design algorithm for genetically highly variable DNA targets. BMC Bioinformatics 2013; 14:255. [PMID: 23965160 PMCID: PMC3765731 DOI: 10.1186/1471-2105-14-255] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 08/20/2013] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Primer design for highly variable DNA sequences is difficult, and experimental success requires attention to many interacting constraints. The advent of next-generation sequencing methods allows the investigation of rare variants otherwise hidden deep in large populations, but requires attention to population diversity and primer localization in relatively conserved regions, in addition to recognized constraints typically considered in primer design. RESULTS Design constraints include degenerate sites to maximize population coverage, matching of melting temperatures, optimizing de novo sequence length, finding optimal bio-barcodes to allow efficient downstream analyses, and minimizing risk of dimerization. To facilitate primer design addressing these and other constraints, we created a novel computer program (PrimerDesign) that automates this complex procedure. We show its powers and limitations and give examples of successful designs for the analysis of HIV-1 populations. CONCLUSIONS PrimerDesign is useful for researchers who want to design DNA primers and probes for analyzing highly variable DNA populations. It can be used to design primers for PCR, RT-PCR, Sanger sequencing, next-generation sequencing, and other experimental protocols targeting highly variable DNA samples.
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Affiliation(s)
- Johanna Brodin
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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79
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Imholte GC, Sauteraud R, Korber B, Bailer RT, Turk ET, Shen X, Tomaras GD, Mascola JR, Koup RA, Montefiori DC, Gottardo R. A computational framework for the analysis of peptide microarray antibody binding data with application to HIV vaccine profiling. J Immunol Methods 2013; 395:1-13. [PMID: 23770318 DOI: 10.1016/j.jim.2013.06.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 04/26/2013] [Accepted: 06/01/2013] [Indexed: 10/26/2022]
Abstract
We present an integrated analytical method for analyzing peptide microarray antibody binding data, from normalization through subject-specific positivity calls and data integration and visualization. Current techniques for the normalization of such data sets do not account for non-specific binding activity. A novel normalization technique based on peptide sequence information quickly and effectively reduced systematic biases. We also employed a sliding mean window technique that borrows strength from peptides sharing similar sequences, resulting in reduced signal variability. A smoothed signal aided in the detection of weak antibody binding hotspots. A new principled FDR method of setting positivity thresholds struck a balance between sensitivity and specificity. In addition, we demonstrate the utility and importance of using baseline control measurements when making subject-specific positivity calls. Data sets from two human clinical trials of candidate HIV-1 vaccines were used to validate the effectiveness of our overall computational framework.
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Affiliation(s)
- Greg C Imholte
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, M2-C200, PO Box 19024, Seattle, WA 98109-1024, United States.
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80
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Abstract
One of the challenges of genetic data analysis is to combine information from sources that are distributed around the world and accessible through a wide array of different methods and interfaces. The HIV database and its footsteps, the hepatitis C virus (HCV) and hemorrhagic fever virus (HFV) databases, have made it their mission to make different data types easily available to their users. This involves a large amount of behind-the-scenes processing, including quality control and analysis of the sequences and their annotation. Gene and protein sequences are distilled from the sequences that are stored in GenBank; to this end, both submitter annotation and script-generated sequences are used. Alignments of both nucleotide and amino acid sequences are generated, manually curated, distilled into an alignment model, and regenerated in an iterative cycle that results in ever better new alignments. Annotation of epidemiological and clinical information is parsed, checked, and added to the database. User interfaces are updated, and new interfaces are added based upon user requests. Vital for its success, the database staff are heavy users of the system, which enables them to fix bugs and find opportunities for improvement. In this chapter we describe some of the infrastructure that keeps these heavily used analysis platforms alive and vital after nearly 25 years of use. The database/analysis platforms described in this chapter can be accessed at http://hiv.lanl.gov http://hcv.lanl.gov http://hfv.lanl.gov.
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Affiliation(s)
- Carla Kuiken
- Los Alamos National Laboratory, Theoretical Biology and Biophysics (MS K710), Los Alamos, NM, USA.
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81
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Parrish NF, Li H, Hora B, Berg A, Wilen CB, Decker J, Iyer SS, Zajic L, O’Brien M, Salazar-Gonzalez JF, Salazar MG, Parrish EH, Ding H, Kumar A, Ochsenbauer C, Bhardwaj N, Doms RW, Kappes JC, Gao F, Haynes BF, Korber B, Hahn BH, Shaw GM. C106 Distinguishing Features of Transmitted/Founder HIV-1. J Acquir Immune Defic Syndr 2013. [DOI: 10.1097/01.qai.0000429225.92253.36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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82
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Zolla-Pazner S, deCamp AC, Cardozo T, Karasavvas N, Gottardo R, Williams C, Morris DE, Tomaras G, Rao M, Billings E, Berman P, Shen X, Andrews C, O'Connell RJ, Ngauy V, Nitayaphan S, de Souza M, Korber B, Koup R, Bailer RT, Mascola JR, Pinter A, Montefiori D, Haynes BF, Robb ML, Rerks-Ngarm S, Michael NL, Gilbert PB, Kim JH. Analysis of V2 antibody responses induced in vaccinees in the ALVAC/AIDSVAX HIV-1 vaccine efficacy trial. PLoS One 2013; 8:e53629. [PMID: 23349725 PMCID: PMC3547933 DOI: 10.1371/journal.pone.0053629] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 11/23/2012] [Indexed: 12/18/2022] Open
Abstract
The RV144 clinical trial of a prime/boost immunizing regimen using recombinant canary pox (ALVAC-HIV) and two gp120 proteins (AIDSVAX B and E) was previously shown to have a 31.2% efficacy rate. Plasma specimens from vaccine and placebo recipients were used in an extensive set of assays to identify correlates of HIV-1 infection risk. Of six primary variables that were studied, only one displayed a significant inverse correlation with risk of infection: the antibody (Ab) response to a fusion protein containing the V1 and V2 regions of gp120 (gp70-V1V2). This finding prompted a thorough examination of the results generated with the complete panel of 13 assays measuring various V2 Abs in the stored plasma used in the initial pilot studies and those used in the subsequent case-control study. The studies revealed that the ALVAC-HIV/AIDSVAX vaccine induced V2-specific Abs that cross-react with multiple HIV-1 subgroups and recognize both conformational and linear epitopes. The conformational epitope was present on gp70-V1V2, while the predominant linear V2 epitope mapped to residues 165–178, immediately N-terminal to the putative α4β7 binding motif in the mid-loop region of V2. Odds ratios (ORs) were calculated to compare the risk of infection with data from 12 V2 assays, and in 11 of these, the ORs were ≤1, reaching statistical significance for two of the variables: Ab responses to gp70-V1V2 and to overlapping V2 linear peptides. It remains to be determined whether anti-V2 Ab responses were directly responsible for the reduced infection rate in RV144 and whether anti-V2 Abs will prove to be important with other candidate HIV vaccines that show efficacy, however, the results support continued dissection of Ab responses to the V2 region which may illuminate mechanisms of protection from HIV-1 infection and may facilitate the development of an effective HIV-1 vaccine.
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Affiliation(s)
- Susan Zolla-Pazner
- Research Service, Veterans Affairs Medical Center, New York, New York, United States of America.
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83
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Fenimore PW, Muhammad MA, Fischer WM, Foley BT, Bakken RR, Thurmond JR, Yusim K, Yoon H, Parker M, Hart MK, Dye JM, Korber B, Kuiken C. Designing and testing broadly-protective filoviral vaccines optimized for cytotoxic T-lymphocyte epitope coverage. PLoS One 2012; 7:e44769. [PMID: 23056184 PMCID: PMC3463593 DOI: 10.1371/journal.pone.0044769] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 08/07/2012] [Indexed: 11/22/2022] Open
Abstract
We report the rational design and in vivo testing of mosaic proteins for a polyvalent pan-filoviral vaccine using a computational strategy designed for the Human Immunodeficiency Virus type 1 (HIV-1) but also appropriate for Hepatitis C virus (HCV) and potentially other diverse viruses. Mosaics are sets of artificial recombinant proteins that are based on natural proteins. The recombinants are computationally selected using a genetic algorithm to optimize the coverage of potential cytotoxic T lymphocyte (CTL) epitopes. Because evolutionary history differs markedly between HIV-1 and filoviruses, we devised an adapted computational technique that is effective for sparsely sampled taxa; our first significant result is that the mosaic technique is effective in creating high-quality mosaic filovirus proteins. The resulting coverage of potential epitopes across filovirus species is superior to coverage by any natural variants, including current vaccine strains with demonstrated cross-reactivity. The mosaic cocktails are also robust: mosaics substantially outperformed natural strains when computationally tested against poorly sampled species and more variable genes. Furthermore, in a computational comparison of cross-reactive potential a design constructed prior to the Bundibugyo outbreak performed nearly as well against all species as an updated design that included Bundibugyo. These points suggest that the mosaic designs would be more resilient than natural-variant vaccines against future Ebola outbreaks dominated by novel viral variants. We demonstrate in vivo immunogenicity and protection against a heterologous challenge in a mouse model. This design work delineates the likely requirements and limitations on broadly-protective filoviral CTL vaccines.
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Affiliation(s)
- Paul W Fenimore
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America.
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84
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Nkolola JP, Kovacs JM, Korber B, Chen B, Seaman M, Barouch D. Stability and neutralization capacity of a novel mosaic HIV-1 gp140 trimer in a guinea pig model. Retrovirology 2012. [PMCID: PMC3441370 DOI: 10.1186/1742-4690-9-s2-p299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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85
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Ford C, Yusim K, Ioerger T, Feng S, Chase M, Greene M, Korber B, Fortune S. Mycobacterium tuberculosis--heterogeneity revealed through whole genome sequencing. Tuberculosis (Edinb) 2012; 92:194-201. [PMID: 22218163 DOI: 10.1016/j.tube.2011.11.003] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 11/07/2011] [Indexed: 11/24/2022]
Abstract
The emergence of whole genome sequencing (WGS) technologies as primary research tools has allowed for the detection of genetic diversity in Mycobacterium tuberculosis (Mtb) with unprecedented resolution. WGS has been used to address a broad range of topics, including the dynamics of evolution, transmission and treatment. Here, we have analyzed 55 publically available genomes to reconstruct the phylogeny of Mtb, and we have addressed complications that arise during the analysis of publically available WGS data. Additionally, we have reviewed the application of WGS to the study of Mtb and discuss those areas still to be addressed, moving from global (phylogeography), to local (transmission chains and circulating strain diversity), to the single patient (clonal heterogeneity) and to the bacterium itself (evolutionary studies). Finally, we discuss the current WGS approaches, their strengths and limitations.
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Affiliation(s)
- Chris Ford
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, 665 Huntington Avenue, Building 1, Boston, MA 02115, USA
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86
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Gnanakaran S, Bhattacharya T, Daniels M, Keele BF, Hraber PT, Lapedes AS, Shen T, Gaschen B, Krishnamoorthy M, Li H, Decker JM, Salazar-Gonzalez JF, Wang S, Jiang C, Gao F, Swanstrom R, Anderson JA, Ping LH, Cohen MS, Markowitz M, Goepfert PA, Saag MS, Eron JJ, Hicks CB, Blattner WA, Tomaras GD, Asmal M, Letvin NL, Gilbert PB, DeCamp AC, Magaret CA, Schief WR, Ban YEA, Zhang M, Soderberg KA, Sodroski JG, Haynes BF, Shaw GM, Hahn BH, Korber B. Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections. PLoS Pathog 2011; 7:e1002209. [PMID: 21980282 PMCID: PMC3182927 DOI: 10.1371/journal.ppat.1002209] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2010] [Accepted: 06/26/2011] [Indexed: 12/15/2022] Open
Abstract
Here we have identified HIV-1 B clade Envelope (Env) amino acid signatures from early in infection that may be favored at transmission, as well as patterns of recurrent mutation in chronic infection that may reflect common pathways of immune evasion. To accomplish this, we compared thousands of sequences derived by single genome amplification from several hundred individuals that were sampled either early in infection or were chronically infected. Samples were divided at the outset into hypothesis-forming and validation sets, and we used phylogenetically corrected statistical strategies to identify signatures, systematically scanning all of Env. Signatures included single amino acids, glycosylation motifs, and multi-site patterns based on functional or structural groupings of amino acids. We identified signatures near the CCR5 co-receptor-binding region, near the CD4 binding site, and in the signal peptide and cytoplasmic domain, which may influence Env expression and processing. Two signatures patterns associated with transmission were particularly interesting. The first was the most statistically robust signature, located in position 12 in the signal peptide. The second was the loss of an N-linked glycosylation site at positions 413-415; the presence of this site has been recently found to be associated with escape from potent and broad neutralizing antibodies, consistent with enabling a common pathway for immune escape during chronic infection. Its recurrent loss in early infection suggests it may impact fitness at the time of transmission or during early viral expansion. The signature patterns we identified implicate Env expression levels in selection at viral transmission or in early expansion, and suggest that immune evasion patterns that recur in many individuals during chronic infection when antibodies are present can be selected against when the infection is being established prior to the adaptive immune response.
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Affiliation(s)
- S. Gnanakaran
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Tanmoy Bhattacharya
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Marcus Daniels
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Brandon F. Keele
- SAIC-Frederick, National Cancer Institute, Frederick, Maryland, United States of America
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Peter T. Hraber
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Alan S. Lapedes
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Tongye Shen
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Center for Molecular Biophysics and Department of Biochemistry, Cellular & Molecular Biology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Brian Gaschen
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Mohan Krishnamoorthy
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Hui Li
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Julie M. Decker
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Jesus F. Salazar-Gonzalez
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Shuyi Wang
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Chunlai Jiang
- National Engineering Laboratory of AIDS Vaccine School of Life Science, Jilin University, Changchun, China
- Duke University Medical Center, the Departments of Medicine and Surgery, and the Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Feng Gao
- Duke University Medical Center, the Departments of Medicine and Surgery, and the Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Ronald Swanstrom
- Department of Biochemistry and Biophysics and the Division of Infectious Diseases Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jeffrey A. Anderson
- Department of Biochemistry and Biophysics and the Division of Infectious Diseases Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Li-Hua Ping
- Department of Biochemistry and Biophysics and the Division of Infectious Diseases Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Myron S. Cohen
- Department of Biochemistry and Biophysics and the Division of Infectious Diseases Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Martin Markowitz
- Aaron Diamond AIDS Research Center, an affiliate of the Rockefeller University, New York, New York, United States of America
| | - Paul A. Goepfert
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Michael S. Saag
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Joseph J. Eron
- Department of Biochemistry and Biophysics and the Division of Infectious Diseases Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Charles B. Hicks
- Duke University Medical Center, the Departments of Medicine and Surgery, and the Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - William A. Blattner
- Institute of Human Virology, University of Maryland, School of Medicine, Baltimore, Maryland, United States of America
| | - Georgia D. Tomaras
- Duke University Medical Center, the Departments of Medicine and Surgery, and the Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Mohammed Asmal
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Norman L. Letvin
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
- Division of Viral Pathogenesis, Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Peter B. Gilbert
- Vaccine Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United State of America
| | - Allan C. DeCamp
- Vaccine Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United State of America
| | - Craig A. Magaret
- Vaccine Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United State of America
| | - William R. Schief
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Yih-En Andrew Ban
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- Arzeda Corporation, Seattle, Washington, United States of America
| | - Ming Zhang
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, Georgia, United States of America
| | - Kelly A. Soderberg
- Duke University Medical Center, the Departments of Medicine and Surgery, and the Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Joseph G. Sodroski
- Dana-Farber Cancer Institute, Department of Cancer Immunology and AIDS, Boston, Massachusetts, United States of America
| | - Barton F. Haynes
- Duke University Medical Center, the Departments of Medicine and Surgery, and the Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - George M. Shaw
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Beatrice H. Hahn
- Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Bette Korber
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- * E-mail:
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87
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Affiliation(s)
- Bette Korber
- Theoretical Biology and Biophysics, T6, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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88
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Korber B, Foley B. AIDS research pioneer Gerry Myers dies. AIDS Res Hum Retroviruses 2011; 27:453-4. [PMID: 21456886 DOI: 10.1089/aid.2011.1500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Bette Korber
- Theorectical Biology and Biophysics, Los Alamos National Laboratory, NM 87545, USA.
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89
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Ganusov V, Goonetilleke N, Liu M, Ferrari G, Shaw G, McMichael A, Borrow P, Korber B, Perelson A. Fitness costs and diversity of CTL response determine the rate of CTL escape during the acute and chronic phases of HIV infection (105.23). The Journal of Immunology 2011. [DOI: 10.4049/jimmunol.186.supp.105.23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Abstract
Human immunodeficiency virus type 1 (HIV-1, or HIV) often evades cytotoxic T cell (CTL) responses by generating variants that are not recognized by CTLs. We used single genome amplification and sequencing of complete HIV genomes to identify longitudinal changes in the transmitted/founder virus from the establishment of infection to the viral set-point at 1 year after the infection. We found that the rate of viral escape from CTL responses in a given patient decreases dramatically from the acute infection to the viral set point. Using a novel mathematical model that tracks the dynamics of viral escape at multiple epitopes we show that a number of factors could potentially contribute to a slower escape in the chronic phase of infection, such as a decreased magnitude of epitope-specific CTL responses, an increased fitness cost of escape mutations, or an increased diversity of the CTL response. In the model, increasing the diversity of the CTL response over time can reduce the rate of viral escape from a given CTL response, particularly if CD8+ T cells compete for killing of infected cells or control virus replication non-lytically. Our mathematical framework of viral escape from multiple CTL responses can be used to predict the breadth and magnitude of HIV-specific CTL response that needs to be induced by vaccination to prevent (or reduce) viral escape following HIV infection.
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Affiliation(s)
- Vitaly Ganusov
- 1Microbiology, University of Tennessee, Knoxville, TN
- 2Los Alamos National Lab., Los Alamos, NM
| | | | | | | | - George Shaw
- 4University of Alabama at Birmingham, Birmingham, AL
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90
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Ferrari G, Korber B, Goonetilleke N, Liu MKP, Turnbull EL, Salazar-Gonzalez JF, Hawkins N, Self S, Watson S, Betts MR, Gay C, McGhee K, Pellegrino P, Williams I, Tomaras GD, Haynes BF, Gray CM, Borrow P, Roederer M, McMichael AJ, Weinhold KJ. Relationship between functional profile of HIV-1 specific CD8 T cells and epitope variability with the selection of escape mutants in acute HIV-1 infection. PLoS Pathog 2011; 7:e1001273. [PMID: 21347345 PMCID: PMC3037354 DOI: 10.1371/journal.ppat.1001273] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Accepted: 01/06/2011] [Indexed: 01/09/2023] Open
Abstract
In the present study, we analyzed the functional profile of CD8+ T-cell responses directed against autologous transmitted/founder HIV-1 isolates during acute and early infection, and examined whether multifunctionality is required for selection of virus escape mutations. Seven anti-retroviral therapy-naïve subjects were studied in detail between 1 and 87 weeks following onset of symptoms of acute HIV-1 infection. Synthetic peptides representing the autologous transmitted/founder HIV-1 sequences were used in multiparameter flow cytometry assays to determine the functionality of HIV-1-specific CD8+ T memory cells. In all seven patients, the earliest T cell responses were predominantly oligofunctional, although the relative contribution of multifunctional cell responses increased significantly with time from infection. Interestingly, only the magnitude of the total and not of the poly-functional T-cell responses was significantly associated with the selection of escape mutants. However, the high contribution of MIP-1β-producing CD8+ T-cells to the total response suggests that mechanisms not limited to cytotoxicity could be exerting immune pressure during acute infection. Lastly, we show that epitope entropy, reflecting the capacity of the epitope to tolerate mutational change and defined as the diversity of epitope sequences at the population level, was also correlated with rate of emergence of escape mutants. An important role for the polyfunctional T-cell fraction of anti-HIV CD8 responses during chronic HIV infection has previously been suggested. This study characterized the role of polyfunctional T-cells directed against the transmitted/founder virus in the selection of viral escape mutants during acute HIV-1 infection within a unique cohort of individuals recruited within 3 weeks from the onset of symptoms at the time when the virus load was still declining. For the first time, the sequences of the transmitted/founder virus isolated from each patient were used. Interestingly, polyfunctionality was not found to be a pre-requisite for selection of escape mutations. A novel significant correlation is found between the order of appearance of escape mutations in different epitope sequences and both the magnitude of the CD8+ T-cell responses and the degree of entropy of the individual epitopes. A high proportion of the T-cells participating in the total response produced MIP-1β, suggesting that mechanisms not limited to the killing of infected cells might play a relevant role in early infection. This highlights the importance of measuring the quality of the CD8+ lymphocyte response and the sequence of the transmitted virus isolates to better understand the mechanisms of control of HIV replication during acute infection.
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Affiliation(s)
- Guido Ferrari
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America.
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91
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Gnanakaran S, Daniels MG, Bhattacharya T, Lapedes AS, Sethi A, Li M, Tang H, Greene K, Gao H, Haynes BF, Cohen MS, Shaw GM, Seaman MS, Kumar A, Gao F, Montefiori DC, Korber B. Genetic signatures in the envelope glycoproteins of HIV-1 that associate with broadly neutralizing antibodies. PLoS Comput Biol 2010; 6:e1000955. [PMID: 20949103 PMCID: PMC2951345 DOI: 10.1371/journal.pcbi.1000955] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Accepted: 09/10/2010] [Indexed: 11/27/2022] Open
Abstract
A steady increase in knowledge of the molecular and antigenic structure of the gp120 and gp41 HIV-1 envelope glycoproteins (Env) is yielding important new insights for vaccine design, but it has been difficult to translate this information to an immunogen that elicits broadly neutralizing antibodies. To help bridge this gap, we used phylogenetically corrected statistical methods to identify amino acid signature patterns in Envs derived from people who have made potently neutralizing antibodies, with the hypothesis that these Envs may share common features that would be useful for incorporation in a vaccine immunogen. Before attempting this, essentially as a control, we explored the utility of our computational methods for defining signatures of complex neutralization phenotypes by analyzing Env sequences from 251 clonal viruses that were differentially sensitive to neutralization by the well-characterized gp120-specific monoclonal antibody, b12. We identified ten b12-neutralization signatures, including seven either in the b12-binding surface of gp120 or in the V2 region of gp120 that have been previously shown to impact b12 sensitivity. A simple algorithm based on the b12 signature pattern was predictive of b12 sensitivity/resistance in an additional blinded panel of 57 viruses. Upon obtaining these reassuring outcomes, we went on to apply these same computational methods to define signature patterns in Env from HIV-1 infected individuals who had potent, broadly neutralizing responses. We analyzed a checkerboard-style neutralization dataset with sera from 69 HIV-1-infected individuals tested against a panel of 25 different Envs. Distinct clusters of sera with high and low neutralization potencies were identified. Six signature positions in Env sequences obtained from the 69 samples were found to be strongly associated with either the high or low potency responses. Five sites were in the CD4-induced coreceptor binding site of gp120, suggesting an important role for this region in the elicitation of broadly neutralizing antibody responses against HIV-1.
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Affiliation(s)
- S. Gnanakaran
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Marcus G. Daniels
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Tanmoy Bhattacharya
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Alan S. Lapedes
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Anurag Sethi
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Ming Li
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Haili Tang
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Kelli Greene
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Hongmei Gao
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Barton F. Haynes
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Myron S. Cohen
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - George M. Shaw
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Michael S. Seaman
- Division of Viral Pathogenesis, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Amit Kumar
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Feng Gao
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - David C. Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
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92
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Bulla I, Schultz AK, Schreiber F, Zhang M, Leitner T, Korber B, Morgenstern B, Stanke M. HIV classification using the coalescent theory. ACTA ACUST UNITED AC 2010; 26:1409-15. [PMID: 20400454 DOI: 10.1093/bioinformatics/btq159] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION Existing coalescent models and phylogenetic tools based on them are not designed for studying the genealogy of sequences like those of HIV, since in HIV recombinants with multiple cross-over points between the parental strains frequently arise. Hence, ambiguous cases in the classification of HIV sequences into subtypes and circulating recombinant forms (CRFs) have been treated with ad hoc methods in lack of tools based on a comprehensive coalescent model accounting for complex recombination patterns. RESULTS We developed the program ARGUS that scores classifications of sequences into subtypes and recombinant forms. It reconstructs ancestral recombination graphs (ARGs) that reflect the genealogy of the input sequences given a classification hypothesis. An ARG with maximal probability is approximated using a Markov chain Monte Carlo approach. ARGUS was able to distinguish the correct classification with a low error rate from plausible alternative classifications in simulation studies with realistic parameters. We applied our algorithm to decide between two recently debated alternatives in the classification of CRF02 of HIV-1 and find that CRF02 is indeed a recombinant of Subtypes A and G. AVAILABILITY ARGUS is implemented in C++ and the source code is available at http://gobics.de/software.
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Affiliation(s)
- Ingo Bulla
- Abteilung Bioinformatik, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Goldschmidtstrasse 1, 37077 Göttingen, Germany.
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93
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Zhang M, Foley B, Schultz AK, Macke JP, Bulla I, Stanke M, Morgenstern B, Korber B, Leitner T. The role of recombination in the emergence of a complex and dynamic HIV epidemic. Retrovirology 2010; 7:25. [PMID: 20331894 PMCID: PMC2855530 DOI: 10.1186/1742-4690-7-25] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Accepted: 03/23/2010] [Indexed: 12/11/2022] Open
Abstract
Background Inter-subtype recombinants dominate the HIV epidemics in three geographical regions. To better understand the role of HIV recombinants in shaping the current HIV epidemic, we here present the results of a large-scale subtyping analysis of 9435 HIV-1 sequences that involve subtypes A, B, C, G, F and the epidemiologically important recombinants derived from three continents. Results The circulating recombinant form CRF02_AG, common in West Central Africa, appears to result from recombination events that occurred early in the divergence between subtypes A and G, followed by additional recent recombination events that contribute to the breakpoint pattern defining the current recombinant lineage. This finding also corrects a recent claim that G is a recombinant and a descendant of CRF02, which was suggested to be a pure subtype. The BC and BF recombinants in China and South America, respectively, are derived from recent recombination between contemporary parental lineages. Shared breakpoints in South America BF recombinants indicate that the HIV-1 epidemics in Argentina and Brazil are not independent. Therefore, the contemporary HIV-1 epidemic has recombinant lineages of both ancient and more recent origins. Conclusions Taken together, we show that these recombinant lineages, which are highly prevalent in the current HIV epidemic, are a mixture of ancient and recent recombination. The HIV pandemic is moving towards having increasing complexity and higher prevalence of recombinant forms, sometimes existing as "families" of related forms. We find that the classification of some CRF designations need to be revised as a consequence of (1) an estimated > 5% error in the original subtype assignments deposited in the Los Alamos sequence database; (2) an increasing number of CRFs are defined while they do not readily fit into groupings for molecular epidemiology and vaccine design; and (3) a dynamic HIV epidemic context.
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Affiliation(s)
- Ming Zhang
- Theoretical Biology & Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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94
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Yusim K, Fischer W, Yoon H, Thurmond J, Fenimore PW, Lauer G, Korber B, Kuiken C. Genotype 1 and global hepatitis C T-cell vaccines designed to optimize coverage of genetic diversity. J Gen Virol 2010; 91:1194-206. [PMID: 20053820 DOI: 10.1099/vir.0.017491-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Immunological control of hepatitis C virus (HCV) is possible and is probably mediated by host T-cell responses, but the genetic diversity of the virus poses a major challenge to vaccine development. We considered monovalent and polyvalent candidates for an HCV vaccine, including natural, consensus and synthetic 'mosaic' sequence cocktails. Mosaic vaccine reagents were designed using a computational approach first applied to and demonstrated experimentally for human immunodeficiency virus type 1 (HIV-Delta). Mosaic proteins resemble natural proteins, but are assembled from fragments of natural sequences via a genetic algorithm and optimized to maximize the coverage of potential T-cell epitopes (all 9-mers) found in natural sequences and to minimize the inclusion of rare 9-mers to avoid vaccine-specific responses. Genotype 1-specific and global vaccine cocktails were evaluated. Among vaccine candidates considered, polyvalent mosaic sequences provided the best coverage of both known and potential epitopes and had the fewest rare epitopes. A global vaccine based on conserved proteins across genotypes may be feasible, as a five-antigen mosaic cocktail provided 90, 77 and 70% coverage of the Core, NS3 and NS4 proteins, respectively; protein coverage diminished with increased protein variability, dropping to 38% for NS2. For the genotype 1-specific vaccine, the H77 prototype vaccine sequence matched only 50% of the potential epitopes in the population, whilst a polyprotein three-antigen mosaic cocktail increased potential epitope coverage to 83%. More than 75% coverage of all HCV proteins was achieved with a three-antigen mosaic cocktail, suggesting that genotype-specific vaccines could also include the more variable proteins.
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Affiliation(s)
- Karina Yusim
- Los Alamos National Laboratory, Theory Division, Los Alamos, NM 87545, USA.
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95
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Abstract
Despite more than 25 years of concerted worldwide research, the development of a safe and effective HIV-1 vaccine remains elusive. Prototype antibody-based and T cell-based HIV-1 vaccines have failed to show efficacy in clinical trials to date. Next-generation HIV-1 vaccine candidates are in various stages of preclinical and clinical development, but key scientific obstacles pose major challenges for the field. Critical hurdles include the enormous global diversity of the virus and the challenges associated with generating broadly reactive neutralizing antibody and cellular immune responses. We review the current state of the HIV-1 vaccine field and outline strategies that are being explored to overcome these roadblocks.
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Affiliation(s)
- Dan H Barouch
- Division of Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, USA.
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96
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Berry IM, Athreya G, Kothari M, Daniels M, Bruno WJ, Korber B, Kuiken C, Ribeiro RM, Leitner T. The evolutionary rate dynamically tracks changes in HIV-1 epidemics: application of a simple method for optimizing the evolutionary rate in phylogenetic trees with longitudinal data. Epidemics 2009; 1:230-9. [PMID: 21352769 PMCID: PMC3053002 DOI: 10.1016/j.epidem.2009.10.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2009] [Revised: 10/06/2009] [Accepted: 10/30/2009] [Indexed: 12/24/2022] Open
Abstract
Large-sequence datasets provide an opportunity to investigate the dynamics of pathogen epidemics. Thus, a fast method to estimate the evolutionary rate from large and numerous phylogenetic trees becomes necessary. Based on minimizing tip height variances, we optimize the root in a given phylogenetic tree to estimate the most homogenous evolutionary rate between samples from at least two different time points. Simulations showed that the method had no bias in the estimation of evolutionary rates and that it was robust to tree rooting and topological errors. We show that the evolutionary rates of HIV-1 subtype B and C epidemics have changed over time, with the rate of evolution inversely correlated to the rate of virus spread. For subtype B, the evolutionary rate slowed down and tracked the start of the HAART era in 1996. Subtype C in Ethiopia showed an increase in the evolutionary rate when the prevalence increase markedly slowed down in 1995. Thus, we show that the evolutionary rate of HIV-1 on the population level dynamically tracks epidemic events.
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Affiliation(s)
- Irina Maljkovic Berry
- Theoretical Biology & Biophysics, MS K710, Los Alamos National Laboratory, Los Alamos, NM 87545, U.S.A
- Center for Nonlinear Studies (CNLS), Los Alamos National Laboratory, Los Alamos, NM 87545, U.S.A
- Department of Virology, Swedish Institute for Infectious Disease Control, SE-171 82 Solna, & Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Gayathri Athreya
- Theoretical Biology & Biophysics, MS K710, Los Alamos National Laboratory, Los Alamos, NM 87545, U.S.A
| | - Moulik Kothari
- Theoretical Biology & Biophysics, MS K710, Los Alamos National Laboratory, Los Alamos, NM 87545, U.S.A
| | - Marcus Daniels
- Theoretical Biology & Biophysics, MS K710, Los Alamos National Laboratory, Los Alamos, NM 87545, U.S.A
| | - William J. Bruno
- Theoretical Biology & Biophysics, MS K710, Los Alamos National Laboratory, Los Alamos, NM 87545, U.S.A
| | - Bette Korber
- Theoretical Biology & Biophysics, MS K710, Los Alamos National Laboratory, Los Alamos, NM 87545, U.S.A
| | - Carla Kuiken
- Theoretical Biology & Biophysics, MS K710, Los Alamos National Laboratory, Los Alamos, NM 87545, U.S.A
| | - Ruy M. Ribeiro
- Theoretical Biology & Biophysics, MS K710, Los Alamos National Laboratory, Los Alamos, NM 87545, U.S.A
| | - Thomas Leitner
- Theoretical Biology & Biophysics, MS K710, Los Alamos National Laboratory, Los Alamos, NM 87545, U.S.A
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97
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Berry IM, Athreya G, Kothari M, Daniels M, Bruno WJ, Korber B, Kuiken C, Ribeiro RM, Leitner T. WITHDRAWN: The evolutionary rate dynamically tracks changes in HIV-1 epidemics: Application of a simple method for optimizing the evolutionary rate in phylogenetic trees with longitudinal data. Epidemics 2009. [DOI: 10.1016/j.epidem.2009.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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98
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Fischer W, Keele B, Bhattacharya T, Lo C, Giorgi E, Hraber P, Leitner T, Han C, Gleasner C, Green L, Hahn B, Shaw G, Haynes B, Korber B. P09-21 LB. Deep sequencing of HIV-1 from acute infection: low initial diversity, and rapid but variable CTL escape. Retrovirology 2009. [PMCID: PMC2767917 DOI: 10.1186/1742-4690-6-s3-p401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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99
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Sirivichayakul S, Felber B, Kulkarni V, Pavlakis G, Buranapraditkun S, Thantiworasit P, Pitakpolrat P, Allen T, Leitner T, Korber B, Ruxrungtham K. P19-01. Pre-clinical immunogenicity of mosaic Asian AE/B HIV-1 DNA vaccine in mice. Retrovirology 2009. [PMCID: PMC2767828 DOI: 10.1186/1742-4690-6-s3-p321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
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100
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Basavapathruni A, Yeh W, Coffey R, Whitney J, Hraber P, Giri A, Rao S, Mascola J, Nabel G, Korber B, Seaman M, Letvin N. P04-41. Kinetics of antibody neutralization and viral evolution following envelope vaccination in SIV-infected rhesus monkeys. Retrovirology 2009. [PMCID: PMC2767972 DOI: 10.1186/1742-4690-6-s3-p69] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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