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Mullen TE, Abdullah R, Boucher J, Brousseau AS, Dasuri NK, Ditto NT, Doucette AM, Emery C, Gabriel J, Greamo B, Patil KS, Rothenberger K, Stolte J, Souders CA. Accelerated antibody discovery targeting the SARS-CoV-2 spike protein for COVID-19 therapeutic potential. Antib Ther 2021; 4:185-196. [PMID: 34541454 PMCID: PMC8444149 DOI: 10.1093/abt/tbab018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 11/13/2022] Open
Abstract
Background Rapid deployment of technologies capable of high-throughput and high-resolution screening is imperative for timely response to viral outbreaks. Risk mitigation in the form of leveraging multiple advanced technologies further increases the likelihood of identifying efficacious treatments in aggressive timelines. Methods In this study, we describe two parallel, yet distinct, in vivo approaches for accelerated discovery of antibodies targeting the severe acute respiratory syndrome coronavirus-2 spike protein. Working with human transgenic Alloy-GK mice, we detail a single B-cell discovery workflow to directly interrogate antibodies secreted from plasma cells for binding specificity and ACE2 receptor blocking activity. Additionally, we describe a concurrent accelerated hybridoma-based workflow utilizing a DiversimAb™ mouse model for increased diversity. Results The panel of antibodies isolated from both workflows revealed binding to distinct epitopes with both blocking and non-blocking profiles. Sequence analysis of the resulting lead candidates uncovered additional diversity with the opportunity for straightforward engineering and affinity maturation. Conclusions By combining in vivo models with advanced integration of screening and selection platforms, lead antibody candidates can be sequenced and fully characterized within one to three months.
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Affiliation(s)
- Tracey E Mullen
- Antibody Discovery, Abveris Inc., 480 Neponset St, Ste 10B, Canton, MA 02021, USA
| | - Rashed Abdullah
- Antibody Discovery, Abveris Inc., 480 Neponset St, Ste 10B, Canton, MA 02021, USA
| | - Jacqueline Boucher
- Antibody Discovery, Abveris Inc., 480 Neponset St, Ste 10B, Canton, MA 02021, USA
| | - Anna Susi Brousseau
- Antibody Discovery, Abveris Inc., 480 Neponset St, Ste 10B, Canton, MA 02021, USA
| | - Narayan K Dasuri
- Antibody Discovery, Abveris Inc., 480 Neponset St, Ste 10B, Canton, MA 02021, USA
| | - Noah T Ditto
- Product Development, Carterra, 825 N 300 W c309, Salt Lake City, UT 84103, USA
| | - Andrew M Doucette
- Antibody Discovery, Abveris Inc., 480 Neponset St, Ste 10B, Canton, MA 02021, USA
| | - Chloe Emery
- Antibody Discovery, Abveris Inc., 480 Neponset St, Ste 10B, Canton, MA 02021, USA
| | - Justin Gabriel
- Antibody Discovery, Abveris Inc., 480 Neponset St, Ste 10B, Canton, MA 02021, USA
| | - Brendan Greamo
- Antibody Discovery, Abveris Inc., 480 Neponset St, Ste 10B, Canton, MA 02021, USA
| | - Ketan S Patil
- Antibody Discovery, Abveris Inc., 480 Neponset St, Ste 10B, Canton, MA 02021, USA
| | - Kelly Rothenberger
- Antibody Discovery, Abveris Inc., 480 Neponset St, Ste 10B, Canton, MA 02021, USA
| | - Justin Stolte
- Antibody Discovery, Abveris Inc., 480 Neponset St, Ste 10B, Canton, MA 02021, USA
| | - Colby A Souders
- Antibody Discovery, Abveris Inc., 480 Neponset St, Ste 10B, Canton, MA 02021, USA
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Hargreaves A, Brady C, Mellors J, Tipton T, Carroll MW, Longet S. Filovirus Neutralising Antibodies: Mechanisms of Action and Therapeutic Application. Pathogens 2021; 10:pathogens10091201. [PMID: 34578233 PMCID: PMC8468515 DOI: 10.3390/pathogens10091201] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/10/2021] [Accepted: 09/12/2021] [Indexed: 12/02/2022] Open
Abstract
Filoviruses, especially Ebola virus, cause sporadic outbreaks of viral haemorrhagic fever with very high case fatality rates in Africa. The 2013–2016 Ebola epidemic in West Africa provided large survivor cohorts spurring a large number of human studies which showed that specific neutralising antibodies played a key role in protection following a natural Ebola virus infection, as part of the overall humoral response and in conjunction with the cellular adaptive response. This review will discuss the studies in survivors and animal models which described protective neutralising antibody response. Their mechanisms of action will be detailed. Furthermore, the importance of neutralising antibodies in antibody-based therapeutics and in vaccine-induced responses will be explained, as well as the strategies to avoid immune escape from neutralising antibodies. Understanding the neutralising antibody response in the context of filoviruses is crucial to furthering our understanding of virus structure and function, in addition to improving current vaccines & antibody-based therapeutics.
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Affiliation(s)
- Alexander Hargreaves
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; (A.H.); (C.B.); (J.M.); (T.T.); (M.W.C.)
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Caolann Brady
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; (A.H.); (C.B.); (J.M.); (T.T.); (M.W.C.)
| | - Jack Mellors
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; (A.H.); (C.B.); (J.M.); (T.T.); (M.W.C.)
- National Infection Service, Public Health England, Porton Down, Salisbury SP4 0JG, UK
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7ZX, UK
| | - Tom Tipton
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; (A.H.); (C.B.); (J.M.); (T.T.); (M.W.C.)
| | - Miles W. Carroll
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; (A.H.); (C.B.); (J.M.); (T.T.); (M.W.C.)
- National Infection Service, Public Health England, Porton Down, Salisbury SP4 0JG, UK
| | - Stephanie Longet
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; (A.H.); (C.B.); (J.M.); (T.T.); (M.W.C.)
- Correspondence: ; Tel.: +44-18-6561-7892
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Gilchuk P, Guthals A, Bonissone SR, Shaw JB, Ilinykh PA, Huang K, Bombardi RG, Liang J, Grinyo A, Davidson E, Chen EC, Gunn BM, Alter G, Saphire EO, Doranz BJ, Bukreyev A, Zeitlin L, Castellana N, Crowe JE. Proteo-Genomic Analysis Identifies Two Major Sites of Vulnerability on Ebolavirus Glycoprotein for Neutralizing Antibodies in Convalescent Human Plasma. Front Immunol 2021; 12:706757. [PMID: 34335620 PMCID: PMC8322977 DOI: 10.3389/fimmu.2021.706757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 06/28/2021] [Indexed: 11/21/2022] Open
Abstract
Three clinically relevant ebolaviruses - Ebola (EBOV), Bundibugyo (BDBV), and Sudan (SUDV) viruses, are responsible for severe disease and occasional deadly outbreaks in Africa. The largest Ebola virus disease (EVD) epidemic to date in 2013-2016 in West Africa highlighted the urgent need for countermeasures, leading to the development and FDA approval of the Ebola virus vaccine rVSV-ZEBOV (Ervebo®) in 2020 and two monoclonal antibody (mAb)-based therapeutics (Inmazeb® [atoltivimab, maftivimab, and odesivimab-ebgn] and Ebanga® (ansuvimab-zykl) in 2020. The humoral response plays an indispensable role in ebolavirus immunity, based on studies of mAbs isolated from the antibody genes in peripheral blood circulating ebolavirus-specific human memory B cells. However, antibodies in the body are not secreted by circulating memory B cells in the blood but rather principally by plasma cells in the bone marrow. Little is known about the protective polyclonal antibody responses in convalescent plasma. Here we exploited both single-cell antibody gene sequencing and proteomic sequencing approaches to assess the composition of the ebolavirus glycoprotein (GP)-reactive antibody repertoire in the plasma of an EVD survivor. We first identified 1,512 GP-specific mAb variable gene sequences from single cells in the memory B cell compartment. Using mass spectrometric analysis of the corresponding GP-specific plasma IgG, we found that only a portion of the large B cell antibody repertoire was represented in the plasma. Molecular and functional analysis of proteomics-identified mAbs revealed recognition of epitopes in three major antigenic sites - the GP head domain, the glycan cap, and the base region, with a high prevalence of neutralizing and protective mAb specificities that targeted the base and glycan cap regions on the GP. Polyclonal plasma antibodies from the survivor reacted broadly to EBOV, BDBV, and SUDV GP, while reactivity of the potently neutralizing mAbs we identified was limited mostly to the homologous EBOV GP. Together these results reveal a restricted diversity of neutralizing humoral response in which mAbs targeting two antigenic sites on GP - glycan cap and base - play a principal role in plasma-antibody-mediated protective immunity against EVD.
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Affiliation(s)
- Pavlo Gilchuk
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Adrian Guthals
- Mapp Biopharmaceutical, Inc. San Diego, CA, United States
| | - Stefano R. Bonissone
- Abterra Biosciences (formerly Digital Proteomics LLC), San Diego, CA, United States
| | - Jared B. Shaw
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Philipp A. Ilinykh
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
- Galveston National Laboratory, Galveston, TX, United States
| | - Kai Huang
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
- Galveston National Laboratory, Galveston, TX, United States
| | - Robin G. Bombardi
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Jenny Liang
- Integral Molecular, Inc., Philadelphia, PA, United States
| | - Ariadna Grinyo
- Integral Molecular, Inc., Philadelphia, PA, United States
| | - Edgar Davidson
- Integral Molecular, Inc., Philadelphia, PA, United States
| | - Elaine C. Chen
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Bronwyn M. Gunn
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | | | - Alexander Bukreyev
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
- Galveston National Laboratory, Galveston, TX, United States
- Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX, United States
| | - Larry Zeitlin
- Mapp Biopharmaceutical, Inc. San Diego, CA, United States
| | - Natalie Castellana
- Abterra Biosciences (formerly Digital Proteomics LLC), San Diego, CA, United States
| | - James E. Crowe
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, United States
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Effective high-throughput isolation of fully human antibodies targeting infectious pathogens. Nat Protoc 2021; 16:3639-3671. [PMID: 34035500 DOI: 10.1038/s41596-021-00554-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/12/2021] [Indexed: 02/04/2023]
Abstract
As exemplified by the ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, there is a strong demand for rapid high-throughput isolation pipelines to identify potent neutralizing antibodies for prevention and therapy of infectious diseases. However, despite substantial progress and extensive efforts, the identification and production of antigen-specific antibodies remains labor- and cost-intensive. We have advanced existing concepts to develop a highly efficient high-throughput protocol with proven application for the isolation of potent antigen-specific antibodies against human immunodeficiency virus 1, hepatitis C virus, human cytomegalovirus, Middle East respiratory syndrome coronavirus, SARS-CoV-2 and Ebola virus. It is based on computationally optimized multiplex primer sets (openPrimeR), which guarantee high coverage of even highly mutated immunoglobulin gene segments as well as on optimized antibody cloning and production strategies. Here, we provide the detailed protocol, which covers all critical steps from sample collection to antibody production within 12-14 d.
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55
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Fels JM, Maurer DP, Herbert AS, Wirchnianski AS, Vergnolle O, Cross RW, Abelson DM, Moyer CL, Mishra AK, Aguilan JT, Kuehne AI, Pauli NT, Bakken RR, Nyakatura EK, Hellert J, Quevedo G, Lobel L, Balinandi S, Lutwama JJ, Zeitlin L, Geisbert TW, Rey FA, Sidoli S, McLellan JS, Lai JR, Bornholdt ZA, Dye JM, Walker LM, Chandran K. Protective neutralizing antibodies from human survivors of Crimean-Congo hemorrhagic fever. Cell 2021; 184:3486-3501.e21. [PMID: 34077751 PMCID: PMC8559771 DOI: 10.1016/j.cell.2021.05.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/19/2021] [Accepted: 04/29/2021] [Indexed: 12/31/2022]
Abstract
Crimean-Congo hemorrhagic fever virus (CCHFV) is a World Health Organization priority pathogen. CCHFV infections cause a highly lethal hemorrhagic fever for which specific treatments and vaccines are urgently needed. Here, we characterize the human immune response to natural CCHFV infection to identify potent neutralizing monoclonal antibodies (nAbs) targeting the viral glycoprotein. Competition experiments showed that these nAbs bind six distinct antigenic sites in the Gc subunit. These sites were further delineated through mutagenesis and mapped onto a prefusion model of Gc. Pairwise screening identified combinations of non-competing nAbs that afford synergistic neutralization. Further enhancements in neutralization breadth and potency were attained by physically linking variable domains of synergistic nAb pairs through bispecific antibody (bsAb) engineering. Although multiple nAbs protected mice from lethal CCHFV challenge in pre- or post-exposure prophylactic settings, only a single bsAb, DVD-121-801, afforded therapeutic protection. DVD-121-801 is a promising candidate suitable for clinical development as a CCHFV therapeutic.
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Affiliation(s)
- J Maximilian Fels
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | | - Andrew S Herbert
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA; The Geneva Foundation, Tacoma, WA 98402, USA
| | - Ariel S Wirchnianski
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Deparment of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Olivia Vergnolle
- Deparment of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Robert W Cross
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77550, USA; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77550, USA
| | | | | | - Akaash K Mishra
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jennifer T Aguilan
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Ana I Kuehne
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | | | - Russell R Bakken
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Elisabeth K Nyakatura
- Deparment of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jan Hellert
- Structural Virology Unit, Department of Virology, CNRS UMR 3569, Institut Pasteur, Paris 75724, France
| | - Gregory Quevedo
- Deparment of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Leslie Lobel
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | | | | | - Larry Zeitlin
- Mapp Biopharmaceutical, Inc., San Diego, CA 92121, USA
| | - Thomas W Geisbert
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77550, USA; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Felix A Rey
- Structural Virology Unit, Department of Virology, CNRS UMR 3569, Institut Pasteur, Paris 75724, France
| | - Simone Sidoli
- Deparment of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jonathan R Lai
- Deparment of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | | - John M Dye
- U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
| | - Laura M Walker
- Adimab, LLC, Lebanon, NH 03766, USA; Adagio Therapeutics, Inc., Waltham, MA 02451, USA.
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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Antibody responses to filovirus infections in humans: protective or not? THE LANCET. INFECTIOUS DISEASES 2021; 21:e348-e355. [PMID: 34175003 DOI: 10.1016/s1473-3099(21)00006-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 12/17/2020] [Accepted: 01/04/2021] [Indexed: 12/16/2022]
Abstract
Disease outbreaks caused by Ebola virus and other filoviruses highlight the urgent need for an in-depth understanding of the role of antibody responses in recovery. In this Personal View we aim to discuss the controversial biological role of antibodies during natural filovirus infections in humans. Survival during natural human filovirus infections correlates with the magnitude of the process of antibodies binding to the filovirus glycoprotein and neutralising the virus. Despite the severity of the disease, highly potent monoclonal antibodies have been isolated from survivors of natural filovirus infections, suggesting that the magnitude of the antibody response is insufficient for prevention of severe disease. Unlike natural infections, filovirus vaccines, which express the viral glycoprotein, do induce protective concentrations of antibodies, albeit only when administered at very high doses. Multiple mechanisms by which filoviruses can delay and reduce the antibody response have been identified in the past decade. Furthermore, subneutralising antibody concentrations have been shown to enhance filovirus infections of immune cells bearing Fc receptors. Understanding the role of antibody responses during natural filovirus infections is important for the development of safe and potent vaccines and antibody-based treatments.
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57
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Bhatia B, Furuyama W, Hoenen T, Feldmann H, Marzi A. Ebola Virus Glycoprotein Domains Associated with Protective Efficacy. Vaccines (Basel) 2021; 9:630. [PMID: 34200548 PMCID: PMC8229685 DOI: 10.3390/vaccines9060630] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/06/2021] [Accepted: 06/08/2021] [Indexed: 11/27/2022] Open
Abstract
Ebola virus (EBOV) is the cause of sporadic outbreaks of human hemorrhagic disease in Africa, and the best-characterized virus in the filovirus family. The West African epidemic accelerated the clinical development of vaccines and therapeutics, leading to licensure of vaccines and antibody-based therapeutics for human use in recent years. The most widely used vaccine is based on vesicular stomatitis virus (VSV) expressing the EBOV glycoprotein (GP) (VSV-EBOV). Due to its favorable immune cell targeting, this vaccine has also been used as a base vector for the development of second generation VSV-based vaccines against Influenza, Nipah, and Zika viruses. However, in these situations, it may be beneficial if the immunogenicity against EBOV GP is minimized to induce a better protective immune response against the other foreign immunogen. Here, we analyzed if EBOV GP can be truncated to be less immunogenic, yet still able to drive replication of the vaccine vector. We found that the EBOV GP glycan cap and the mucin-like domain are both dispensable for VSV-EBOV replication. The glycan cap, however, appears critical for mediating a protective immune response against lethal EBOV challenge in mice.
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Affiliation(s)
- Bharti Bhatia
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA; (B.B.); (W.F.); (H.F.)
| | - Wakako Furuyama
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA; (B.B.); (W.F.); (H.F.)
| | - Thomas Hoenen
- Institute for Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany;
| | - Heinz Feldmann
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA; (B.B.); (W.F.); (H.F.)
| | - Andrea Marzi
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA; (B.B.); (W.F.); (H.F.)
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Structural basis for broad coronavirus neutralization. Nat Struct Mol Biol 2021; 28:478-486. [PMID: 33981021 DOI: 10.1038/s41594-021-00596-4] [Citation(s) in RCA: 151] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/21/2021] [Indexed: 02/03/2023]
Abstract
Three highly pathogenic β-coronaviruses have crossed the animal-to-human species barrier in the past two decades: SARS-CoV, MERS-CoV and SARS-CoV-2. To evaluate the possibility of identifying antibodies with broad neutralizing activity, we isolated a monoclonal antibody, termed B6, that cross-reacts with eight β-coronavirus spike glycoproteins, including all five human-infecting β-coronaviruses. B6 broadly neutralizes entry of pseudotyped viruses from lineages A and C, but not from lineage B, and the latter includes SARS-CoV and SARS-CoV-2. Cryo-EM, X-ray crystallography and membrane fusion assays reveal that B6 binds to a conserved cryptic epitope located in the fusion machinery. The data indicate that antibody binding sterically interferes with the spike conformational changes leading to membrane fusion. Our data provide a structural framework explaining B6 cross-reactivity with β-coronaviruses from three lineages, along with a proof of concept for antibody-mediated broad coronavirus neutralization elicited through vaccination. This study unveils an unexpected target for next-generation structure-guided design of a pan-β-coronavirus vaccine.
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59
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Chuang GY, Shen CH, Cheung CSF, Gorman J, Creanga A, Joyce MG, Leung K, Rawi R, Wang L, Yang ES, Yang Y, Zhang B, Zhang Y, Kanekiyo M, Zhou T, DeKosky BJ, Graham BS, Mascola JR, Kwong PD. Sequence-Signature Optimization Enables Improved Identification of Human HV6-1-Derived Class Antibodies That Neutralize Diverse Influenza A Viruses. Front Immunol 2021; 12:662909. [PMID: 34135892 PMCID: PMC8201785 DOI: 10.3389/fimmu.2021.662909] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/26/2021] [Indexed: 11/13/2022] Open
Abstract
Sequence signatures of multidonor broadly neutralizing influenza antibodies can be used to quantify the prevalence of B cells with virus-neutralizing potential to accelerate development of broadly protective vaccine strategies. Antibodies of the same class share similar recognition modes and developmental pathways, and several antibody classes have been identified that neutralize diverse group 1- and group 2-influenza A viruses and have been observed in multiple human donors. One such multidonor antibody class, the HV6-1-derived class, targets the stem region of hemagglutinin with extraordinary neutralization breadth. Here, we use an iterative process to combine informatics, biochemical, and structural analyses to delineate an improved sequence signature for HV6-1-class antibodies. Based on sequence and structure analyses of known HV6-1 class antibodies, we derived a more inclusive signature (version 1), which we used to search for matching B-cell transcripts from published next-generation sequencing datasets of influenza vaccination studies. We expressed selected antibodies, evaluated their function, and identified amino acid-level requirements from which to refine the sequence signature (version 2). The cryo-electron microscopy structure for one of the signature-identified antibodies in complex with hemagglutinin confirmed motif recognition to be similar to known HV6-1-class members, MEDI8852 and 56.a.09, despite differences in recognition-loop length. Threading indicated the refined signature to have increased accuracy, and signature-identified heavy chains, when paired with the light chain of MEDI8852, showed neutralization comparable to the most potent members of the class. Incorporating sequences of additional class members thus enables an improved sequence signature for HV6-1-class antibodies, which can identify class members with increased accuracy.
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Affiliation(s)
- Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Chen-Hsiang Shen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Crystal Sao-Fong Cheung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Adrian Creanga
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - M Gordon Joyce
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Kwanyee Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Yongping Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Brandon J DeKosky
- Department of Pharmaceutical Chemistry and Department of Chemical Engineering, University of Kansas, Lawrence, KS, United States
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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60
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Keeler SP, Fox JM. Requirement of Fc-Fc Gamma Receptor Interaction for Antibody-Based Protection against Emerging Virus Infections. Viruses 2021; 13:v13061037. [PMID: 34072720 PMCID: PMC8226613 DOI: 10.3390/v13061037] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/13/2022] Open
Abstract
Identification of therapeutics against emerging and re-emerging viruses remains a continued priority that is only reinforced by the recent SARS-CoV-2 pandemic. Advances in monoclonal antibody (mAb) isolation, characterization, and production make it a viable option for rapid treatment development. While mAbs are traditionally screened and selected based on potency of neutralization in vitro, it is clear that additional factors contribute to the in vivo efficacy of a mAb beyond viral neutralization. These factors include interactions with Fc receptors (FcRs) and complement that can enhance neutralization, clearance of infected cells, opsonization of virions, and modulation of the innate and adaptive immune response. In this review, we discuss recent studies, primarily using mouse models, that identified a role for Fc-FcγR interactions for optimal antibody-based protection against emerging and re-emerging virus infections.
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Affiliation(s)
- Shamus P. Keeler
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA;
| | - Julie M. Fox
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Correspondence:
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61
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Paquin-Proulx D, Gunn BM, Alrubayyi A, Clark DV, Creegan M, Kim D, Kibuuka H, Millard M, Wakabi S, Eller LA, Michael NL, Schoepp RJ, Hepburn MJ, Hensley LE, Robb ML, Alter G, Eller MA. Associations Between Antibody Fc-Mediated Effector Functions and Long-Term Sequelae in Ebola Virus Survivors. Front Immunol 2021; 12:682120. [PMID: 34093585 PMCID: PMC8173169 DOI: 10.3389/fimmu.2021.682120] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/05/2021] [Indexed: 11/13/2022] Open
Abstract
Antibodies that mediate non-neutralizing functions play an important role in the immune response to Ebola virus (EBOV) and are thought to impact disease outcome. EBOV has also been associated with long term sequelae in survivors, however, the extent to which antibodies that mediate non-neutralizing functions are associated with the development of these sequelae is unknown. Here, the presence of antibodies mediating different effector functions and how they relate to long-term sequelae two years after the 2007 Bundibugyo Ebola virus (BDBV) outbreak was investigated. The majority of survivors demonstrated robust antibody effector functional activity and demonstrated persistent polyfunctional antibody profiles to the EBOV glycoprotein (GP) two years after infection. These functions were strongly associated with the levels of GP-specific IgG1. The odds of developing hearing loss, one of the more common sequelae to BDBV was reduced when antibodies mediating antibody dependent cellular phagocytosis (ADCP), antibody dependent complement deposition (ADCD), or activating NK cells (ADNKA) were observed. In addition, hearing loss was associated with increased levels of several pro-inflammatory cytokines and levels of these pro-inflammatory cytokines were associated with lower ADCP. These results are indicating that a skewed antibody profile and persistent inflammation may contribute to long term outcome in survivors of BDBV infection.
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Affiliation(s)
- Dominic Paquin-Proulx
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
| | - Bronwyn M Gunn
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
| | - Aljawharah Alrubayyi
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
| | - Danielle V Clark
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
| | - Matthew Creegan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
| | - Dohoon Kim
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
| | - Hannah Kibuuka
- Makerere University Walter Reed Project, Kampala, Uganda
| | - Monica Millard
- Makerere University Walter Reed Project, Kampala, Uganda
| | - Salim Wakabi
- Makerere University Walter Reed Project, Kampala, Uganda
| | - Leigh Anne Eller
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
| | - Nelson L Michael
- Center for Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Randal J Schoepp
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, United States
| | - Matthew J Hepburn
- Medical Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, United States
| | - Lisa E Hensley
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, United States
| | - Merlin L Robb
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
| | - Michael A Eller
- Vaccine Research Program, Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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62
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He L, Chaudhary A, Lin X, Sou C, Alkutkar T, Kumar S, Ngo T, Kosviner E, Ozorowski G, Stanfield RL, Ward AB, Wilson IA, Zhu J. Single-component multilayered self-assembling nanoparticles presenting rationally designed glycoprotein trimers as Ebola virus vaccines. Nat Commun 2021; 12:2633. [PMID: 33976149 DOI: 10.1101/2020.08.22.262634] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 04/06/2021] [Indexed: 05/27/2023] Open
Abstract
Ebola virus (EBOV) glycoprotein (GP) can be recognized by neutralizing antibodies (NAbs) and is the main target for vaccine design. Here, we first investigate the contribution of the stalk and heptad repeat 1-C (HR1C) regions to GP metastability. Specific stalk and HR1C modifications in a mucin-deleted form (GPΔmuc) increase trimer yield, whereas alterations of HR1C exert a more complex effect on thermostability. Crystal structures are determined to validate two rationally designed GPΔmuc trimers in their unliganded state. We then display a modified GPΔmuc trimer on reengineered protein nanoparticles that encapsulate a layer of locking domains (LD) and a cluster of helper T-cell epitopes. In mice and rabbits, GP trimers and nanoparticles elicit cross-ebolavirus NAbs, as well as non-NAbs that enhance pseudovirus infection. Repertoire sequencing reveals quantitative profiles of vaccine-induced B-cell responses. This study demonstrates a promising vaccine strategy for filoviruses, such as EBOV, based on GP stabilization and nanoparticle display.
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MESH Headings
- Animals
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
- Antigens, Viral/administration & dosage
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Antigens, Viral/ultrastructure
- B-Lymphocytes/immunology
- Crystallography, X-Ray
- Disease Models, Animal
- Ebola Vaccines/administration & dosage
- Ebola Vaccines/genetics
- Ebola Vaccines/immunology
- Ebolavirus/genetics
- Ebolavirus/immunology
- Epitopes, T-Lymphocyte/administration & dosage
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/ultrastructure
- Female
- Glycoproteins/administration & dosage
- Glycoproteins/genetics
- Glycoproteins/immunology
- Glycoproteins/ultrastructure
- Hemorrhagic Fever, Ebola/blood
- Hemorrhagic Fever, Ebola/immunology
- Hemorrhagic Fever, Ebola/therapy
- Hemorrhagic Fever, Ebola/virology
- Humans
- Mice
- Nanoparticles/chemistry
- Protein Domains/genetics
- Protein Domains/immunology
- Protein Engineering
- Protein Multimerization/genetics
- Protein Multimerization/immunology
- Protein Stability
- Rabbits
- T-Lymphocytes, Helper-Inducer/immunology
- Vaccines, Subunit/administration & dosage
- Vaccines, Subunit/genetics
- Vaccines, Subunit/immunology
- Viral Proteins/administration & dosage
- Viral Proteins/genetics
- Viral Proteins/immunology
- Viral Proteins/ultrastructure
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Affiliation(s)
- Linling He
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Anshul Chaudhary
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Xiaohe Lin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Cindy Sou
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Tanwee Alkutkar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sonu Kumar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Timothy Ngo
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ezra Kosviner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Robyn L Stanfield
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Jiang Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
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63
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He L, Chaudhary A, Lin X, Sou C, Alkutkar T, Kumar S, Ngo T, Kosviner E, Ozorowski G, Stanfield RL, Ward AB, Wilson IA, Zhu J. Single-component multilayered self-assembling nanoparticles presenting rationally designed glycoprotein trimers as Ebola virus vaccines. Nat Commun 2021; 12:2633. [PMID: 33976149 PMCID: PMC8113551 DOI: 10.1038/s41467-021-22867-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 04/06/2021] [Indexed: 12/17/2022] Open
Abstract
Ebola virus (EBOV) glycoprotein (GP) can be recognized by neutralizing antibodies (NAbs) and is the main target for vaccine design. Here, we first investigate the contribution of the stalk and heptad repeat 1-C (HR1C) regions to GP metastability. Specific stalk and HR1C modifications in a mucin-deleted form (GPΔmuc) increase trimer yield, whereas alterations of HR1C exert a more complex effect on thermostability. Crystal structures are determined to validate two rationally designed GPΔmuc trimers in their unliganded state. We then display a modified GPΔmuc trimer on reengineered protein nanoparticles that encapsulate a layer of locking domains (LD) and a cluster of helper T-cell epitopes. In mice and rabbits, GP trimers and nanoparticles elicit cross-ebolavirus NAbs, as well as non-NAbs that enhance pseudovirus infection. Repertoire sequencing reveals quantitative profiles of vaccine-induced B-cell responses. This study demonstrates a promising vaccine strategy for filoviruses, such as EBOV, based on GP stabilization and nanoparticle display. Ebola virus glycoprotein (GP) is a major target for vaccine design. Here, the authors identify mutations to improve GP stability and yield, design two multilayered nanoparticle carriers, and demonstrate good immunogenicity of the modified GP on nanoparticles in mice and rabbits.
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Affiliation(s)
- Linling He
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Anshul Chaudhary
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Xiaohe Lin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Cindy Sou
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Tanwee Alkutkar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sonu Kumar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Timothy Ngo
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ezra Kosviner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Robyn L Stanfield
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA. .,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Jiang Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA. .,Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
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64
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Wec AZ, Lin KS, Kwasnieski JC, Sinai S, Gerold J, Kelsic ED. Overcoming Immunological Challenges Limiting Capsid-Mediated Gene Therapy With Machine Learning. Front Immunol 2021; 12:674021. [PMID: 33986759 PMCID: PMC8112259 DOI: 10.3389/fimmu.2021.674021] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/09/2021] [Indexed: 12/11/2022] Open
Abstract
A key hurdle to making adeno-associated virus (AAV) capsid mediated gene therapy broadly beneficial to all patients is overcoming pre-existing and therapy-induced immune responses to these vectors. Recent advances in high-throughput DNA synthesis, multiplexing and sequencing technologies have accelerated engineering of improved capsid properties such as production yield, packaging efficiency, biodistribution and transduction efficiency. Here we outline how machine learning, advances in viral immunology, and high-throughput measurements can enable engineering of a new generation of de-immunized capsids beyond the antigenic landscape of natural AAVs, towards expanding the therapeutic reach of gene therapy.
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Affiliation(s)
- Anna Z. Wec
- Applied Biology, Dyno Therapeutics Inc, Cambridge, MA, United States
| | - Kathy S. Lin
- Data Science, Dyno Therapeutics Inc, Cambridge, MA, United States
| | | | - Sam Sinai
- Data Science, Dyno Therapeutics Inc, Cambridge, MA, United States
| | - Jeff Gerold
- Data Science, Dyno Therapeutics Inc, Cambridge, MA, United States
| | - Eric D. Kelsic
- Applied Biology, Dyno Therapeutics Inc, Cambridge, MA, United States
- Data Science, Dyno Therapeutics Inc, Cambridge, MA, United States
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65
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Gunn BM, Lu R, Slein MD, Ilinykh PA, Huang K, Atyeo C, Schendel SL, Kim J, Cain C, Roy V, Suscovich TJ, Takada A, Halfmann PJ, Kawaoka Y, Pauthner MG, Momoh M, Goba A, Kanneh L, Andersen KG, Schieffelin JS, Grant D, Garry RF, Saphire EO, Bukreyev A, Alter G. A Fc engineering approach to define functional humoral correlates of immunity against Ebola virus. Immunity 2021; 54:815-828.e5. [PMID: 33852832 PMCID: PMC8111768 DOI: 10.1016/j.immuni.2021.03.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 01/28/2021] [Accepted: 03/16/2021] [Indexed: 01/31/2023]
Abstract
Protective Ebola virus (EBOV) antibodies have neutralizing activity and induction of antibody constant domain (Fc)-mediated innate immune effector functions. Efforts to enhance Fc effector functionality often focus on maximizing antibody-dependent cellular cytotoxicity, yet distinct combinations of functions could be critical for antibody-mediated protection. As neutralizing antibodies have been cloned from EBOV disease survivors, we sought to identify survivor Fc effector profiles to help guide Fc optimization strategies. Survivors developed a range of functional antibody responses, and we therefore applied a rapid, high-throughput Fc engineering platform to define the most protective profiles. We generated a library of Fc variants with identical antigen-binding fragments (Fabs) from an EBOV neutralizing antibody. Fc variants with antibody-mediated complement deposition and moderate natural killer (NK) cell activity demonstrated complete protective activity in a stringent in vivo mouse model. Our findings highlight the importance of specific effector functions in antibody-mediated protection, and the experimental platform presents a generalizable resource for identifying correlates of immunity to guide therapeutic antibody design.
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Affiliation(s)
- Bronwyn M Gunn
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Richard Lu
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Matthew D Slein
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Philipp A Ilinykh
- Department of Pathology, University of Texas Medical Branch at Galveston, Galveston, TX, USA; Galveston National Laboratory, Galveston, TX, USA
| | - Kai Huang
- Department of Pathology, University of Texas Medical Branch at Galveston, Galveston, TX, USA; Galveston National Laboratory, Galveston, TX, USA
| | - Caroline Atyeo
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | | | - Jiyoung Kim
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Caitlin Cain
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Vicky Roy
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | | | - Ayato Takada
- Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Peter J Halfmann
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI, USA
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI, USA
| | - Matthias G Pauthner
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA, USA
| | - Mambu Momoh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
| | - Augustine Goba
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
| | - Lansana Kanneh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
| | - Kristian G Andersen
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA, USA; Scripps Research Translational Institute, La Jolla, CA, USA
| | - John S Schieffelin
- Department of Pediatrics, Tulane University School of Medicine, New Orleans, LA, USA
| | - Donald Grant
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Robert F Garry
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, USA
| | | | - Alexander Bukreyev
- Department of Pathology, University of Texas Medical Branch at Galveston, Galveston, TX, USA; Galveston National Laboratory, Galveston, TX, USA; Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, TX, USA.
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.
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66
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Convergence of a common solution for broad ebolavirus neutralization by glycan cap-directed human antibodies. Cell Rep 2021; 35:108984. [PMID: 33852862 PMCID: PMC8133395 DOI: 10.1016/j.celrep.2021.108984] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 02/19/2021] [Accepted: 03/23/2021] [Indexed: 11/23/2022] Open
Abstract
Antibodies that target the glycan cap epitope on the ebolavirus glycoprotein (GP) are common in the adaptive response of survivors. A subset is known to be broadly neutralizing, but the details of their epitopes and basis for neutralization are not well understood. Here, we present cryoelectron microscopy (cryo-EM) structures of diverse glycan cap antibodies that variably synergize with GP base-binding antibodies. These structures describe a conserved site of vulnerability that anchors the mucin-like domains (MLDs) to the glycan cap, which we call the MLD anchor and cradle. Antibodies that bind to the MLD cradle share common features, including use of IGHV1–69 and IGHJ6 germline genes, which exploit hydrophobic residues and form β-hairpin structures to mimic the MLD anchor, disrupt MLD attachment, destabilize GP quaternary structure, and block cleavage events required for receptor binding. Our results provide a molecular basis for ebolavirus neutralization by broadly reactive glycan cap antibodies. A rare subset of ebolavirus antibodies targeting the glycan cap are broadly neutralizing. Murin et al. report cryo-EM structures and custom in vitro assays identifying a conserved site of vulnerability in the glycan cap and detail mechanisms of action, including structural mimicry, trimer instability, and blocking cleavage.
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67
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Cross RW, Bornholdt ZA, Prasad AN, Borisevich V, Agans KN, Deer DJ, Abelson DM, Kim DH, Shestowsky WS, Campbell LA, Bunyan E, Geisbert JB, Fenton KA, Zeitlin L, Porter DP, Geisbert TW. Combination therapy protects macaques against advanced Marburg virus disease. Nat Commun 2021; 12:1891. [PMID: 33767178 PMCID: PMC7994808 DOI: 10.1038/s41467-021-22132-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/03/2021] [Indexed: 11/08/2022] Open
Abstract
Monoclonal antibodies (mAbs) and remdesivir, a small-molecule antiviral, are promising monotherapies for many viruses, including members of the genera Marburgvirus and Ebolavirus (family Filoviridae), and more recently, SARS-CoV-2. One of the major challenges of acute viral infections is the treatment of advanced disease. Thus, extending the window of therapeutic intervention is critical. Here, we explore the benefit of combination therapy with a mAb and remdesivir in a non-human primate model of Marburg virus (MARV) disease. While rhesus monkeys are protected against lethal infection when treatment with either a human mAb (MR186-YTE; 100%), or remdesivir (80%), is initiated 5 days post-inoculation (dpi) with MARV, no animals survive when either treatment is initiated alone beginning 6 dpi. However, by combining MR186-YTE with remdesivir beginning 6 dpi, significant protection (80%) is achieved, thereby extending the therapeutic window. These results suggest value in exploring combination therapy in patients presenting with advanced filovirus disease.
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Affiliation(s)
- Robert W Cross
- Galveston National Laboratory, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, USA
| | | | - Abhishek N Prasad
- Galveston National Laboratory, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, USA
| | - Viktoriya Borisevich
- Galveston National Laboratory, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, USA
| | - Krystle N Agans
- Galveston National Laboratory, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, USA
| | - Daniel J Deer
- Galveston National Laboratory, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, USA
| | - Dafna M Abelson
- Mapp Biopharmaceutical, Inc., 6160 Lusk Blvd Ste C200, San Diego, CA, USA
| | - Do H Kim
- Mapp Biopharmaceutical, Inc., 6160 Lusk Blvd Ste C200, San Diego, CA, USA
| | | | | | - Elaine Bunyan
- Gilead Sciences, Inc., 333 Lakeside Dr, Foster City, CA, USA
| | - Joan B Geisbert
- Galveston National Laboratory, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, USA
| | - Karla A Fenton
- Galveston National Laboratory, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, USA
| | - Larry Zeitlin
- Mapp Biopharmaceutical, Inc., 6160 Lusk Blvd Ste C200, San Diego, CA, USA.
| | | | - Thomas W Geisbert
- Galveston National Laboratory, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, USA.
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, USA.
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68
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Wang Y, Howell KA, Brannan J, Agans KN, Turner HL, Wirchnianski AS, Kailasan S, Fusco M, Galkin A, Chiang CI, Zhao X, Saphire EO, Chandran K, Ward AB, Dye JM, Aman MJ, Geisbert TW, Li Y. Prominent Neutralizing Antibody Response Targeting the Ebolavirus Glycoprotein Subunit Interface Elicited by Immunization. J Virol 2021; 95:JVI.01907-20. [PMID: 33536172 PMCID: PMC8103683 DOI: 10.1128/jvi.01907-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/13/2021] [Indexed: 12/21/2022] Open
Abstract
The severe death toll caused by the recent outbreak of Ebola virus disease reinforces the importance of developing ebolavirus prevention and treatment strategies. Here, we have explored the immunogenicity of a novel immunization regimen priming with vesicular stomatitis virus particles bearing Sudan Ebola virus (SUDV) glycoprotein (GP) that consists of GP1 & GP2 subunits and boosting with soluble SUDV GP in macaques, which developed robust neutralizing antibody (nAb) responses following immunizations. Moreover, EB46, a protective nAb isolated from one of the immune macaques, is found to target the GP1/GP2 interface, with GP-binding mode and neutralization mechanism similar to a number of ebolavirus nAbs from human and mouse, indicating that the ebolavirus GP1/GP2 interface is a common immunological target in different species. Importantly, selected immune macaque polyclonal sera showed nAb specificity similar to EB46 at substantial titers, suggesting that the GP1/GP2 interface region is a viable target for ebolavirus vaccine.Importance: The elicitation of sustained neutralizing antibody (nAb) responses against diverse ebolavirus strains remains as a high priority for the vaccine field. The most clinically advanced rVSV-ZEBOV vaccine could elicit moderate nAb responses against only one ebolavirus strain, EBOV, among the five ebolavirus strains, which last less than 6 months. Boost immunization strategies are desirable to effectively recall the rVSV vector-primed nAb responses to prevent infections in prospective epidemics, while an in-depth understanding of the specificity of immunization-elicited nAb responses is essential for improving vaccine performance. Here, using non-human primate animal model, we demonstrated that booster immunization with a stabilized trimeric soluble form of recombinant glycoprotein derived from the ebolavirus Sudan strain following the priming rVSV vector immunization led to robust nAb responses that substantially map to the subunit interface of ebolavirus glycoprotein, a common B cell repertoire target of multiple species including primates and rodents.
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Affiliation(s)
- Yimeng Wang
- Institute for Bioscience and Biotechnology Research, Rockville, MD
| | | | - Jennifer Brannan
- US Army Medical Research Institute of Infectious Diseases, Frederick, MD
| | - Krystle N Agans
- Galveston National Laboratory and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX
- Galveston National Laboratory and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX
| | - Hannah L Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA
| | - Ariel S Wirchnianski
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY
| | | | - Marnie Fusco
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA
| | - Andrey Galkin
- Institute for Bioscience and Biotechnology Research, Rockville, MD
- La Jolla Institute for Immunology, La Jolla, CA
| | - Chi-I Chiang
- Institute for Bioscience and Biotechnology Research, Rockville, MD
| | - Xuelian Zhao
- Institute for Bioscience and Biotechnology Research, Rockville, MD
| | | | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA
| | - John M Dye
- US Army Medical Research Institute of Infectious Diseases, Frederick, MD
| | | | - Thomas W Geisbert
- Galveston National Laboratory and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX
- Galveston National Laboratory and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX
| | - Yuxing Li
- Institute for Bioscience and Biotechnology Research, Rockville, MD
- Department of Microbiology and Immunology and Center of Biomolecular Therapeutics, University of Maryland School of Medicine, Baltimore, MD
- Department of Microbiology and Immunology and Center of Biomolecular Therapeutics, University of Maryland School of Medicine, Baltimore, MD
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69
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Ripoll DR, Chaudhury S, Wallqvist A. Using the antibody-antigen binding interface to train image-based deep neural networks for antibody-epitope classification. PLoS Comput Biol 2021; 17:e1008864. [PMID: 33780441 PMCID: PMC8032195 DOI: 10.1371/journal.pcbi.1008864] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 04/08/2021] [Accepted: 03/10/2021] [Indexed: 12/05/2022] Open
Abstract
High-throughput B-cell sequencing has opened up new avenues for investigating complex mechanisms underlying our adaptive immune response. These technological advances drive data generation and the need to mine and analyze the information contained in these large datasets, in particular the identification of therapeutic antibodies (Abs) or those associated with disease exposure and protection. Here, we describe our efforts to use artificial intelligence (AI)-based image-analyses for prospective classification of Abs based solely on sequence information. We hypothesized that Abs recognizing the same part of an antigen share a limited set of features at the binding interface, and that the binding site regions of these Abs share share common structure and physicochemical property patterns that can serve as a "fingerprint" to recognize uncharacterized Abs. We combined large-scale sequence-based protein-structure predictions to generate ensembles of 3-D Ab models, reduced the Ab binding interface to a 2-D image (fingerprint), used pre-trained convolutional neural networks to extract features, and trained deep neural networks (DNNs) to classify Abs. We evaluated this approach using Ab sequences derived from human HIV and Ebola viral infections to differentiate between two Abs, Abs belonging to specific B-cell family lineages, and Abs with different epitope preferences. In addition, we explored a different type of DNN method to detect one class of Abs from a larger pool of Abs. Testing on Ab sets that had been kept aside during model training, we achieved average prediction accuracies ranging from 71-96% depending on the complexity of the classification task. The high level of accuracies reached during these classification tests suggests that the DNN models were able to learn a series of structural patterns shared by Abs belonging to the same class. The developed methodology provides a means to apply AI-based image recognition techniques to analyze high-throughput B-cell sequencing datasets (repertoires) for Ab classification.
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Affiliation(s)
- Daniel R. Ripoll
- DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. (HJF), Bethesda, Maryland, United States of America
| | - Sidhartha Chaudhury
- DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, Maryland, United States of America
- Center for Enabling Capabilities, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Anders Wallqvist
- DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, Maryland, United States of America
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70
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Misasi J, Sullivan NJ. Immunotherapeutic strategies to target vulnerabilities in the Ebolavirus glycoprotein. Immunity 2021; 54:412-436. [PMID: 33691133 DOI: 10.1016/j.immuni.2021.01.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 01/15/2021] [Accepted: 01/20/2021] [Indexed: 12/18/2022]
Abstract
The 2014 Ebola virus disease (EVD) outbreak in West Africa and the subsequent outbreaks of 2018-2020 in Equator and North Kivu provinces of the Democratic Republic of the Congo illustrate the public health challenges of emerging and reemerging viruses. EVD has a high case fatality rate with a rapidly progressing syndrome of fever, rash, vomiting, diarrhea, and bleeding diathesis. Recently, two monoclonal-antibody-based therapies received United States Food and Drug Administration (FDA) approval, and there are several other passive immunotherapies that hold promise as therapeutics against other species of Ebolavirus. Here, we review concepts needed to understand mechanisms of action, present an expanded schema to define additional sites of vulnerability on the viral glycoprotein, and review current antibody-based therapeutics. The concepts described are used to gain insights into the key characteristics that represent functional targets for immunotherapies against Zaire Ebolavirus and other emerging viruses within the Ebolavirus genus.
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Affiliation(s)
- John Misasi
- National Institutes of Health, National Institute of Allergy and Infectious Diseases, Vaccine Research Center, 40 Convent Drive, Bethesda, MD 20892, USA
| | - Nancy J Sullivan
- National Institutes of Health, National Institute of Allergy and Infectious Diseases, Vaccine Research Center, 40 Convent Drive, Bethesda, MD 20892, USA.
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71
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Longet S, Mellors J, Carroll MW, Tipton T. Ebolavirus: Comparison of Survivor Immunology and Animal Models in the Search for a Correlate of Protection. Front Immunol 2021; 11:599568. [PMID: 33679690 PMCID: PMC7935512 DOI: 10.3389/fimmu.2020.599568] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 12/29/2020] [Indexed: 01/21/2023] Open
Abstract
Ebola viruses are enveloped, single-stranded RNA viruses belonging to the Filoviridae family and can cause Ebola virus disease (EVD), a serious haemorrhagic illness with up to 90% mortality. The disease was first detected in Zaire (currently the Democratic Republic of Congo) in 1976. Since its discovery, Ebola virus has caused sporadic outbreaks in Africa and was responsible for the largest 2013-2016 EVD epidemic in West Africa, which resulted in more than 28,600 cases and over 11,300 deaths. This epidemic strengthened international scientific efforts to contain the virus and develop therapeutics and vaccines. Immunology studies in animal models and survivors, as well as clinical trials have been crucial to understand Ebola virus pathogenesis and host immune responses, which has supported vaccine development. This review discusses the major findings that have emerged from animal models, studies in survivors and vaccine clinical trials and explains how these investigations have helped in the search for a correlate of protection.
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Affiliation(s)
- Stephanie Longet
- Public Health England, National Infection Service, Salisbury, United Kingdom
| | - Jack Mellors
- Public Health England, National Infection Service, Salisbury, United Kingdom
| | - Miles W. Carroll
- Public Health England, National Infection Service, Salisbury, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Tom Tipton
- Public Health England, National Infection Service, Salisbury, United Kingdom
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72
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Fan P, Chi X, Liu G, Zhang G, Chen Z, Liu Y, Fang T, Li J, Banadyga L, He S, Yu C, Qiu X, Chen W. Potent neutralizing monoclonal antibodies against Ebola virus isolated from vaccinated donors. MAbs 2021; 12:1742457. [PMID: 32213108 PMCID: PMC7153831 DOI: 10.1080/19420862.2020.1742457] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Ebola virus (EBOV) can cause severe hemorrhagic fever in humans, and no approved treatment is currently available. Although several antibodies have achieved good protection in animal models, the potential emerging isolates of ebolavirus and the unknown effects of experimental antibodies in humans underscore the need to develop additional antibodies to address the threat of Ebola. Here, we isolated a series of memory B cell-derived monoclonal antibodies from healthy Chinese adults vaccinated with Ad5-EBOV. These antibodies were encoded by diverse germline genes and had high levels of somatic hypermutation. Most antibodies were cross-reactive and could bind at least two ebolavirus glycoproteins (GPs). Seven neutralizing antibodies were identified using HIV-EBOV GP-Luc pseudovirus, and they effectively neutralized authentic EBOV. In particular, monoclonal antibody 2G1 exhibited potent cross-neutralization against HIV-EBOV/SUDV/BDBV GP-Luc bearing different ebolavirus GPs. We used truncated GPs, competition assays, and software prediction to analyze seven neutralizing antibodies, which bound four different epitopes on GP. Importantly, three of these antibodies provided complete protection in mice when administered one day post-infection. Our study expands the list of candidate antibodies and the options for successfully treating ebolavirus infection.
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Affiliation(s)
- Pengfei Fan
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Xiangyang Chi
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Guodong Liu
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Guanying Zhang
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Zhengshan Chen
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Yujiao Liu
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Ting Fang
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Jianmin Li
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Logan Banadyga
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Shihua He
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Changming Yu
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Xiangguo Qiu
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Wei Chen
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China
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73
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Powell A, Zhang K, Sanyal M, Tang S, Weidenbacher PA, Li S, Pham TD, Pak JE, Chiu W, Kim PS. A Single Immunization with Spike-Functionalized Ferritin Vaccines Elicits Neutralizing Antibody Responses against SARS-CoV-2 in Mice. ACS CENTRAL SCIENCE 2021; 7:183-199. [PMID: 33527087 PMCID: PMC7805605 DOI: 10.1021/acscentsci.0c01405] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Indexed: 05/05/2023]
Abstract
The development of a safe and effective SARS-CoV-2 vaccine is a public health priority. We designed subunit vaccine candidates using self-assembling ferritin nanoparticles displaying one of two multimerized SARS-CoV-2 spikes: full-length ectodomain (S-Fer) or a C-terminal 70 amino-acid deletion (SΔC-Fer). Ferritin is an attractive nanoparticle platform for production of vaccines, and ferritin-based vaccines have been investigated in humans in two separate clinical trials. We confirmed proper folding and antigenicity of spike on the surface of ferritin by cryo-EM and binding to conformation-specific monoclonal antibodies. After a single immunization of mice with either of the two spike ferritin particles, a lentiviral SARS-CoV-2 pseudovirus assay revealed mean neutralizing antibody titers at least 2-fold greater than those in convalescent plasma from COVID-19 patients. Additionally, a single dose of SΔC-Fer elicited significantly higher neutralizing responses as compared to immunization with the spike receptor binding domain (RBD) monomer or spike ectodomain trimer alone. After a second dose, mice immunized with SΔC-Fer exhibited higher neutralizing titers than all other groups. Taken together, these results demonstrate that multivalent presentation of SARS-CoV-2 spike on ferritin can notably enhance elicitation of neutralizing antibodies, thus constituting a viable strategy for single-dose vaccination against COVID-19.
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Affiliation(s)
- Abigail
E. Powell
- Department
of Biochemistry & Stanford ChEM-H, Stanford
University, Stanford, California 94305, United States
| | - Kaiming Zhang
- Department
of Bioengineering & James H. Clark Center, Stanford University, Stanford, California 94305, United States
| | - Mrinmoy Sanyal
- Department
of Biochemistry & Stanford ChEM-H, Stanford
University, Stanford, California 94305, United States
| | - Shaogeng Tang
- Department
of Biochemistry & Stanford ChEM-H, Stanford
University, Stanford, California 94305, United States
| | - Payton A. Weidenbacher
- Department
of Biochemistry & Stanford ChEM-H, Stanford
University, Stanford, California 94305, United States
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Shanshan Li
- Department
of Bioengineering & James H. Clark Center, Stanford University, Stanford, California 94305, United States
| | - Tho D. Pham
- Department
of Pathology, Stanford University, Stanford, California 94305, United States
- Stanford
Blood Center, Palo Alto, California 94304, United States
| | - John E. Pak
- Chan Zuckerberg
Biohub, San Francisco, California 94158, United States
| | - Wah Chiu
- Department
of Bioengineering & James H. Clark Center, Stanford University, Stanford, California 94305, United States
- Chan Zuckerberg
Biohub, San Francisco, California 94158, United States
- Division
of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Peter S. Kim
- Department
of Biochemistry & Stanford ChEM-H, Stanford
University, Stanford, California 94305, United States
- Chan Zuckerberg
Biohub, San Francisco, California 94158, United States
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74
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Direct Intracellular Visualization of Ebola Virus-Receptor Interaction by In Situ Proximity Ligation. mBio 2021; 12:mBio.03100-20. [PMID: 33436438 PMCID: PMC7844541 DOI: 10.1128/mbio.03100-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Ebola virus causes episodic but increasingly frequent outbreaks of severe disease in Middle Africa, as shown by the recently overcome second largest outbreak on record in the Democratic Republic of Congo. Despite considerable effort, FDA-approved antifiloviral therapeutics or targeted interventions are not available yet. Ebola virus (EBOV) entry into host cells comprises stepwise and extensive interactions of the sole viral surface glycoprotein (GP) with multiple host factors. During the intricate process, following virus uptake and trafficking to late endosomal/lysosomal compartments, GP is proteolytically processed to cleaved GP (GPCL) by the endosomal proteases cathepsin B and L, unmasking GP’s receptor-binding site. Engagement of GPCL with the universal filoviral intracellular receptor Niemann-Pick C1 (NPC1) eventually culminates in fusion between viral and cellular membranes, cytoplasmic escape of the viral nucleocapsid, and subsequent infection. Mechanistic delineation of the indispensable GPCL-NPC1-binding step has been severely hampered by the unavailability of a robust cell-based assay assessing interaction of GPCL with full-length endosomal NPC1. Here, we describe a novel in situ assay to monitor GPCL-NPC1 engagement in intact, infected cells. Visualization of the subcellular localization of binding complexes is based on the principle of DNA-assisted, antibody-mediated proximity ligation. Virus-receptor binding monitored by proximity ligation was contingent on GP’s proteolytic cleavage and was sensitive to perturbations in the GPCL-NPC1 interface. Our assay also specifically decoupled detection of virus-receptor binding from steps post-receptor binding, such as membrane fusion and infection. Testing of multiple FDA-approved small-molecule inhibitors revealed that drug treatments inhibited virus entry and GPCL-NPC1 recognition by distinctive mechanisms. Together, here we present a newly established proximity ligation assay, which will allow us to dissect cellular and viral requirements for filovirus-receptor binding and to delineate the mechanisms of action of inhibitors on filovirus entry in a cell-based system.
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75
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Sauer MM, Tortorici MA, Park YJ, Walls AC, Homad L, Acton O, Bowen J, Wang C, Xiong X, de van der Schueren W, Quispe J, Hoffstrom BG, Bosch BJ, McGuire AT, Veesler D. Structural basis for broad coronavirus neutralization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2020.12.29.424482. [PMID: 33398277 PMCID: PMC7781312 DOI: 10.1101/2020.12.29.424482] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Three highly pathogenic β-coronaviruses crossed the animal-to-human species barrier in the past two decades: SARS-CoV, MERS-CoV and SARS-CoV-2. SARS-CoV-2 has infected more than 64 million people worldwide, claimed over 1.4 million lives and is responsible for the ongoing COVID-19 pandemic. We isolated a monoclonal antibody, termed B6, cross-reacting with eight β-coronavirus spike glycoproteins, including all five human-infecting β-coronaviruses, and broadly inhibiting entry of pseudotyped viruses from two coronavirus lineages. Cryo-electron microscopy and X-ray crystallography characterization reveal that B6 binds to a conserved cryptic epitope located in the fusion machinery and indicate that antibody binding sterically interferes with spike conformational changes leading to membrane fusion. Our data provide a structural framework explaining B6 cross-reactivity with β-coronaviruses from three lineages along with proof-of-concept for antibody-mediated broad coronavirus neutralization elicited through vaccination. This study unveils an unexpected target for next-generation structure-guided design of a pan-coronavirus vaccine.
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Affiliation(s)
- Maximilian M. Sauer
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - M. Alexandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institut Pasteur, Unité de Virologie Structurale, Paris, France; CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Leah Homad
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Oliver Acton
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - John Bowen
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Chunyan Wang
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Xiaoli Xiong
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | | | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Benjamin G. Hoffstrom
- Antibody Technology Resource, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Berend-Jan Bosch
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Andrew T. McGuire
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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76
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Ali MG, Zhang Z, Gao Q, Pan M, Rowan EG, Zhang J. Recent advances in therapeutic applications of neutralizing antibodies for virus infections: an overview. Immunol Res 2020; 68:325-339. [PMID: 33161557 PMCID: PMC7648849 DOI: 10.1007/s12026-020-09159-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 10/21/2020] [Indexed: 12/14/2022]
Abstract
Antibodies are considered as an excellent foundation to neutralize pathogens and as highly specific therapeutic agents. Antibodies are generated in response to a vaccine but little use as immunotherapy to combat virus infections. A new generation of broadly cross-reactive and highly potent antibodies has led to a unique chance for them to be used as a medical intervention. Neutralizing antibodies (monoclonal and polyclonal antibodies) are desirable for pharmaceutical products because of their ability to target specific epitopes with their variable domains by precise neutralization mechanisms. The isolation of neutralizing antiviral antibodies has been achieved by Phage displayed antibody libraries, transgenic mice, B cell approaches, and hybridoma technology. Antibody engineering technologies have led to efficacy improvements, to further boost antibody in vivo activities. "Although neutralizing antiviral antibodies have some limitations that hinder their full development as therapeutic agents, the potential for prevention and treatment of infections, including a range of viruses (HIV, Ebola, MERS-COV, CHIKV, SARS-CoV, and SARS-CoV2), are being actively pursued in human clinical trials."
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Affiliation(s)
- Manasik Gumah Ali
- Antibody Engineering Laboratory, School of Life Science & Technology, China Pharmaceutical University, Nanjing, China
| | - Zhening Zhang
- Antibody Engineering Laboratory, School of Life Science & Technology, China Pharmaceutical University, Nanjing, China
| | - Qi Gao
- Antibody Engineering Laboratory, School of Life Science & Technology, China Pharmaceutical University, Nanjing, China
| | - Mingzhu Pan
- Antibody Engineering Laboratory, School of Life Science & Technology, China Pharmaceutical University, Nanjing, China
| | - Edward G Rowan
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University Strathclyde, Glasgow, UK
| | - Juan Zhang
- Antibody Engineering Laboratory, School of Life Science & Technology, China Pharmaceutical University, Nanjing, China.
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77
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Sevvana M, Rogers TF, Miller AS, Long F, Klose T, Beutler N, Lai YC, Parren M, Walker LM, Buda G, Burton DR, Rossmann MG, Kuhn RJ. Structural Basis of Zika Virus Specific Neutralization in Subsequent Flavivirus Infections. Viruses 2020; 12:v12121346. [PMID: 33255202 PMCID: PMC7760643 DOI: 10.3390/v12121346] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/19/2020] [Accepted: 11/20/2020] [Indexed: 02/06/2023] Open
Abstract
Zika virus (ZIKV), a mosquito-borne human flavivirus that causes microcephaly and other neurological disorders, has been a recent focus for the development of flavivirus vaccines and therapeutics. We report here a 4.0 Å resolution structure of the mature ZIKV in complex with ADI-30056, a ZIKV-specific human monoclonal antibody (hMAb) isolated from a ZIKV infected donor with a prior dengue virus infection. The structure shows that the hMAb interactions span across the E protein dimers on the virus surface, inhibiting conformational changes required for the formation of infectious fusogenic trimers similar to the hMAb, ZIKV-117. Structure-based functional analysis, and structure and sequence comparisons, identified ZIKV residues essential for neutralization and crucial for the evolution of highly potent E protein crosslinking Abs in ZIKV. Thus, this epitope, ZIKV’s “Achilles heel”, defined by the contacts between ZIKV and ADI-30056, could be a suitable target for the design of therapeutic antibodies.
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Affiliation(s)
- Madhumati Sevvana
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (M.S.); (A.S.M.); (F.L.); (T.K.); (G.B.); (M.G.R.)
| | - Thomas F. Rogers
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; (T.F.R.); (N.B.); (Y.-C.L.); (M.P.); (D.R.B.)
| | - Andrew S. Miller
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (M.S.); (A.S.M.); (F.L.); (T.K.); (G.B.); (M.G.R.)
| | - Feng Long
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (M.S.); (A.S.M.); (F.L.); (T.K.); (G.B.); (M.G.R.)
| | - Thomas Klose
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (M.S.); (A.S.M.); (F.L.); (T.K.); (G.B.); (M.G.R.)
| | - Nathan Beutler
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; (T.F.R.); (N.B.); (Y.-C.L.); (M.P.); (D.R.B.)
| | - Yen-Chung Lai
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; (T.F.R.); (N.B.); (Y.-C.L.); (M.P.); (D.R.B.)
| | - Mara Parren
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; (T.F.R.); (N.B.); (Y.-C.L.); (M.P.); (D.R.B.)
| | | | - Geeta Buda
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (M.S.); (A.S.M.); (F.L.); (T.K.); (G.B.); (M.G.R.)
| | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; (T.F.R.); (N.B.); (Y.-C.L.); (M.P.); (D.R.B.)
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Michael G. Rossmann
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (M.S.); (A.S.M.); (F.L.); (T.K.); (G.B.); (M.G.R.)
| | - Richard J. Kuhn
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (M.S.); (A.S.M.); (F.L.); (T.K.); (G.B.); (M.G.R.)
- Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA
- Correspondence:
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78
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Rghei AD, van Lieshout LP, Santry LA, Guilleman MM, Thomas SP, Susta L, Karimi K, Bridle BW, Wootton SK. AAV Vectored Immunoprophylaxis for Filovirus Infections. Trop Med Infect Dis 2020; 5:tropicalmed5040169. [PMID: 33182447 PMCID: PMC7709665 DOI: 10.3390/tropicalmed5040169] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 01/07/2023] Open
Abstract
Filoviruses are among the deadliest infectious agents known to man, causing severe hemorrhagic fever, with up to 90% fatality rates. The 2014 Ebola outbreak in West Africa resulted in over 28,000 infections, demonstrating the large-scale human health and economic impact generated by filoviruses. Zaire ebolavirus is responsible for the greatest number of deaths to date and consequently there is now an approved vaccine, Ervebo, while other filovirus species have similar epidemic potential and remain without effective vaccines. Recent clinical success of REGN-EB3 and mAb-114 monoclonal antibody (mAb)-based therapies supports further investigation of this treatment approach for other filoviruses. While efficacious, protection from passive mAb therapies is short-lived, requiring repeat dosing to maintain therapeutic concentrations. An alternative strategy is vectored immunoprophylaxis (VIP), which utilizes an adeno-associated virus (AAV) vector to generate sustained expression of selected mAbs directly in vivo. This approach takes advantage of validated mAb development and enables vectorization of the top candidates to provide long-term immunity. In this review, we summarize the history of filovirus outbreaks, mAb-based therapeutics, and highlight promising AAV vectorized approaches to providing immunity against filoviruses where vaccines are not yet available.
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79
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Heiss K, Heidepriem J, Fischer N, Weber LK, Dahlke C, Jaenisch T, Loeffler FF. Rapid Response to Pandemic Threats: Immunogenic Epitope Detection of Pandemic Pathogens for Diagnostics and Vaccine Development Using Peptide Microarrays. J Proteome Res 2020; 19:4339-4354. [PMID: 32892628 PMCID: PMC7640972 DOI: 10.1021/acs.jproteome.0c00484] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Indexed: 12/18/2022]
Abstract
Emergence and re-emergence of pathogens bearing the risk of becoming a pandemic threat are on the rise. Increased travel and trade, growing population density, changes in urbanization, and climate have a critical impact on infectious disease spread. Currently, the world is confronted with the emergence of a novel coronavirus SARS-CoV-2, responsible for yet more than 800 000 deaths globally. Outbreaks caused by viruses, such as SARS-CoV-2, HIV, Ebola, influenza, and Zika, have increased over the past decade, underlining the need for a rapid development of diagnostics and vaccines. Hence, the rational identification of biomarkers for diagnostic measures on the one hand, and antigenic targets for vaccine development on the other, are of utmost importance. Peptide microarrays can display large numbers of putative target proteins translated into overlapping linear (and cyclic) peptides for a multiplexed, high-throughput antibody analysis. This enabled for example the identification of discriminant/diagnostic epitopes in Zika or influenza and mapping epitope evolution in natural infections versus vaccinations. In this review, we highlight synthesis platforms that facilitate fast and flexible generation of high-density peptide microarrays. We further outline the multifaceted applications of these peptide array platforms for the development of serological tests and vaccines to quickly encounter pandemic threats.
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Affiliation(s)
- Kirsten Heiss
- PEPperPRINT
GmbH, Rischerstrasse
12, 69123 Heidelberg, Germany
| | - Jasmin Heidepriem
- Max
Planck Institute of Colloids and Interfaces, Department of Biomolecular Systems, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - Nico Fischer
- Section
Clinical Tropical Medicine, Department of Infectious Diseases, Heidelberg University Hospital, INF 324, 69120 Heidelberg, Germany
| | - Laura K. Weber
- PEPperPRINT
GmbH, Rischerstrasse
12, 69123 Heidelberg, Germany
- Institute
of Microstructure Technology, Karlsruhe
Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Christine Dahlke
- Division
of Infectious Diseases, First Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- Department
of Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
- German
Center for Infection Research, Partner Site
Hamburg-Lübeck-Borstel-Riems, 38124 Braunschweig, Germany
| | - Thomas Jaenisch
- Heidelberg
Institute of Global Health (HIGH), Heidelberg
University Hospital, Im Neuenheimer Feld 130, 69120 Heidelberg, Germany
- Center
for Global Health, Colorado School of Public Health, University of Colorado, Aurora, Colorado 80045, United States
- Department
of Epidemiology, Colorado School of Public Health, University of Colorado, Aurora, Colorado 80045, United States
| | - Felix F. Loeffler
- Max
Planck Institute of Colloids and Interfaces, Department of Biomolecular Systems, Am Muehlenberg 1, 14476 Potsdam, Germany
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80
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Ralph DK, Matsen FA. Using B cell receptor lineage structures to predict affinity. PLoS Comput Biol 2020; 16:e1008391. [PMID: 33175831 PMCID: PMC7682889 DOI: 10.1371/journal.pcbi.1008391] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 11/23/2020] [Accepted: 08/30/2020] [Indexed: 11/18/2022] Open
Abstract
We are frequently faced with a large collection of antibodies, and want to select those with highest affinity for their cognate antigen. When developing a first-line therapeutic for a novel pathogen, for instance, we might look for such antibodies in patients that have recovered. There exist effective experimental methods of accomplishing this, such as cell sorting and baiting; however they are time consuming and expensive. Next generation sequencing of B cell receptor (BCR) repertoires offers an additional source of sequences that could be tapped if we had a reliable method of selecting those coding for the best antibodies. In this paper we introduce a method that uses evolutionary information from the family of related sequences that share a naive ancestor to predict the affinity of each resulting antibody for its antigen. When combined with information on the identity of the antigen, this method should provide a source of effective new antibodies. We also introduce a method for a related task: given an antibody of interest and its inferred ancestral lineage, which branches in the tree are likely to harbor key affinity-increasing mutations? We evaluate the performance of these methods on a wide variety of simulated samples, as well as two real data samples. These methods are implemented as part of continuing development of the partis BCR inference package, available at https://github.com/psathyrella/partis. Comments Please post comments or questions on this paper as new issues at https://git.io/Jvxkn.
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Affiliation(s)
- Duncan K. Ralph
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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81
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Kofman A, Linderman S, Su K, Purpura LJ, Ervin E, Brown S, Morales-Betoulle M, Graziano J, Cannon DL, Klena JD, Desamu-Thorpe R, Fankhauser J, Orone R, Soka M, Glaybo U, Massaquoi M, Nysenswah T, Nichol ST, Kollie J, Kiawu A, Freeman E, Giah G, Tony H, Faikai M, Jawara M, Kamara K, Kamara S, Flowers B, Mohammed K, Chiriboga D, Williams DE, Hinrichs SH, Ahmed R, Vonhm B, Rollin PE, Choi MJ. Characteristics of Ebola Virus Disease Survivor Blood and Semen in Liberia: Serology and RT-PCR. Clin Infect Dis 2020; 73:e3641-e3646. [PMID: 32894277 DOI: 10.1093/cid/ciaa1331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Indexed: 11/12/2022] Open
Abstract
INTRODUCTION Ebola virus (EBOV), species Zaire ebolavirus, may persist in the semen of male survivors of Ebola Virus Disease (EVD). We conducted a study of male survivors of the 2014-2016 EVD outbreak in Liberia and evaluated their immune responses to EBOV. We report here findings from the serologic testing of blood for EBOV-specific antibodies, molecular testing for EBOV in blood and semen, and serologic testing of peripheral blood mononuclear cells (PBMCs) in a subset of study participants. METHODS We tested for EBOV RNA in blood by qRT-PCR, and for anti-EBOV-specific IgM and IgG antibodies by enzyme-linked immunosorbent assay (ELISA) for 126 study participants. We performed peripheral blood mononuclear cell (PBMC) analysis on a subgroup of 26 IgG-negative participants. RESULTS All 126 participants tested negative for EBOV RNA in blood by qRT-PCR. The blood of 26 participants tested negative for EBOV-specific IgG antibodies by ELISA. PBMCs were collected from 23/26 EBOV IgG-negative participants. Of these, 1/23 participants had PBMCs which produced anti-EBOV-specific IgG antibodies upon stimulation with EBOV-specific GP and NP antigens. DISCUSSION The blood of EVD survivors, collected when they did not have symptoms meeting the case definition for acute or relapsed EVD, is unlikely to pose a risk for EBOV transmission. We identified one IgM/IgG negative participant who had PBMCs which produced anti-EBOV-specific antibodies upon stimulation. Immunogenicity following acute EBOV infection may exist along a spectrum and absence of antibody response should not be exclusionary in determining an individual's status as a survivor of EVD.
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Affiliation(s)
- Aaron Kofman
- Epidemic Intelligence Service, CDC.,Division of High-Consequence Pathogens and Pathology, National Center, for Emerging and Zoonotic Infectious Diseases, CDC
| | | | - Kaihong Su
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - Lawrence J Purpura
- Division of High-Consequence Pathogens and Pathology, National Center, for Emerging and Zoonotic Infectious Diseases, CDC
| | - Elizabeth Ervin
- Division of High-Consequence Pathogens and Pathology, National Center, for Emerging and Zoonotic Infectious Diseases, CDC
| | - Shelley Brown
- Division of High-Consequence Pathogens and Pathology, National Center, for Emerging and Zoonotic Infectious Diseases, CDC
| | - Maria Morales-Betoulle
- Division of High-Consequence Pathogens and Pathology, National Center, for Emerging and Zoonotic Infectious Diseases, CDC
| | | | - Deborah L Cannon
- Division of High-Consequence Pathogens and Pathology, National Center, for Emerging and Zoonotic Infectious Diseases, CDC
| | - John D Klena
- Division of High-Consequence Pathogens and Pathology, National Center, for Emerging and Zoonotic Infectious Diseases, CDC
| | - Rodel Desamu-Thorpe
- Office of, Public Health Preparedness and Response, Center for Preparedness and Response, CDC
| | - John Fankhauser
- ELWA Hospital, Samaritan's Purse.,Ventura County Medical Center, Ventura, CA', CA
| | | | - Moses Soka
- Ministry of Health Liberia, Men's, Health Screening Program, Liberia
| | | | - Moses Massaquoi
- Ministry of Health Liberia, Men's, Health Screening Program, Liberia
| | | | - Stuart T Nichol
- Division of High-Consequence Pathogens and Pathology, National Center, for Emerging and Zoonotic Infectious Diseases, CDC
| | - Jomah Kollie
- Ministry of Health Liberia, Men's, Health Screening Program, Liberia
| | - Armah Kiawu
- University of Massachusetts Medical School, Worcester, MA
| | - Edna Freeman
- University of Massachusetts Medical School, Worcester, MA
| | - Giovanni Giah
- University of Massachusetts Medical School, Worcester, MA
| | - Henry Tony
- University of Massachusetts Medical School, Worcester, MA
| | - Mylene Faikai
- University of Massachusetts Medical School, Worcester, MA
| | - Mary Jawara
- University of Massachusetts Medical School, Worcester, MA
| | - Kuku Kamara
- University of Massachusetts Medical School, Worcester, MA
| | - Samuel Kamara
- Ministry of Health Liberia, Men's, Health Screening Program, Liberia
| | - Benjamin Flowers
- Ministry of Health Liberia, Men's, Health Screening Program, Liberia
| | - Kromah Mohammed
- Ministry of Health Liberia, Men's, Health Screening Program, Liberia
| | | | | | - Steven H Hinrichs
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - Rafi Ahmed
- Emory Vaccine Center, Emory University, Atlanta, GA
| | | | - Pierre E Rollin
- Division of High-Consequence Pathogens and Pathology, National Center, for Emerging and Zoonotic Infectious Diseases, CDC
| | - Mary J Choi
- Division of High-Consequence Pathogens and Pathology, National Center, for Emerging and Zoonotic Infectious Diseases, CDC
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82
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Powell AE, Zhang K, Sanyal M, Tang S, Weidenbacher PA, Li S, Pham TD, Pak JE, Chiu W, Kim PS. A single immunization with spike-functionalized ferritin vaccines elicits neutralizing antibody responses against SARS-CoV-2 in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.08.28.272518. [PMID: 32869030 PMCID: PMC7457616 DOI: 10.1101/2020.08.28.272518] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Development of a safe and effective SARS-CoV-2 vaccine is a public health priority. We designed subunit vaccine candidates using self-assembling ferritin nanoparticles displaying one of two multimerized SARS-CoV-2 spikes: full-length ectodomain (S-Fer) or a C-terminal 70 amino-acid deletion (SΔC-Fer). Ferritin is an attractive nanoparticle platform for production of vaccines and ferritin-based vaccines have been investigated in humans in two separate clinical trials. We confirmed proper folding and antigenicity of spike on the surface of ferritin by cryo-EM and binding to conformation-specific monoclonal antibodies. After a single immunization of mice with either of the two spike ferritin particles, a lentiviral SARS-CoV-2 pseudovirus assay revealed mean neutralizing antibody titers at least 2-fold greater than those in convalescent plasma from COVID-19 patients. Additionally, a single dose of SΔC-Fer elicited significantly higher neutralizing responses as compared to immunization with the spike receptor binding domain (RBD) monomer or spike ectodomain trimer alone. After a second dose, mice immunized with SΔC-Fer exhibited higher neutralizing titers than all other groups. Taken together, these results demonstrate that multivalent presentation of SARS-CoV-2 spike on ferritin can notably enhance elicitation of neutralizing antibodies, thus constituting a viable strategy for single-dose vaccination against COVID-19.
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Affiliation(s)
- Abigail E. Powell
- Department of Biochemistry & Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Kaiming Zhang
- Department of Bioengineering & James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | - Mrinmoy Sanyal
- Department of Biochemistry & Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Shaogeng Tang
- Department of Biochemistry & Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Payton A. Weidenbacher
- Department of Biochemistry & Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Shanshan Li
- Department of Bioengineering & James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | - Tho D. Pham
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- Stanford Blood Center, Palo Alto, CA 94304, USA
| | - John E. Pak
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Wah Chiu
- Department of Bioengineering & James H. Clark Center, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Peter S. Kim
- Department of Biochemistry & Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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83
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Fukuyama J, Olson BJ, Matsen FA. Lack of Evidence for a Substantial Rate of Templated Mutagenesis in B Cell Diversification. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2020; 205:936-944. [PMID: 32669310 PMCID: PMC7593666 DOI: 10.4049/jimmunol.2000092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 06/17/2020] [Indexed: 11/19/2022]
Abstract
BCR sequences diversify through mutations introduced by purpose-built cellular machinery. A recent paper has concluded that a "templated mutagenesis" process is a major contributor to somatic hypermutation and therefore Ig diversification in mice and humans. In this proposed process, mutations in the Ig locus are introduced by copying short segments from other Ig genes. If true, this would overturn decades of research on B cell diversification and would require a complete rewrite of computational methods to analyze B cell data for these species. In this paper, we re-evaluate the templated mutagenesis hypothesis. By applying the original inferential method using potential donor templates absent from B cell genomes, we obtain estimates of the methods' false positive rates. We find false positive rates of templated mutagenesis in murine and human Ig loci that are similar to or even higher than the original rate inferences, and by considering the bases used in substitution, we find evidence that if templated mutagenesis occurs, it is at a low rate. We also show that the statistically significant results in the original paper can easily result from a slight misspecification of the null model.
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Affiliation(s)
- Julia Fukuyama
- Department of Statistics, Indiana University Bloomington, Bloomington, IN 47408
| | - Branden J Olson
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109; and
- Department of Statistics, University of Washington, Seattle, WA 98195
| | - Frederick A Matsen
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109; and
- Department of Statistics, University of Washington, Seattle, WA 98195
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84
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Mapping the diverse structural landscape of the flavivirus antibody repertoire. Curr Opin Virol 2020; 45:51-64. [PMID: 32801077 DOI: 10.1016/j.coviro.2020.07.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/01/2020] [Accepted: 07/07/2020] [Indexed: 02/08/2023]
Abstract
Flaviviruses are emerging arthropod-borne RNA viruses, causing a broad spectrum of life-threatening disease symptoms such as encephalitis and hemorrhagic fever. Successful vaccines exist against yellow fever virus, Japanese encephalitis virus and tick-borne encephalitis virus. However, vaccine development against other flaviviruses like dengue virus is not straightforward. This is partly because of the high sequence conservation and immunological cross-reactivity among flavivirus envelope glycoproteins leading to antibody mediated enhancement of disease. A comprehensive analyses of the structural landscape of humoral immune response against flaviviruses is crucial for antigen design. Here, we compare the available structural data of several flavivirus antibody complexes with a major focus on Zika virus and dengue virus and discuss the mapped epitopes, the stoichiometry of antibody binding and mechanisms of neutralization.
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85
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Gunn BM, Roy V, Karim MM, Hartnett JN, Suscovich TJ, Goba A, Momoh M, Sandi JD, Kanneh L, Andersen KG, Shaffer JG, Schieffelin JS, Garry RF, Grant DS, Alter G. Survivors of Ebola Virus Disease Develop Polyfunctional Antibody Responses. J Infect Dis 2020; 221:156-161. [PMID: 31301137 PMCID: PMC7184900 DOI: 10.1093/infdis/jiz364] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 07/11/2019] [Indexed: 11/21/2022] Open
Abstract
Monoclonal antibodies can mediate protection against Ebola virus (EBOV) infection through direct neutralization as well as through the recruitment of innate immune effector functions. However, the antibody functional response following survival of acute EBOV disease has not been well characterized. In this study, serum antibodies from Ebola virus disease (EVD) survivors from Sierra Leone were profiled to capture variation in overall subclass/isotype abundance, neutralizing activity, and innate immune effector functions. Antibodies from EVD survivors exhibited robust innate immune effector functions, mediated primarily by IgG1 and IgA1. In conclusion, development of functional antibodies follows survival of acute EVD.
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Affiliation(s)
- Bronwyn M Gunn
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts
| | - Vicky Roy
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts
| | - Marcus M Karim
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts
| | - Jessica N Hartnett
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana
| | - Todd J Suscovich
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts
| | - Augustine Goba
- Viral Hemorrhagic Fever Program, Kenema Government Hospital
| | - Mambu Momoh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital.,Eastern Polytechnic University, Kenema, Sierra Leone
| | | | - Lansana Kanneh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital
| | - Kristian G Andersen
- Department of Immunology and Microbiology, Scripps Research Institute.,Scripps Research Translational Institute, La Jolla, California
| | - Jeffrey G Shaffer
- Department of Biostatistics and Bioinformatics, Tulane School of Public Health and Tropical Medicine, New Orleans, Louisiana
| | - John S Schieffelin
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana
| | - Robert F Garry
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana
| | - Donald S Grant
- Viral Hemorrhagic Fever Program, Kenema Government Hospital.,Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Galit Alter
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts
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86
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Integrated pipeline for the accelerated discovery of antiviral antibody therapeutics. Nat Biomed Eng 2020; 4:1030-1043. [PMID: 32747832 PMCID: PMC7655621 DOI: 10.1038/s41551-020-0594-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/26/2020] [Indexed: 02/06/2023]
Abstract
The emergence and re-emergence of highly virulent viral pathogens with pandemic potential creates an urgent need for the accelerated discovery of antiviral therapeutics. Antiviral human monoclonal antibodies (mAbs) are promising candidates to prevent or treat severe viral diseases, but their long development timeframes limit their rapid deployment and use. Here, we report the development of an integrated sequence of technologies, including single-cell mRNA sequence analysis, bioinformatics, synthetic biology and high-throughput functional analysis, that enabled the rapid discovery of highly potent antiviral human mAbs, whose activity we validated in vivo. In a 78-day study modelling the deployment of a rapid response to an outbreak, we isolated more than 100 human mAbs specific for the Zika virus, assessed their function, identified 29 of those as having broadly neutralizing activity, and verified the therapeutic potency of the lead candidates in mice and non-human primate models of infection via the delivery of an antibody-encoding mRNA formulation and of the respective IgG antibody. The pipeline provides a roadmap for rapid antibody-discovery programs against viral pathogens of global concern.
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87
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Loos C, Lauffenburger DA, Alter G. Dissecting the antibody-OME: past, present, and future. Curr Opin Immunol 2020; 65:89-96. [PMID: 32755751 DOI: 10.1016/j.coi.2020.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/24/2020] [Indexed: 02/08/2023]
Abstract
Humoral immunity is key to protection for nearly all licensed vaccines. Yet, the design of vaccines has been more difficult for some of our most deadly killers (e.g. HIV, influenza, Dengue virus, etc.), likely due to our incomplete understanding of the precise immunological mechanisms associated with protection. Humoral immunity is governed both by B-cells and their bi-functional secreted antibodies, all of which have a unique capacity to evolve during an immune response. Current OMIC technologies capture individual features of the humoral immune response, providing a glimpse into humoral components (Fab/Fc/B-cell-omic), but fail to provide a wholistic view of the humoral response as a collective functional arm. Here, we dissect current OMIC strategies reviewing experimental and computational approaches, that if integrated could provide a true systems-level view of the humoral immune response.
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Affiliation(s)
- Carolin Loos
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Galit Alter
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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88
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Yuan TZ, Lujan Hernandez AG, Keane E, Liu Q, Axelrod F, Kailasan S, Noonan-Shueh M, Aman MJ, Sato AK, Abdiche YN. Rapid exploration of the epitope coverage produced by an Ebola survivor to guide the discovery of therapeutic antibody cocktails. Antib Ther 2020; 3:167-178. [PMID: 33912793 PMCID: PMC7454256 DOI: 10.1093/abt/tbaa016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/24/2020] [Accepted: 07/28/2020] [Indexed: 11/17/2022] Open
Abstract
Background Development of successful neutralizing antibodies is dependent upon broad epitope coverage to increase the likelihood of achieving therapeutic function. Recent advances in synthetic biology have allowed us to conduct an epitope binning study on a large panel of antibodies identified to bind to Ebola virus glycoprotein with only published sequences. Methods and Results A rapid, first-pass epitope binning experiment revealed seven distinct epitope families that overlapped with known structural epitopes from the literature. A focused set of antibodies was selected from representative clones per bin to guide a second-pass binning that revealed previously unassigned epitopes, confirmed epitopes known to be associated with neutralizing antibodies, and demonstrated asymmetric blocking of EBOV GP from allosteric effectors reported from literature. Conclusions Critically, this workflow allows us to probe the epitope landscape of EBOV GP without any prior structural knowledge of the antigen or structural benchmark clones. Incorporating epitope binning on hundreds of antibodies during early stage antibody characterization ensures access to a library’s full epitope coverage, aids in the identification of high quality reagents within the library that recapitulate this diversity for use in other studies, and ultimately enables the rational development of therapeutic cocktails that take advantage of multiple mechanisms of action such as cooperative synergistic effects to enhance neutralization function and minimize the risk of mutagenic escape. The use of high-throughput epitope binning during new outbreaks such as the current COVID-19 pandemic is particularly useful in accelerating timelines due to the large amount of information gained in a single experiment.
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Affiliation(s)
- Tom Z Yuan
- Twist Biopharma, Twist Bioscience, South San Francisco, CA 94080, USA
| | | | - Erica Keane
- Twist Biopharma, Twist Bioscience, South San Francisco, CA 94080, USA
| | - Qiang Liu
- Twist Biopharma, Twist Bioscience, South San Francisco, CA 94080, USA
| | - Fumiko Axelrod
- Twist Biopharma, Twist Bioscience, South San Francisco, CA 94080, USA
| | | | | | | | - Aaron K Sato
- Twist Biopharma, Twist Bioscience, South San Francisco, CA 94080, USA
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89
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Ng TW, Wirchnianski AS, Wec AZ, Fels JM, Johndrow CT, Saunders KO, Liao HX, Chan J, Jacobs WR, Chandran K, Porcelli SA. Exploiting Pre-Existing CD4 + T Cell Help from Bacille Calmette-Guérin Vaccination to Improve Antiviral Antibody Responses. THE JOURNAL OF IMMUNOLOGY 2020; 205:425-437. [PMID: 32513849 DOI: 10.4049/jimmunol.2000191] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/12/2020] [Indexed: 12/12/2022]
Abstract
The continuing emergence of viral pathogens and their rapid spread into heavily populated areas around the world underscore the urgency for development of highly effective vaccines to generate protective antiviral Ab responses. Many established and newly emerging viral pathogens, including HIV and Ebola viruses, are most prevalent in regions of the world in which Mycobacterium tuberculosis infection remains endemic and vaccination at birth with M. bovis bacille Calmette-Guérin (BCG) is widely used. We have investigated the potential for using CD4+ T cells arising in response to BCG as a source of help for driving Ab responses against viral vaccines. To test this approach, we designed vaccines comprised of protein immunogens fused to an immunodominant CD4+ T cell epitope of the secreted Ag 85B protein of BCG. Proof-of-concept experiments showed that the presence of BCG-specific Th cells in previously BCG-vaccinated mice had a dose-sparing effect for subsequent vaccination with fusion proteins containing the Ag 85B epitope and consistently induced isotype switching to the IgG2c subclass. Studies using an Ebola virus glycoprotein fused to the Ag 85B epitope showed that prior BCG vaccination promoted high-affinity IgG1 responses that neutralized viral infection. The design of fusion protein vaccines with the ability to recruit BCG-specific CD4+ Th cells may be a useful and broadly applicable approach to generating improved vaccines against a range of established and newly emergent viral pathogens.
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Affiliation(s)
- Tony W Ng
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Ariel S Wirchnianski
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Anna Z Wec
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461.,Adimab, Lebanon, NH 03766
| | - J Maximilian Fels
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Christopher T Johndrow
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Kevin O Saunders
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710; and
| | - Hua-Xin Liao
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710; and
| | - John Chan
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461.,Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461
| | - William R Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Steven A Porcelli
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461; .,Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461
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90
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Rijal P, Elias SC, Machado SR, Xiao J, Schimanski L, O'Dowd V, Baker T, Barry E, Mendelsohn SC, Cherry CJ, Jin J, Labbé GM, Donnellan FR, Rampling T, Dowall S, Rayner E, Findlay-Wilson S, Carroll M, Guo J, Xu XN, Huang KYA, Takada A, Burgess G, McMillan D, Popplewell A, Lightwood DJ, Draper SJ, Townsend AR. Therapeutic Monoclonal Antibodies for Ebola Virus Infection Derived from Vaccinated Humans. Cell Rep 2020; 27:172-186.e7. [PMID: 30943399 DOI: 10.1016/j.celrep.2019.03.020] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 12/10/2018] [Accepted: 03/05/2019] [Indexed: 12/17/2022] Open
Abstract
We describe therapeutic monoclonal antibodies isolated from human volunteers vaccinated with recombinant adenovirus expressing Ebola virus glycoprotein (EBOV GP) and boosted with modified vaccinia virus Ankara. Among 82 antibodies isolated from peripheral blood B cells, almost half neutralized GP pseudotyped influenza virus. The antibody response was diverse in gene usage and epitope recognition. Although close to germline in sequence, neutralizing antibodies with binding affinities in the nano- to pico-molar range, similar to "affinity matured" antibodies from convalescent donors, were found. They recognized the mucin-like domain, glycan cap, receptor binding region, and the base of the glycoprotein. A cross-reactive cocktail of four antibodies, targeting the latter three non-overlapping epitopes, given on day 3 of EBOV infection, completely protected guinea pigs. This study highlights the value of experimental vaccine trials as a rich source of therapeutic human monoclonal antibodies.
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Affiliation(s)
- Pramila Rijal
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Sean C Elias
- Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Samara Rosendo Machado
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Julie Xiao
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Lisa Schimanski
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | | | | | | | - Simon C Mendelsohn
- Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Catherine J Cherry
- Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Jing Jin
- Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Geneviève M Labbé
- Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Francesca R Donnellan
- Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Tommy Rampling
- Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | | | - Emma Rayner
- Public Health England, Porton Down, Wiltshire, UK
| | | | | | - Jia Guo
- Centre for Immunology and Vaccinology, Chelsea & Westminster Hospital, Faculty of Medicine, Imperial College, London, UK
| | - Xiao-Ning Xu
- Centre for Immunology and Vaccinology, Chelsea & Westminster Hospital, Faculty of Medicine, Imperial College, London, UK
| | - Kuan-Ying A Huang
- Division of Paediatric Infectious Diseases, Department of Paediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Ayato Takada
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | | | | | | | | | - Simon J Draper
- Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Alain R Townsend
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
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91
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Wec AZ, Wrapp D, Herbert AS, Maurer D, Haslwanter D, Sakharkar M, Jangra RK, Dieterle ME, Lilov A, Huang D, Tse LV, Johnson NV, Hsieh CL, Wang N, Nett JH, Champney E, Burnina I, Brown M, Lin S, Sinclair M, Johnson C, Pudi S, Bortz R, Wirchnianski AS, Laudermilch E, Florez C, Fels JM, O’Brien CM, Graham BS, Nemazee D, Burton DR, Baric RS, Voss JE, Chandran K, Dye JM, McLellan JS, Walker LM. Broad sarbecovirus neutralizing antibodies define a key site of vulnerability on the SARS-CoV-2 spike protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.05.15.096511. [PMID: 32511337 PMCID: PMC7241100 DOI: 10.1101/2020.05.15.096511] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Broadly protective vaccines against known and pre-emergent coronaviruses are urgently needed. Critical to their development is a deeper understanding of cross-neutralizing antibody responses induced by natural human coronavirus (HCoV) infections. Here, we mined the memory B cell repertoire of a convalescent SARS donor and identified 200 SARS-CoV-2 binding antibodies that target multiple conserved sites on the spike (S) protein. A large proportion of the antibodies display high levels of somatic hypermutation and cross-react with circulating HCoVs, suggesting recall of pre-existing memory B cells (MBCs) elicited by prior HCoV infections. Several antibodies potently cross-neutralize SARS-CoV, SARS-CoV-2, and the bat SARS-like virus WIV1 by blocking receptor attachment and inducing S1 shedding. These antibodies represent promising candidates for therapeutic intervention and reveal a new target for the rational design of pan-sarbecovirus vaccines.
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Affiliation(s)
| | - Daniel Wrapp
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Andrew S. Herbert
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | | | - Denise Haslwanter
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | | | - Rohit K. Jangra
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - M. Eugenia Dieterle
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | | | - Deli Huang
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Longping V. Tse
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nicole V. Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Nianshuang Wang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | | | | | | | | | - Shu Lin
- Adimab LLC, Lebanon, NH 03766, USA
| | | | | | | | - Robert Bortz
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - Ariel S. Wirchnianski
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - Ethan Laudermilch
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - Catalina Florez
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - J. Maximilian Fels
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - Cecilia M. O’Brien
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | | | - David Nemazee
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis R. Burton
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard
| | - Ralph S. Baric
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Departments of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - James E. Voss
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - John M. Dye
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
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92
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Cohen-Dvashi H, Zehner M, Ehrhardt S, Katz M, Elad N, Klein F, Diskin R. Structural Basis for a Convergent Immune Response against Ebola Virus. Cell Host Microbe 2020; 27:418-427.e4. [DOI: 10.1016/j.chom.2020.01.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/31/2019] [Accepted: 01/14/2020] [Indexed: 11/29/2022]
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93
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Fuentes S, Ravichandran S, Coyle EM, Klenow L, Khurana S. Human Antibody Repertoire following Ebola Virus Infection and Vaccination. iScience 2020; 23:100920. [PMID: 32145646 PMCID: PMC7058406 DOI: 10.1016/j.isci.2020.100920] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 01/14/2020] [Accepted: 02/12/2020] [Indexed: 02/07/2023] Open
Abstract
Limited knowledge exists on the quality of polyclonal antibody response generated following Ebola virus (EBOV) infection compared with vaccination. Polyclonal antibody repertoire in plasma following EBOV infection in survivors was compared with ChAd3-MVA prime-boost human vaccination. Higher antibody binding and affinity to GP was observed in survivors compared with vaccinated plasma that correlated with EBOV neutralization. Surprisingly, a predominant IgM response was generated after prime-boost vaccination, whereas survivors demonstrated IgG-dominant antibody response. EBOV infection induced more diverse antibody epitope repertoire compared with vaccination. A strong binding to antigenic sites in the fusion peptide and another in the highly conserved GP2-HR2 domain was preferentially recognized by EBOV survivors than vaccinated individuals that correlated strongly with EBOV neutralization titers. These findings will help development and evaluation of effective Ebola countermeasures including therapeutics and vaccines. EBOV infection induced a more diverse antibody repertoire than vaccination Ebola survivors demonstrated long-lasting, high-affinity, IgG antibody response Several novel antigenic sites recognized by post-EBOV infection sera
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Affiliation(s)
- Sandra Fuentes
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration (FDA), 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Supriya Ravichandran
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration (FDA), 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Elizabeth M Coyle
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration (FDA), 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Laura Klenow
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration (FDA), 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Surender Khurana
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration (FDA), 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA.
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94
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Gilchuk P, Murin CD, Milligan JC, Cross RW, Mire CE, Ilinykh PA, Huang K, Kuzmina N, Altman PX, Hui S, Gunn BM, Bryan AL, Davidson E, Doranz BJ, Turner HL, Alkutkar T, Flinko R, Orlandi C, Carnahan R, Nargi R, Bombardi RG, Vodzak ME, Li S, Okoli A, Ibeawuchi M, Ohiaeri B, Lewis GK, Alter G, Bukreyev A, Saphire EO, Geisbert TW, Ward AB, Crowe JE. Analysis of a Therapeutic Antibody Cocktail Reveals Determinants for Cooperative and Broad Ebolavirus Neutralization. Immunity 2020; 52:388-403.e12. [PMID: 32023489 PMCID: PMC7111202 DOI: 10.1016/j.immuni.2020.01.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 11/14/2019] [Accepted: 01/08/2020] [Indexed: 01/14/2023]
Abstract
Structural principles underlying the composition of protective antiviral monoclonal antibody (mAb) cocktails are poorly defined. Here, we exploited antibody cooperativity to develop a therapeutic mAb cocktail against Ebola virus. We systematically analyzed the antibody repertoire in human survivors and identified a pair of potently neutralizing mAbs that cooperatively bound to the ebolavirus glycoprotein (GP). High-resolution structures revealed that in a two-antibody cocktail, molecular mimicry was a major feature of mAb-GP interactions. Broadly neutralizing mAb rEBOV-520 targeted a conserved epitope on the GP base region. mAb rEBOV-548 bound to a glycan cap epitope, possessed neutralizing and Fc-mediated effector function activities, and potentiated neutralization by rEBOV-520. Remodeling of the glycan cap structures by the cocktail enabled enhanced GP binding and virus neutralization. The cocktail demonstrated resistance to virus escape and protected non-human primates (NHPs) against Ebola virus disease. These data illuminate structural principles of antibody cooperativity with implications for development of antiviral immunotherapeutics.
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Affiliation(s)
- Pavlo Gilchuk
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Charles D. Murin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jacob C. Milligan
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Robert W. Cross
- Galveston National Laboratory, Galveston, TX 77550, USA,Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Chad E. Mire
- Galveston National Laboratory, Galveston, TX 77550, USA,Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Philipp A. Ilinykh
- Galveston National Laboratory, Galveston, TX 77550, USA,Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Kai Huang
- Galveston National Laboratory, Galveston, TX 77550, USA,Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Natalia Kuzmina
- Galveston National Laboratory, Galveston, TX 77550, USA,Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Pilar X. Altman
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sean Hui
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bronwyn M. Gunn
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | | | | | | | - Hannah L. Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tanwee Alkutkar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Robin Flinko
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Chiara Orlandi
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Robert Carnahan
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Rachel Nargi
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Robin G. Bombardi
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Megan E. Vodzak
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Sheng Li
- Department of Medicine, University of California, San Diego, San Diego, CA 92093, USA
| | - Adaora Okoli
- First Consultants Medical Center, Lagos, Nigeria
| | | | | | - George K. Lewis
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Alexander Bukreyev
- Galveston National Laboratory, Galveston, TX 77550, USA,Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA,Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Erica Ollmann Saphire
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA,The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Thomas W. Geisbert
- Galveston National Laboratory, Galveston, TX 77550, USA,Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James E. Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA,Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA,Corresponding author
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95
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Development of an antibody cocktail for treatment of Sudan virus infection. Proc Natl Acad Sci U S A 2020; 117:3768-3778. [PMID: 32015126 DOI: 10.1073/pnas.1914985117] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Antibody-based therapies are a promising treatment option for managing ebolavirus infections. Several Ebola virus (EBOV)-specific and, more recently, pan-ebolavirus antibody cocktails have been described. Here, we report the development and assessment of a Sudan virus (SUDV)-specific antibody cocktail. We produced a panel of SUDV glycoprotein (GP)-specific human chimeric monoclonal antibodies (mAbs) using both plant and mammalian expression systems and completed head-to-head in vitro and in vivo evaluations. Neutralizing activity, competitive binding groups, and epitope specificity of SUDV mAbs were defined before assessing protective efficacy of individual mAbs using a mouse model of SUDV infection. Of the mAbs tested, GP base-binding mAbs were more potent neutralizers and more protective than glycan cap- or mucin-like domain-binding mAbs. No significant difference was observed between plant and mammalian mAbs in any of our in vitro or in vivo evaluations. Based on in vitro and rodent testing, a combination of two SUDV-specific mAbs, one base binding (16F6) and one glycan cap binding (X10H2), was down-selected for assessment in a macaque model of SUDV infection. This cocktail, RIID F6-H2, provided protection from SUDV infection in rhesus macaques when administered at 50 mg/kg on days 4 and 6 postinfection. RIID F6-H2 is an effective postexposure SUDV therapy and provides a potential treatment option for managing human SUDV infection.
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96
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Gardill B, Huang J, Tu L, Van Petegem F, Oxenoid K, Thomson CA. Nanodisc technology facilitates identification of monoclonal antibodies targeting multi-pass membrane proteins. Sci Rep 2020; 10:1130. [PMID: 31980674 PMCID: PMC6981118 DOI: 10.1038/s41598-020-58002-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 01/08/2020] [Indexed: 12/31/2022] Open
Abstract
Multi-pass membrane proteins are important targets of biologic medicines. Given the inherent difficulties in working with membrane proteins, we sought to investigate the utility of membrane scaffold protein nanodiscs as a means of solubilizing membrane proteins to aid antibody discovery. Using a model multi-pass membrane protein, we demonstrate how incorporation of a multi-pass membrane protein into nanodiscs can be used in flow cytometry to identify antigen-specific hybridoma. The use of target protein-loaded nanodiscs to sort individual hybridoma early in the screening process can reduce the time required to identify antibodies against multi-pass membrane proteins.
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Affiliation(s)
- Bernd Gardill
- Amgen Research, Biologic Discovery, Burnaby, BC, Canada.,The University of British Columbia, Department of Biochemistry and Molecular Biology, Life Sciences Institute, Vancouver, BC, Canada.,Amgen Research, Munich, Germany
| | - Jerry Huang
- Amgen Research, Biologic Discovery, Burnaby, BC, Canada
| | - Lawrence Tu
- Amgen Research, Biologic Discovery, Burnaby, BC, Canada
| | - Filip Van Petegem
- The University of British Columbia, Department of Biochemistry and Molecular Biology, Life Sciences Institute, Vancouver, BC, Canada
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97
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98
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Durham ND, Howard AR, Govindan R, Senjobe F, Fels JM, Diehl WE, Luban J, Chandran K, Munro JB. Real-Time Analysis of Individual Ebola Virus Glycoproteins Reveals Pre-Fusion, Entry-Relevant Conformational Dynamics. Viruses 2020; 12:v12010103. [PMID: 31952255 PMCID: PMC7019799 DOI: 10.3390/v12010103] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/09/2020] [Accepted: 01/10/2020] [Indexed: 12/21/2022] Open
Abstract
The Ebola virus (EBOV) envelope glycoprotein (GP) mediates the fusion of the virion membrane with the membrane of susceptible target cells during infection. While proteolytic cleavage of GP by endosomal cathepsins and binding of the cellular receptor Niemann-Pick C1 protein (NPC1) are essential steps for virus entry, the detailed mechanisms by which these events promote membrane fusion remain unknown. Here, we applied single-molecule Förster resonance energy transfer (smFRET) imaging to investigate the structural dynamics of the EBOV GP trimeric ectodomain, and the functional transmembrane protein on the surface of pseudovirions. We show that in both contexts, pre-fusion GP is dynamic and samples multiple conformations. Removal of the glycan cap and NPC1 binding shift the conformational equilibrium, suggesting stabilization of conformations relevant to viral fusion. Furthermore, several neutralizing antibodies enrich alternative conformational states. This suggests that these antibodies neutralize EBOV by restricting access to GP conformations relevant to fusion. This work demonstrates previously unobserved dynamics of pre-fusion EBOV GP and presents a platform with heightened sensitivity to conformational changes for the study of GP function and antibody-mediated neutralization.
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Affiliation(s)
- Natasha D. Durham
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA;
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Sackler School of Graduate Biomedical Sciences, Boston, MA 02111, USA; (A.R.H.); (F.S.)
- Correspondence: (N.D.D.); (J.B.M.)
| | - Angela R. Howard
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Sackler School of Graduate Biomedical Sciences, Boston, MA 02111, USA; (A.R.H.); (F.S.)
| | - Ramesh Govindan
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA;
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Sackler School of Graduate Biomedical Sciences, Boston, MA 02111, USA; (A.R.H.); (F.S.)
| | - Fernando Senjobe
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Sackler School of Graduate Biomedical Sciences, Boston, MA 02111, USA; (A.R.H.); (F.S.)
| | - J. Maximilian Fels
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (J.M.F.); (K.C.)
| | - William E. Diehl
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA; (W.E.D.); (J.L.)
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA; (W.E.D.); (J.L.)
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (J.M.F.); (K.C.)
| | - James B. Munro
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA;
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Sackler School of Graduate Biomedical Sciences, Boston, MA 02111, USA; (A.R.H.); (F.S.)
- Correspondence: (N.D.D.); (J.B.M.)
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99
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Shaw JB, Liu W, Vasil′ev YV, Bracken CC, Malhan N, Guthals A, Beckman JS, Voinov VG. Direct Determination of Antibody Chain Pairing by Top-down and Middle-down Mass Spectrometry Using Electron Capture Dissociation and Ultraviolet Photodissociation. Anal Chem 2020; 92:766-773. [PMID: 31769659 PMCID: PMC7819135 DOI: 10.1021/acs.analchem.9b03129] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
One challenge associated with the discovery and development of monoclonal antibody (mAb) therapeutics is the determination of heavy chain and light chain pairing. Advances in MS instrumentation and MS/MS methods have greatly enhanced capabilities for the analysis of large intact proteins yielding much more detailed and accurate proteoform characterization. Consequently, direct interrogation of intact antibodies or F(ab')2 and Fab fragments has the potential to significantly streamline therapeutic mAb discovery processes. Here, we demonstrate for the first time the ability to efficiently cleave disulfide bonds linking heavy and light chains of mAbs using electron capture dissociation (ECD) and 157 nm ultraviolet photodissociation (UVPD). The combination of intact mAb, Fab, or F(ab')2 mass, intact LC and Fd masses, and CDR3 sequence coverage enabled determination of heavy chain and light chain pairing from a single experiment and experimental condition. These results demonstrate the potential of top-down and middle-down proteomics to significantly streamline therapeutic antibody discovery.
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Affiliation(s)
- Jared B. Shaw
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Weijing Liu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Yury V. Vasil′ev
- e-MSion Inc., 2121 NE Jack London Drive, Corvallis, Oregon 97330, United States
- Linus Pauling Institute and the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Carter C. Bracken
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Neha Malhan
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Adrian Guthals
- Mapp Biopharmaceutical Inc., 6160 Lusk Boulevard #105, San Diego, California 92121, United States
| | - Joseph S. Beckman
- e-MSion Inc., 2121 NE Jack London Drive, Corvallis, Oregon 97330, United States
- Linus Pauling Institute and the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Valery G. Voinov
- e-MSion Inc., 2121 NE Jack London Drive, Corvallis, Oregon 97330, United States
- Linus Pauling Institute and the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
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100
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Sanchez-Lockhart M, Reyes DS, Gonzalez JC, Garcia KY, Villa EC, Pfeffer BP, Trefry JC, Kugelman JR, Pitt ML, Palacios GF. Qualitative Profiling of the Humoral Immune Response Elicited by rVSV-ΔG-EBOV-GP Using a Systems Serology Assay, Domain Programmable Arrays. Cell Rep 2020; 24:1050-1059.e5. [PMID: 30044972 DOI: 10.1016/j.celrep.2018.06.077] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 04/20/2018] [Accepted: 06/18/2018] [Indexed: 01/02/2023] Open
Abstract
Development of an effective vaccine became a worldwide priority after the devastating 2013-2016 Ebola disease outbreak. To qualitatively profile the humoral response against advanced filovirus vaccine candidates, we developed Domain Programmable Arrays (DPA), a systems serology platform to identify epitopes targeted after vaccination or filovirus infection. We optimized the assay using a panel of well-characterized monoclonal antibodies. After optimization, we utilized the system to longitudinally characterize the immunoglobulin (Ig) isotype-specific responses in non-human primates vaccinated with rVSV-ΔG-EBOV-glycoprotein (GP). Strikingly, we observed that, although the IgM response was directed against epitopes over the whole GP, the IgG and IgA responses were almost exclusively directed against the mucin-like domain (MLD) of the glycan cap. Further research will be needed to characterize this possible biased IgG and IgA response toward the MLD, but the results corroborate that DPA is a valuable tool to qualitatively measure the humoral response after vaccination.
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Affiliation(s)
- Mariano Sanchez-Lockhart
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA; Departments of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Daniel S Reyes
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA; Departments of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Jeanette C Gonzalez
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA
| | - Karla Y Garcia
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA; Departments of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Erika C Villa
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bradley P Pfeffer
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA
| | - John C Trefry
- Virology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA
| | - Jeffrey R Kugelman
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA
| | - Margaret L Pitt
- Virology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA
| | - Gustavo F Palacios
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD 21702, USA.
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