1
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Guerrero RF, Dorji T, Harris RM, Shoulders MD, Ogbunugafor CB. Evolutionary druggability for low-dimensional fitness landscapes toward new metrics for antimicrobial applications. eLife 2024; 12:RP88480. [PMID: 38833384 PMCID: PMC11149929 DOI: 10.7554/elife.88480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024] Open
Abstract
The term 'druggability' describes the molecular properties of drugs or targets in pharmacological interventions and is commonly used in work involving drug development for clinical applications. There are no current analogues for this notion that quantify the drug-target interaction with respect to a given target variant's sensitivity across a breadth of drugs in a panel, or a given drug's range of effectiveness across alleles of a target protein. Using data from low-dimensional empirical fitness landscapes composed of 16 β-lactamase alleles and 7 β-lactam drugs, we introduce two metrics that capture (i) the average susceptibility of an allelic variant of a drug target to any available drug in a given panel ('variant vulnerability'), and (ii) the average applicability of a drug (or mixture) across allelic variants of a drug target ('drug applicability'). Finally, we (iii) disentangle the quality and magnitude of interactions between loci in the drug target and the seven drug environments in terms of their mutation by mutation by environment (G x G x E) interactions, offering mechanistic insight into the variant variability and drug applicability metrics. Summarizing, we propose that our framework can be applied to other datasets and pathogen-drug systems to understand which pathogen variants in a clinical setting are the most concerning (low variant vulnerability), and which drugs in a panel are most likely to be effective in an infection defined by standing genetic variation in the pathogen drug target (high drug applicability).
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Affiliation(s)
- Rafael F Guerrero
- Department of Biological Sciences, North Carolina State UniversityRaleighUnited States
| | - Tandin Dorji
- Department of Mathematics and Statistics, University of VermontBurlingtonUnited States
| | - Ra'Mal M Harris
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Matthew D Shoulders
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
| | - C Brandon Ogbunugafor
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Ecology and Evolutionary Biology, Yale UniversityNew HavenUnited States
- Santa Fe InstituteSanta FeUnited States
- Public Health Modeling Unit, Yale School of Public HealthNew HavenUnited States
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2
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Furey C, Scher G, Ye N, Kercher L, DeBeauchamp J, Crumpton JC, Jeevan T, Patton C, Franks J, Rubrum A, Alameh MG, Fan SHY, Phan AT, Hunter CA, Webby RJ, Weissman D, Hensley SE. Development of a nucleoside-modified mRNA vaccine against clade 2.3.4.4b H5 highly pathogenic avian influenza virus. Nat Commun 2024; 15:4350. [PMID: 38782954 PMCID: PMC11116520 DOI: 10.1038/s41467-024-48555-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
mRNA lipid nanoparticle (LNP) vaccines would be useful during an influenza virus pandemic since they can be produced rapidly and do not require the generation of egg-adapted vaccine seed stocks. Highly pathogenic avian influenza viruses from H5 clade 2.3.4.4b are circulating at unprecedently high levels in wild and domestic birds and have the potential to adapt to humans. Here, we generate an mRNA lipid nanoparticle (LNP) vaccine encoding the hemagglutinin (HA) glycoprotein from a clade 2.3.4.4b H5 isolate. The H5 mRNA-LNP vaccine elicits strong T cell and antibody responses in female mice, including neutralizing antibodies and broadly-reactive anti-HA stalk antibodies. The H5 mRNA-LNP vaccine elicits antibodies at similar levels compared to whole inactivated vaccines in female mice with and without prior H1N1 exposures. Finally, we find that the H5 mRNA-LNP vaccine is immunogenic in male ferrets and prevents morbidity and mortality of animals following 2.3.4.4b H5N1 challenge. Together, our data demonstrate that a monovalent mRNA-LNP vaccine expressing 2.3.4.4b H5 is immunogenic and protective in pre-clinical animal models.
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MESH Headings
- Animals
- Influenza Vaccines/immunology
- Influenza Vaccines/administration & dosage
- Female
- Mice
- Ferrets
- Nanoparticles/chemistry
- Male
- Influenza A Virus, H5N1 Subtype/immunology
- Influenza A Virus, H5N1 Subtype/genetics
- Antibodies, Viral/immunology
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Orthomyxoviridae Infections/prevention & control
- Orthomyxoviridae Infections/immunology
- Orthomyxoviridae Infections/virology
- mRNA Vaccines/immunology
- Antibodies, Neutralizing/immunology
- Mice, Inbred BALB C
- Influenza in Birds/prevention & control
- Influenza in Birds/immunology
- Influenza in Birds/virology
- Humans
- RNA, Messenger/genetics
- RNA, Messenger/immunology
- RNA, Messenger/metabolism
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza A Virus, H1N1 Subtype/genetics
- Birds/virology
- Lipids/chemistry
- Liposomes
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Affiliation(s)
- Colleen Furey
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gabrielle Scher
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Naiqing Ye
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lisa Kercher
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jennifer DeBeauchamp
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeri Carol Crumpton
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Trushar Jeevan
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Christopher Patton
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - John Franks
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Adam Rubrum
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mohamad-Gabriel Alameh
- Infectious Disease Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Institute for RNA Innovation, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Anthony T Phan
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christopher A Hunter
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Richard J Webby
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Drew Weissman
- Infectious Disease Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Institute for RNA Innovation, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Scott E Hensley
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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3
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Luczo JM, Spackman E. Epitopes in the HA and NA of H5 and H7 avian influenza viruses that are important for antigenic drift. FEMS Microbiol Rev 2024; 48:fuae014. [PMID: 38734891 PMCID: PMC11149724 DOI: 10.1093/femsre/fuae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 04/23/2024] [Accepted: 05/10/2024] [Indexed: 05/13/2024] Open
Abstract
Avian influenza viruses evolve antigenically to evade host immunity. Two influenza A virus surface glycoproteins, the haemagglutinin and neuraminidase, are the major targets of host immunity and undergo antigenic drift in response to host pre-existing humoral and cellular immune responses. Specific sites have been identified as important epitopes in prominent subtypes such as H5 and H7, which are of animal and public health significance due to their panzootic and pandemic potential. The haemagglutinin is the immunodominant immunogen, it has been extensively studied, and the antigenic reactivity is closely monitored to ensure candidate vaccine viruses are protective. More recently, the neuraminidase has received increasing attention for its role as a protective immunogen. The neuraminidase is expressed at a lower abundance than the haemagglutinin on the virus surface but does elicit a robust antibody response. This review aims to compile the current information on haemagglutinin and neuraminidase epitopes and immune escape mutants of H5 and H7 highly pathogenic avian influenza viruses. Understanding the evolution of immune escape mutants and the location of epitopes is critical for identification of vaccine strains and development of broadly reactive vaccines that can be utilized in humans and animals.
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Affiliation(s)
- Jasmina M Luczo
- Australian Animal Health Laboratory, Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation, East Geelong, Victoria 3219, Australia
| | - Erica Spackman
- Exotic & Emerging Avian Viral Diseases Research, Southeast Poultry Research Laboratory, United States National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, Athens, GA 30605, United States
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4
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Maurer DP, Vu M, Schmidt AG. Antigenic drift expands viral escape pathways from imprinted host humoral immunity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.20.585891. [PMID: 38562862 PMCID: PMC10983950 DOI: 10.1101/2024.03.20.585891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
An initial virus exposure can imprint antibodies such that future responses to antigenically drifted strains are dependent on the identity of the imprinting strain. Subsequent exposure to antigenically distinct strains followed by affinity maturation can guide immune responses toward generation of cross-reactive antibodies. How viruses evolve in turn to escape these imprinted broad antibody responses is unclear. Here, we used clonal antibody lineages from two human donors recognizing conserved influenza virus hemagglutinin (HA) epitopes to assess viral escape potential using deep mutational scanning. We show that even though antibody affinity maturation does restrict the number of potential escape routes in the imprinting strain through repositioning the antibody variable domains, escape is still readily observed in drifted strains and attributed to epistatic networks within HA. These data explain how influenza virus continues to evolve in the human population by escaping even broad antibody responses.
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5
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Loes AN, Tarabi RAL, Huddleston J, Touyon L, Wong SS, Cheng SMS, Leung NHL, Hannon WW, Bedford T, Cobey S, Cowling BJ, Bloom JD. High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.584176. [PMID: 38496577 PMCID: PMC10942427 DOI: 10.1101/2024.03.08.584176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The high genetic diversity of influenza viruses means that traditional serological assays have too low throughput to measure serum antibody neutralization titers against all relevant strains. To overcome this challenge, we have developed a sequencing-based neutralization assay that simultaneously measures titers against many viral strains using small serum volumes via a workflow similar to traditional neutralization assays. The key innovation is to incorporate unique nucleotide barcodes into the hemagglutinin (HA) genomic segment, and then pool viruses with numerous different barcoded HA variants and quantify infectivity of all of them simultaneously using next-generation sequencing. With this approach, a single researcher performed the equivalent of 2,880 traditional neutralization assays (80 serum samples against 36 viral strains) in approximately one month. We applied the sequencing-based assay to quantify the impact of influenza vaccination on neutralization titers against recent human H1N1 strains for individuals who had or had not also received a vaccine in the previous year. We found that the viral strain specificities of the neutralizing antibodies elicited by vaccination vary among individuals, and that vaccination induced a smaller increase in titers for individuals who had also received a vaccine the previous year-although the titers six months after vaccination were similar in individuals with and without the previous-year vaccination. We also identified a subset of individuals with low titers to a subclade of recent H1N1 even after vaccination. This study demonstrates the utility of high-throughput sequencing-based neutralization assays that enable titers to be simultaneously measured against many different viral strains. We provide a detailed experimental protocol (DOI: https://dx.doi.org/10.17504/protocols.io.kqdg3xdmpg25/v1) and a computational pipeline (https://github.com/jbloomlab/seqneut-pipeline) for the sequencing-based neutralization assays to facilitate the use of this method by others.
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Affiliation(s)
- Andrea N Loes
- Howard Hughes Medical Institute, Seattle, WA
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Rosario Araceli L Tarabi
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - John Huddleston
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Lisa Touyon
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
| | - Sook San Wong
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
| | - Samuel M S Cheng
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
| | - Nancy H L Leung
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
| | - William W Hannon
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98109, USA
| | - Trevor Bedford
- Howard Hughes Medical Institute, Seattle, WA
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, IL
| | - Benjamin J Cowling
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong, SAR, China
| | - Jesse D Bloom
- Howard Hughes Medical Institute, Seattle, WA
- Division of Basic Sciences, Computational Biology Program, and Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
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6
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Irvine EB, Reddy ST. Advancing Antibody Engineering through Synthetic Evolution and Machine Learning. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:235-243. [PMID: 38166249 DOI: 10.4049/jimmunol.2300492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/20/2023] [Indexed: 01/04/2024]
Abstract
Abs are versatile molecules with the potential to achieve exceptional binding to target Ags, while also possessing biophysical properties suitable for therapeutic drug development. Protein display and directed evolution systems have transformed synthetic Ab discovery, engineering, and optimization, vastly expanding the number of Ab clones able to be experimentally screened for binding. Moreover, the burgeoning integration of high-throughput screening, deep sequencing, and machine learning has further augmented in vitro Ab optimization, promising to accelerate the design process and massively expand the Ab sequence space interrogated. In this Brief Review, we discuss the experimental and computational tools employed in synthetic Ab engineering and optimization. We also explore the therapeutic challenges posed by developing Abs for infectious diseases, and the prospects for leveraging machine learning-guided protein engineering to prospectively design Abs resistant to viral escape.
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Affiliation(s)
- Edward B Irvine
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
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7
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Musunuri S, Weidenbacher PAB, Kim PS. Bringing immunofocusing into focus. NPJ Vaccines 2024; 9:11. [PMID: 38195562 PMCID: PMC10776678 DOI: 10.1038/s41541-023-00792-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 12/07/2023] [Indexed: 01/11/2024] Open
Abstract
Immunofocusing is a strategy to create immunogens that redirect humoral immune responses towards a targeted epitope and away from non-desirable epitopes. Immunofocusing methods often aim to develop "universal" vaccines that provide broad protection against highly variant viruses such as influenza virus, human immunodeficiency virus (HIV-1), and most recently, severe acute respiratory syndrome coronavirus (SARS-CoV-2). We use existing examples to illustrate five main immunofocusing strategies-cross-strain boosting, mosaic display, protein dissection, epitope scaffolding, and epitope masking. We also discuss obstacles for immunofocusing like immune imprinting. A thorough understanding, advancement, and application of the methods we outline here will enable the design of high-resolution vaccines that protect against future viral outbreaks.
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Affiliation(s)
- Sriharshita Musunuri
- Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
| | - Payton A B Weidenbacher
- Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Peter S Kim
- Stanford ChEM-H, Stanford University, Stanford, CA, 94305, USA.
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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8
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Kikawa C, Cartwright-Acar CH, Stuart JB, Contreras M, Levoir LM, Evans MJ, Bloom JD, Goo L. The effect of single mutations in Zika virus envelope on escape from broadly neutralizing antibodies. J Virol 2023; 97:e0141423. [PMID: 37943046 PMCID: PMC10688354 DOI: 10.1128/jvi.01414-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 10/19/2023] [Indexed: 11/10/2023] Open
Abstract
IMPORTANCE The wide endemic range of mosquito-vectored flaviviruses-such as Zika virus and dengue virus serotypes 1-4-places hundreds of millions of people at risk of infection every year. Despite this, there are no widely available vaccines, and treatment of severe cases is limited to supportive care. An avenue toward development of more widely applicable vaccines and targeted therapies is the characterization of monoclonal antibodies that broadly neutralize all these viruses. Here, we measure how single amino acid mutations in viral envelope protein affect neutralizing antibodies with both broad and narrow specificities. We find that broadly neutralizing antibodies with potential as vaccine prototypes or biological therapeutics are quantifiably more difficult to escape than narrow, virus-specific neutralizing antibodies.
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Affiliation(s)
- Caroline Kikawa
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Medical Scientist Training Program, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, Washington, USA
| | | | - Jackson B. Stuart
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, Washington, USA
| | - Maya Contreras
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, Washington, USA
| | - Lisa M. Levoir
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, Washington, USA
| | - Matthew J. Evans
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jesse D. Bloom
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Basic Sciences, Fred Hutch Cancer Center, Seattle, Washington, USA
- Computational Biology, Fred Hutch Cancer Center, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, Washington, USA
| | - Leslie Goo
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, Washington, USA
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9
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Li Y, Arcos S, Sabsay KR, te Velthuis AJW, Lauring AS. Deep mutational scanning reveals the functional constraints and evolutionary potential of the influenza A virus PB1 protein. J Virol 2023; 97:e0132923. [PMID: 37882522 PMCID: PMC10688322 DOI: 10.1128/jvi.01329-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/08/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE The influenza virus polymerase is important for adaptation to new hosts and, as a determinant of mutation rate, for the process of adaptation itself. We performed a deep mutational scan of the polymerase basic 1 (PB1) protein to gain insights into the structural and functional constraints on the influenza RNA-dependent RNA polymerase. We find that PB1 is highly constrained at specific sites that are only moderately predicted by the global structure or larger domain. We identified a number of beneficial mutations, many of which have been shown to be functionally important or observed in influenza virus' natural evolution. Overall, our atlas of PB1 mutations and their fitness impacts serves as an important resource for future studies of influenza replication and evolution.
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Affiliation(s)
- Yuan Li
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Sarah Arcos
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kimberly R. Sabsay
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
- Lewis-Sigler Institute, Princeton University, Princeton, New Jersey, USA
| | | | - Adam S. Lauring
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
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10
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Álvarez-Rodríguez B, Buceta J, Geller R. Comprehensive profiling of neutralizing polyclonal sera targeting coxsackievirus B3. Nat Commun 2023; 14:6417. [PMID: 37828013 PMCID: PMC10570382 DOI: 10.1038/s41467-023-42144-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023] Open
Abstract
Despite their fundamental role in resolving viral infections, our understanding of how polyclonal neutralizing antibody responses target non-enveloped viruses remains limited. To define these responses, we obtained the full antigenic profile of multiple human and mouse polyclonal sera targeting the capsid of a prototypical picornavirus, coxsackievirus B3. Our results uncover significant variation in the breadth and strength of neutralization sites targeted by individual human polyclonal responses, which contrasted with homogenous responses observed in experimentally infected mice. We further use these comprehensive antigenic profiles to define key structural and evolutionary parameters that are predictive of escape, assess epitope dominance at the population level, and reveal a need for at least two mutations to achieve significant escape from multiple sera. Overall, our data provide a comprehensive analysis of how polyclonal sera target a non-enveloped viral capsid and help define both immune dominance and escape at the population level.
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Affiliation(s)
- Beatriz Álvarez-Rodríguez
- Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia-CSIC, Valencia, 46980, Spain.
| | - Javier Buceta
- Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia-CSIC, Valencia, 46980, Spain.
| | - Ron Geller
- Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia-CSIC, Valencia, 46980, Spain.
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11
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Kikawa C, Cartwright-Acar CH, Stuart JB, Contreras M, Levoir LM, Evans MJ, Bloom JD, Goo L. The effect of single mutations in Zika virus envelope on escape from broadly neutralizing antibodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.13.557606. [PMID: 37808848 PMCID: PMC10557620 DOI: 10.1101/2023.09.13.557606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Zika virus and dengue virus are co-circulating flaviviruses with a widespread endemic range. Eliciting broad and potent neutralizing antibodies is an attractive goal for developing a vaccine to simultaneously protect against these viruses. However, the capacity of viral mutations to confer escape from broadly neutralizing antibodies remains undescribed, due in part to limited throughput and scope of traditional approaches. Here, we use deep mutational scanning to map how all possible single amino acid mutations in Zika virus envelope protein affect neutralization by antibodies of varying breadth and potency. While all antibodies selected viral escape mutations, the mutations selected by broadly neutralizing antibodies conferred less escape relative to those selected by narrow, virus-specific antibodies. Surprisingly, even for broadly neutralizing antibodies with similar binding footprints, different single mutations led to escape, indicating distinct functional requirements for neutralization not captured by existing structures. Additionally, the antigenic effects of mutations selected by broadly neutralizing antibodies were conserved across divergent, albeit related, flaviviruses. Our approach identifies residues critical for antibody neutralization, thus comprehensively defining the as-yet-unknown functional epitopes of antibodies with clinical potential.
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Affiliation(s)
- Caroline Kikawa
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98109, USA
- Medical Scientist Training Program, University of Washington, Seattle, Washington, 98109, USA
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, Washington, 98109, USA
| | | | - Jackson B. Stuart
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, Washington, 98109, USA
| | - Maya Contreras
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, Washington, 98109, USA
| | - Lisa M. Levoir
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, Washington, 98109, USA
| | - Matthew J. Evans
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
| | - Jesse D. Bloom
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98109, USA
- Basic Sciences and Computational Biology, Fred Hutch Cancer Center, Seattle Washington, 98109, USA
- Howard Hughes Medical Institute, Seattle, WA, 98109, USA
| | - Leslie Goo
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, Washington, 98109, USA
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12
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Guerrero RF, Dorji T, Harris RM, Shoulders MD, Ogbunugafor CB. Evolutionary druggability: leveraging low-dimensional fitness landscapes towards new metrics for antimicrobial applications. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.08.536116. [PMID: 37066376 PMCID: PMC10104179 DOI: 10.1101/2023.04.08.536116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
The term "druggability" describes the molecular properties of drugs or targets in pharmacological interventions and is commonly used in work involving drug development for clinical applications. There are no current analogues for this notion that quantify the drug-target interaction with respect to a given target variant's sensitivity across a breadth of drugs in a panel, or a given drug's range of effectiveness across alleles of a target protein. Using data from low-dimensional empirical fitness landscapes composed of 16 β-lactamase alleles and seven β-lactam drugs, we introduce two metrics that capture (i) the average susceptibility of an allelic variant of a drug target to any available drug in a given panel ("variant vulnerability"), and (ii) the average applicability of a drug (or mixture) across allelic variants of a drug target ("drug applicability"). Finally, we (iii) disentangle the quality and magnitude of interactions between loci in the drug target and the seven drug environments in terms of their mutation by mutation by environment (G × G × E) interactions, offering mechanistic insight into the variant variability and drug applicability metrics. Summarizing, we propose that our framework can be applied to other datasets and pathogen-drug systems to understand which pathogen variants in a clinical setting are the most concerning (low variant vulnerability), and which drugs in a panel are most likely to be effective in an infection defined by standing genetic variation in the pathogen drug target (high drug applicability).
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Affiliation(s)
| | - Tandin Dorji
- Department of Mathematics and Statistics, University of Vermont, Burlington, VT
| | - Ra’Mal M. Harris
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA
| | | | - C. Brandon Ogbunugafor
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA
- DDepartment of Ecology and Evolutionary Biology, Yale University, New Haven, CT
- Santa Fe Institute, Santa Fe, NM
- Public Health Modeling Unit, Yale School of Public Health, New Haven, CT
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13
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Haddox HK, Galloway JG, Dadonaite B, Bloom JD, Matsen IV FA, DeWitt WS. Jointly modeling deep mutational scans identifies shifted mutational effects among SARS-CoV-2 spike homologs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.31.551037. [PMID: 37577604 PMCID: PMC10418112 DOI: 10.1101/2023.07.31.551037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Deep mutational scanning (DMS) is a high-throughput experimental technique that measures the effects of thousands of mutations to a protein. These experiments can be performed on multiple homologs of a protein or on the same protein selected under multiple conditions. It is often of biological interest to identify mutations with shifted effects across homologs or conditions. However, it is challenging to determine if observed shifts arise from biological signal or experimental noise. Here, we describe a method for jointly inferring mutational effects across multiple DMS experiments while also identifying mutations that have shifted in their effects among experiments. A key aspect of our method is to regularize the inferred shifts, so that they are nonzero only when strongly supported by the data. We apply this method to DMS experiments that measure how mutations to spike proteins from SARS-CoV-2 variants (Delta, Omicron BA.1, and Omicron BA.2) affect cell entry. Most mutational effects are conserved between these spike homologs, but a fraction have markedly shifted. We experimentally validate a subset of the mutations inferred to have shifted effects, and confirm differences of > 1,000-fold in the impact of the same mutation on spike-mediated viral infection across spikes from different SARS-CoV-2 variants. Overall, our work establishes a general approach for comparing sets of DMS experiments to identify biologically important shifts in mutational effects.
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Affiliation(s)
- Hugh K. Haddox
- Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA
| | - Jared G. Galloway
- Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA
| | - Bernadeta Dadonaite
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jesse D. Bloom
- Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Frederick A. Matsen IV
- Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
- Department of Statistics, University of Washington, Seattle, WA 98195, USA
| | - William S. DeWitt
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720, USA
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14
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Radford CE, Schommers P, Gieselmann L, Crawford KHD, Dadonaite B, Yu TC, Dingens AS, Overbaugh J, Klein F, Bloom JD. Mapping the neutralizing specificity of human anti-HIV serum by deep mutational scanning. Cell Host Microbe 2023; 31:1200-1215.e9. [PMID: 37327779 PMCID: PMC10351223 DOI: 10.1016/j.chom.2023.05.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/15/2023] [Accepted: 05/23/2023] [Indexed: 06/18/2023]
Abstract
Understanding the specificities of human serum antibodies that broadly neutralize HIV can inform prevention and treatment strategies. Here, we describe a deep mutational scanning system that can measure the effects of combinations of mutations to HIV envelope (Env) on neutralization by antibodies and polyclonal serum. We first show that this system can accurately map how all functionally tolerated mutations to Env affect neutralization by monoclonal antibodies. We then comprehensively map Env mutations that affect neutralization by a set of human polyclonal sera that neutralize diverse strains of HIV and target the site engaging the host receptor CD4. The neutralizing activities of these sera target different epitopes, with most sera having specificities reminiscent of individual characterized monoclonal antibodies, but one serum targeting two epitopes within the CD4-binding site. Mapping the specificity of the neutralizing activity in polyclonal human serum will aid in assessing anti-HIV immune responses to inform prevention strategies.
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Affiliation(s)
- Caelan E Radford
- Molecular and Cellular Biology Graduate Program, University of Washington and Basic Sciences Division, Fred Hutch Cancer Center, Seattle, WA 98109, USA; Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Philipp Schommers
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany; German Center for Infection Research, partner site Bonn-Cologne, 50931 Cologne, Germany; Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
| | - Lutz Gieselmann
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany; German Center for Infection Research, partner site Bonn-Cologne, 50931 Cologne, Germany; Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
| | - Katharine H D Crawford
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, WA 98109, USA
| | - Bernadeta Dadonaite
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Timothy C Yu
- Molecular and Cellular Biology Graduate Program, University of Washington and Basic Sciences Division, Fred Hutch Cancer Center, Seattle, WA 98109, USA; Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Adam S Dingens
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany; German Center for Infection Research, partner site Bonn-Cologne, 50931 Cologne, Germany; Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA.
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15
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Moulana A, Dupic T, Phillips AM, Desai MM. Genotype-phenotype landscapes for immune-pathogen coevolution. Trends Immunol 2023; 44:384-396. [PMID: 37024340 PMCID: PMC10147585 DOI: 10.1016/j.it.2023.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 04/07/2023]
Abstract
Our immune systems constantly coevolve with the pathogens that challenge them, as pathogens adapt to evade our defense responses, with our immune repertoires shifting in turn. These coevolutionary dynamics take place across a vast and high-dimensional landscape of potential pathogen and immune receptor sequence variants. Mapping the relationship between these genotypes and the phenotypes that determine immune-pathogen interactions is crucial for understanding, predicting, and controlling disease. Here, we review recent developments applying high-throughput methods to create large libraries of immune receptor and pathogen protein sequence variants and measure relevant phenotypes. We describe several approaches that probe different regions of the high-dimensional sequence space and comment on how combinations of these methods may offer novel insight into immune-pathogen coevolution.
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Affiliation(s)
- Alief Moulana
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Thomas Dupic
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Angela M Phillips
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, CA 94143, USA
| | - Michael M Desai
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Department of Physics, Harvard University, Cambridge, MA 02138, USA; NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, MA 02138, USA; Quantitative Biology Initiative, Harvard University, Cambridge, MA 02138, USA.
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16
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Radford CE, Schommers P, Gieselmann L, Crawford KHD, Dadonaite B, Yu TC, Dingens AS, Overbaugh J, Klein F, Bloom JD. Mapping the neutralizing specificity of human anti-HIV serum by deep mutational scanning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.23.533993. [PMID: 36993197 PMCID: PMC10055425 DOI: 10.1101/2023.03.23.533993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Understanding the specificities of human serum antibodies that broadly neutralize HIV can inform prevention and treatment strategies. Here we describe a deep mutational scanning system that can measure the effects of combinations of mutations to HIV envelope (Env) on neutralization by antibodies and polyclonal serum. We first show that this system can accurately map how all functionally tolerated mutations to Env affect neutralization by monoclonal antibodies. We then comprehensively map Env mutations that affect neutralization by a set of human polyclonal sera known to target the CD4-binding site that neutralize diverse strains of HIV. The neutralizing activities of these sera target different epitopes, with most sera having specificities reminiscent of individual characterized monoclonal antibodies, but one sera targeting two epitopes within the CD4 binding site. Mapping the specificity of the neutralizing activity in polyclonal human serum will aid in assessing anti-HIV immune responses to inform prevention strategies.
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17
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Lei R, Hernandez Garcia A, Tan TJC, Teo QW, Wang Y, Zhang X, Luo S, Nair SK, Peng J, Wu NC. Mutational fitness landscape of human influenza H3N2 neuraminidase. Cell Rep 2023; 42:111951. [PMID: 36640354 PMCID: PMC9931530 DOI: 10.1016/j.celrep.2022.111951] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/24/2022] [Accepted: 12/16/2022] [Indexed: 01/07/2023] Open
Abstract
Influenza neuraminidase (NA) has received increasing attention as an effective vaccine target. However, its mutational tolerance is not well characterized. Here, the fitness effects of >6,000 mutations in human H3N2 NA are probed using deep mutational scanning. Our result shows that while its antigenic regions have high mutational tolerance, there are solvent-exposed regions with low mutational tolerance. We also find that protein stability is a major determinant of NA mutational fitness. The deep mutational scanning result correlates well with mutational fitness inferred from natural sequences using a protein language model, substantiating the relevance of our findings to the natural evolution of circulating strains. Additional analysis further suggests that human H3N2 NA is far from running out of mutations despite already evolving for >50 years. Overall, this study advances our understanding of the evolutionary potential of NA and the underlying biophysical constraints, which in turn provide insights into NA-based vaccine design.
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Affiliation(s)
- Ruipeng Lei
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Andrea Hernandez Garcia
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Timothy J C Tan
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Qi Wen Teo
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yiquan Wang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | | | | | - Satish K Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jian Peng
- HeliXon Limited, Beijing 100084, China; Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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18
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Chu JT, Gu H, Sun W, Fan RL, Nicholls JM, Valkenburg SA, Poon LL. Heterosubtypic immune pressure accelerates emergence of influenza A virus escape phenotypes in mice. Virus Res 2023; 323:198991. [PMID: 36302472 PMCID: PMC10194115 DOI: 10.1016/j.virusres.2022.198991] [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: 09/29/2022] [Revised: 10/21/2022] [Accepted: 10/22/2022] [Indexed: 11/07/2022]
Abstract
Rapid antigenic evolution of the influenza A virus surface antigen hemagglutinin undermines protection conferred by seasonal vaccines. Protective correlates targeted by universal vaccines such as cytotoxic T cells or HA stem directed broadly neutralizing antibodies have been shown to select for immune escape mutants during infection. We developed an in vivo serial passage mouse model for viral adaptation and used next generation sequencing to evaluate full genome viral evolution in the context of broadly protective immunity. Heterosubtypic immune pressure increased the incidence of genome-wide single nucleotide variants, though mutations found in early adapted populations were predominantly stochastic in nature. Prolonged adaptation under heterosubtypic immune selection resulted in the manifestation of highly virulent phenotypes that ablated vaccine mediated protection from mortality. High frequency mutations unique to escape phenotypes were identified within the polymerase encoding segments. These findings suggest that a suboptimial usage of population-wide universal influenza vaccine may drive formation of escape variants attributed to polygenic changes.
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Affiliation(s)
- Julie Ts Chu
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Haogao Gu
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Wanying Sun
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Rebecca Ly Fan
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - John M Nicholls
- Department of Pathology, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Sophie A Valkenburg
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Leo Lm Poon
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; HKU-Pasteur Research Pole, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; Centre for Immunology & Infection, Hong Kong Science Park, Hong Kong Special Administrative Region, China.
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19
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Yu TC, Thornton ZT, Hannon WW, DeWitt WS, Radford CE, Matsen FA, Bloom JD. A biophysical model of viral escape from polyclonal antibodies. Virus Evol 2022; 8:veac110. [PMID: 36582502 PMCID: PMC9793855 DOI: 10.1093/ve/veac110] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 11/12/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022] Open
Abstract
A challenge in studying viral immune escape is determining how mutations combine to escape polyclonal antibodies, which can potentially target multiple distinct viral epitopes. Here we introduce a biophysical model of this process that partitions the total polyclonal antibody activity by epitope and then quantifies how each viral mutation affects the antibody activity against each epitope. We develop software that can use deep mutational scanning data to infer these properties for polyclonal antibody mixtures. We validate this software using a computationally simulated deep mutational scanning experiment and demonstrate that it enables the prediction of escape by arbitrary combinations of mutations. The software described in this paper is available at https://jbloomlab.github.io/polyclonal.
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Affiliation(s)
- Timothy C Yu
- Basic Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Computational Biology Program, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, 1959 NE Pacifc Street, Seattle, WA 98195, USA
| | - Zorian T Thornton
- Computational Biology Program, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195, USA
| | - William W Hannon
- Basic Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Computational Biology Program, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, 1959 NE Pacifc Street, Seattle, WA 98195, USA
| | - William S DeWitt
- Computational Biology Program, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195, USA
| | - Caelan E Radford
- Basic Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Computational Biology Program, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, 1959 NE Pacifc Street, Seattle, WA 98195, USA
| | - Frederick A Matsen
- Computational Biology Program, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Jesse D Bloom
- Basic Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Computational Biology Program, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, 1100 Fairview Ave N, Seattle, WA 98109, USA
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20
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Arevalo CP, Bolton MJ, Le Sage V, Ye N, Furey C, Muramatsu H, Alameh MG, Pardi N, Drapeau EM, Parkhouse K, Garretson T, Morris JS, Moncla LH, Tam YK, Fan SHY, Lakdawala SS, Weissman D, Hensley SE. A multivalent nucleoside-modified mRNA vaccine against all known influenza virus subtypes. Science 2022; 378:899-904. [PMID: 36423275 PMCID: PMC10790309 DOI: 10.1126/science.abm0271] [Citation(s) in RCA: 104] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Seasonal influenza vaccines offer little protection against pandemic influenza virus strains. It is difficult to create effective prepandemic vaccines because it is uncertain which influenza virus subtype will cause the next pandemic. In this work, we developed a nucleoside-modified messenger RNA (mRNA)-lipid nanoparticle vaccine encoding hemagglutinin antigens from all 20 known influenza A virus subtypes and influenza B virus lineages. This multivalent vaccine elicited high levels of cross-reactive and subtype-specific antibodies in mice and ferrets that reacted to all 20 encoded antigens. Vaccination protected mice and ferrets challenged with matched and mismatched viral strains, and this protection was at least partially dependent on antibodies. Our studies indicate that mRNA vaccines can provide protection against antigenically variable viruses by simultaneously inducing antibodies against multiple antigens.
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Affiliation(s)
- Claudia P. Arevalo
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Marcus J. Bolton
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Valerie Le Sage
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
| | - Naiqing Ye
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Colleen Furey
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Hiromi Muramatsu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Mohamad-Gabriel Alameh
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Norbert Pardi
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Elizabeth M. Drapeau
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Kaela Parkhouse
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Tyler Garretson
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Jeffrey S. Morris
- Department of Biostatistics Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Louise H. Moncla
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center; Seattle, WA, USA
| | - Ying K. Tam
- Acuitas Therapeutics; Vancouver, BC, V6T 1Z3
| | | | - Seema S. Lakdawala
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
- Center for Vaccine Research, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
| | - Drew Weissman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Scott E. Hensley
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
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21
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Liu T, Wang Y, Tan TJC, Wu NC, Brooke CB. The evolutionary potential of influenza A virus hemagglutinin is highly constrained by epistatic interactions with neuraminidase. Cell Host Microbe 2022; 30:1363-1369.e4. [PMID: 36150395 PMCID: PMC9588755 DOI: 10.1016/j.chom.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/27/2022] [Accepted: 09/02/2022] [Indexed: 11/03/2022]
Abstract
Antigenic evolution of the influenza A virus (IAV) hemagglutinin (HA) gene limits efforts to effectively control the spread of the virus in the population. Efforts to understand the mechanisms governing HA antigenic evolution typically examine the HA gene in isolation. This can ignore the importance of balancing HA receptor binding activities with the receptor-destroying activities of the viral neuraminidase (NA) to maintain viral fitness. We hypothesize that the need to maintain functional balance with NA significantly constrains the evolutionary potential of the HA. We use deep mutational scanning and show that variation in NA activity significantly reshapes the HA fitness landscape by modulating the overall mutational robustness of HA. Consistent with this, we observe that different NA backgrounds support the emergence of distinct repertoires of HA escape variants under neutralizing antibody pressure. Our results reveal a critical role for intersegment epistasis in influencing the evolutionary potential of the HA gene.
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Affiliation(s)
- Tongyu Liu
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yiquan Wang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Timothy J C Tan
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Christopher B Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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22
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Cui J, Cui P, Shi J, Fan W, Xing X, Gu W, Zhang Y, Zhang Y, Zeng X, Jiang Y, Chen P, Yang H, Chen Y, Liu J, Liu L, Tian G, Lu Y, Chen H, Li C, Deng G. Continued evolution of H6 avian influenza viruses isolated from farms in China between 2014 and 2018. Transbound Emerg Dis 2022; 69:2156-2172. [PMID: 34192815 DOI: 10.1111/tbed.14212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/04/2021] [Accepted: 06/27/2021] [Indexed: 12/22/2022]
Abstract
H6 avian influenza virus (AIV) is one of the most prevalent AIV subtypes in the world. Our previous studies have demonstrated that H6 AIVs isolated from live poultry markets pose a potential threat to human health. In recent years, increasing number of H6 AIVs has been constantly isolated from poultry farms. In order to understand the biological characteristics of H6 AIVs in the context of farms, here, we analyzed the phylogenetic relationships, antigenicity, replication in mice and receptor binding properties of H6 AIVs isolated from farms in China between 2014 and 2018. Phylogenetic analysis showed that 19 different genotypes were formed among 20 representative H6 viruses. Notably, the internal genes of these H6 viruses exhibited complicated relationships with different subtypes of AIVs worldwide, indicating that these viruses are the products of complex and frequent reassortment events. Antigenic analysis revealed that 13 viruses tested were divided into three antigenic groups. 10 viruses examined could all replicate in the respiratory organs of infected mice without prior adaptation. Receptor binding analysis demonstrated that some of the H6 AIVs bound to both α-2, 3-linked glycans (avian-type receptor) and α-2, 6-linked glycans (human-type receptor), thereby posing a potential threat to human health. Together, these findings revealed the prevalence, complicated genetic evolution, diverse antigenicity, and dual receptor binding specificity of H6 AIVs in the settings of poultry farms, which emphasize the importance to continuously monitor the evolution and biological properties of H6 AIVs in nature.
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Affiliation(s)
- Jiaqi Cui
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P. R. China
| | - Pengfei Cui
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Jianzhong Shi
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Weifeng Fan
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Xin Xing
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Wenli Gu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Yuancheng Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Yaping Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Xianying Zeng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Yongping Jiang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Pucheng Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Huanliang Yang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Yan Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Jinxiong Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Liling Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Guobin Tian
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Yixin Lu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P. R. China
| | - Hualan Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Chengjun Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
| | - Guohua Deng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, P. R. China
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23
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Muralidharan A, Gravel C, Harris G, Hashem AM, Zhang W, Safronetz D, Van Domselaar G, Krammer F, Sauve S, Rosu-Myles M, Wang L, Chen W, Li X. Universal antibody targeting the highly conserved fusion peptide provides cross-protection in mice. Hum Vaccin Immunother 2022; 18:2083428. [PMID: 35724343 PMCID: PMC9621047 DOI: 10.1080/21645515.2022.2083428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Influenza is a major public health concern causing millions of hospitalizations every year. The current vaccines need annual updating based on prediction of likely strains in the upcoming season. However, mismatches between vaccines and the actual circulating viruses can occur, reducing vaccine effectiveness significantly because of the remarkably high rate of mutation in the viral glycoprotein, hemagglutinin (HA). Clearly, it would be of great interest to determine the potential role of universally conserved epitopes in inducing protective immunity. Here, an antibody against the 14-aa fusion peptide sequence at the N-terminus of the HA2 subunit (Uni-1) was investigated for its ability to elicit antibody-dependent cellular cytotoxicity (ADCC) in vitro and cross-protection against lethal infection in animals. Uni-1, known to neutralize influenza type A (IAV) in vitro, was found to induce strong ADCC against diverse influenza viruses, including human and avian IAVs and both lineages of type B (IBV). The ADCC effects against human IAVs by Uni-1 was comparable to ADCC induced by well-characterized antibodies, F10 and FI6V3. Importantly, mice treated with Uni-1 were protected against lethal challenge of IAV and IBV. These results revealed the versatile effector functions of this universal antibody against markedly diverse strains of both IAV and IBV. The fusion peptide is the only universally conserved epitope in both IAV and IBV Mono-specific universal antibody induces strong ADCC against human and avian IAV Mono-specific universal antibody induces strong ADCC against IBV from both genetic lineages of IBV The antibody has bi-functional effector functions against several influenza viruses
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Affiliation(s)
- Abenaya Muralidharan
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada.,Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Caroline Gravel
- Centre for Biologics Evaluation, Biologic and Radiopharmaceutical Drugs Directorate, HPFB, Health Canada and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Ottawa, Canada
| | - Greg Harris
- Human Health Therapeutics (HHT) Research Center, National Research Council of Canada, Ottawa, Canada
| | - Anwar M Hashem
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Wanyue Zhang
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada.,Centre for Biologics Evaluation, Biologic and Radiopharmaceutical Drugs Directorate, HPFB, Health Canada and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Ottawa, Canada
| | - David Safronetz
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Simon Sauve
- Centre for Biologics Evaluation, Biologic and Radiopharmaceutical Drugs Directorate, HPFB, Health Canada and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Ottawa, Canada
| | - Michael Rosu-Myles
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada.,Centre for Biologics Evaluation, Biologic and Radiopharmaceutical Drugs Directorate, HPFB, Health Canada and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Ottawa, Canada
| | - Lisheng Wang
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Wangxue Chen
- Human Health Therapeutics (HHT) Research Center, National Research Council of Canada, Ottawa, Canada
| | - Xuguang Li
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada.,Centre for Biologics Evaluation, Biologic and Radiopharmaceutical Drugs Directorate, HPFB, Health Canada and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Ottawa, Canada
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24
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Zhu R, Xu S, Sun W, Li Q, Wang S, Shi H, Liu X. HA gene amino acid mutations contribute to antigenic variation and immune escape of H9N2 influenza virus. Vet Res 2022; 53:43. [PMID: 35706014 PMCID: PMC9202205 DOI: 10.1186/s13567-022-01058-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/11/2022] [Indexed: 11/10/2022] Open
Abstract
Based on differences in the amino acid sequence of the protein haemagglutinin (HA), the H9N2 avian influenza virus (H9N2 virus) has been clustered into multiple lineages, and its rapidly ongoing evolution increases the difficulties faced by prevention and control programs. The HA protein, a major antigenic protein, and the amino acid mutations that alter viral antigenicity in particular have always been of interest. Likewise, it has been well documented that some amino acid mutations in HA alter viral antigenicity in the H9N2 virus, but little has been reported regarding how these antibody escape mutations affect antigenic variation. In this study, we were able to identify 15 HA mutations that were potentially relevant to viral antigenic drift, and we also found that a key amino acid mutation, A180V, at position 180 in HA (the numbering for mature H9 HA), the only site of the receptor binding sites that is not conserved, was directly responsible for viral antigenic variation. Moreover, the recombinant virus with alanine to valine substitution at position 180 in HA in the SH/F/98 backbone (rF/HAA180V virus) showed poor cross-reactivity to immune sera from animals immunized with the SH/F/98 (F/98, A180), SD/SS/94 (A180), JS/Y618/12 (T180), and rF/HAA180V (V180) viruses by microneutralization (MN) assay. The A180V substitution in the parent virus caused a significant decrease in cross-MN titres by enhancing the receptor binding activity, but it did not physically prevent antibody (Ab) binding. The strong receptor binding avidity prevented viral release from cells. Moreover, the A180V substitution promoted H9N2 virus escape from an in vitro pAb-neutralizing reaction, which also slightly affected the cross-protection in vivo. Our results suggest that the A180V mutation with a strong receptor binding avidity contributed to the low reactors in MN/HI assays and slightly affected vaccine efficacy but was not directly responsible for immune escape, which suggested that the A180V mutation might play a key role in the process of the adaptive evolution of H9N2 virus.
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Affiliation(s)
- Rui Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.,Jiangsu Key Laboratory for High-Tech Research and Development of Veterinary Biopharmaceuticals, Jiangsu Agri-Animal Husbandry Vocational College, Taizhou, 225300, Jiangsu, China
| | - Shunshun Xu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - Wangyangji Sun
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - Quan Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
| | - Shifeng Wang
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611-0880, USA
| | - Huoying Shi
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China. .,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China. .,Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611-0880, USA.
| | - Xiufan Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
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25
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Diefenbacher M, Tan TJC, Bauer DLV, Stadtmueller BM, Wu NC, Brooke CB. Interactions between Influenza A Virus Nucleoprotein and Gene Segment Untranslated Regions Facilitate Selective Modulation of Viral Gene Expression. J Virol 2022; 96:e0020522. [PMID: 35467364 PMCID: PMC9131868 DOI: 10.1128/jvi.00205-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/29/2022] [Indexed: 11/20/2022] Open
Abstract
The influenza A virus (IAV) genome is divided into eight negative-sense, single-stranded RNA segments. Each segment exhibits a unique level and temporal pattern of expression; however, the exact mechanisms underlying the patterns of individual gene segment expression are poorly understood. We previously demonstrated that a single substitution in the viral nucleoprotein (NP:F346S) selectively modulates neuraminidase (NA) gene segment expression while leaving other segments largely unaffected. Given what is currently known about NP function, there is no obvious explanation for how changes in NP can selectively modulate the replication of individual gene segments. In this study, we found that the specificity of this effect for the NA segment is virus strain specific and depends on the untranslated region (UTR) sequences of the NA segment. While the NP:F346S substitution did not significantly alter the RNA binding or oligomerization activities of NP in vitro, it specifically decreased the ability of NP to promote NA segment viral RNA (vRNA) synthesis. In addition to NP residue F346, we identified two other adjacent aromatic residues in NP (Y385 and F479) capable of similarly regulating NA gene segment expression, suggesting a larger role for this domain in gene-segment specific regulation. Our findings reveal a novel role for NP in selective regulation of viral gene segment replication and provide a framework for understanding how the expression patterns of individual viral gene segments can be modulated during adaptation to new host environments. IMPORTANCE Influenza A virus (IAV) is a respiratory pathogen that remains a significant source of morbidity and mortality. Escape from host immunity or emergence into new host species often requires mutations that modulate the functional activities of the viral glycoproteins hemagglutinin (HA) and neuraminidase (NA), which are responsible for virus attachment to and release from host cells, respectively. Maintaining the functional balance between the activities of HA and NA is required for fitness across multiple host systems. Thus, selective modulation of viral gene expression patterns may be a key determinant of viral immune escape and cross-species transmission potential. We identified a novel mechanism by which the viral nucleoprotein (NP) gene can selectively modulate NA segment replication and gene expression through interactions with the segment UTRs. Our work highlights an unexpected role for NP in selective regulation of expression from the individual IAV gene segments.
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Affiliation(s)
- Meghan Diefenbacher
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Timothy J. C. Tan
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - David L. V. Bauer
- RNA Virus Replication Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Beth M. Stadtmueller
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Nicholas C. Wu
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Christopher B. Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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26
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Abstract
Vertebrate immune systems suppress viral infection using both innate restriction factors and adaptive immunity. Viruses mutate to escape these defenses, driving hosts to counterevolve to regain fitness. This cycle recurs repeatedly, resulting in an evolutionary arms race whose outcome depends on the pace and likelihood of adaptation by host and viral genes. Although viruses evolve faster than their vertebrate hosts, their proteins are subject to numerous functional constraints that impact the probability of adaptation. These constraints are globally defined by evolutionary landscapes, which describe the fitness and adaptive potential of all possible mutations. We review deep mutational scanning experiments mapping the evolutionary landscapes of both host and viral proteins engaged in arms races. For restriction factors and some broadly neutralizing antibodies, landscapes favor the host, which may help to level the evolutionary playing field against rapidly evolving viruses. We discuss the biophysical underpinnings of these landscapes and their therapeutic implications.
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Affiliation(s)
- Jeannette L Tenthorey
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA; , ,
| | - Michael Emerman
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA; , , .,Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA; , , .,Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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27
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Abstract
Antibodies have been used to prevent or treat viral infections since the nineteenth century, but the full potential to use passive immunization for infectious diseases has yet to be realized. The advent of efficient methods for isolating broad and potently neutralizing human monoclonal antibodies is enabling us to develop antibodies with unprecedented activities. The discovery of IgG Fc region modifications that extend antibody half-life in humans to three months or more suggests that antibodies could become the principal tool with which we manage future viral epidemics. Antibodies for members of most virus families that cause severe disease in humans have been isolated, and many of them are in clinical development, an area that has accelerated during the effort to prevent or treat COVID-19 (coronavirus disease 2019). Broad and potently neutralizing antibodies are also important research reagents for identification of protective epitopes that can be engineered into active vaccines through structure-based reverse vaccinology. Expected final online publication date for the Annual Review of Immunology, Volume 40 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- James E Crowe
- Vanderbilt Vaccine Center, Department of Pediatrics, and Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
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28
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Guthmiller JJ, Han J, Utset HA, Li L, Lan LYL, Henry C, Stamper CT, McMahon M, O'Dell G, Fernández-Quintero ML, Freyn AW, Amanat F, Stovicek O, Gentles L, Richey ST, de la Peña AT, Rosado V, Dugan HL, Zheng NY, Tepora ME, Bitar DJ, Changrob S, Strohmeier S, Huang M, García-Sastre A, Liedl KR, Bloom JD, Nachbagauer R, Palese P, Krammer F, Coughlan L, Ward AB, Wilson PC. Broadly neutralizing antibodies target a haemagglutinin anchor epitope. Nature 2022; 602:314-320. [PMID: 34942633 PMCID: PMC8828479 DOI: 10.1038/s41586-021-04356-8] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 12/15/2021] [Indexed: 11/09/2022]
Abstract
Broadly neutralizing antibodies that target epitopes of haemagglutinin on the influenza virus have the potential to provide near universal protection against influenza virus infection1. However, viral mutants that escape broadly neutralizing antibodies have been reported2,3. The identification of broadly neutralizing antibody classes that can neutralize viral escape mutants is critical for universal influenza virus vaccine design. Here we report a distinct class of broadly neutralizing antibodies that target a discrete membrane-proximal anchor epitope of the haemagglutinin stalk domain. Anchor epitope-targeting antibodies are broadly neutralizing across H1 viruses and can cross-react with H2 and H5 viruses that are a pandemic threat. Antibodies that target this anchor epitope utilize a highly restricted repertoire, which encodes two public binding motifs that make extensive contacts with conserved residues in the fusion peptide. Moreover, anchor epitope-targeting B cells are common in the human memory B cell repertoire and were recalled in humans by an oil-in-water adjuvanted chimeric haemagglutinin vaccine4,5, which is a potential universal influenza virus vaccine. To maximize protection against seasonal and pandemic influenza viruses, vaccines should aim to boost this previously untapped source of broadly neutralizing antibodies that are widespread in the human memory B cell pool.
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Affiliation(s)
- Jenna J Guthmiller
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA.
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Henry A Utset
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | - Lei Li
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | | | - Carole Henry
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
- Moderna Inc., Cambridge, MA, USA
| | | | - Meagan McMahon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - George O'Dell
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Monica L Fernández-Quintero
- Center for Molecular Biosciences Innsbruck, Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Alec W Freyn
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Moderna Inc., Cambridge, MA, USA
| | - Fatima Amanat
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Olivia Stovicek
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | - Lauren Gentles
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Sara T Richey
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Alba Torrents de la Peña
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Victoria Rosado
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Haley L Dugan
- Committee on Immunology, University of Chicago, Chicago, IL, USA
| | - Nai-Ying Zheng
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | - Micah E Tepora
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | - Dalia J Bitar
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | - Siriruk Changrob
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | - Shirin Strohmeier
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Min Huang
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Klaus R Liedl
- Center for Molecular Biosciences Innsbruck, Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Jesse D Bloom
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Microbiology, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Raffael Nachbagauer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Moderna Inc., Cambridge, MA, USA
| | - Peter Palese
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lynda Coughlan
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
- Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, MD, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Patrick C Wilson
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA.
- Committee on Immunology, University of Chicago, Chicago, IL, USA.
- Drukier Institute for Children's Health, Department of Pediatrics, Weill Cornell Medicine, New York, NY, USA.
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29
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Viral surface geometry shapes influenza and coronavirus spike evolution through antibody pressure. PLoS Comput Biol 2021; 17:e1009664. [PMID: 34898597 PMCID: PMC8699686 DOI: 10.1371/journal.pcbi.1009664] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 12/23/2021] [Accepted: 11/19/2021] [Indexed: 01/02/2023] Open
Abstract
The evolution of circulating viruses is shaped by their need to evade antibody response, which mainly targets the viral spike. Because of the high density of spikes on the viral surface, not all antigenic sites are targeted equally by antibodies. We offer here a geometry-based approach to predict and rank the probability of surface residues of SARS spike (S protein) and influenza H1N1 spike (hemagglutinin) to acquire antibody-escaping mutations utilizing in-silico models of viral structure. We used coarse-grained MD simulations to estimate the on-rate (targeting) of an antibody model to surface residues of the spike protein. Analyzing publicly available sequences, we found that spike surface sequence diversity of the pre-pandemic seasonal influenza H1N1 and the sarbecovirus subgenus highly correlates with our model prediction of antibody targeting. In particular, we identified an antibody-targeting gradient, which matches a mutability gradient along the main axis of the spike. This identifies the role of viral surface geometry in shaping the evolution of circulating viruses. For the 2009 H1N1 and SARS-CoV-2 pandemics, a mutability gradient along the main axis of the spike was not observed. Our model further allowed us to identify key residues of the SARS-CoV-2 spike at which antibody escape mutations have now occurred. Therefore, it can inform of the likely functional role of observed mutations and predict at which residues antibody-escaping mutation might arise. The immune system responds to viruses by making neutralizing antibodies to regions of the viral spike protein, which mutates to escape. To inform vaccine design and understand how the fitness landscape of the viral spike changes over time, it is necessary to identify and quantify the factors directing its evolution. Based on the 3D structure of the viral surface and spike as captured with Cryo-EM and crystallography, we aimed to create a coarse-grained model for the effect of antibodies in forcing surface residues of the spike to mutate. We found that for pre-pandemic influenza (hemagglutinin) and the corona sarbecovirus subgenus (S protein), the location of a residue on the spike protein, which modulates its accessibility to antibodies, highly correlates with its propensity to mutate. Hence, a mechanistic approach can be used to identify aspects of viral spike sequence diversity related to antibody escape.
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30
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Mendes M, Russell AB. Library-based analysis reveals segment and length dependent characteristics of defective influenza genomes. PLoS Pathog 2021; 17:e1010125. [PMID: 34882752 PMCID: PMC8691639 DOI: 10.1371/journal.ppat.1010125] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 12/21/2021] [Accepted: 11/17/2021] [Indexed: 12/14/2022] Open
Abstract
Found in a diverse set of viral populations, defective interfering particles are parasitic variants that are unable to replicate on their own yet rise to relatively high frequencies. Their presence is associated with a loss of population fitness, both through the depletion of key cellular resources and the stimulation of innate immunity. For influenza A virus, these particles contain large internal deletions in the genomic segments which encode components of the heterotrimeric polymerase. Using a library-based approach, we comprehensively profile the growth and replication of defective influenza species, demonstrating that they possess an advantage during genome replication, and that exclusion during population expansion reshapes population composition in a manner consistent with their final, observed, distribution in natural populations. We find that an innate immune response is not linked to the size of a deletion; however, replication of defective segments can enhance their immunostimulatory properties. Overall, our results address several key questions in defective influenza A virus biology, and the methods we have developed to answer those questions may be broadly applied to other defective viruses.
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Affiliation(s)
- Marisa Mendes
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Alistair B. Russell
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
- * E-mail:
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31
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Hanning KR, Minot M, Warrender AK, Kelton W, Reddy ST. Deep mutational scanning for therapeutic antibody engineering. Trends Pharmacol Sci 2021; 43:123-135. [PMID: 34895944 DOI: 10.1016/j.tips.2021.11.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/02/2021] [Accepted: 11/10/2021] [Indexed: 12/24/2022]
Abstract
The biophysical and functional properties of monoclonal antibody (mAb) drug candidates are often improved by protein engineering methods to increase the probability of clinical efficacy. One emerging method is deep mutational scanning (DMS) which combines the power of exhaustive protein mutagenesis and functional screening with deep sequencing and bioinformatics. The application of DMS has yielded significant improvements to the affinity, specificity, and stability of several preclinical antibodies alongside novel applications such as introducing multi-specific binding properties. DMS has also been applied directly on target antigens to precisely map antibody-binding epitopes and notably to profile the mutational escape potential of viral targets (e.g., SARS-CoV-2 variants). Finally, DMS combined with machine learning is enabling advances in the computational screening and engineering of therapeutic antibodies.
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Affiliation(s)
- Kyrin R Hanning
- Te Huataki Waiora School of Health, University of Waikato, Hamilton 3240, New Zealand
| | - Mason Minot
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel 4058, Switzerland
| | - Annmaree K Warrender
- Te Huataki Waiora School of Health, University of Waikato, Hamilton 3240, New Zealand
| | - William Kelton
- Te Huataki Waiora School of Health, University of Waikato, Hamilton 3240, New Zealand.
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel 4058, Switzerland.
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32
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Creytens S, Pascha MN, Ballegeer M, Saelens X, de Haan CAM. Influenza Neuraminidase Characteristics and Potential as a Vaccine Target. Front Immunol 2021; 12:786617. [PMID: 34868073 PMCID: PMC8635103 DOI: 10.3389/fimmu.2021.786617] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 10/29/2021] [Indexed: 12/28/2022] Open
Abstract
Neuraminidase of influenza A and B viruses plays a critical role in the virus life cycle and is an important target of the host immune system. Here, we highlight the current understanding of influenza neuraminidase structure, function, antigenicity, immunogenicity, and immune protective potential. Neuraminidase inhibiting antibodies have been recognized as correlates of protection against disease caused by natural or experimental influenza A virus infection in humans. In the past years, we have witnessed an increasing interest in the use of influenza neuraminidase to improve the protective potential of currently used influenza vaccines. A number of well-characterized influenza neuraminidase-specific monoclonal antibodies have been described recently, most of which can protect in experimental challenge models by inhibiting the neuraminidase activity or by Fc receptor-dependent mechanisms. The relative instability of the neuraminidase poses a challenge for protein-based antigen design. We critically review the different solutions that have been proposed to solve this problem, ranging from the inclusion of stabilizing heterologous tetramerizing zippers to the introduction of inter-protomer stabilizing mutations. Computationally engineered neuraminidase antigens have been generated that offer broad, within subtype protection in animal challenge models. We also provide an overview of modern vaccine technology platforms that are compatible with the induction of robust neuraminidase-specific immune responses. In the near future, we will likely see the implementation of influenza vaccines that confront the influenza virus with a double punch: targeting both the hemagglutinin and the neuraminidase.
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MESH Headings
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Antigenic Drift and Shift
- Antigens, Viral/immunology
- Antigens, Viral/ultrastructure
- Catalytic Domain/genetics
- Catalytic Domain/immunology
- Cross Protection
- Evolution, Molecular
- Humans
- Immunogenicity, Vaccine
- Influenza Vaccines/administration & dosage
- Influenza Vaccines/genetics
- Influenza Vaccines/immunology
- Influenza, Human/immunology
- Influenza, Human/prevention & control
- Influenza, Human/virology
- Alphainfluenzavirus/enzymology
- Alphainfluenzavirus/genetics
- Alphainfluenzavirus/immunology
- Betainfluenzavirus/enzymology
- Betainfluenzavirus/genetics
- Betainfluenzavirus/immunology
- Mutation
- Nanoparticles
- Neuraminidase/administration & dosage
- Neuraminidase/genetics
- Neuraminidase/immunology
- Neuraminidase/ultrastructure
- Vaccines, Synthetic/administration & dosage
- Vaccines, Synthetic/genetics
- Vaccines, Synthetic/immunology
- Vaccines, Synthetic/ultrastructure
- Viral Proteins/administration & dosage
- Viral Proteins/genetics
- Viral Proteins/immunology
- Viral Proteins/ultrastructure
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Affiliation(s)
- Sarah Creytens
- Vlaams Instituut voor Biotechnologie (VIB)-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Mirte N. Pascha
- Section Virology, Division Infectious Diseases & Immunology, Department of Biomolecular Health Sciences, Utrecht University, Utrecht, Netherlands
| | - Marlies Ballegeer
- Vlaams Instituut voor Biotechnologie (VIB)-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Xavier Saelens
- Vlaams Instituut voor Biotechnologie (VIB)-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Cornelis A. M. de Haan
- Section Virology, Division Infectious Diseases & Immunology, Department of Biomolecular Health Sciences, Utrecht University, Utrecht, Netherlands
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Zolotarova O, Fesenko A, Holubka O, Radchenko L, Bortz E, Budzanivska I, Mironenko A. Genotypic Variants of Pandemic H1N1 Influenza A Viruses Isolated from Severe Acute Respiratory Infections in Ukraine during the 2015/16 Influenza Season. Viruses 2021; 13:2125. [PMID: 34834932 PMCID: PMC8619959 DOI: 10.3390/v13112125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/05/2021] [Accepted: 10/15/2021] [Indexed: 01/15/2023] Open
Abstract
Human type A influenza viruses A(H1N1)pdm09 have caused seasonal epidemics of influenza since the 2009-2010 pandemic. A(H1N1)pdm09 viruses had a leading role in the severe epidemic season of 2015/16 in the Northern Hemisphere and caused a high incidence of acute respiratory infection (ARI) in Ukraine. Serious complications of influenza-associated severe ARI (SARI) were observed in the very young and individuals at increased risk, and 391 fatal cases occurred in the 2015/16 epidemic season. We analyzed the genetic changes in the genomes of A(H1N1)pdm09 influenza viruses isolated from SARI cases in Ukraine during the 2015/16 season. The viral hemagglutinin (HA) fell in H1 group 6B.1 for all but four isolates, with known mutations affecting glycosylation, the Sa antigenic site (S162N in all 6B.1 isolates), or virulence (D222G/N in two isolates). Other mutations occurred in antigenic site Ca (A141P and S236P), and a subgroup of four strains were in group 6B.2, with potential alterations to antigenicity in A(H1N1)pdm09 viruses circulating in 2015/16 in Ukraine. A cluster of Ukrainian isolates exhibited novel D2E and N48S mutations in the RNA binding domain, and E125D in the effector domain, of immune evasion nonstructural protein 1 (NS1). The diverse spectrum of amino-acid substitutions in HA, NS1, and other viral proteins including nucleoprotein (NP) and the polymerase complex suggested the concurrent circulation of multiple lineages of A(H1N1)pdm09 influenza viruses in the human population in Ukraine, a country with low vaccination coverage, complicating public health measures against influenza.
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Affiliation(s)
- Oksana Zolotarova
- Educational Scientific Centre “Institute of Biology and Medicine”, Taras Shevchenko National University of Kyiv, 01601 Kyiv, Ukraine;
| | - Anna Fesenko
- Gromashevsky L.V. Institute of Epidemiology and Infectious Diseases, National Academy of Medical Sciences of Ukraine, 03680 Kyiv, Ukraine; (A.F.); (O.H.); (L.R.); (A.M.)
| | - Olga Holubka
- Gromashevsky L.V. Institute of Epidemiology and Infectious Diseases, National Academy of Medical Sciences of Ukraine, 03680 Kyiv, Ukraine; (A.F.); (O.H.); (L.R.); (A.M.)
| | - Larysa Radchenko
- Gromashevsky L.V. Institute of Epidemiology and Infectious Diseases, National Academy of Medical Sciences of Ukraine, 03680 Kyiv, Ukraine; (A.F.); (O.H.); (L.R.); (A.M.)
| | - Eric Bortz
- Department of Biological Sciences, University of Alaska, 3211 Providence Dr., Anchorage, AK 99508, USA;
| | - Iryna Budzanivska
- Educational Scientific Centre “Institute of Biology and Medicine”, Taras Shevchenko National University of Kyiv, 01601 Kyiv, Ukraine;
| | - Alla Mironenko
- Gromashevsky L.V. Institute of Epidemiology and Infectious Diseases, National Academy of Medical Sciences of Ukraine, 03680 Kyiv, Ukraine; (A.F.); (O.H.); (L.R.); (A.M.)
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34
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Walti CS, Loes AN, Shuey K, Krantz EM, Boonyaratanakornkit J, Keane-Candib J, Loeffelholz T, Wolf CR, Taylor JJ, Gardner RA, Green DJ, Cowan AJ, Maloney DG, Turtle CJ, Pergam SA, Chu HY, Bloom JD, Hill JA. Humoral immunogenicity of the seasonal influenza vaccine before and after CAR-T-cell therapy: a prospective observational study. J Immunother Cancer 2021; 9:jitc-2021-003428. [PMID: 34702753 PMCID: PMC8549667 DOI: 10.1136/jitc-2021-003428] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2021] [Indexed: 11/23/2022] Open
Abstract
Recipients of chimeric antigen receptor-modified T (CAR-T) cell therapies for B cell malignancies have profound and prolonged immunodeficiencies and are at risk for serious infections, including respiratory virus infections. Vaccination may be important for infection prevention, but there are limited data on vaccine immunogenicity in this population. We conducted a prospective observational study of the humoral immunogenicity of commercially available 2019-2020 inactivated influenza vaccines in adults immediately prior to or while in durable remission after CD19-, CD20-, or B cell maturation antigen-targeted CAR-T-cell therapy, as well as controls. We tested for antibodies to all four vaccine strains using neutralization and hemagglutination inhibition (HAI) assays. Antibody responses were defined as at least fourfold titer increases from baseline. Seroprotection was defined as a HAI titer ≥40. Enrolled CAR-T-cell recipients were vaccinated 14-29 days prior to (n=5) or 13-57 months following therapy (n=13), and the majority had hypogammaglobulinemia and cellular immunodeficiencies prevaccination. Eight non-immunocompromised adults served as controls. Antibody responses to ≥1 vaccine strain occurred in 2 (40%) individuals before CAR-T-cell therapy and in 4 (31%) individuals vaccinated after CAR-T-cell therapy. An additional 1 (20%) and 6 (46%) individuals had at least twofold increases, respectively. One individual vaccinated prior to CAR-T-cell therapy maintained a response for >3 months following therapy. Across all tested vaccine strains, seroprotection was less frequent in CAR-T-cell recipients than in controls. There was evidence of immunogenicity even among individuals with low immunoglobulin, CD19+ B cell, and CD4+ T-cell counts. These data support consideration for vaccination before and after CAR-T-cell therapy for influenza and other relevant pathogens such as SARS-CoV-2, irrespective of hypogammaglobulinemia or B cell aplasia. However, relatively impaired humoral vaccine immunogenicity indicates the need for additional infection-prevention strategies. Larger studies are needed to refine our understanding of potential correlates of vaccine immunogenicity, and durability of immune responses, in CAR-T-cell therapy recipients.
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Affiliation(s)
- Carla S Walti
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Andrea N Loes
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, Washington, USA
| | - Kiel Shuey
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Elizabeth M Krantz
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jim Boonyaratanakornkit
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Jacob Keane-Candib
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Tillie Loeffelholz
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Caitlin R Wolf
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Justin J Taylor
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Rebecca A Gardner
- Division of Hematology-Oncology, Seattle Children's Hospital, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Damian J Green
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Andrew J Cowan
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - David G Maloney
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Cameron J Turtle
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Steven A Pergam
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, and Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Helen Y Chu
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Jesse D Bloom
- Howard Hughes Medical Institute, Seattle, Washington, USA
- Basic Sciences Division, Computational Biology Program, and Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Joshua A Hill
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, and Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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35
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Li T, Cai H, Yao H, Zhou B, Zhang N, van Vlissingen MF, Kuiken T, Han W, GeurtsvanKessel CH, Gong Y, Zhao Y, Shen Q, Qin W, Tian XX, Peng C, Lai Y, Wang Y, Hutter CAJ, Kuo SM, Bao J, Liu C, Wang Y, Richard AS, Raoul H, Lan J, Seeger MA, Cong Y, Rockx B, Wong G, Bi Y, Lavillette D, Li D. A synthetic nanobody targeting RBD protects hamsters from SARS-CoV-2 infection. Nat Commun 2021; 12:4635. [PMID: 34330908 PMCID: PMC8324831 DOI: 10.1038/s41467-021-24905-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 07/15/2021] [Indexed: 01/15/2023] Open
Abstract
SARS-CoV-2, the causative agent of COVID-191, features a receptor-binding domain (RBD) for binding to the host cell ACE2 protein1-6. Neutralizing antibodies that block RBD-ACE2 interaction are candidates for the development of targeted therapeutics7-17. Llama-derived single-domain antibodies (nanobodies, ~15 kDa) offer advantages in bioavailability, amenability, and production and storage owing to their small sizes and high stability. Here, we report the rapid selection of 99 synthetic nanobodies (sybodies) against RBD by in vitro selection using three libraries. The best sybody, MR3 binds to RBD with high affinity (KD = 1.0 nM) and displays high neutralization activity against SARS-CoV-2 pseudoviruses (IC50 = 0.42 μg mL-1). Structural, biochemical, and biological characterization suggests a common neutralizing mechanism, in which the RBD-ACE2 interaction is competitively inhibited by sybodies. Various forms of sybodies with improved potency have been generated by structure-based design, biparatopic construction, and divalent engineering. Two divalent forms of MR3 protect hamsters from clinical signs after live virus challenge and a single dose of the Fc-fusion construct of MR3 reduces viral RNA load by 6 Log10. Our results pave the way for the development of therapeutic nanobodies against COVID-19 and present a strategy for rapid development of targeted medical interventions during an outbreak.
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Affiliation(s)
- Tingting Li
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Hongmin Cai
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Hebang Yao
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Bingjie Zhou
- University of CAS, Beijing, China
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, Shanghai, China
| | - Ning Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), CAS, Beijing, China
| | - Martje Fentener van Vlissingen
- Erasmus Laboratory Animal Science Center, Erasmus University Medical Center, Rotterdam, Netherlands
- European Research Infrastructure on Highly Pathogenic Agents (ERINHA-AISBL), Paris, France
| | - Thijs Kuiken
- European Research Infrastructure on Highly Pathogenic Agents (ERINHA-AISBL), Paris, France
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Wenyu Han
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), Shanghai, China
- University of CAS, Beijing, China
| | - Corine H GeurtsvanKessel
- European Research Infrastructure on Highly Pathogenic Agents (ERINHA-AISBL), Paris, France
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Yuhuan Gong
- University of CAS, Beijing, China
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), CAS, Beijing, China
| | - Yapei Zhao
- University of CAS, Beijing, China
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, Shanghai, China
| | - Quan Shen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), CAS, Beijing, China
| | - Wenming Qin
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute (Zhangjiang Laboratory), CAS, Shanghai, China
| | - Xiao-Xu Tian
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute (Zhangjiang Laboratory), CAS, Shanghai, China
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute (Zhangjiang Laboratory), CAS, Shanghai, China
| | - Yanling Lai
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), Shanghai, China
- University of CAS, Beijing, China
| | - Yanxing Wang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Cedric A J Hutter
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Shu-Ming Kuo
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, Shanghai, China
| | - Juan Bao
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Caixuan Liu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), Shanghai, China
- University of CAS, Beijing, China
| | - Yifan Wang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), Shanghai, China
- University of CAS, Beijing, China
| | - Audrey S Richard
- European Research Infrastructure on Highly Pathogenic Agents (ERINHA-AISBL), Paris, France
| | - Hervé Raoul
- European Research Infrastructure on Highly Pathogenic Agents (ERINHA-AISBL), Paris, France
| | - Jiaming Lan
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, Shanghai, China
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Yao Cong
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Barry Rockx
- European Research Infrastructure on Highly Pathogenic Agents (ERINHA-AISBL), Paris, France
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Gary Wong
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, Shanghai, China.
- Département de microbiologie-infectiologie et d'immunologie, Université Laval, Québec, QC, Canada.
| | - Yuhai Bi
- University of CAS, Beijing, China.
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), CAS, Beijing, China.
| | - Dimitri Lavillette
- CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS, Shanghai, China.
- Pasteurien College, Soochow University, Jiangsu, China.
| | - Dianfan Li
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), Shanghai, China.
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36
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Shipley MM, Mangala Prasad V, Doepker LE, Dingens A, Ralph DK, Harkins E, Dhar A, Arenz D, Chohan V, Weight H, Mandaliya K, Bloom JD, Matsen FA, Lee KK, Overbaugh JM. Functional development of a V3/glycan-specific broadly neutralizing antibody isolated from a case of HIV superinfection. eLife 2021; 10:68110. [PMID: 34263727 PMCID: PMC8376252 DOI: 10.7554/elife.68110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/14/2021] [Indexed: 12/12/2022] Open
Abstract
Stimulating broadly neutralizing antibodies (bnAbs) directly from germline remains a barrier for HIV vaccines. HIV superinfection elicits bnAbs more frequently than single infection, providing clues of how to elicit such responses. We used longitudinal antibody sequencing and structural studies to characterize bnAb development from a superinfection case. BnAb QA013.2 bound initial and superinfecting viral Env, despite its probable naive progenitor only recognizing the superinfecting strain, suggesting both viruses influenced this lineage. A 4.15 Å cryo-EM structure of QA013.2 bound to native-like trimer showed recognition of V3 signatures (N301/N332 and GDIR). QA013.2 relies less on CDRH3 and more on framework and CDRH1 for affinity and breadth compared to other V3/glycan-specific bnAbs. Antigenic profiling revealed that viral escape was achieved by changes in the structurally-defined epitope and by mutations in V1. These results highlight shared and novel properties of QA013.2 relative to other V3/glycan-specific bnAbs in the setting of sequential, diverse antigens.
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Affiliation(s)
- Mackenzie M Shipley
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Vidya Mangala Prasad
- Department of Medicinal Chemistry, University of Washington, Seattle, United States
| | - Laura E Doepker
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Adam Dingens
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Duncan K Ralph
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Elias Harkins
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Amrit Dhar
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Dana Arenz
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Vrasha Chohan
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Haidyn Weight
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Kishor Mandaliya
- Coast Provincial General Hospital, Women's Health Project, Mombasa, Kenya
| | - Jesse D Bloom
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States.,Department of Genome Sciences, University of Washington, Seattle, United States.,Howard Hughes Medical Institute, Chevy Chase, United States
| | - Frederick A Matsen
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Kelly K Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, United States
| | - Julie M Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, United States
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37
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Comprehensive Profiling of Mutations to Influenza Virus PB2 That Confer Resistance to the Cap-Binding Inhibitor Pimodivir. Viruses 2021; 13:v13071196. [PMID: 34206520 PMCID: PMC8310130 DOI: 10.3390/v13071196] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 06/06/2021] [Accepted: 06/17/2021] [Indexed: 12/14/2022] Open
Abstract
Antivirals are used not only in the current treatment of influenza but are also stockpiled as a first line of defense against novel influenza strains for which vaccines have yet to be developed. Identifying drug resistance mutations can guide the clinical deployment of the antiviral and can additionally define the mechanisms of drug action and drug resistance. Pimodivir is a first-in-class inhibitor of the polymerase basic protein 2 (PB2) subunit of the influenza A virus polymerase complex. A number of resistance mutations have previously been identified in treated patients or cell culture. Here, we generate a complete map of the effect of all single-amino-acid mutations to an avian PB2 on resistance to pimodivir. We identified both known and novel resistance mutations not only in the previously implicated cap-binding and mid-link domains, but also in the N-terminal domain. Our complete map of pimodivir resistance thus enables the evaluation of whether new viral strains contain mutations that will confer pimodivir resistance.
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38
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An Antigenic Thrift-Based Approach to Influenza Vaccine Design. Vaccines (Basel) 2021; 9:vaccines9060657. [PMID: 34208489 PMCID: PMC8235769 DOI: 10.3390/vaccines9060657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/04/2021] [Accepted: 06/05/2021] [Indexed: 11/19/2022] Open
Abstract
The antigenic drift theory states that influenza evolves via the gradual accumulation of mutations, decreasing a host’s immune protection against previous strains. Influenza vaccines are designed accordingly, under the premise of antigenic drift. However, a paradox exists at the centre of influenza research. If influenza evolved primarily through mutation in multiple epitopes, multiple influenza strains should co-circulate. Such a multitude of strains would render influenza vaccines quickly inefficacious. Instead, a single or limited number of strains dominate circulation each influenza season. Unless additional constraints are placed on the evolution of influenza, antigenic drift does not adequately explain these observations. Here, we explore the constraints placed on antigenic drift and a competing theory of influenza evolution – antigenic thrift. In contrast to antigenic drift, antigenic thrift states that immune selection targets epitopes of limited variability, which constrain the variability of the virus. We explain the implications of antigenic drift and antigenic thrift and explore their current and potential uses in the context of influenza vaccine design.
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39
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Boonnak K, Mansanguan C, Schuerch D, Boonyuen U, Lerdsamran H, Jiamsomboon K, Sae Wang F, Huntrup A, Prasertsopon J, Kosoltanapiwat N, Puthavathana P. Molecular Characterization of Seasonal Influenza A and B from Hospitalized Patients in Thailand in 2018-2019. Viruses 2021; 13:977. [PMID: 34070388 PMCID: PMC8228477 DOI: 10.3390/v13060977] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/21/2021] [Accepted: 05/22/2021] [Indexed: 12/11/2022] Open
Abstract
Influenza viruses continue to be a major public health threat due to the possible emergence of more virulent influenza virus strains resulting from dynamic changes in virus adaptability, consequent of functional mutations and antigenic drift in surface proteins, especially hemagglutinin (HA) and neuraminidase (NA). In this study, we describe the genetic and evolutionary characteristics of H1N1, H3N2, and influenza B strains detected in severe cases of seasonal influenza in Thailand from 2018 to 2019. We genetically characterized seven A/H1N1 isolates, seven A/H3N2 isolates, and six influenza B isolates. Five of the seven A/H1N1 viruses were found to belong to clade 6B.1 and were antigenically similar to A/Switzerland/3330/2017 (H1N1), whereas two isolates belonged to clade 6B.1A1 and clustered with A/Brisbane/02/2018 (H1N1). Interestingly, we observed additional mutations at antigenic sites (S91R, S181T, T202I) as well as a unique mutation at a receptor binding site (S200P). Three-dimensional (3D) protein structure analysis of hemagglutinin protein reveals that this unique mutation may lead to the altered binding of the HA protein to a sialic acid receptor. A/H3N2 isolates were found to belong to clade 3C.2a2 and 3C.2a1b, clustering with A/Switzerland/8060/2017 (H3N2) and A/South Australia/34/2019 (H3N2), respectively. Amino acid sequence analysis revealed 10 mutations at antigenic sites including T144A/I, T151K, Q213R, S214P, T176K, D69N, Q277R, N137K, N187K, and E78K/G. All influenza B isolates in this study belong to the Victoria lineage. Five out of six isolates belong to clade 1A3-DEL, which relate closely to B/Washington/02/2009, with one isolate lacking the three amino acid deletion on the HA segment at position K162, N163, and D164. In comparison to the B/Colorado/06/2017, which is the representative of influenza B Victoria lineage vaccine strain, these substitutions include G129D, G133R, K136E, and V180R for HA protein. Importantly, the susceptibility to oseltamivir of influenza B isolates, but not A/H1N1 and A/H3N2 isolates, were reduced as assessed by the phenotypic assay. This study demonstrates the importance of monitoring genetic variation in influenza viruses regarding how acquired mutations could be associated with an improved adaptability for efficient transmission.
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Affiliation(s)
- Kobporn Boonnak
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (K.B.); (D.S.); (K.J.); (F.S.W.); (N.K.)
| | - Chayasin Mansanguan
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
| | - Dennis Schuerch
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (K.B.); (D.S.); (K.J.); (F.S.W.); (N.K.)
| | - Usa Boonyuen
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
| | - Hatairat Lerdsamran
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Nakhon Pathom 73170, Thailand; (H.L.); (J.P.)
| | - Kultida Jiamsomboon
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (K.B.); (D.S.); (K.J.); (F.S.W.); (N.K.)
| | - Fanny Sae Wang
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (K.B.); (D.S.); (K.J.); (F.S.W.); (N.K.)
| | - Arun Huntrup
- Hospital for Tropical Diseases, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
| | - Jarunee Prasertsopon
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Nakhon Pathom 73170, Thailand; (H.L.); (J.P.)
| | - Nathamon Kosoltanapiwat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (K.B.); (D.S.); (K.J.); (F.S.W.); (N.K.)
| | - Pilaipan Puthavathana
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Nakhon Pathom 73170, Thailand; (H.L.); (J.P.)
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40
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Pucci F, Rooman M. Prediction and Evolution of the Molecular Fitness of SARS-CoV-2 Variants: Introducing SpikePro. Viruses 2021; 13:935. [PMID: 34070055 PMCID: PMC8158131 DOI: 10.3390/v13050935] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/11/2021] [Accepted: 05/14/2021] [Indexed: 12/18/2022] Open
Abstract
The understanding of the molecular mechanisms driving the fitness of the SARS-CoV-2 virus and its mutational evolution is still a critical issue. We built a simplified computational model, called SpikePro, to predict the SARS-CoV-2 fitness from the amino acid sequence and structure of the spike protein. It contains three contributions: the inter-human transmissibility of the virus predicted from the stability of the spike protein, the infectivity computed in terms of the affinity of the spike protein for the ACE2 receptor, and the ability of the virus to escape from the human immune response based on the binding affinity of the spike protein for a set of neutralizing antibodies. Our model reproduces well the available experimental, epidemiological and clinical data on the impact of variants on the biophysical characteristics of the virus. For example, it is able to identify circulating viral strains that, by increasing their fitness, recently became dominant at the population level. SpikePro is a useful, freely available instrument which predicts rapidly and with good accuracy the dangerousness of new viral strains. It can be integrated and play a fundamental role in the genomic surveillance programs of the SARS-CoV-2 virus that, despite all the efforts, remain time-consuming and expensive.
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Affiliation(s)
- Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium;
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium;
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
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41
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Pucci F, Rooman M. Prediction and Evolution of the Molecular Fitness of SARS-CoV-2 Variants: Introducing SpikePro. Viruses 2021; 13:v13050935. [PMID: 34070055 DOI: 10.1101/2021.04.11.439322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/11/2021] [Accepted: 05/14/2021] [Indexed: 05/25/2023] Open
Abstract
The understanding of the molecular mechanisms driving the fitness of the SARS-CoV-2 virus and its mutational evolution is still a critical issue. We built a simplified computational model, called SpikePro, to predict the SARS-CoV-2 fitness from the amino acid sequence and structure of the spike protein. It contains three contributions: the inter-human transmissibility of the virus predicted from the stability of the spike protein, the infectivity computed in terms of the affinity of the spike protein for the ACE2 receptor, and the ability of the virus to escape from the human immune response based on the binding affinity of the spike protein for a set of neutralizing antibodies. Our model reproduces well the available experimental, epidemiological and clinical data on the impact of variants on the biophysical characteristics of the virus. For example, it is able to identify circulating viral strains that, by increasing their fitness, recently became dominant at the population level. SpikePro is a useful, freely available instrument which predicts rapidly and with good accuracy the dangerousness of new viral strains. It can be integrated and play a fundamental role in the genomic surveillance programs of the SARS-CoV-2 virus that, despite all the efforts, remain time-consuming and expensive.
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Affiliation(s)
- Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
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42
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Walti CS, Loes AN, Shuey K, Krantz EM, Boonyaratanakornkit J, Keane-Candib J, Loeffelholz T, Wolf CR, Taylor JJ, Gardner RA, Green DJ, Cowan AJ, Maloney DG, Turtle CJ, Pergam SA, Chu HY, Bloom JD, Hill JA. Humoral immunogenicity of the seasonal influenza vaccine before and after CAR-T-cell therapy. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021. [PMID: 34013294 PMCID: PMC8132269 DOI: 10.1101/2021.05.10.21256634] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Recipients of chimeric antigen receptor-modified T (CAR-T) cell therapies for B-cell malignancies are immunocompromised and at risk for serious infections. Vaccine immunogenicity is unknown in this population. We conducted a prospective observational study of the humoral immunogenicity of 2019-2020 inactivated influenza vaccines (IIV) in children and adults immediately prior to (n=7) or 13-57 months after (n=15) CD19-, CD20-, or BCMA-targeted CAR-T-cell therapy, as well as controls (n=8). Individuals post-CAR-T-cell therapy were in remission. We tested for antibodies to 4 vaccine strains at baseline and ≥1 time point after IIV using neutralization and hemagglutination inhibition assays. An antibody response was defined as a ≥4-fold titer increase from baseline at the first post-vaccine time point. Baseline A(H1N1) titers in the CAR-T cohorts were significantly lower compared to controls. Antibody responses to ≥1 vaccine strain occurred in 2 (29%) individuals before CAR-T-cell therapy; one individual maintained a response for >3 months post-CAR-T-cell therapy. Antibody responses to ≥1 vaccine strain occurred in 6 (40%) individuals vaccinated after CAR-T-cell therapy. An additional 2 (29%) and 6 (40%) individuals had ≥2-fold increases (at any time) in the pre- and post-CAR-T cohorts, respectively. There were no identified clinical or immunologic predictors of antibody responses. Neither severe hypogammaglobulinemia nor B-cell aplasia precluded antibody responses. These data support consideration for vaccination before and after CAR-T-cell therapy for influenza and other relevant pathogens such as SARS-CoV-2, irrespective of hypogammaglobulinemia or B-cell aplasia. Larger studies are needed to determine correlates of vaccine immunogenicity and durability in CAR-T-cell therapy recipients. Key Points Influenza vaccination was immunogenic pre- and post-CAR-T-cell therapy, despite hypogammaglobulinemia and B-cell aplasia.Vaccination with inactivated vaccines can be considered before CAR-T-cell therapy and in individuals with remission after therapy.
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43
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Garrett ME, Galloway J, Chu HY, Itell HL, Stoddard CI, Wolf CR, Logue JK, McDonald D, Weight H, Matsen FA, Overbaugh J. High-resolution profiling of pathways of escape for SARS-CoV-2 spike-binding antibodies. Cell 2021; 184:2927-2938.e11. [PMID: 34010620 PMCID: PMC8096189 DOI: 10.1016/j.cell.2021.04.045] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/26/2021] [Accepted: 04/23/2021] [Indexed: 01/02/2023]
Abstract
Defining long-term protective immunity to SARS-CoV-2 is one of the most pressing questions of our time and will require a detailed understanding of potential ways this virus can evolve to escape immune protection. Immune protection will most likely be mediated by antibodies that bind to the viral entry protein, spike (S). Here, we used Phage-DMS, an approach that comprehensively interrogates the effect of all possible mutations on binding to a protein of interest, to define the profile of antibody escape to the SARS-CoV-2 S protein using coronavirus disease 2019 (COVID-19) convalescent plasma. Antibody binding was common in two regions, the fusion peptide and the linker region upstream of the heptad repeat region 2. However, escape mutations were variable within these immunodominant regions. There was also individual variation in less commonly targeted epitopes. This study provides a granular view of potential antibody escape pathways and suggests there will be individual variation in antibody-mediated virus evolution.
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Affiliation(s)
- Meghan E Garrett
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA; Molecular and Cellular Biology Graduate Program, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, WA 98195, USA
| | - Jared Galloway
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA
| | - Helen Y Chu
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Hannah L Itell
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA; Molecular and Cellular Biology Graduate Program, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, WA 98195, USA
| | - Caitlin I Stoddard
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA
| | - Caitlin R Wolf
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jennifer K Logue
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Dylan McDonald
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Haidyn Weight
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA
| | - Frederick A Matsen
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA; Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA
| | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA.
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44
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Ortega JT, Pujol FH, Jastrzebska B, Rangel HR. Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. EXCLI JOURNAL 2021; 20:585-600. [PMID: 33883984 PMCID: PMC8056063 DOI: 10.17179/excli2021-3471] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 02/22/2021] [Indexed: 12/12/2022]
Abstract
The increasing number of SARS-CoV-2 variants associated with highly transmissible phenotypes is a health-public concern in the current pandemic scenario. Herein, we developed a comprehensive in silico analysis of the changes occurring upon mutations in the viral spike. We focused on mutants located in the receptor-binding domain of the viral spike protein and analyzed whether these mutants modulate the interaction with the human host receptor angiotensin-converting enzyme II (ACE2). Thirty-two highly prevalent mutants were retrieved from the GISAID database, and their structural models were built using the SWISS-Model server. The stabilization effect for each mutation was assessed by the DUET and DeepDGG software. By applying molecular docking using both Z-Dock and Haddock software we found that multiple mutations, including A475V, V455E, V445L, and V445I, resulted in the higher binding free energy as compared to the wild type (WT) spike protein, thus had a destabilizing effect on the binding to ACE2. On the other hand, several mutants, including the most prevalent N501Y and B.1.1.7 variants, as well as the K444R, L455F, Q493R, and Y505W variants exhibited lower binding free energy as compared to the WT spike. These mutants showed an increased number of electrostatic interactions with ACE2 than the WT spike protein, and they changed the interaction pattern of the neighboring residues. Together, the results presented in this study contribute to a better understanding of the changes in the interaction between SARS-CoV-2 and the human host ACE2 receptor associated with point mutations in the viral spike protein.
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Affiliation(s)
- Joseph Thomas Ortega
- Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Flor Helene Pujol
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Apdo 20632, Caracas 1020A, Venezuela
| | - Beata Jastrzebska
- Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Hector R. Rangel
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas, Apdo 20632, Caracas 1020A, Venezuela
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Dingens AS, Pratap P, Malone K, Hilton SK, Ketas T, Cottrell CA, Overbaugh J, Moore JP, Klasse PJ, Ward AB, Bloom JD. High-resolution mapping of the neutralizing and binding specificities of polyclonal sera post-HIV Env trimer vaccination. eLife 2021; 10:e64281. [PMID: 33438580 PMCID: PMC7864656 DOI: 10.7554/elife.64281] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/12/2021] [Indexed: 01/01/2023] Open
Abstract
Mapping polyclonal serum responses is critical to rational vaccine design. However, most high-resolution mapping approaches involve isolating and characterizing individual antibodies, which incompletely defines the polyclonal response. Here we use two complementary approaches to directly map the specificities of the neutralizing and binding antibodies of polyclonal anti-HIV-1 sera from rabbits immunized with BG505 Env SOSIP trimers. We used mutational antigenic profiling to determine how all mutations in Env affected viral neutralization and electron microscopy polyclonal epitope mapping (EMPEM) to directly visualize serum Fabs bound to Env trimers. The dominant neutralizing specificities were generally only a subset of the more diverse binding specificities. Additional differences between binding and neutralization reflected antigenicity differences between virus and soluble Env trimer. Furthermore, we refined residue-level epitope specificity directly from sera, revealing subtle differences across sera. Together, mutational antigenic profiling and EMPEM yield a holistic view of the binding and neutralizing specificity of polyclonal sera.
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Affiliation(s)
- Adam S Dingens
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Payal Pratap
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Keara Malone
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Sarah K Hilton
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Thomas Ketas
- Department of Microbiology and Immunology, Weill Cornell Medical CollegeNew YorkUnited States
| | - Christopher A Cottrell
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Julie Overbaugh
- Human Biology Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - John P Moore
- Department of Microbiology and Immunology, Weill Cornell Medical CollegeNew YorkUnited States
| | - PJ Klasse
- Department of Microbiology and Immunology, Weill Cornell Medical CollegeNew YorkUnited States
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research CenterSeattleUnited States
- Howard Hughes Medical InstituteSeattleUnited States
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Characterizing genetic and antigenic divergence from vaccine strain of influenza A and B viruses circulating in Thailand, 2017-2020. Sci Rep 2021; 11:735. [PMID: 33437008 PMCID: PMC7803983 DOI: 10.1038/s41598-020-80895-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 12/30/2020] [Indexed: 01/29/2023] Open
Abstract
We monitored the circulating strains and genetic variation among seasonal influenza A and B viruses in Thailand between July 2017 and March 2020. The hemagglutinin gene was amplified and sequenced. We identified amino acid (AA) changes and computed antigenic relatedness using the Pepitope model. Phylogenetic analyses revealed multiple clades/subclades of influenza A(H1N1)pdm09 and A(H3N2) were circulating simultaneously and evolved away from their vaccine strain, but not the influenza B virus. The predominant circulating strains of A(H1N1)pdm09 belonged to 6B.1A1 (2017-2018) and 6B.1A5 (2019-2020) with additional AA substitutions. Clade 3C.2a1b and 3C.2a2 viruses co-circulated in A(H3N2) and clade 3C.3a virus was found in 2020. The B/Victoria-like lineage predominated since 2019 with an additional three AA deletions. Antigenic drift was dominantly facilitated at epitopes Sa and Sb of A(H1N1)pdm09, epitopes A, B, D and E of A(H3N2), and the 120 loop and 190 helix of influenza B virus. Moderate computed antigenic relatedness was observed in A(H1N1)pdm09. The computed antigenic relatedness of A(H3N2) indicated a significant decline in 2019 (9.17%) and 2020 (- 18.94%) whereas the circulating influenza B virus was antigenically similar (94.81%) with its vaccine strain. Our findings offer insights into the genetic divergence from vaccine strains, which could aid vaccine updating.
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Amitai A. Viral surface geometry shapes influenza and coronavirus spike evolution through antibody pressure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.10.20.347641. [PMID: 33106808 PMCID: PMC7587782 DOI: 10.1101/2020.10.20.347641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The evolution of circulating viruses is shaped by their need to evade antibody response, which mainly targets the glycoprotein (spike). However, not all antigenic sites are targeted equally by antibodies, leading to complex immunodominance patterns. We used 3D computational models to estimate antibody pressure on the seasonal influenza H1N1 and SARS spikes. Analyzing publically available sequences, we show that antibody pressure, through the geometrical organization of spikes on the viral surface, shaped their mutability. Studying the mutability patterns of SARS-CoV-2 and the 2009 H1N1 pandemic spikes, we find that they are not predominantly shaped by antibody pressure. However, for SARS-CoV-2, we find that over time, it acquired mutations at antibody-accessible positions, which could indicate possible escape as define by our model. We offer a geometry-based approach to predict and rank the probability of surface resides of SARS-CoV-2 spike to acquire antibody escaping mutations.
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Affiliation(s)
- Assaf Amitai
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
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48
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Linsky TW, Vergara R, Codina N, Nelson JW, Walker MJ, Su W, Barnes CO, Hsiang TY, Esser-Nobis K, Yu K, Reneer ZB, Hou YJ, Priya T, Mitsumoto M, Pong A, Lau UY, Mason ML, Chen J, Chen A, Berrocal T, Peng H, Clairmont NS, Castellanos J, Lin YR, Josephson-Day A, Baric RS, Fuller DH, Walkey CD, Ross TM, Swanson R, Bjorkman PJ, Gale M, Blancas-Mejia LM, Yen HL, Silva DA. De novo design of potent and resilient hACE2 decoys to neutralize SARS-CoV-2. Science 2020; 370:1208-1214. [PMID: 33154107 PMCID: PMC7920261 DOI: 10.1126/science.abe0075] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/30/2020] [Indexed: 01/04/2023]
Abstract
We developed a de novo protein design strategy to swiftly engineer decoys for neutralizing pathogens that exploit extracellular host proteins to infect the cell. Our pipeline allowed the design, validation, and optimization of de novo human angiotensin-converting enzyme 2 (hACE2) decoys to neutralize severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The best monovalent decoy, CTC-445.2, bound with low nanomolar affinity and high specificity to the receptor-binding domain (RBD) of the spike protein. Cryo-electron microscopy (cryo-EM) showed that the design is accurate and can simultaneously bind to all three RBDs of a single spike protein. Because the decoy replicates the spike protein target interface in hACE2, it is intrinsically resilient to viral mutational escape. A bivalent decoy, CTC-445.2d, showed ~10-fold improvement in binding. CTC-445.2d potently neutralized SARS-CoV-2 infection of cells in vitro, and a single intranasal prophylactic dose of decoy protected Syrian hamsters from a subsequent lethal SARS-CoV-2 challenge.
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Affiliation(s)
| | | | | | | | | | - Wen Su
- School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tien-Ying Hsiang
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, WA, USA
| | - Katharina Esser-Nobis
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, WA, USA
| | - Kevin Yu
- Neoleukin Therapeutics Inc., Seattle, WA, USA
| | - Z Beau Reneer
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA
| | - Yixuan J Hou
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, WA, USA
| | - Tanu Priya
- Neoleukin Therapeutics Inc., Seattle, WA, USA
| | | | - Avery Pong
- Neoleukin Therapeutics Inc., Seattle, WA, USA
| | - Uland Y Lau
- Neoleukin Therapeutics Inc., Seattle, WA, USA
| | | | - Jerry Chen
- Neoleukin Therapeutics Inc., Seattle, WA, USA
| | - Alex Chen
- Neoleukin Therapeutics Inc., Seattle, WA, USA
| | | | - Hong Peng
- Neoleukin Therapeutics Inc., Seattle, WA, USA
| | | | | | - Yu-Ru Lin
- Neoleukin Therapeutics Inc., Seattle, WA, USA
| | | | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Deborah H Fuller
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | | | - Ted M Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA
- Department of Infectious Diseases, University of Georgia, Athens, GA, USA
| | | | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Michael Gale
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, WA, USA
| | | | - Hui-Ling Yen
- School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
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49
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Koel BF, Vigeveno RM, Pater M, Koekkoek SM, Han AX, Tuan HM, Anh TTN, Hung NT, Thinh LQ, Hai LT, Ngoc HTB, Chau NVV, Ngoc NM, Chokephaibulkit K, Puthavathana P, Kinh NV, Trinh T, Lee RTC, Maurer-Stroh S, Eggink D, Thanh TT, Tan LV, van Doorn HR, de Jong MD. Longitudinal sampling is required to maximize detection of intrahost A/H3N2 virus variants. Virus Evol 2020; 6:veaa088. [PMID: 33343927 PMCID: PMC7733607 DOI: 10.1093/ve/veaa088] [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] [Indexed: 12/20/2022] Open
Abstract
Seasonal human influenza viruses continually change antigenically to escape from neutralizing antibodies. It remains unclear how genetic variation in the intrahost virus population and selection at the level of individual hosts translates to the fast-paced evolution observed at the global level because emerging intrahost antigenic variants are rarely detected. We tracked intrahost variants in the hemagglutinin and neuraminidase surface proteins using longitudinally collected samples from 52 patients infected by A/H3N2 influenza virus, mostly young children, who received oseltamivir treatment. We identified emerging putative antigenic variants and oseltamivir-resistant variants, most of which remained detectable in samples collected at subsequent days, and identified variants that emerged intrahost immediately prior to increases in global rates. In contrast to most putative antigenic variants, oseltamivir-resistant variants rapidly increased to high frequencies in the virus population. Importantly, the majority of putative antigenic variants and oseltamivir-resistant variants were first detectable four or more days after onset of symptoms or start of treatment, respectively. Our observations demonstrate that de novo variants emerge, and may be positively selected, during the course of infection. Additionally, based on the 4–7 days post-treatment delay in emergence of oseltamivir-resistant variants in six out of the eight individuals with such variants, we find that limiting sample collection for routine surveillance and diagnostic testing to early timepoints after onset of symptoms can potentially preclude detection of emerging, positively selected variants.
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Affiliation(s)
- B F Koel
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - R M Vigeveno
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - M Pater
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - S M Koekkoek
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - A X Han
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | | | | | - N T Hung
- Children's Hospital 1, Ho Chi Minh City, Vietnam
| | - L Q Thinh
- Children's Hospital 1, Ho Chi Minh City, Vietnam
| | - L T Hai
- Vietnam National Children's Hospital, Hanoi, Vietnam
| | - H T B Ngoc
- Vietnam National Children's Hospital, Hanoi, Vietnam
| | - N V V Chau
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - N M Ngoc
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | | | | | - N V Kinh
- National Hospital of Tropical Diseases, Hanoi, Vietnam
| | - T Trinh
- National Hospital of Tropical Diseases, Hanoi, Vietnam
| | - R T C Lee
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore 138671 Singapore
| | - S Maurer-Stroh
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore 138671 Singapore.,Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore.,National Public Health Laboratory, National Centre for Infectious Diseases, Ministry of Health, Singapore 308442, Singapore
| | - D Eggink
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - T T Thanh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - L V Tan
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - H R van Doorn
- Oxford University Clinical Research Unit, Hanoi, Vietnam.,Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - M D de Jong
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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Garrett ME, Galloway J, Chu HY, Itell HL, Stoddard CI, Wolf CR, Logue JK, McDonald D, Matsen FA, Overbaugh J. High resolution profiling of pathways of escape for SARS-CoV-2 spike-binding antibodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.11.16.385278. [PMID: 33236010 PMCID: PMC7685320 DOI: 10.1101/2020.11.16.385278] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Defining long-term protective immunity to SARS-CoV-2 is one of the most pressing questions of our time and will require a detailed understanding of potential ways this virus can evolve to escape immune protection. Immune protection will most likely be mediated by antibodies that bind to the viral entry protein, Spike (S). Here we used Phage-DMS, an approach that comprehensively interrogates the effect of all possible mutations on binding to a protein of interest, to define the profile of antibody escape to the SARS-CoV-2 S protein using COVID-19 convalescent plasma. Antibody binding was common in two regions: the fusion peptide and linker region upstream of the heptad repeat region 2. However, escape mutations were variable within these immunodominant regions. There was also individual variation in less commonly targeted epitopes. This study provides a granular view of potential antibody escape pathways and suggests there will be individual variation in antibody-mediated virus evolution.
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Affiliation(s)
- Meghan E Garrett
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jared Galloway
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Helen Y Chu
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Hannah L Itell
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Caitlin I Stoddard
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Caitlin R Wolf
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jennifer K Logue
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Dylan McDonald
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Frederick A Matsen
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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