1
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Maltseva M, Keeshan A, Cooper C, Langlois MA. Immune imprinting: The persisting influence of the first antigenic encounter with rapidly evolving viruses. Hum Vaccin Immunother 2024; 20:2384192. [PMID: 39149872 PMCID: PMC11328881 DOI: 10.1080/21645515.2024.2384192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 07/08/2024] [Accepted: 07/21/2024] [Indexed: 08/17/2024] Open
Abstract
Immune imprinting is a phenomenon that stems from the fundamentals of immunological memory. Upon recurrent exposures to an evolving pathogen, the immune system must weigh the benefits of rapidly recalling established antibody repertoires with greater affinity to the initial variant or invest additional time and energy in producing de novo responses specific to the emerging variant. In this review, we delve into the mechanistic complexities of immune imprinting and its role in shaping subsequent immune responses, both de novo and recall, against rapidly evolving respiratory viruses such as influenza and coronaviruses. By exploring the duality of immune imprinting, we examine its potential to both enhance or hinder immune protection against disease, while emphasizing the role of host and viral factors. Finally, we explore how different vaccine platforms may affect immune imprinting and comment on vaccine strategies that can favor de novo variant-specific antibody responses.
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Affiliation(s)
- Mariam Maltseva
- Department of Biochemistry, Microbiology & Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Alexa Keeshan
- School of Epidemiology and Public Health, University of Ottawa Faculty of Medicine, Ottawa, ON, Canada
- Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Curtis Cooper
- School of Epidemiology and Public Health, University of Ottawa Faculty of Medicine, Ottawa, ON, Canada
- Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Medicine, University of Ottawa, Ottawa, ON, Canada
- Division of Infectious Diseases, Ottawa Hospital Research Institute Clinical Epidemiology Program, Ottawa, ON, Canada
| | - Marc-André Langlois
- Department of Biochemistry, Microbiology & Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- Center for Infection, Immunity, and Inflammation (CI3), University of Ottawa, Ottawa, ON, Canada
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2
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Lin Y, Wang Y, Li H, Liu T, Zhang J, Guo X, Guo W, Wang Y, Liu X, Huang S, Liao H, Wang X. A platform for the rapid screening of equine immunoglobins F (ab)2 derived from single equine memory B cells able to cross-neutralize to influenza virus. Emerg Microbes Infect 2024; 13:2396864. [PMID: 39331815 PMCID: PMC11441081 DOI: 10.1080/22221751.2024.2396864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 07/26/2024] [Accepted: 08/22/2024] [Indexed: 09/29/2024]
Abstract
Single B cells-based antibody platforms offer an effective approach for the discovery of useful antibodies for therapeutic or research purposes. Here we present a method for screening equine immunoglobins F(ab)2, which offers the potential advantage of reacting with multiple epitopes on the virus. Using equine influenza virus (EIV) as model, a hemagglutinin (HA) trimer was constructed to bait B cells in vaccinated horses. We screened 370 HA-specific B cells from 1 × 106 PBMCs and identified a diverse set of equine variable region gene sequences of heavy and light chains and then recombined with humanized Ig Fc. Recombinant equine Ig was then self-assembled in co-transfected 293 T cells, and subsequently optimized to obtain HA binding B-cell receptor (s). The recombinant antibodies exhibited a high binding affinity to the HA protein. Antibody H81 exhibited the highest cross neutralizing activities against EIV strains in vitro. Furthermore, it effectively protected EIV-challenged mice, resulting in significantly improved survival, reduced pulmonary inflammation and decreased viral titers. In silico predication identified a functional region of H81 comprising 27 key amino acids cross the main circulating EIV strains. The 12 amino acid residues in this region with the highest binding affinities were screened. Notably, the predicted epitopes of H81 encompassed the documented equine HA receptor binding site, validating its cross-neutralization. In summary, a rapid platform was successfully established to investigate the profiling of equine antigen-recognizing receptors (BCRs) following infection. This platform has the potential to optimize the screening of virus-neutralizing antibodies and aid in vaccine design.
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Affiliation(s)
- Yuezhi Lin
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Yayu Wang
- Zhuhai Trinomab Pharmaceutical Co., Ltd, Zhuhai, People’s Republic of China
| | - Hongxin Li
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Tong Liu
- Zhuhai Trinomab Pharmaceutical Co., Ltd, Zhuhai, People’s Republic of China
| | - Jiaqi Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Xing Guo
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Wei Guo
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
- Institute of Western Agriculture, the Chinese Academy of Agricultural sciences, Changji, People’s Republic of China
| | - Yaoxin Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Xiangning Liu
- Clinical Research Platform for Interdiscipline of Stomatology, The First Affiliated Hospital of Jinan University, Guangzhou, People's Republic of China
- Department of Stomatology, College of Stomatology, Jinan University, Guangzhou, People’s Republic of China
| | - Shaoli Huang
- The Hong Kong University of Science and Technology, School of Engineering, Hong Kong, People’s Republic of China
| | - Huaxin Liao
- Zhuhai Trinomab Pharmaceutical Co., Ltd, Zhuhai, People’s Republic of China
| | - XiaoJun Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
- Institute of Western Agriculture, the Chinese Academy of Agricultural sciences, Changji, People’s Republic of China
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3
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Cobey S. Vaccination against rapidly evolving pathogens and the entanglements of memory. Nat Immunol 2024:10.1038/s41590-024-01970-2. [PMID: 39384979 DOI: 10.1038/s41590-024-01970-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 08/26/2024] [Indexed: 10/11/2024]
Abstract
Immune memory determines infection risk and responses to future infections and vaccinations over potentially decades of life. Despite its centrality, the dynamics of memory to antigenically variable pathogens remains poorly understood. This Review examines how past exposures shape B cell responses to vaccinations with influenza and SARS-CoV-2. An overriding feature of vaccinations with these pathogens is the recall of primary responses, often termed 'imprinting' or 'original antigenic sin'. These recalled responses can inhibit the generation of new responses unless some incompletely defined conditions are met. Depending on the context, immune memory can increase or decrease the total neutralizing antibody response to variant antigens, with apparent consequences for protection. These effects are easier to measure experimentally than epidemiologically, but there is evidence that both early and recent exposures influence vaccine effectiveness. A few immunological interactions between adaptive immune responses and antigens might explain the seemingly discrepant effects of memory. Overall, the complex observations point to a need for more quantitative approaches to integrate high-dimensional immune data from populations with diverse exposure histories. Such approaches could help identify optimal vaccination strategies against antigenically diverse pathogens.
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Affiliation(s)
- Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.
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4
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Wang W, Bhushan G, Paz S, Stauft CB, Selvaraj P, Goguet E, Bishop-Lilly KA, Subramanian R, Vassell R, Lusvarghi S, Cong Y, Agan B, Richard SA, Epsi NJ, Fries A, Fung CK, Conte MA, Holbrook MR, Wang TT, Burgess TH, Pollett SD, Mitre E, Katzelnick LC, Weiss CD. Human and hamster sera correlate well in identifying antigenic drift among SARS-CoV-2 variants, including JN.1. J Virol 2024:e0094824. [PMID: 39365051 DOI: 10.1128/jvi.00948-24] [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: 06/07/2024] [Accepted: 09/14/2024] [Indexed: 10/05/2024] Open
Abstract
Antigenic assessments of SARS-CoV-2 variants inform decisions to update COVID-19 vaccines. Primary infection sera are often used for assessments, but such sera are rare due to population immunity from SARS-CoV-2 infections and COVID-19 vaccinations. Here, we show that neutralization titers and breadth of matched human and hamster pre-Omicron variant primary infection sera correlate well and generate similar antigenic maps. The hamster antigenic map shows modest antigenic drift among XBB sub-lineage variants, with JN.1 and BA.4/BA.5 variants within the XBB cluster, but with fivefold to sixfold antigenic differences between these variants and XBB.1.5. Compared to sera following only ancestral or bivalent COVID-19 vaccinations, or with post-vaccination infections, XBB.1.5 booster sera had the broadest neutralization against XBB sub-lineage variants, although a fivefold titer difference was still observed between JN.1 and XBB.1.5 variants. These findings suggest that antibody coverage of antigenically divergent JN.1 could be improved with a matched vaccine antigen.IMPORTANCEUpdates to COVID-19 vaccine antigens depend on assessing how much vaccine antigens differ antigenically from newer SARS-CoV-2 variants. Human sera from single variant infections are ideal for discriminating antigenic differences among variants, but such primary infection sera are now rare due to high population immunity. It remains unclear whether sera from experimentally infected animals could substitute for human sera for antigenic assessments. This report shows that neutralization titers of variant-matched human and hamster primary infection sera correlate well and recognize variants similarly, indicating that hamster sera can be a proxy for human sera for antigenic assessments. We further show that human sera following an XBB.1.5 booster vaccine broadly neutralized XBB sub-lineage variants but titers were fivefold lower against the more recent JN.1 variant. These findings support updating the current COVID-19 vaccine variant composition and developing a framework for assessing antigenic differences in future variants using hamster primary infection sera.
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Affiliation(s)
- Wei Wang
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Gitanjali Bhushan
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Stephanie Paz
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Charles B Stauft
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Prabhuanand Selvaraj
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Emilie Goguet
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Kimberly A Bishop-Lilly
- Biological Defense Research Directorate, Naval Medical Research Command, Fort Detrick, Maryland, USA
| | - Rahul Subramanian
- Office of Data Science and Emerging Technologies, Office of Science Management and Operations, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Russell Vassell
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Sabrina Lusvarghi
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Yu Cong
- Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
| | - Brian Agan
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Stephanie A Richard
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Nusrat J Epsi
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Anthony Fries
- US Air Force School of Aerospace Medicine, Dayton, Ohio, USA
| | - Christian K Fung
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Matthew A Conte
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Michael R Holbrook
- Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
| | - Tony T Wang
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Timothy H Burgess
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Simon D Pollett
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Edward Mitre
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Leah C Katzelnick
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Carol D Weiss
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
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5
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Pardi N, Krammer F. mRNA vaccines for infectious diseases - advances, challenges and opportunities. Nat Rev Drug Discov 2024:10.1038/s41573-024-01042-y. [PMID: 39367276 DOI: 10.1038/s41573-024-01042-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2024] [Indexed: 10/06/2024]
Abstract
The concept of mRNA-based vaccines emerged more than three decades ago. Groundbreaking discoveries and technological advancements over the past 20 years have resolved the major roadblocks that initially delayed application of this new vaccine modality. The rapid development of nucleoside-modified COVID-19 mRNA vaccines demonstrated that this immunization platform is easy to develop, has an acceptable safety profile and can be produced at a large scale. The flexibility and ease of antigen design have enabled mRNA vaccines to enter development for a wide range of viruses as well as for various bacteria and parasites. However, gaps in our knowledge limit the development of next-generation mRNA vaccines with increased potency and safety. A deeper understanding of the mechanisms of action of mRNA vaccines, application of novel technologies enabling rational antigen design, and innovative vaccine delivery strategies and vaccination regimens will likely yield potent novel vaccines against a wide range of pathogens.
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Affiliation(s)
- Norbert Pardi
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), 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.
- Ignaz Semmelweis Institute, Interuniversity Institute for Infection Research, Medical University of Vienna, Vienna, Austria.
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6
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Underwood AP, Gupta M, Wu BR, Eltahla AA, Boo I, Wang JJ, Agapiou D, Abayasingam A, Reynaldi A, Keoshkerian E, Zhao Y, Brasher N, Walker MR, Bukh J, Maher L, Gordon T, Davenport MP, Luciani F, Drummer HE, Lloyd AR, Bull RA. B-cell characteristics define HCV reinfection outcome. J Hepatol 2024; 81:415-428. [PMID: 38604387 DOI: 10.1016/j.jhep.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 03/20/2024] [Accepted: 04/03/2024] [Indexed: 04/13/2024]
Abstract
BACKGROUND & AIMS In individuals highly exposed to HCV, reinfection is common, suggesting that natural development of sterilising immunity is difficult. In those that are reinfected, some will develop a persistent infection, while a small proportion repeatedly clear the virus, suggesting natural protection is possible. The aim of this study was to characterise immune responses associated with rapid natural clearance of HCV reinfection. METHODS Broad neutralising antibodies (nAbs) and Envelope 2 (E2)-specific memory B cell (MBC) responses were examined longitudinally in 15 individuals with varied reinfection outcomes. RESULTS Broad nAb responses were associated with MBC recall, but not with clearance of reinfection. Strong evidence of antigen imprinting was found, and the B-cell receptor repertoire showed a high level of clonality with ongoing somatic hypermutation of many clones over subsequent reinfection events. Single-cell transcriptomic analyses showed that cleared reinfections featured an activated transcriptomic profile in HCV-specific B cells that rapidly expanded upon reinfection. CONCLUSIONS MBC quality, but not necessarily breadth of nAb responses, is important for protection against antigenically diverse variants, which is encouraging for HCV vaccine development. IMPACT AND IMPLICATIONS HCV continues to have a major health burden globally. Limitations in the health infrastructure for diagnosis and treatment, as well as high rates of reinfection, indicate that a vaccine that can protect against chronic HCV infection will greatly complement current efforts to eliminate HCV-related disease. With alternative approaches to testing vaccines, such as controlled human inoculation trials under consideration, we desperately need to identify the correlates of immune protection. In this study, in a small but rare cohort of high-risk injecting drug users who were reinfected multiple times, breadth of neutralisation was not associated with ultimate clearance of the reinfection event. Alternatively, characteristics of the HCV-specific B-cell response associated with B-cell proliferation were. This study indicates that humoral responses are important for protection and suggests that for genetically very diverse viruses, such as HCV, it may be beneficial to look beyond just antibodies as correlates of protection.
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Affiliation(s)
- Alexander P Underwood
- School of Biomedical Science, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia; The Kirby Institute, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia; Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Money Gupta
- School of Biomedical Science, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia; The Kirby Institute, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia
| | - Bing-Ru Wu
- School of Biomedical Science, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia; The Kirby Institute, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia
| | - Auda A Eltahla
- School of Biomedical Science, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia; The Kirby Institute, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia
| | - Irene Boo
- Burnet Institute, Melbourne, VIC, Australia
| | - Jing Jing Wang
- Department of Immunology Flinders Medical Centre and Flinders University, SA Pathology Bedford Park, SA, Australia
| | - David Agapiou
- The Kirby Institute, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia
| | - Arunasingam Abayasingam
- School of Biomedical Science, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia; The Kirby Institute, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia
| | - Arnold Reynaldi
- The Kirby Institute, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia
| | | | - Yanran Zhao
- The Kirby Institute, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia
| | - Nicholas Brasher
- School of Biomedical Science, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia; The Kirby Institute, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia
| | - Melanie R Walker
- School of Biomedical Science, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia; The Kirby Institute, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lisa Maher
- The Kirby Institute, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia
| | - Tom Gordon
- Department of Immunology Flinders Medical Centre and Flinders University, SA Pathology Bedford Park, SA, Australia
| | - Miles P Davenport
- The Kirby Institute, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia
| | - Fabio Luciani
- School of Biomedical Science, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia; The Kirby Institute, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia
| | - Heidi E Drummer
- Burnet Institute, Melbourne, VIC, Australia; Department of Microbiology, Monash University, Clayton, VIC, Australia; Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Andrew R Lloyd
- The Kirby Institute, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia
| | - Rowena A Bull
- School of Biomedical Science, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia; The Kirby Institute, Faculty of Medicine and Health, UNSW, Sydney, NSW, Australia.
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7
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Zhang Y, Cui P, Shi J, Zeng X, Jiang Y, Chen Y, Zhang J, Wang C, Wang Y, Tian G, Chen H, Kong H, Deng G. A broad-spectrum vaccine candidate against H5 viruses bearing different sub-clade 2.3.4.4 HA genes. NPJ Vaccines 2024; 9:152. [PMID: 39160189 PMCID: PMC11333769 DOI: 10.1038/s41541-024-00947-4] [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: 04/01/2024] [Accepted: 08/06/2024] [Indexed: 08/21/2024] Open
Abstract
The global spread of H5 clade 2.3.4.4 highly pathogenic avian influenza (HPAI) viruses threatens poultry and public health. The continuous circulation of these viruses has led to their considerable genetic and antigenic evolution, resulting in the formation of eight subclades (2.3.4.4a-h). Here, we examined the antigenic sites that determine the antigenic differences between two H5 vaccine strains, H5-Re8 (clade 2.3.4.4g) and H5-Re11 (clade 2.3.4.4h). Epitope mapping data revealed that all eight identified antigenic sites were located within two classical antigenic regions, with five sites in region A (positions 115, 120, 124, 126, and 140) and three in region B (positions 151, 156, and 185). Through antigenic cartography analysis of mutants with varying numbers of substitutions, we confirmed that a combination of mutations in these eight sites reverses the antigenicity of H5-Re11 to that of H5-Re8, and vice versa. More importantly, our analyses identified H5-Re11_Q115L/R120S/A156T (H5-Re11 + 3) as a promising candidate for a broad-spectrum vaccine, positioned centrally in the antigenic map, and offering potential universal protection against all variants within the clade 2.3.4.4. H5-Re11 + 3 serum has better cross-reactivity than sera generated with other 2.3.4.4 vaccines, and H5-Re11 + 3 vaccine provided 100% protection of chickens against antigenically drifted H5 viruses from various 2.3.4.4 antigenic groups. Our findings suggest that antigenic regions A and B are immunodominant in H5 viruses, and that antigenic cartography-guided vaccine design is a promising strategy for selecting a broad-spectrum vaccine.
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Affiliation(s)
- Yuancheng Zhang
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Pengfei Cui
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jianzhong Shi
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xianying Zeng
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yongping Jiang
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yuan Chen
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jie Zhang
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Congcong Wang
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yan Wang
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Guobin Tian
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hualan Chen
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Huihui Kong
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
| | - Guohua Deng
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
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8
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Welsh FC, Eguia RT, Lee JM, Haddox HK, Galloway J, Van Vinh Chau N, Loes AN, Huddleston J, Yu TC, Quynh Le M, Nhat NTD, Thi Le Thanh N, Greninger AL, Chu HY, Englund JA, Bedford T, Matsen FA, Boni MF, Bloom JD. Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin. Cell Host Microbe 2024; 32:1397-1411.e11. [PMID: 39032493 PMCID: PMC11329357 DOI: 10.1016/j.chom.2024.06.015] [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: 12/12/2023] [Revised: 04/19/2024] [Accepted: 06/25/2024] [Indexed: 07/23/2024]
Abstract
Human influenza virus evolves to escape neutralization by polyclonal antibodies. However, we have a limited understanding of how the antigenic effects of viral mutations vary across the human population and how this heterogeneity affects virus evolution. Here, we use deep mutational scanning to map how mutations to the hemagglutinin (HA) proteins of two H3N2 strains, A/Hong Kong/45/2019 and A/Perth/16/2009, affect neutralization by serum from individuals of a variety of ages. The effects of HA mutations on serum neutralization differ across age groups in ways that can be partially rationalized in terms of exposure histories. Mutations that were fixed in influenza variants after 2020 cause greater escape from sera from younger individuals compared with adults. Overall, these results demonstrate that influenza faces distinct antigenic selection regimes from different age groups and suggest approaches to understand how this heterogeneous selection shapes viral evolution.
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MESH Headings
- Humans
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/immunology
- Mutation
- Adult
- Antibodies, Viral/immunology
- Antibodies, Viral/blood
- Influenza, Human/virology
- Influenza, Human/immunology
- Age Factors
- Middle Aged
- Young Adult
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/blood
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Adolescent
- Evolution, Molecular
- Aged
- Child
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Affiliation(s)
- Frances C Welsh
- 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
| | - Rachel T Eguia
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Juhye M Lee
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Hugh K Haddox
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Jared Galloway
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Nguyen Van Vinh Chau
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Andrea N Loes
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - John Huddleston
- Vaccine and Infectious Disease Division, 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
| | - Mai Quynh Le
- National Institutes for Hygiene and Epidemiology, Hanoi, Vietnam
| | - Nguyen T D Nhat
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam; Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Nguyen Thi Le Thanh
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA; Division of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Helen Y Chu
- Division of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Janet A Englund
- Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Trevor Bedford
- Howard Hughes Medical Institute, Seattle, WA 98109, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Frederick A Matsen
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Maciej F Boni
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam; Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - 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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9
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Mühlemann B, Trimpert J, Walper F, Schmidt ML, Jansen J, Schroeder S, Jeworowski LM, Beheim-Schwarzbach J, Bleicker T, Niemeyer D, Richter A, Adler JM, Vidal RM, Langner C, Vladimirova D, Wilks SH, Smith DJ, Voß M, Paltzow L, Martínez Christophersen C, Rose R, Krumbholz A, Jones TC, Corman VM, Drosten C. Antigenic cartography using variant-specific hamster sera reveals substantial antigenic variation among Omicron subvariants. Proc Natl Acad Sci U S A 2024; 121:e2310917121. [PMID: 39078681 PMCID: PMC11317614 DOI: 10.1073/pnas.2310917121] [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: 07/04/2023] [Accepted: 05/31/2024] [Indexed: 07/31/2024] Open
Abstract
Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) has developed substantial antigenic variability. As the majority of the population now has pre-existing immunity due to infection or vaccination, the use of experimentally generated animal immune sera can be valuable for measuring antigenic differences between virus variants. Here, we immunized Syrian hamsters by two successive infections with one of nine SARS-CoV-2 variants. Their sera were titrated against 16 SARS-CoV-2 variants, and the resulting titers were visualized using antigenic cartography. The antigenic map shows a condensed cluster containing all pre-Omicron variants (D614G, Alpha, Delta, Beta, Mu, and an engineered B.1+E484K variant) and considerably more diversity among a selected panel of Omicron subvariants (BA.1, BA.2, BA.4/BA.5, the BA.5 descendants BF.7 and BQ.1.18, the BA.2.75 descendant BN.1.3.1, the BA.2-derived recombinants XBB.2 and EG.5.1, and the BA.2.86 descendant JN.1). Some Omicron subvariants were as antigenically distinct from each other as the wildtype is from the Omicron BA.1 variant. Compared to titers measured in human sera, titers in hamster sera are of higher magnitude, show less fold change, and result in a more compact antigenic map topology. The results highlight the potential of sera from hamsters for the continued antigenic characterization of SARS-CoV-2.
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Affiliation(s)
- Barbara Mühlemann
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
- German Centre for Infection Research (Deutsches Zentrum für Infektionsforschung), Berlin10117, Germany
| | - Jakob Trimpert
- Institut für Virologie, Freie Universität Berlin, Berlin14163, Germany
| | - Felix Walper
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Marie L. Schmidt
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Jenny Jansen
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Simon Schroeder
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Lara M. Jeworowski
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Jörn Beheim-Schwarzbach
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Tobias Bleicker
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Daniela Niemeyer
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Anja Richter
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
| | - Julia M. Adler
- Institut für Virologie, Freie Universität Berlin, Berlin14163, Germany
| | | | - Christine Langner
- Institut für Virologie, Freie Universität Berlin, Berlin14163, Germany
| | - Daria Vladimirova
- Institut für Virologie, Freie Universität Berlin, Berlin14163, Germany
| | - Samuel H. Wilks
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, CambridgeCB2 3EJ, United Kingdom
| | - Derek J. Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, CambridgeCB2 3EJ, United Kingdom
| | - Mathias Voß
- Institute for Infection Medicine, Christian-Albrechts-Universität zu Kiel and University Medical Center Schleswig-Holstein, Kiel24105, Germany
| | - Lea Paltzow
- Labor Dr. Krause und Kollegen Medizinisches Versorgungszentrum GmbH, Kiel24106, Germany
| | | | - Ruben Rose
- Institute for Infection Medicine, Christian-Albrechts-Universität zu Kiel and University Medical Center Schleswig-Holstein, Kiel24105, Germany
| | - Andi Krumbholz
- Institute for Infection Medicine, Christian-Albrechts-Universität zu Kiel and University Medical Center Schleswig-Holstein, Kiel24105, Germany
- Labor Dr. Krause und Kollegen Medizinisches Versorgungszentrum GmbH, Kiel24106, Germany
| | - Terry C. Jones
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
- German Centre for Infection Research (Deutsches Zentrum für Infektionsforschung), Berlin10117, Germany
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, CambridgeCB2 3EJ, United Kingdom
| | - Victor M. Corman
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
- German Centre for Infection Research (Deutsches Zentrum für Infektionsforschung), Berlin10117, Germany
- Labor Berlin–Charité Vivantes GmbH, Berlin13353, Germany
| | - Christian Drosten
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin10117, Germany
- German Centre for Infection Research (Deutsches Zentrum für Infektionsforschung), Berlin10117, Germany
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10
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Avanthay R, Garcia-Nicolas O, Ruggli N, Grau-Roma L, Párraga-Ros E, Summerfield A, Zimmer G. Evaluation of a novel intramuscular prime/intranasal boost vaccination strategy against influenza in the pig model. PLoS Pathog 2024; 20:e1012393. [PMID: 39116029 PMCID: PMC11309389 DOI: 10.1371/journal.ppat.1012393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 07/03/2024] [Indexed: 08/10/2024] Open
Abstract
Live-attenuated influenza vaccines (LAIV) offer advantages over the commonly used inactivated split influenza vaccines. However, finding the optimal balance between sufficient attenuation and immunogenicity has remained a challenge. We recently developed an alternative LAIV based on the 2009 pandemic H1N1 virus with a truncated NS1 protein and lacking PA-X protein expression (NS1(1-126)-ΔPAX). This virus showed a blunted replication and elicited a strong innate immune response. In the present study, we evaluated the efficacy of this vaccine candidate in the porcine animal model as a pertinent in vivo system. Immunization of pigs via the nasal route with the novel NS1(1-126)-ΔPAX LAIV did not cause disease and elicited a strong mucosal immune response that completely blocked replication of the homologous challenge virus in the respiratory tract. However, we observed prolonged shedding of our vaccine candidate from the upper respiratory tract. To improve LAIV safety, we developed a novel prime/boost vaccination strategy combining primary intramuscular immunization with a haemagglutinin-encoding propagation-defective vesicular stomatitis virus (VSV) replicon, followed by a secondary immunization with the NS1(1-126)-ΔPAX LAIV via the nasal route. This two-step immunization procedure significantly reduced LAIV shedding, increased the production of specific serum IgG, neutralizing antibodies, and Th1 memory cells, and resulted in sterilizing immunity against homologous virus challenge. In conclusion, our novel intramuscular prime/intranasal boost regimen interferes with virus shedding and transmission, a feature that will help combat influenza epidemics and pandemics.
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MESH Headings
- Animals
- Swine
- Influenza Vaccines/immunology
- Influenza Vaccines/administration & dosage
- Orthomyxoviridae Infections/prevention & control
- Orthomyxoviridae Infections/immunology
- Injections, Intramuscular
- Administration, Intranasal
- Vaccines, Attenuated/immunology
- Vaccines, Attenuated/administration & dosage
- Influenza A Virus, H1N1 Subtype/immunology
- Disease Models, Animal
- Antibodies, Viral/immunology
- Immunization, Secondary/methods
- Vaccination/methods
- Influenza, Human/prevention & control
- Influenza, Human/immunology
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Affiliation(s)
- Robin Avanthay
- Institute of Virology and Immunology IVI, Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Obdulio Garcia-Nicolas
- Institute of Virology and Immunology IVI, Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nicolas Ruggli
- Institute of Virology and Immunology IVI, Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Llorenç Grau-Roma
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Institute of Animal Pathology, COMPATH, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Ester Párraga-Ros
- Department of Anatomy and Comparative Pathology, Veterinary Faculty, University of Murcia, Murcia, Spain
| | - Artur Summerfield
- Institute of Virology and Immunology IVI, Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Gert Zimmer
- Institute of Virology and Immunology IVI, Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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11
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Gong X, Peng L, Wang F, Liu J, Tang Y, Peng Y, Niu S, Yin J, Guo L, Lu H, Liu Y, Yang Y. Repeated Omicron infection dampens immune imprinting from previous vaccination and induces broad neutralizing antibodies against Omicron sub-variants. J Infect 2024; 89:106208. [PMID: 38908522 DOI: 10.1016/j.jinf.2024.106208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 06/15/2024] [Indexed: 06/24/2024]
Abstract
OBJECTIVE Similar with influenza virus, antigenic drift is highly relevant to SARS-CoV-2 evolution, and immune imprinting has been found to limit the performance of updated vaccines based on the emerging variants of SARS-CoV-2. We aimed to investigate whether repeated exposure to Omicron variant could reduce the immune imprinting from previous vaccination. METHODS A total of 194 participants with different status of vaccination (unvaccinated, regular vaccination and booster vaccination) confirmed for first infection and re-infection with BA.5, BF.7 and XBB variants were enrolled, and the neutralizing profiles against wild type (WT) SARS-CoV-2 and Omicron sub-variants were analyzed. RESULTS Neutralizing potency against the corresponding infected variant is significantly hampered along with the doses of vaccination during first infection. However, for the participants with first infection of BA.5/BF.7 variants and re-infection of XBB variant, immune imprinting was obviously alleviated, indicated as significantly increased ratio of the corresponding infected variant/WT ID50 titers and higher percentage of samples with high neutralizing activities (ID50 > 500) against BA.5, BF.7 and XBB variants. Moreover, repeated Omicron infection could induce strong neutralizing potency with broad neutralizing profiles against a series of other Omicron sub-variants, both in the vaccine naive and vaccine experienced individuals. CONCLUSIONS Our results demonstrate that repeated Omicron infection dampens immune imprinting from vaccination with WT SARS-CoV-2 and induces broad neutralizing profiles against Omicron sub-variants.
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Affiliation(s)
- Xiaohua Gong
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China; Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China; National Clinical Research Center for Infectious Disease, Shenzhen, China
| | - Ling Peng
- Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China; National Clinical Research Center for Infectious Disease, Shenzhen, China
| | - Fuxiang Wang
- Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China; National Clinical Research Center for Infectious Disease, Shenzhen, China
| | - Jiexiang Liu
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China; Shenzhen Clinical School of Medicine, Guangzhou University of Chinese Medicine, China
| | - Yimin Tang
- Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China; National Clinical Research Center for Infectious Disease, Shenzhen, China
| | - Yun Peng
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China; Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China; National Clinical Research Center for Infectious Disease, Shenzhen, China
| | - Shiyu Niu
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China; Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China
| | - Juzhen Yin
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China; Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China
| | - Liping Guo
- Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China; National Clinical Research Center for Infectious Disease, Shenzhen, China
| | - Hongzhou Lu
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China; Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China; National Clinical Research Center for Infectious Disease, Shenzhen, China.
| | - Yingxia Liu
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China; Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China; National Clinical Research Center for Infectious Disease, Shenzhen, China.
| | - Yang Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China; Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, China; National Clinical Research Center for Infectious Disease, Shenzhen, China.
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12
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Edler P, Schwab LSU, Aban M, Wille M, Spirason N, Deng YM, Carlock MA, Ross TM, Juno JA, Rockman S, Wheatley AK, Kent SJ, Barr IG, Price DJ, Koutsakos M. Immune imprinting in early life shapes cross-reactivity to influenza B virus haemagglutinin. Nat Microbiol 2024; 9:2073-2083. [PMID: 38890491 DOI: 10.1038/s41564-024-01732-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 05/15/2024] [Indexed: 06/20/2024]
Abstract
Influenza exposures early in life are believed to shape future susceptibility to influenza infections by imprinting immunological biases that affect cross-reactivity to future influenza viruses. However, direct serological evidence linked to susceptibility is limited. Here we analysed haemagglutination-inhibition titres in 1,451 cross-sectional samples collected between 1992 and 2020, from individuals born between 1917 and 2008, against influenza B virus (IBV) isolates from 1940 to 2021. We included testing of 'future' isolates that circulated after sample collection. We show that immunological biases are conferred by early life IBV infection and result in lineage-specific cross-reactivity of a birth cohort towards future IBV isolates. This translates into differential estimates of susceptibility between birth cohorts towards the B/Yamagata and B/Victoria lineages, predicting lineage-specific birth-cohort distributions of observed medically attended IBV infections. Our data suggest that immunological measurements of imprinting could be important in modelling and predicting virus epidemiology.
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Affiliation(s)
- Peta Edler
- Department of Infectious Diseases, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Lara S U Schwab
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Malet Aban
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Michelle Wille
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
| | - Natalie Spirason
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Yi-Mo Deng
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Michael A Carlock
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA
- Department of Infectious Diseases, University of Georgia, Athens, GA, USA
- Florida Research and Innovation Centre, Cleveland Clinic, Port Saint Lucie, FL, 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
- Florida Research and Innovation Centre, Cleveland Clinic, Port Saint Lucie, FL, USA
- Department of Infection Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jennifer A Juno
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Steve Rockman
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Vaccine Product Development, CSL Seqirus Ltd, Parkville, Victoria, Australia
| | - Adam K Wheatley
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Melbourne Sexual Health Centre and Department of Infectious Diseases, Alfred Health, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Ian G Barr
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - David J Price
- Department of Infectious Diseases, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Marios Koutsakos
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia.
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13
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Kim K, Vieira MC, Gouma S, Weirick ME, Hensley SE, Cobey S. Measures of population immunity can predict the dominant clade of influenza A (H3N2) in the 2017-2018 season and reveal age-associated differences in susceptibility and antibody-binding specificity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.10.26.23297569. [PMID: 37961288 PMCID: PMC10635207 DOI: 10.1101/2023.10.26.23297569] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Background For antigenically variable pathogens such as influenza, strain fitness is partly determined by the relative availability of hosts susceptible to infection with that strain compared to others. Antibodies to the hemagglutinin (HA) and neuraminidase (NA) confer substantial protection against influenza infection. We asked if a cross-sectionalantibody-derived estimate of population susceptibility to different clades of influenza A (H3N2) could predict the success of clades in the following season. Methods We collected sera from 483 healthy individuals aged 1 to 90 years in the summer of 2017 and analyzed neutralizing responses to the HA and NA of representative strains using Focus Reduction Neutralization Tests (FNRT) and Enzyme-Linked Lectin Assays (ELLA). We estimated relative population-average and age-specific susceptibilities to circulating viral clades and compared those estimates to changes in clade frequencies in the following 2017-18 season. Results The clade to which neutralizing antibody titers were lowest, indicating greater population susceptibility, dominated the next season. Titers to different HA and NA clades varied dramatically between individuals but showed significant associations with age, suggesting dependence on correlated past exposures. Conclusions This study indicates how representative measures of population immunity might improve evolutionary forecasts and inform selective pressures on influenza.
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Affiliation(s)
- Kangchon Kim
- Department of Ecology and Evolution, The University of Chicago, USA
| | - Marcos C. Vieira
- Department of Ecology and Evolution, The University of Chicago, USA
| | - Sigrid Gouma
- Department of Microbiology, Perelman School of Medicine, The University of Pennsylvania, USA
| | - Madison E. Weirick
- Department of Microbiology, Perelman School of Medicine, The University of Pennsylvania, USA
| | - Scott E. Hensley
- Department of Microbiology, Perelman School of Medicine, The University of Pennsylvania, USA
| | - Sarah Cobey
- Department of Ecology and Evolution, The University of Chicago, USA
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14
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Carlock MA, Allen JD, Hanley HB, Ross TM. Longitudinal assessment of human antibody binding to hemagglutinin elicited by split-inactivated influenza vaccination over six consecutive seasons. PLoS One 2024; 19:e0301157. [PMID: 38917104 PMCID: PMC11198804 DOI: 10.1371/journal.pone.0301157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 06/07/2024] [Indexed: 06/27/2024] Open
Abstract
Participants between the ages of 10-86 years old were vaccinated with split-inactivated influenza vaccine (Fluzone®) in six consecutive influenza seasons from 2016-2017 to 2021-2022. Vaccine effectiveness varies from season to season as a result of both host immune responses as well as evolutionary changes in the influenza virus surface glycoproteins that provide challenges to vaccine manufacturers to produce more effective annual vaccines. Next generation influenza vaccines are in development and may provide protective immune responses against a broader number of influenza viruses and reduce the need for annual vaccination. An improved understanding how current influenza vaccines are influenced by human host immune responses in people of different ages and co-morbidities is necessary for designing the next-generation of 'universal' or broadly-protective influenza vaccines. Overall, pre-existing immune responses to previous influenza virus exposures, either by past infections or vaccinations, is a critical factor influencing host responses to seasonal influenza vaccination. Participants vaccinated in consecutive seasons had reduced serum hemagglutination-inhibition (HAI) activity against strains included in the vaccine compared to participants that had not been vaccinated in the preceding 1-2 years prior to entering this study. The magnitude and breadth of these antibody responses were also modulated by the age of the participant. Elderly participants over 65 years of age, in general, had lower pre-existing HAI titers each season prior to vaccination with lower post-vaccination titers compared to children or young adults under the age of 35. The administration of higher doses (HD) of the split-inactivated vaccine enhanced the antibody titers in the elderly. This report showcases 6 consecutive years of antibody HAI activity in human subjects receiving seasonal split-inactivated influenza vaccine.
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Affiliation(s)
- Michael A. Carlock
- Center for Vaccines and Immunology, Athens, GA, United States of America
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States of America
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, United States of America
| | - James D. Allen
- Center for Vaccines and Immunology, Athens, GA, United States of America
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States of America
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, United States of America
| | - Hannah B. Hanley
- Center for Vaccines and Immunology, Athens, GA, United States of America
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States of America
| | - Ted M. Ross
- Center for Vaccines and Immunology, Athens, GA, United States of America
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States of America
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, United States of America
- Department of Infection Biology, Lehner Research Institute, Cleveland Clinic, Cleveland, OH, United States of America
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15
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McGough L, Cobey S. A speed limit on serial strain replacement from original antigenic sin. Proc Natl Acad Sci U S A 2024; 121:e2400202121. [PMID: 38857397 PMCID: PMC11194583 DOI: 10.1073/pnas.2400202121] [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: 01/04/2024] [Accepted: 05/06/2024] [Indexed: 06/12/2024] Open
Abstract
Many pathogens evolve to escape immunity, yet it remains difficult to predict whether immune pressure will lead to diversification, serial replacement of one variant by another, or more complex patterns. Pathogen strain dynamics are mediated by cross-protective immunity, whereby exposure to one strain partially protects against infection by antigenically diverged strains. There is growing evidence that this protection is influenced by early exposures, a phenomenon referred to as original antigenic sin (OAS) or imprinting. In this paper, we derive constraints on the emergence of the pattern of successive strain replacements demonstrated by influenza, SARS-CoV-2, seasonal coronaviruses, and other pathogens. We find that OAS implies that the limited diversity found with successive strain replacement can only be maintained if [Formula: see text] is less than a threshold set by the characteristic antigenic distances for cross-protection and for the creation of new immune memory. This bound implies a "speed limit" on the evolution of new strains and a minimum variance of the distribution of infecting strains in antigenic space at any time. To carry out this analysis, we develop a theoretical model of pathogen evolution in antigenic space that implements OAS by decoupling the antigenic distances required for protection from infection and strain-specific memory creation. Our results demonstrate that OAS can play an integral role in the emergence of strain structure from host immune dynamics, preventing highly transmissible pathogens from maintaining serial strain replacement without diversification.
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Affiliation(s)
- Lauren McGough
- Department of Ecology and EvolutionThe University of Chicago, Chicago, IL60637
| | - Sarah Cobey
- Department of Ecology and EvolutionThe University of Chicago, Chicago, IL60637
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16
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Wang D, Huot M, Mohanty V, Shakhnovich EI. Biophysical principles predict fitness of SARS-CoV-2 variants. Proc Natl Acad Sci U S A 2024; 121:e2314518121. [PMID: 38820002 PMCID: PMC11161772 DOI: 10.1073/pnas.2314518121] [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: 08/22/2023] [Accepted: 04/19/2024] [Indexed: 06/02/2024] Open
Abstract
SARS-CoV-2 employs its spike protein's receptor binding domain (RBD) to enter host cells. The RBD is constantly subjected to immune responses, while requiring efficient binding to host cell receptors for successful infection. However, our understanding of how RBD's biophysical properties contribute to SARS-CoV-2's epidemiological fitness remains largely incomplete. Through a comprehensive approach, comprising large-scale sequence analysis of SARS-CoV-2 variants and the identification of a fitness function based on binding thermodynamics, we unravel the relationship between the biophysical properties of RBD variants and their contribution to viral fitness. We developed a biophysical model that uses statistical mechanics to map the molecular phenotype space, characterized by dissociation constants of RBD to ACE2, LY-CoV016, LY-CoV555, REGN10987, and S309, onto an epistatic fitness landscape. We validate our findings through experimentally measured and machine learning (ML) estimated binding affinities, coupled with infectivity data derived from population-level sequencing. Our analysis reveals that this model effectively predicts the fitness of novel RBD variants and can account for the epistatic interactions among mutations, including explaining the later reversal of Q493R. Our study sheds light on the impact of specific mutations on viral fitness and delivers a tool for predicting the future epidemiological trajectory of previously unseen or emerging low-frequency variants. These insights offer not only greater understanding of viral evolution but also potentially aid in guiding public health decisions in the battle against COVID-19 and future pandemics.
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Affiliation(s)
- Dianzhuo Wang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
| | - Marian Huot
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
- École Polytechnique, Institut Polytechnique de Paris, Palaiseau91128, France
| | - Vaibhav Mohanty
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
- Harvard/MIT MD-PhD Program, Harvard Medical School, Boston, MA02115
- Massachusetts Institute of Technology, Cambridge, MA02139
| | - Eugene I. Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
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17
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Mühlemann B, Wilks SH, Baracco L, Bekliz M, Carreño JM, Corman VM, Davis-Gardner ME, Dejnirattisai W, Diamond MS, Douek DC, Drosten C, Eckerle I, Edara VV, Ellis M, Fouchier RAM, Frieman M, Godbole S, Haagmans B, Halfmann PJ, Henry AR, Jones TC, Katzelnick LC, Kawaoka Y, Kimpel J, Krammer F, Lai L, Liu C, Lusvarghi S, Meyer B, Mongkolsapaya J, Montefiori DC, Mykytyn A, Netzl A, Pollett S, Rössler A, Screaton GR, Shen X, Sigal A, Simon V, Subramanian R, Supasa P, Suthar MS, Türeli S, Wang W, Weiss CD, Smith DJ. Comparative analysis of SARS-CoV-2 neutralization titers reveals consistency between human and animal model serum and across assays. Sci Transl Med 2024; 16:eadl1722. [PMID: 38748773 DOI: 10.1126/scitranslmed.adl1722] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 04/11/2024] [Indexed: 08/31/2024]
Abstract
The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires ongoing monitoring to judge the ability of newly arising variants to escape the immune response. A surveillance system necessitates an understanding of differences in neutralization titers measured in different assays and using human and animal serum samples. We compared 18 datasets generated using human, hamster, and mouse serum and six different neutralization assays. Datasets using animal model serum samples showed higher titer magnitudes than datasets using human serum samples in this comparison. Fold change in neutralization of variants compared to ancestral SARS-CoV-2, immunodominance patterns, and antigenic maps were similar among serum samples and assays. Most assays yielded consistent results, except for differences in fold change in cytopathic effect assays. Hamster serum samples were a consistent surrogate for human first-infection serum samples. These results inform the transition of surveillance of SARS-CoV-2 antigenic variation from dependence on human first-infection serum samples to the utilization of serum samples from animal models.
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Affiliation(s)
- Barbara Mühlemann
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | - Samuel H Wilks
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Lauren Baracco
- Center for Pathogen Research, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Meriem Bekliz
- Department of Medicine, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
- Centre for Emerging Viral Diseases, University Hospitals of Geneva and University of Geneva, CH-1211, Geneva, Switzerland
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Victor M Corman
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | - Meredith E Davis-Gardner
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Wanwisa Dejnirattisai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Division of Emerging Infectious Disease, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok Noi, Bangkok 10700, Thailand
| | - Michael S Diamond
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Andrew M. and Jane M. Bursky the Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christian Drosten
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | - Isabella Eckerle
- Department of Medicine, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
- Centre for Emerging Viral Diseases, University Hospitals of Geneva and University of Geneva, CH-1211, Geneva, Switzerland
- Division of Infectious Diseases, Geneva University Hospitals, CH-1211 Geneva, Switzerland
| | - Venkata-Viswanadh Edara
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Madison Ellis
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Ron A M Fouchier
- Viroscience Department, Erasmus Medical Center, 3015 Rotterdam, Netherlands
| | - Matthew Frieman
- Center for Pathogen Research, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Sucheta Godbole
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bart Haagmans
- Viroscience Department, Erasmus Medical Center, 3015 Rotterdam, Netherlands
| | - Peter J Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Amy R Henry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Terry C Jones
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Leah C Katzelnick
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
- Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), University of Tokyo, Tokyo 162-8655, Japan
| | - Janine Kimpel
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pathology, Cellular and Molecular Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lilin Lai
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7BN, UK
| | - Sabrina Lusvarghi
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20903, USA
| | - Benjamin Meyer
- Centre of Vaccinology, Department of Pathology and Immunology, University of Geneva, CH-1211 Geneva, Switzerland
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7BN, UK
| | - David C Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Anna Mykytyn
- Viroscience Department, Erasmus Medical Center, 3015 Rotterdam, Netherlands
| | - Antonia Netzl
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Simon Pollett
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Annika Rössler
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020 Innsbruck, Austria
| | - Gavin R Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Xiaoying Shen
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Alex Sigal
- Africa Health Research Institute, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
- Centre for the AIDS Programme of Research in South Africa, Durban 4001, South Africa
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pathology, Cellular and Molecular Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rahul Subramanian
- Office of Data Science and Emerging Technologies, Office of Science Management and Operations, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Mehul S Suthar
- Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Sina Türeli
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Wei Wang
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20903, USA
| | - Carol D Weiss
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20903, USA
| | - Derek J Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
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18
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Meijers M, Ruchnewitz D, Eberhardt J, Karmakar M, Łuksza M, Lässig M. Concepts and methods for predicting viral evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585703. [PMID: 38746108 PMCID: PMC11092427 DOI: 10.1101/2024.03.19.585703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The seasonal human influenza virus undergoes rapid evolution, leading to significant changes in circulating viral strains from year to year. These changes are typically driven by adaptive mutations, particularly in the antigenic epitopes, the regions of the viral surface protein haemagglutinin targeted by human antibodies. Here we describe a consistent set of methods for data-driven predictive analysis of viral evolution. Our pipeline integrates four types of data: (1) sequence data of viral isolates collected on a worldwide scale, (2) epidemiological data on incidences, (3) antigenic characterization of circulating viruses, and (4) intrinsic viral phenotypes. From the combined analysis of these data, we obtain estimates of relative fitness for circulating strains and predictions of clade frequencies for periods of up to one year. Furthermore, we obtain comparative estimates of protection against future viral populations for candidate vaccine strains, providing a basis for pre-emptive vaccine strain selection. Continuously updated predictions obtained from the prediction pipeline for influenza and SARS-CoV-2 are available on the website previr.app .
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19
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Meijers M, Ruchnewitz D, Eberhardt J, Karmakar M, Łuksza M, Lässig M. Concepts and methods for predicting viral evolution. ARXIV 2024:arXiv:2403.12684v2. [PMID: 38745695 PMCID: PMC11092678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The seasonal human influenza virus undergoes rapid evolution, leading to significant changes in circulating viral strains from year to year. These changes are typically driven by adaptive mutations, particularly in the antigenic epitopes, the regions of the viral surface protein haemagglutinin targeted by human antibodies. Here we describe a consistent set of methods for data-driven predictive analysis of viral evolution. Our pipeline integrates four types of data: (1) sequence data of viral isolates collected on a worldwide scale, (2) epidemiological data on incidences, (3) antigenic characterization of circulating viruses, and (4) intrinsic viral phenotypes. From the combined analysis of these data, we obtain estimates of relative fitness for circulating strains and predictions of clade frequencies for periods of up to one year. Furthermore, we obtain comparative estimates of protection against future viral populations for candidate vaccine strains, providing a basis for pre-emptive vaccine strain selection. Continuously updated predictions obtained from the prediction pipeline for influenza and SARS-CoV-2 are available on the website previr.app.
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Affiliation(s)
- Matthijs Meijers
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937, Köln, Germany
| | - Denis Ruchnewitz
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937, Köln, Germany
| | - Jan Eberhardt
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937, Köln, Germany
| | - Malancha Karmakar
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937, Köln, Germany
| | - Marta Łuksza
- Tisch Cancer Institute, Departments of Oncological Sciences and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Lässig
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937, Köln, Germany
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20
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Astakhova EA, Morozov AA, Vavilova JD, Filatov AV. Antigenic Cartography of SARS-CoV-2. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:862-871. [PMID: 38880647 DOI: 10.1134/s0006297924050079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/14/2024] [Accepted: 01/17/2024] [Indexed: 06/18/2024]
Abstract
Antigenic cartography is a tool for interpreting and visualizing antigenic differences between virus variants based on virus neutralization data. This approach has been successfully used in the selection of influenza vaccine seed strains. With the emergence of SARS-CoV-2 variants escaping vaccine-induced antibody response, adjusting COVID-19 vaccines has become essential. This review provides information on the antigenic differences between SARS-CoV-2 variants revealed by antigenic cartography and explores a potential of antigenic cartography-based methods (e.g., building antibody landscapes and neutralization breadth gain plots) for the quantitative assessment of the breadth of the antibody response. Understanding the antigenic differences of SARS-CoV-2 and the possibilities of the formed humoral immunity aids in the prompt modification of preventative vaccines against COVID-19.
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Affiliation(s)
- Ekaterina A Astakhova
- National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, Moscow, 115522, Russia.
- Department of Immunology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Alexey A Morozov
- National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, Moscow, 115522, Russia
- Department of Immunology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Julia D Vavilova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Alexander V Filatov
- National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, Moscow, 115522, Russia
- Department of Immunology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
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21
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Guiomar R, Pereira da Silva S, Costa I, Conde P, Cristóvão P, Rodrigues A, Fernandes A, Dias A, Couto A, Ramos A, Moita C, Rodrigues C, Vale F, Caldeira F, Bruges Armas J, Pereira‐Vaz J, Alves J, Freitas L, Martins L, Milho L, Mota‐Vieira L, Lopes L, Freitas M, Pessanha M, Correia M, Marques M, Cardoso M, Peres M, Cunha M, Amantegui P, Mota P, Lopes P, Pereira P, Viseu R, Cabral R, Côrte‐Real R, Almeida S, Soares V, Mansinho K, Hungnes O, Nunes B. Seroprevalence of Protective Antibodies Against Influenza and the Reduction of the Influenza Incidence Rate: An Annual Repeated Cross-Sectional Study From 2014 to 2019. Influenza Other Respir Viruses 2024; 18:e13307. [PMID: 38798072 PMCID: PMC11128746 DOI: 10.1111/irv.13307] [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: 12/27/2023] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 05/29/2024] Open
Abstract
BACKGROUND Seroepidemiological studies provide estimates of population-level immunity, prevalence/incidence of infections, and evaluation of vaccination programs. We assessed the seroprevalence of protective antibodies against influenza and evaluated the correlation of seroprevalence with the cumulative annual influenza incidence rate. METHODS We conducted an annual repeated cross-sectional seroepidemiological survey, during June-August, from 2014 to 2019, in Portugal. A total of 4326 sera from all age groups, sex, and regions was tested by hemagglutination inhibition assay. Seroprevalence and geometric mean titers (GMT) of protective antibodies against influenza were assessed by age group, sex, and vaccine status (65+ years old). The association between summer annual seroprevalence and the difference of influenza incidence rates between one season and the previous one was measured by Pearson correlation coefficient (r). RESULTS Significant differences in seroprevalence of protective antibodies against influenza were observed in the population. Higher seroprevalence and GMT for A(H1N1)pdm09 and A(H3N2) were observed in children (5-14); influenza B seroprevalence in adults 65+ was 1.6-4.4 times than in children (0-4). Vaccinated participants (65+) showed significant higher seroprevalence/GMT for influenza. A strong negative and significant correlation was found between seroprevalence and ILI incidence rate for A(H1N1)pdm09 in children between 5 and 14 (r = -0.84; 95% CI, -0.98 to -0.07); a weak negative correlation was observed for A(H3N2) and B/Yamagata (r ≤ -0.1). CONCLUSIONS The study provides new insight into the anti-influenza antibodies seroprevalence measured in summer on the ILI incidence rate in the next season and the need for adjusted preventive health care measures to prevent influenza infection and transmission.
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Affiliation(s)
- Raquel Guiomar
- National Reference Laboratory for Influenza and Other Respiratory Viruses, Infectious Diseases DepartmentNational Institute of Health Dr. Ricardo Jorge, IPLisbonPortugal
| | | | - Inês Costa
- National Reference Laboratory for Influenza and Other Respiratory Viruses, Infectious Diseases DepartmentNational Institute of Health Dr. Ricardo Jorge, IPLisbonPortugal
| | - Patricia Conde
- National Reference Laboratory for Influenza and Other Respiratory Viruses, Infectious Diseases DepartmentNational Institute of Health Dr. Ricardo Jorge, IPLisbonPortugal
| | - Paula Cristóvão
- National Reference Laboratory for Influenza and Other Respiratory Viruses, Infectious Diseases DepartmentNational Institute of Health Dr. Ricardo Jorge, IPLisbonPortugal
| | - Ana Paula Rodrigues
- Department of EpidemiologyNational Institute of Health Dr. Ricardo Jorge, IPLisbonPortugal
| | - Aida Fernandes
- Laboratório de Saúde Pública Dr.ª Laura AyresFaroPortugal
| | - Ana Paula Dias
- Centro Hospitalar de Lisboa Ocidental, E. P. E.LisbonPortugal
| | - Ana Rita Couto
- Hospital de Santo Espírito da Ilha Terceira, E. P. E.R.Angra do HeroísmoPortugal
| | - Angélica Ramos
- Centro Hospitalar Universitário de São João, E. P. E.PortoPortugal
- EPIUnit – Instituto de Saúde PúblicaUniversidade do PortoPortoPortugal
| | - Carina Moita
- Unidade Local de Saúde da Guarda, E. P. E.GuardaPortugal
| | | | - Fátima Vale
- Unidade Local de Saúde da Guarda, E. P. E.GuardaPortugal
| | | | - Jácome Bruges Armas
- Hospital de Santo Espírito da Ilha Terceira, E. P. E.R.Angra do HeroísmoPortugal
| | - João Pereira‐Vaz
- Centro Hospitalar e Universitário de Coimbra, E. P. E.CoimbraPortugal
| | - José Alves
- Hospital Central e Universitário da MadeiraFunchalPortugal
| | | | - Luis Martins
- Instituto Português de Oncologia de Lisboa, Francisco Gentil, E.P. E.LisbonPortugal
| | - Luís Milho
- Laboratório de Saúde Pública Dr.ª Laura AyresFaroPortugal
| | - Luisa Mota‐Vieira
- Hospital do Divino Espirito Santo de Ponta Delgada, E. P. E. R.Ponta DelgadaPortugal
| | - Lurdes Lopes
- Centro Hospitalar e Universitário de Lisboa Central, E. P. E.LisbonPortugal
| | - Margarida Freitas
- Hospital da Senhora da Oliveira Guimarães, E. P. E.GuimarãesPortugal
| | | | - Maria Correia
- Centro Hospitalar e Universitário de Coimbra, E. P. E.CoimbraPortugal
| | | | | | | | - Mário Cunha
- Instituto Português de Oncologia de Lisboa, Francisco Gentil, E.P. E.LisbonPortugal
| | | | - Paula Mota
- Hospital da Senhora da Oliveira Guimarães, E. P. E.GuimarãesPortugal
| | - Paulo Lopes
- Centro Hospitalar de Vila Nova de Gaia/Espinho, E. P. E.Vila Nova de GaiaPortugal
| | - Paulo Pereira
- Centro Hospitalar Universitário do Porto, E. P. E.PortoPortugal
| | - Regina Viseu
- Centro Hospitalar de Setúbal, E. P. E.SetúbalPortugal
| | - Rita Cabral
- Hospital do Divino Espirito Santo de Ponta Delgada, E. P. E. R.Ponta DelgadaPortugal
| | - Rita Côrte‐Real
- Centro Hospitalar e Universitário de Lisboa Central, E. P. E.LisbonPortugal
| | - Sofia Almeida
- Centro Hospitalar Universitário Cova da Beira, E. P. E.CovilhãPortugal
| | - Vânia Soares
- Centro Hospitalar de Vila Nova de Gaia/Espinho, E. P. E.Vila Nova de GaiaPortugal
| | - Kamal Mansinho
- Centro Hospitalar de Lisboa Ocidental, E. P. E.LisbonPortugal
| | - Olav Hungnes
- Norwegian National Influenza CentreNorwegian Institute of Public HealthOsloNorway
| | - Baltazar Nunes
- Department of EpidemiologyNational Institute of Health Dr. Ricardo Jorge, IPLisbonPortugal
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22
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Wang L, Huang AT, Katzelnick LC, Lefrancq N, Escoto AC, Duret L, Chowdhury N, Jarman R, Conte MA, Berry IM, Fernandez S, Klungthong C, Thaisomboonsuk B, Suntarattiwong P, Vandepitte W, Whitehead SS, Cauchemez S, Cummings DAT, Salje H. Antigenic distance between primary and secondary dengue infections correlates with disease risk. Sci Transl Med 2024; 16:eadk3259. [PMID: 38657027 DOI: 10.1126/scitranslmed.adk3259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 03/21/2024] [Indexed: 04/26/2024]
Abstract
Many pathogens continuously change their protein structure in response to immune-driven selection, resulting in weakened protection even in previously exposed individuals. In addition, for some pathogens, such as dengue virus, poorly targeted immunity is associated with increased risk of severe disease through a mechanism known as antibody-dependent enhancement. However, it remains unclear whether the antigenic distances between an individual's first infection and subsequent exposures dictate disease risk, explaining the observed large-scale differences in dengue hospitalizations across years. Here, we develop a framework that combines detailed antigenic and genetic characterization of viruses with details on hospitalized cases from 21 years of dengue surveillance in Bangkok, Thailand, to identify the role of the antigenic profile of circulating viruses in determining disease risk. We found that the risk of hospitalization depended on both the specific order of infecting serotypes and the antigenic distance between an individual's primary and secondary infections, with risk maximized at intermediate antigenic distances. These findings suggest that immune imprinting helps determine dengue disease risk and provide a pathway to monitor the changing risk profile of populations and to quantifying risk profiles of candidate vaccines.
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Affiliation(s)
- Lin Wang
- Department of Genetics, University of Cambridge, Cambridge CB2 1TN, UK
| | - Angkana T Huang
- Department of Genetics, University of Cambridge, Cambridge CB2 1TN, UK
| | - Leah C Katzelnick
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Noémie Lefrancq
- Department of Genetics, University of Cambridge, Cambridge CB2 1TN, UK
| | - Ana Coello Escoto
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Loréna Duret
- Department of Genetics, University of Cambridge, Cambridge CB2 1TN, UK
| | - Nayeem Chowdhury
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard Jarman
- Coalition for Epidemic Preparedness Initiative, Washington, DC 20006, USA
| | - Matthew A Conte
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Stefan Fernandez
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand
| | - Chonticha Klungthong
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand
| | - Butsaya Thaisomboonsuk
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand
| | | | - Warunee Vandepitte
- Queen Sirikit National Institute of Child Health, Bangkok 10400, Thailand
| | - Stephen S Whitehead
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Paris 75015, France
| | - Derek A T Cummings
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA
| | - Henrik Salje
- Department of Genetics, University of Cambridge, Cambridge CB2 1TN, UK
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA
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23
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McGough L, Cobey S. A speed limit on serial strain replacement from original antigenic sin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.04.574172. [PMID: 38260288 PMCID: PMC10802292 DOI: 10.1101/2024.01.04.574172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Many pathogens evolve to escape immunity, yet it remains difficult to predict whether immune pressure will lead to diversification, serial replacement of one variant by another, or more complex patterns. Pathogen strain dynamics are mediated by cross-protective immunity, whereby exposure to one strain partially protects against infection by antigenically diverged strains. There is growing evidence that this protection is influenced by early exposures, a phenomenon referred to as original antigenic sin (OAS) or imprinting. In this paper, we derive new constraints on the emergence of the pattern of successive strain replacements demonstrated by influenza, SARS-CoV-2, seasonal coronaviruses, and other pathogens. We find that OAS implies that the limited diversity found with successive strain replacement can only be maintained if R 0 is less than a threshold set by the characteristic antigenic distances for cross-protection and for the creation of new immune memory. This bound implies a "speed limit" on the evolution of new strains and a minimum variance of the distribution of infecting strains in antigenic space at any time. To carry out this analysis, we develop a theoretical model of pathogen evolution in antigenic space that implements OAS by decoupling the antigenic distances required for protection from infection and strain-specific memory creation. Our results demonstrate that OAS can play an integral role in the emergence of strain structure from host immune dynamics, preventing highly transmissible pathogens from maintaining serial strain replacement without diversification.
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Affiliation(s)
- Lauren McGough
- Department of Ecology and Evolution, University of Chicago, Chicago, IL
| | - Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, IL
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24
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Kasten-Jolly J, Lawrence DA. Cellular and Molecular Immunity to Influenza Viruses and Vaccines. Vaccines (Basel) 2024; 12:389. [PMID: 38675771 PMCID: PMC11154265 DOI: 10.3390/vaccines12040389] [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: 03/18/2024] [Revised: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 04/28/2024] Open
Abstract
Immune responses to influenza (flu) antigens reflect memory of prior infections or vaccinations, which might influence immunity to new flu antigens. Memory of past antigens has been termed "original antigenic sin" or, more recently, "immune imprinting" and "seniority". We have researched a comparison between the immune response to live flu infections and inactivated flu vaccinations. A brief history of antibody generation theories is presented, culminating in new findings about the immune-network theory and suggesting that a network of clones exists between anti-idiotypic antibodies and T cell receptors. Findings regarding the 2009 pandemic flu strain and immune responses to it are presented, including memory B cells and conserved regions within the hemagglutinin protein. The importance of CD4+ memory T cells and cytotoxic CD8+ T cells responding to both infections and vaccinations are discussed and compared. Innate immune cells, like natural killer (NK) cells and macrophages, are discussed regarding their roles in adaptive immune responses. Antigen presentation via macroautophagy processes is described. New vaccines in development are mentioned along with the results of some clinical trials. The manuscript concludes with how repeated vaccinations are impacting the immune system and a sketch of what might be behind the imprinting phenomenon, including future research directions.
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Affiliation(s)
- Jane Kasten-Jolly
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA;
| | - David A. Lawrence
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA;
- Departments of Biomedical Science and Environmental Health Science, University at Albany School of Public Health, Rensselaer, NY 12144, USA
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25
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Wang W, Bhushan GL, Paz S, Stauft CB, Selvaraj P, Goguet E, Bishop-Lilly KA, Subramanian R, Vassell R, Lusvarghi S, Cong Y, Agan B, Richard SA, Epsi NJ, Fries A, Fung CK, Conte MA, Holbrook MR, Wang TT, Burgess TH, Mitre E, Pollett SD, Katzelnick LC, Weiss CD. Antigenic cartography using hamster sera identifies SARS-CoV-2 JN.1 evasion seen in human XBB.1.5 booster sera. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.05.588359. [PMID: 38712124 PMCID: PMC11071293 DOI: 10.1101/2024.04.05.588359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Antigenic assessments of SARS-CoV-2 variants inform decisions to update COVID-19 vaccines. Primary infection sera are often used for assessments, but such sera are rare due to population immunity from SARS-CoV-2 infections and COVID-19 vaccinations. Here, we show that neutralization titers and breadth of matched human and hamster pre-Omicron variant primary infection sera correlate well and generate similar antigenic maps. The hamster antigenic map shows modest antigenic drift among XBB sub-lineage variants, with JN.1 and BA.4/BA.5 variants within the XBB cluster, but with five to six-fold antigenic differences between these variants and XBB.1.5. Compared to sera following only ancestral or bivalent COVID-19 vaccinations, or with post-vaccination infections, XBB.1.5 booster sera had the broadest neutralization against XBB sub-lineage variants, although a five-fold titer difference was still observed between JN.1 and XBB.1.5 variants. These findings suggest that antibody coverage of antigenically divergent JN.1 could be improved with a matched vaccine antigen.
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Affiliation(s)
- Wei Wang
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Gitanjali L. Bhushan
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Stephanie Paz
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Charles B. Stauft
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Prabhu Selvaraj
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Emilie Goguet
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, Maryland, USA
| | - Kimberly A. Bishop-Lilly
- Biological Defense Research Directorate, Naval Medical Research Command, Fort Detrick, Maryland, USA
| | - Rahul Subramanian
- Office of Data Science and Emerging Technologies, Office of Science Management and Operations, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Russell Vassell
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Sabrina Lusvarghi
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Yu Cong
- Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Ft. Detrick, Frederick, Maryland, USA
| | - Brian Agan
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, Maryland, USA
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Stephanie A. Richard
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, Maryland, USA
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Nusrat J. Epsi
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, Maryland, USA
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Anthony Fries
- US Air Force School of Aerospace Medicine, Dayton, Ohio, USA
| | - Christian K. Fung
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Matthew A. Conte
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Michael R. Holbrook
- Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Ft. Detrick, Frederick, Maryland, USA
| | - Tony T. Wang
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Timothy H. Burgess
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Edward Mitre
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Simon D. Pollett
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, Maryland, USA
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Leah C. Katzelnick
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Carol D. Weiss
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
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26
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Roberts MG, Hickson RI, McCaw JM. How immune dynamics shape multi-season epidemics: a continuous-discrete model in one dimensional antigenic space. J Math Biol 2024; 88:48. [PMID: 38538962 PMCID: PMC10973021 DOI: 10.1007/s00285-024-02076-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 02/25/2024] [Accepted: 03/05/2024] [Indexed: 04/01/2024]
Abstract
We extend a previously published model for the dynamics of a single strain of an influenza-like infection. The model incorporates a waning acquired immunity to infection and punctuated antigenic drift of the virus, employing a set of coupled integral equations within a season and a discrete map between seasons. The long term behaviour of the model is demonstrated by examples where immunity to infection depends on the time since a host was last infected, and where immunity depends on the number of times that a host has been infected. The first scenario leads to complicated dynamics in some regions of parameter space, and to regions of parameter space with more than one attractor. The second scenario leads to a stable fixed point, corresponding to an identical epidemic each season. We also examine the model with both paradigms in combination, almost always but not exclusively observing a stable fixed point or periodic solution. Adding stochastic perturbations to the between season map fails to destroy the model's qualitative dynamics. Our results suggest that if the level of host immunity depends on the elapsed time since the last infection then the epidemiological dynamics may be unpredictable.
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Affiliation(s)
- M G Roberts
- New Zealand Institute for Advanced Study and the Infectious Disease Research Centre, Massey University, Auckland, New Zealand.
| | - R I Hickson
- Health and Biosecurity, CSIRO, Townsville, QLD, 4814, Australia
- Australian Institute of Tropical Medicine and Hygiene, and College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, 4814, Australia
- School of Mathematics and Statistics, Faculty of Science, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - J M McCaw
- School of Mathematics and Statistics, Faculty of Science, University of Melbourne, Melbourne, VIC, 3010, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, 3010, Australia
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27
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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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28
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Rössler A, Knabl L, Netzl A, Bante D, Borena W, von Laer D, Smith DJ, Kimpel J. Durability of Cross-Neutralizing Antibodies 5.5 Months After Bivalent Coronavirus Disease 2019 Vaccine Booster. J Infect Dis 2024; 229:644-647. [PMID: 38016020 PMCID: PMC10938204 DOI: 10.1093/infdis/jiad472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/16/2023] [Accepted: 10/20/2023] [Indexed: 11/30/2023] Open
Abstract
We analyzed neutralizing antibodies in samples from ancestral + BA.1 and ancestral + BA.4/5 boosted individuals, collected around 5.5 months after booster. Titers of neutralizing antibodies generally decreased compared to a time point early after the bivalent booster immunization. This was more pronounced for individuals without infection history and for recently emerged Omicron variants.
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Affiliation(s)
- Annika Rössler
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Austria
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Antonia Netzl
- Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, United Kingdom
| | - David Bante
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Austria
| | - Wegene Borena
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Austria
| | - Dorothee von Laer
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Austria
| | - Derek J Smith
- Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, United Kingdom
| | - Janine Kimpel
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Austria
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29
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Srivastava K, Carreño JM, Gleason C, Monahan B, Singh G, Abbad A, Tcheou J, Raskin A, Kleiner G, van Bakel H, Sordillo EM, Krammer F, Simon V. SARS-CoV-2-infection- and vaccine-induced antibody responses are long lasting with an initial waning phase followed by a stabilization phase. Immunity 2024; 57:587-599.e4. [PMID: 38395697 PMCID: PMC11066813 DOI: 10.1016/j.immuni.2024.01.017] [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: 10/05/2023] [Revised: 12/06/2023] [Accepted: 01/29/2024] [Indexed: 02/25/2024]
Abstract
It is thought that mRNA-based vaccine-induced immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) wanes quickly, based mostly on short-term studies. Here, we analyzed the kinetics and durability of the humoral responses to SARS-CoV-2 infection and vaccination using >8,000 longitudinal samples collected over a 3-year period in New York City. Upon primary immunization, participants with pre-existing immunity mounted higher antibody responses faster and achieved higher steady-state antibody titers than naive individuals. Antibody kinetics were characterized by two phases: an initial rapid decay, followed by a stabilization phase with very slow decay. Booster vaccination equalized the differences in antibody concentration between participants with and without hybrid immunity, but the peak antibody titers decreased with each successive antigen exposure. Breakthrough infections increased antibodies to similar titers as an additional vaccine dose in naive individuals. Our study provides strong evidence that SARS-CoV-2 antibody responses are long lasting, with initial waning followed by stabilization.
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Affiliation(s)
- Komal Srivastava
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Charles Gleason
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brian Monahan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gagandeep Singh
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anass Abbad
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Johnstone Tcheou
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ariel Raskin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Giulio Kleiner
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Harm van Bakel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emilia Mia Sordillo
- Department of Pathology, Molecular and Cell-Based Medicine, 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; Center for Vaccine Research and Pandemic Preparedness (C-VARPP), 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.
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center for Vaccine Research and Pandemic Preparedness (C-VARPP), 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; Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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30
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Chang S, Shin KS, Park B, Park S, Shin J, Park H, Jung IK, Kim JH, Bae SE, Kim JO, Baek SH, Kim G, Hong JJ, Seo H, Volz E, Kang CY. Strategy to develop broadly effective multivalent COVID-19 vaccines against emerging variants based on Ad5/35 platform. Proc Natl Acad Sci U S A 2024; 121:e2313681121. [PMID: 38408238 DOI: 10.1073/pnas.2313681121] [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: 08/18/2023] [Accepted: 01/28/2024] [Indexed: 02/28/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron strain has evolved into highly divergent variants with several sub-lineages. These newly emerging variants threaten the efficacy of available COVID-19 vaccines. To mitigate the occurrence of breakthrough infections and re-infections, and more importantly, to reduce the disease burden, it is essential to develop a strategy for producing updated multivalent vaccines that can provide broad neutralization against both currently circulating and emerging variants. We developed bivalent vaccine AdCLD-CoV19-1 BA.5/BA.2.75 and trivalent vaccines AdCLD-CoV19-1 XBB/BN.1/BQ.1.1 and AdCLD-CoV19-1 XBB.1.5/BN.1/BQ.1.1 using an Ad5/35 platform-based non-replicating recombinant adenoviral vector. We compared immune responses elicited by the monovalent and multivalent vaccines in mice and macaques. We found that the BA.5/BA.2.75 bivalent and the XBB/BN.1/BQ.1.1 and XBB.1.5/BN.1/BQ.1.1 trivalent vaccines exhibited improved cross-neutralization ability compared to their respective monovalent vaccines. These data suggest that the developed multivalent vaccines enhance immunity against circulating Omicron subvariants and effectively elicit neutralizing antibodies across a broad spectrum of SARS-CoV-2 variants.
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Affiliation(s)
- Soojeong Chang
- Research & Development Center, Cellid Co., Ltd., Seoul 08826, Republic of Korea
| | - Kwang-Soo Shin
- Research & Development Center, Cellid Co., Ltd., Seoul 08826, Republic of Korea
| | - Bongju Park
- Research & Development Center, Cellid Co., Ltd., Seoul 08826, Republic of Korea
| | - Seowoo Park
- Research & Development Center, Cellid Co., Ltd., Seoul 08826, Republic of Korea
| | - Jieun Shin
- Research & Development Center, Cellid Co., Ltd., Seoul 08826, Republic of Korea
| | - Hyemin Park
- Research & Development Center, Cellid Co., Ltd., Seoul 08826, Republic of Korea
| | - In Kyung Jung
- Research & Development Center, Cellid Co., Ltd., Seoul 08826, Republic of Korea
| | - Jong Heon Kim
- Research & Development Center, Cellid Co., Ltd., Seoul 08826, Republic of Korea
| | - Seong Eun Bae
- Science Unit, International Vaccine Institute, Seoul 08826, Republic of Korea
| | - Jae-Ouk Kim
- Science Unit, International Vaccine Institute, Seoul 08826, Republic of Korea
| | - Seung Ho Baek
- National Primate Research Centre, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungcheongbuk 28116, Republic of Korea
| | - Green Kim
- National Primate Research Centre, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungcheongbuk 28116, Republic of Korea
| | - Jung Joo Hong
- National Primate Research Centre, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungcheongbuk 28116, Republic of Korea
- Korea Research Institute of Bioscience and Biotechnology School of Bioscience, Korea University of Science & Technology, Daejeon 34141, Republic of Korea
| | - Hyungseok Seo
- Laboratory of Cell & Gene Therapy, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Erik Volz
- Department of Infectious Disease Epidemiology, Medical Research Council Centre for Global Infectious Disease Analysis, Imperial College London, London W2 1PG, United Kingdom
| | - Chang-Yuil Kang
- Research & Development Center, Cellid Co., Ltd., Seoul 08826, Republic of Korea
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31
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Shin KS, Kim BS, Chang S, Jung IK, Park H, Park S, Shin J, Kim JH, Han SJ, Park B, Kim JO, Lee JA, Lee TY, Kang CY. Boosting with variant-matched adenovirus-based vaccines promotes neutralizing antibody responses against SARS-CoV-2 Omicron sublineages in mice. Int J Antimicrob Agents 2024; 63:107082. [PMID: 38163552 DOI: 10.1016/j.ijantimicag.2023.107082] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/15/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
Global spread of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Omicron subvariants, such as BA.4, BA.5 and XBB.1.5, has been leading the recent wave of coronavirus disease 2019 (COVID-19). Unique mutations in the spike proteins of these emerging Omicron subvariants caused immune evasion from the pre-existing protective immunity induced by vaccination or natural infection. Previously, we developed AdCLD-CoV19-1, a non-replicating recombinant adenoviral vector that encodes the receptor binding domain of the spike protein of the ancestral SARS-CoV-2 strain. Based on the same recombinant adenoviral vector platform, updated vaccines that cover unique mutations found in each Omicron subvariant, including BA.1, BA.2, BA.4.1 and BA.5, were constructed. Preclinical studies revealed that each updated vaccine as a booster shot following primary vaccination targeting the ancestral strain improved neutralizing antibody responses against the pseudovirus of its respective strain most effectively. Of note, boosting with a vaccine targeting the BA.1 or BA.2 Omicron subvariant was most effective in neutralization against the pseudovirus of the BA.2.75 strain, whereas BA.4.1/5-adapted booster shots were most effective in neutralization against the BQ.1, BQ1.1 and BF.7 strains. Therefore, it is imperative to develop a vaccination strategy that can cover the unique spike mutations of currently circulating Omicron subvariants in order to prevent the next wave of COVID-19.
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Affiliation(s)
- Kwang-Soo Shin
- Cellid Co., Ltd., Seoul, Republic of Korea; Research Institute of Pharmaceutical Science, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Byung-Seok Kim
- Division of Life Sciences, College of Life Science and Bioengineering, Incheon National University, Incheon, Republic of Korea
| | | | | | | | | | - Jieun Shin
- Cellid Co., Ltd., Seoul, Republic of Korea
| | | | - Sang Jun Han
- Division of Life Sciences, College of Life Science and Bioengineering, Incheon National University, Incheon, Republic of Korea
| | | | - Jae-Ouk Kim
- Science Unit, International Vaccine Institute, Seoul, Republic of Korea
| | - Jung-Ah Lee
- Division of Infectious Disease Vaccine Research, Centre for Vaccine Research, National Institute of Infectious Diseases, National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Tae-Young Lee
- Division of Infectious Disease Vaccine Research, Centre for Vaccine Research, National Institute of Infectious Diseases, National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
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32
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Costa Rocha VP, Souza Machado BA, Barreto BC, Quadros HC, Santana Fernandes AM, Lima EDS, Bandeira ME, Meira CS, Moraes dos Santos Fonseca L, Erasmus J, Khandhar A, Berglund P, Reed S, José da Silva Badaró R, Pereira Soares MB. A polyvalent RNA vaccine reduces the immune imprinting phenotype in mice and induces neutralizing antibodies against omicron SARS-CoV-2. Heliyon 2024; 10:e25539. [PMID: 38370238 PMCID: PMC10869778 DOI: 10.1016/j.heliyon.2024.e25539] [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: 12/02/2023] [Revised: 01/29/2024] [Accepted: 01/29/2024] [Indexed: 02/20/2024] Open
Abstract
Immune imprinting is now evident in COVID-19 vaccinated people. This phenomenon may impair the development of effective neutralizing antibodies against variants of concern (VoCs), mainly Omicron and its subvariants. Consequently, the boost doses with bivalent vaccines have not shown a significant gain of function regarding the neutralization of Omicron. The approach to design COVID-19 vaccines must be revised to improve the effectiveness against VoCs. Here, we took advantage of the self-amplifying characteristic of RepRNA and developed a polyvalent formulation composed of mRNA from five VoCs. LION/RepRNA Polyvalent induced neutralizing antibodies in mice previously immunized with LION/RepRNA D614G and reduced the imprinted phenotype associated with low neutralization capacity of Omicron B.1.1.529 pseudoviruses. The polyvalent vaccine can be a strategy to handle the low neutralization of Omicron VoC, despite booster doses with either monovalent or bivalent vaccines.
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Affiliation(s)
- Vinicius Pinto Costa Rocha
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CIMATEC, Salvador, Bahia, Brazil
- Gonçalo Moniz Institute, FIOCRUZ, Salvador, Bahia, Brazil
| | - Bruna Aparecida Souza Machado
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CIMATEC, Salvador, Bahia, Brazil
- University Center SENAI CIMATEC, Salvador, Bahia, Brazil
| | | | - Helenita Costa Quadros
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CIMATEC, Salvador, Bahia, Brazil
- Gonçalo Moniz Institute, FIOCRUZ, Salvador, Bahia, Brazil
| | | | - Eduarda dos Santos Lima
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CIMATEC, Salvador, Bahia, Brazil
| | - Mariana Evangelista Bandeira
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CIMATEC, Salvador, Bahia, Brazil
| | - Cássio Santana Meira
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CIMATEC, Salvador, Bahia, Brazil
- Gonçalo Moniz Institute, FIOCRUZ, Salvador, Bahia, Brazil
| | | | | | | | | | | | - Roberto José da Silva Badaró
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CIMATEC, Salvador, Bahia, Brazil
| | - Milena Botelho Pereira Soares
- SENAI Institute of Innovation (ISI) in Health Advanced Systems (CIMATEC ISI SAS), SENAI CIMATEC, Salvador, Bahia, Brazil
- Gonçalo Moniz Institute, FIOCRUZ, Salvador, Bahia, Brazil
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33
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Port JR, Morris DH, Riopelle JC, Yinda CK, Avanzato VA, Holbrook MG, Bushmaker T, Schulz JE, Saturday TA, Barbian K, Russell CA, Perry-Gottschalk R, Shaia C, Martens C, Lloyd-Smith JO, Fischer RJ, Munster VJ. Host and viral determinants of airborne transmission of SARS-CoV-2 in the Syrian hamster. eLife 2024; 12:RP87094. [PMID: 38416804 PMCID: PMC10942639 DOI: 10.7554/elife.87094] [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: 03/01/2024] Open
Abstract
It remains poorly understood how SARS-CoV-2 infection influences the physiological host factors important for aerosol transmission. We assessed breathing pattern, exhaled droplets, and infectious virus after infection with Alpha and Delta variants of concern (VOC) in the Syrian hamster. Both VOCs displayed a confined window of detectable airborne virus (24-48 hr), shorter than compared to oropharyngeal swabs. The loss of airborne shedding was linked to airway constriction resulting in a decrease of fine aerosols (1-10 µm) produced, which are suspected to be the major driver of airborne transmission. Male sex was associated with increased viral replication and virus shedding in the air. Next, we compared the transmission efficiency of both variants and found no significant differences. Transmission efficiency varied mostly among donors, 0-100% (including a superspreading event), and aerosol transmission over multiple chain links was representative of natural heterogeneity of exposure dose and downstream viral kinetics. Co-infection with VOCs only occurred when both viruses were shed by the same donor during an increased exposure timeframe (24-48 hr). This highlights that assessment of host and virus factors resulting in a differential exhaled particle profile is critical for understanding airborne transmission.
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Affiliation(s)
- Julia R Port
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Dylan H Morris
- Department of Ecology and Evolutionary Biology, University of California, Los AngelesLos AngelesUnited States
| | - Jade C Riopelle
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Claude Kwe Yinda
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Victoria A Avanzato
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Myndi G Holbrook
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Trenton Bushmaker
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Jonathan E Schulz
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Taylor A Saturday
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Kent Barbian
- Rocky Mountain Research and Technologies Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Colin A Russell
- Department of Medical Microbiology | Amsterdam University Medical Center, University of AmsterdamAmsterdamNetherlands
| | - Rose Perry-Gottschalk
- Rocky Mountain Visual and Medical Arts Unit, Research Technologies Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Carl Shaia
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Craig Martens
- Rocky Mountain Research and Technologies Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - James O Lloyd-Smith
- Department of Ecology and Evolutionary Biology, University of California, Los AngelesLos AngelesUnited States
| | - Robert J Fischer
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Vincent J Munster
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
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Hinke DM, Anderson AM, Katta K, Laursen MF, Tesfaye DY, Werninghaus IC, Angeletti D, Grødeland G, Bogen B, Braathen R. Applying valency-based immuno-selection to generate broadly cross-reactive antibodies against influenza hemagglutinins. Nat Commun 2024; 15:850. [PMID: 38346952 PMCID: PMC10861589 DOI: 10.1038/s41467-024-44889-w] [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: 10/26/2022] [Accepted: 01/09/2024] [Indexed: 02/15/2024] Open
Abstract
Conserved epitopes shared between virus subtypes are often subdominant, making it difficult to induce broadly reactive antibodies by immunization. Here, we generate a plasmid DNA mix vaccine that encodes protein heterodimers with sixteen different influenza A virus hemagglutinins (HA) representing all HA subtypes except H1 (group 1) and H7 (group 2). Each single heterodimer expresses two different HA subtypes and is targeted to MHC class II on antigen presenting cells (APC). Female mice immunized with the plasmid mix produce antibodies not only against the 16 HA subtypes, but also against non-included H1 and H7. We demonstrate that individual antibody molecules cross-react between different HAs. Furthermore, the mix vaccine induces T cell responses to conserved HA epitopes. Immunized mice are partially protected against H1 viruses. The results show that application of valency-based immuno-selection to diversified antigens can be used to direct antibody responses towards conserved (subdominant) epitopes on viral antigens.
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Affiliation(s)
- Daniëla Maria Hinke
- K.G. Jebsen Centre for Influenza Vaccine Research, University of Oslo, Oslo, Norway
- Institute of Immunology (IMM), University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Ane Marie Anderson
- K.G. Jebsen Centre for Influenza Vaccine Research, University of Oslo, Oslo, Norway
- Institute of Immunology (IMM), University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Kirankumar Katta
- Institute of Immunology (IMM), University of Oslo and Oslo University Hospital, Oslo, Norway
| | | | - Demo Yemane Tesfaye
- Institute of Immunology (IMM), University of Oslo and Oslo University Hospital, Oslo, Norway
| | | | - Davide Angeletti
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Gunnveig Grødeland
- K.G. Jebsen Centre for Influenza Vaccine Research, University of Oslo, Oslo, Norway
- Institute of Immunology (IMM), University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Bjarne Bogen
- K.G. Jebsen Centre for Influenza Vaccine Research, University of Oslo, Oslo, Norway.
- Institute of Immunology (IMM), University of Oslo and Oslo University Hospital, Oslo, Norway.
| | - Ranveig Braathen
- K.G. Jebsen Centre for Influenza Vaccine Research, University of Oslo, Oslo, Norway.
- Institute of Immunology (IMM), University of Oslo and Oslo University Hospital, Oslo, Norway.
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35
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Wang D, Huot M, Mohanty V, Shakhnovich EI. Biophysical principles predict fitness of SARS-CoV-2 variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.23.549087. [PMID: 37577536 PMCID: PMC10418099 DOI: 10.1101/2023.07.23.549087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
SARS-CoV-2 employs its spike protein's receptor binding domain (RBD) to enter host cells. The RBD is constantly subjected to immune responses, while requiring efficient binding to host cell receptors for successful infection. However, our understanding of how RBD's biophysical properties contribute to SARS-CoV-2's epidemiological fitness remains largely incomplete. Through a comprehensive approach, comprising large-scale sequence analysis of SARS-CoV-2 variants and the discovery of a fitness function based on binding thermodynamics, we unravel the relationship between the biophysical properties of RBD variants and their contribution to viral fitness. We developed a biophysical model that uses statistical mechanics to map the molecular phenotype space, characterized by binding constants of RBD to ACE2, LY-CoV016, LY-CoV555, REGN10987, and S309, onto a epistatic fitness landscape. We validate our findings through experimentally measured and machine learning (ML) estimated binding affinities, coupled with infectivity data derived from population-level sequencing. Our analysis reveals that this model effectively predicts the fitness of novel RBD variants and can account for the epistatic interactions among mutations, including explaining the later reversal of Q493R. Our study sheds light on the impact of specific mutations on viral fitness and delivers a tool for predicting the future epidemiological trajectory of previously unseen or emerging low frequency variants. These insights offer not only greater understanding of viral evolution but also potentially aid in guiding public health decisions in the battle against COVID-19 and future pandemics.
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Affiliation(s)
- Dianzhuo Wang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA
| | - Marian Huot
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA
- Ecole Polytechnique, Institut Polytechnique de Paris
| | - Vaibhav Mohanty
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA
- Harvard-MIT MD-PhD Program and Program in Health Sciences and Technology, Harvard Medical School, Boston, MA and Massachusetts Institute of Technology, Cambridge, MA
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36
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de Jong SPJ, Felix Garza ZC, Gibson JC, van Leeuwen S, de Vries RP, Boons GJ, van Hoesel M, de Haan K, van Groeningen LE, Hulme KD, van Willigen HDG, Wynberg E, de Bree GJ, Matser A, Bakker M, van der Hoek L, Prins M, Kootstra NA, Eggink D, Nichols BE, Han AX, de Jong MD, Russell CA. Determinants of epidemic size and the impacts of lulls in seasonal influenza virus circulation. Nat Commun 2024; 15:591. [PMID: 38238318 PMCID: PMC10796432 DOI: 10.1038/s41467-023-44668-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 12/21/2023] [Indexed: 01/22/2024] Open
Abstract
During the COVID-19 pandemic, levels of seasonal influenza virus circulation were unprecedentedly low, leading to concerns that a lack of exposure to influenza viruses, combined with waning antibody titres, could result in larger and/or more severe post-pandemic seasonal influenza epidemics. However, in most countries the first post-pandemic influenza season was not unusually large and/or severe. Here, based on an analysis of historical influenza virus epidemic patterns from 2002 to 2019, we show that historic lulls in influenza virus circulation had relatively minor impacts on subsequent epidemic size and that epidemic size was more substantially impacted by season-specific effects unrelated to the magnitude of circulation in prior seasons. From measurements of antibody levels from serum samples collected each year from 2017 to 2021, we show that the rate of waning of antibody titres against influenza virus during the pandemic was smaller than assumed in predictive models. Taken together, these results partially explain why the re-emergence of seasonal influenza virus epidemics was less dramatic than anticipated and suggest that influenza virus epidemic dynamics are not currently amenable to multi-season prediction.
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Affiliation(s)
- Simon P J de Jong
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Zandra C Felix Garza
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Joseph C Gibson
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Sarah van Leeuwen
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Robert P de Vries
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Geert-Jan Boons
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
- Department of Chemistry, University of Georgia, Athens, GA, USA
| | - Marliek van Hoesel
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Karen de Haan
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Laura E van Groeningen
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Katina D Hulme
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Hugo D G van Willigen
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Elke Wynberg
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
- Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, The Netherlands
| | - Godelieve J de Bree
- Department of Infectious Diseases, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Amy Matser
- Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, The Netherlands
| | - Margreet Bakker
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Lia van der Hoek
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Maria Prins
- Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, The Netherlands
- Department of Infectious Diseases, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Neeltje A Kootstra
- Department of Experimental Immunology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Dirk Eggink
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Brooke E Nichols
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
- Department of Global Health, School of Public Health, Boston University, Boston, MA, USA
| | - Alvin X Han
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Menno D de Jong
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Colin A Russell
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.
- Department of Global Health, School of Public Health, Boston University, Boston, MA, USA.
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37
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Fox A. Drift and shape-new insights into human immunity against influenza virus neuraminidase. mBio 2023; 14:e0165423. [PMID: 37933976 PMCID: PMC10746272 DOI: 10.1128/mbio.01654-23] [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] [Indexed: 11/08/2023] Open
Abstract
Influenza virus hemagglutinin mediates infection by binding sialic acids, whereas neuraminidase cleaves sialic acids to release progeny virions. Both are targets of protective antibodies, but influenza vaccine strain selection and antigen dose are based on hemagglutinin alone. Virus characterization using first infection ferret sera indicates that escape from hemagglutination inhibiting (HI) antibodies occurs more frequently and is not coordinated with escape from neuraminidase inhibiting (NI) antibodies. A key question addressed by Daulagala et al. (P. Daulagala, B. R. Mann, K. Leung, E. H. Y. Lau, et al., mBio 14:e00084-23, 2023, https://doi.org/10.1128/mbio.00084-23) is how this translates to humans who encounter multiple influenza viruses throughout life. Their cross-sectional study, using sera from a wide age range of participants and H1N1 viruses spanning 1977-2015, indicates that NI antibodies are more broadly cross-reactive than HI antibodies. Both HI and NI titers were highest against strains encountered in childhood indicating that both are shaped by priming exposures. The study further supports the development of NA-optimized vaccines.
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Affiliation(s)
- Annette Fox
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
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38
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Nuñez IA, Jang H, Huang Y, Kelvin A, Ross TM. Influenza virus immune imprinting dictates the clinical outcomes in ferrets challenged with highly pathogenic avian influenza virus H5N1. Front Vet Sci 2023; 10:1286758. [PMID: 38170075 PMCID: PMC10759238 DOI: 10.3389/fvets.2023.1286758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/28/2023] [Indexed: 01/05/2024] Open
Abstract
Zoonotic transmission of H5N1 highly pathogenic avian influenza virus (HPAIV) into the human population is an increasing global threat. The recent 2022 HPAIV outbreak significantly highlighted this possibility, increasing concern in the general population. The clinical outcomes of H5N1 influenza virus exposure can be determined by an individual's primary influenza virus infection (imprinting) or vaccination status. Immunological imprinting with Group 1 - (H1N1, H2N2, and H2N3) increases survival rates following H5N1 viral infection compared to Group 2 - (H3N2) imprinted individuals. Vaccination against H5N1 influenza viruses can offer protection to at-risk populations; however, stockpiled inactivated H5N1 influenza vaccines are not readily available to the public. We hypothesize that the immunological response to vaccination and subsequent clinical outcome following H5N1 influenza virus infection is correlated with the immunological imprinting status of an individual. To test this hypothesis, our lab established a ferret pre-immune model of disease. Naïve ferrets were intranasally inoculated with seasonal influenza viruses and allowed to recover for 84 days prior to H5N1 virus infection. Ferrets imprinted following H1N1 and H2N3 virus infections were completely protected against lethal H5N1 influenza virus challenge (100% survival), with few to no clinical symptoms. In comparison, H3N2 influenza virus-imprinted ferrets had severe clinical symptoms, delayed disease progression, and a sublethal phenotype (40% mortality). Consecutive infections with H1N1 influenza viruses followed by an H3N2 influenza virus infection did not abrogate the immune protection induced by the original H1N1 influenza virus infection. In addition, ferrets consecutively infected with H1N1 and H2N3 viruses had no clinical symptoms or weight loss. H3N2 pre-immune ferrets were vaccinated with a broadly reactive H5 HA-based or H1 NA-based vaccine (Hu-CO 2). These ferrets were protected against H5N1 influenza virus challenge, whereas ferrets vaccinated with the H1N1 wild-type CA/09 rHA vaccine had similar phenotypes as non-vaccinated H3N2-imprinted ferrets with 40% survival. Overall, Group 2 imprinted ferrets, which were vaccinated with heterologous Group 1 HA vaccines, had redirected immune responses to Group 1 influenza viral antigens and rescued a sublethal phenotype to complete protection.
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Affiliation(s)
- Ivette A. Nuñez
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States
| | - Hyesun Jang
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
| | - Ying Huang
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
| | - Alyson Kelvin
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
| | - Ted M. Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States
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39
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Welsh FC, Eguia RT, Lee JM, Haddox HK, Galloway J, Chau NVV, Loes AN, Huddleston J, Yu TC, Le MQ, Nhat NTD, Thanh NTL, Greninger AL, Chu HY, Englund JA, Bedford T, Matsen FA, Boni MF, Bloom JD. Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.571235. [PMID: 38168237 PMCID: PMC10760046 DOI: 10.1101/2023.12.12.571235] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Human influenza virus evolves to escape neutralization by polyclonal antibodies. However, we have a limited understanding of how the antigenic effects of viral mutations vary across the human population, and how this heterogeneity affects virus evolution. Here we use deep mutational scanning to map how mutations to the hemagglutinin (HA) proteins of the A/Hong Kong/45/2019 (H3N2) and A/Perth/16/2009 (H3N2) strains affect neutralization by serum from individuals of a variety of ages. The effects of HA mutations on serum neutralization differ across age groups in ways that can be partially rationalized in terms of exposure histories. Mutations that fixed in influenza variants after 2020 cause the greatest escape from sera from younger individuals. Overall, these results demonstrate that influenza faces distinct antigenic selection regimes from different age groups, and suggest approaches to understand how this heterogeneous selection shapes viral evolution.
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Affiliation(s)
- Frances C Welsh
- 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
| | - Rachel T Eguia
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
- Howard Hughes Medical Institute, Seattle, WA, 98109, USA
| | - Juhye M Lee
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
- Howard Hughes Medical Institute, Seattle, WA, 98109, USA
| | - Hugh K Haddox
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Jared Galloway
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Nguyen Van Vinh Chau
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Andrea N Loes
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
- Howard Hughes Medical Institute, Seattle, WA, 98109, USA
| | - John Huddleston
- Vaccine and Infectious Disease Division, 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
| | - Mai Quynh Le
- National Institutes for Hygiene and Epidemiology, Hanoi, Vietnam
| | - Nguyen T D Nhat
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Nguyen Thi Le Thanh
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98195, USA
- Division of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Helen Y Chu
- Division of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Janet A Englund
- Seattle Children's Research Institute, Seattle, WA, 98109, USA
| | - Trevor Bedford
- Howard Hughes Medical Institute, Seattle, WA, 98109, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Frederick A Matsen
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
- Howard Hughes Medical Institute, Seattle, WA, 98109, USA
| | - Maciej F Boni
- Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - 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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40
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Han AX, de Jong SPJ, Russell CA. Co-evolution of immunity and seasonal influenza viruses. Nat Rev Microbiol 2023; 21:805-817. [PMID: 37532870 DOI: 10.1038/s41579-023-00945-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2023] [Indexed: 08/04/2023]
Abstract
Seasonal influenza viruses cause recurring global epidemics by continually evolving to escape host immunity. The viral constraints and host immune responses that limit and drive the evolution of these viruses are increasingly well understood. However, it remains unclear how most of these advances improve the capacity to reduce the impact of seasonal influenza viruses on human health. In this Review, we synthesize recent progress made in understanding the interplay between the evolution of immunity induced by previous infections or vaccination and the evolution of seasonal influenza viruses driven by the heterogeneous accumulation of antibody-mediated immunity in humans. We discuss the functional constraints that limit the evolution of the viruses, the within-host evolutionary processes that drive the emergence of new virus variants, as well as current and prospective options for influenza virus control, including the viral and immunological barriers that must be overcome to improve the effectiveness of vaccines and antiviral drugs.
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Affiliation(s)
- Alvin X Han
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Simon P J de Jong
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Colin A Russell
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
- Department of Global Health, School of Public Health, Boston University, Boston, MA, USA.
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41
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Zhang Y, Cui P, Shi J, Chen Y, Zeng X, Jiang Y, Tian G, Li C, Chen H, Kong H, Deng G. Key Amino Acid Residues That Determine the Antigenic Properties of Highly Pathogenic H5 Influenza Viruses Bearing the Clade 2.3.4.4 Hemagglutinin Gene. Viruses 2023; 15:2249. [PMID: 38005926 PMCID: PMC10674173 DOI: 10.3390/v15112249] [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: 10/21/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
The H5 subtype highly pathogenic avian influenza viruses bearing the clade 2.3.4.4 HA gene have been pervasive among domestic poultry and wild birds worldwide since 2014, presenting substantial risks to human and animal health. Continued circulation of clade 2.3.4.4 viruses has resulted in the emergence of eight subclades (2.3.4.4a-h) and multiple distinct antigenic groups. However, the key antigenic substitutions responsible for the antigenic change of these viruses remain unknown. In this study, we analyzed the HA gene sequences of 5713 clade 2.3.4.4 viruses obtained from a public database and found that 23 amino acid residues were highly variable among these strains. We then generated a series of single-amino-acid mutants based on the H5-Re8 (a vaccine seed virus) background and tested their reactivity with a panel of eight monoclonal antibodies (mAbs). Six mutants bearing amino acid substitutions at positions 120, 126, 141, 156, 185, or 189 (H5 numbering) led to reduced or lost reactivity to these mAbs. Further antigenic cartography analysis revealed that the amino acid residues at positions 126, 156, and 189 acted as immunodominant epitopes of H5 viruses. Collectively, our findings offer valuable guidance for the surveillance and early detection of emerging antigenic variants.
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Affiliation(s)
- Yuancheng Zhang
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150009, China; (Y.Z.); (P.C.); (J.S.); (Y.C.); (X.Z.); (Y.J.); (G.T.); (C.L.); (H.C.)
| | - Pengfei Cui
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150009, China; (Y.Z.); (P.C.); (J.S.); (Y.C.); (X.Z.); (Y.J.); (G.T.); (C.L.); (H.C.)
| | - Jianzhong Shi
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150009, China; (Y.Z.); (P.C.); (J.S.); (Y.C.); (X.Z.); (Y.J.); (G.T.); (C.L.); (H.C.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yuan Chen
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150009, China; (Y.Z.); (P.C.); (J.S.); (Y.C.); (X.Z.); (Y.J.); (G.T.); (C.L.); (H.C.)
| | - Xianying Zeng
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150009, China; (Y.Z.); (P.C.); (J.S.); (Y.C.); (X.Z.); (Y.J.); (G.T.); (C.L.); (H.C.)
| | - Yongping Jiang
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150009, China; (Y.Z.); (P.C.); (J.S.); (Y.C.); (X.Z.); (Y.J.); (G.T.); (C.L.); (H.C.)
| | - Guobin Tian
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150009, China; (Y.Z.); (P.C.); (J.S.); (Y.C.); (X.Z.); (Y.J.); (G.T.); (C.L.); (H.C.)
| | - Chengjun Li
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150009, China; (Y.Z.); (P.C.); (J.S.); (Y.C.); (X.Z.); (Y.J.); (G.T.); (C.L.); (H.C.)
| | - Hualan Chen
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150009, China; (Y.Z.); (P.C.); (J.S.); (Y.C.); (X.Z.); (Y.J.); (G.T.); (C.L.); (H.C.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Huihui Kong
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150009, China; (Y.Z.); (P.C.); (J.S.); (Y.C.); (X.Z.); (Y.J.); (G.T.); (C.L.); (H.C.)
| | - Guohua Deng
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150009, China; (Y.Z.); (P.C.); (J.S.); (Y.C.); (X.Z.); (Y.J.); (G.T.); (C.L.); (H.C.)
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Moyo-Gwete T, Richardson SI, Keeton R, Hermanus T, Spencer H, Manamela NP, Ayres F, Makhado Z, Motlou T, Tincho MB, Benede N, Ngomti A, Baguma R, Chauke MV, Mennen M, Adriaanse M, Skelem S, Goga A, Garrett N, Bekker LG, Gray G, Ntusi NAB, Riou C, Burgers WA, Moore PL. Homologous Ad26.COV2.S vaccination results in reduced boosting of humoral responses in hybrid immunity, but elicits antibodies of similar magnitude regardless of prior infection. PLoS Pathog 2023; 19:e1011772. [PMID: 37943890 PMCID: PMC10684107 DOI: 10.1371/journal.ppat.1011772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 11/28/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023] Open
Abstract
The impact of previous SARS-CoV-2 infection on the durability of Ad26.COV2.S vaccine-elicited responses, and the effect of homologous boosting has not been well explored. We followed a cohort of healthcare workers for 6 months after receiving the Ad26.COV2.S vaccine and a further one month after they received an Ad26.COV2.S booster dose. We assessed longitudinal spike-specific antibody and T cell responses in individuals who had never had SARS-CoV-2 infection, compared to those who were infected with either the D614G or Beta variants prior to vaccination. Antibody and T cell responses elicited by the primary dose were durable against several variants of concern over the 6 month follow-up period, regardless of infection history. However, at 6 months after first vaccination, antibody binding, neutralization and ADCC were as much as 59-fold higher in individuals with hybrid immunity compared to those with no prior infection. Antibody cross-reactivity profiles of the previously infected groups were similar at 6 months, unlike at earlier time points, suggesting that the effect of immune imprinting diminishes by 6 months. Importantly, an Ad26.COV2.S booster dose increased the magnitude of the antibody response in individuals with no prior infection to similar levels as those with previous infection. The magnitude of spike T cell responses and proportion of T cell responders remained stable after homologous boosting, concomitant with a significant increase in long-lived early differentiated CD4 memory T cells. Thus, these data highlight that multiple antigen exposures, whether through infection and vaccination or vaccination alone, result in similar boosts after Ad26.COV2.S vaccination.
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Affiliation(s)
- Thandeka Moyo-Gwete
- SA MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
| | - Simone I. Richardson
- SA MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
| | - Roanne Keeton
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology; University of Cape Town; Observatory, South Africa
| | - Tandile Hermanus
- SA MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
| | - Holly Spencer
- SA MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
| | - Nelia P. Manamela
- SA MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
| | - Frances Ayres
- SA MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
| | - Zanele Makhado
- SA MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
| | - Thopisang Motlou
- SA MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
| | - Marius B. Tincho
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology; University of Cape Town; Observatory, South Africa
| | - Ntombi Benede
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology; University of Cape Town; Observatory, South Africa
| | - Amkele Ngomti
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology; University of Cape Town; Observatory, South Africa
| | - Richard Baguma
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology; University of Cape Town; Observatory, South Africa
| | - Masego V. Chauke
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology; University of Cape Town; Observatory, South Africa
| | - Mathilda Mennen
- Department of Medicine, University of Cape Town and Groote Schuur Hospital; Observatory, South Africa
- Cape Heart Institute, Faculty of Health Sciences, University of Cape Town; Observatory, South Africa
- South African Medical Research Council Extramural Unit on Intersection of Non-communicable Diseases and Infectious Diseases, University of Cape Town, Cape Town, South Africa
| | - Marguerite Adriaanse
- Department of Medicine, University of Cape Town and Groote Schuur Hospital; Observatory, South Africa
- Cape Heart Institute, Faculty of Health Sciences, University of Cape Town; Observatory, South Africa
- South African Medical Research Council Extramural Unit on Intersection of Non-communicable Diseases and Infectious Diseases, University of Cape Town, Cape Town, South Africa
| | - Sango Skelem
- Department of Medicine, University of Cape Town and Groote Schuur Hospital; Observatory, South Africa
- Cape Heart Institute, Faculty of Health Sciences, University of Cape Town; Observatory, South Africa
- South African Medical Research Council Extramural Unit on Intersection of Non-communicable Diseases and Infectious Diseases, University of Cape Town, Cape Town, South Africa
| | - Ameena Goga
- South African Medical Research Council, Cape Town, South Africa
| | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Discipline of Public Health Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Linda-Gail Bekker
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Desmond Tutu HIV Centre, Cape Town, South Africa
| | - Glenda Gray
- South African Medical Research Council, Cape Town, South Africa
| | - Ntobeko A. B. Ntusi
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Department of Medicine, University of Cape Town and Groote Schuur Hospital; Observatory, South Africa
- Cape Heart Institute, Faculty of Health Sciences, University of Cape Town; Observatory, South Africa
- South African Medical Research Council Extramural Unit on Intersection of Non-communicable Diseases and Infectious Diseases, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | - Catherine Riou
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology; University of Cape Town; Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | - Wendy A. Burgers
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology; University of Cape Town; Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | - Penny L. Moore
- SA MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
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Kok A, Scheuer R, Bestebroer TM, Burke DF, Wilks SH, Spronken MI, de Meulder D, Lexmond P, Pronk M, Smith DJ, Herfst S, Fouchier RAM, Richard M. Characterization of A/H7 influenza virus global antigenic diversity and key determinants in the hemagglutinin globular head mediating A/H7N9 antigenic evolution. mBio 2023; 14:e0048823. [PMID: 37565755 PMCID: PMC10655666 DOI: 10.1128/mbio.00488-23] [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: 02/23/2023] [Accepted: 04/26/2023] [Indexed: 08/12/2023] Open
Abstract
IMPORTANCE A/H7 avian influenza viruses cause outbreaks in poultry globally, resulting in outbreaks with significant socio-economical impact and zoonotic risks. Occasionally, poultry vaccination programs have been implemented to reduce the burden of these viruses, which might result in an increased immune pressure accelerating antigenic evolution. In fact, evidence for antigenic diversification of A/H7 influenza viruses exists, posing challenges to pandemic preparedness and the design of vaccination strategies efficacious against drifted variants. Here, we performed a comprehensive analysis of the global antigenic diversity of A/H7 influenza viruses and identified the main substitutions in the hemagglutinin responsible for antigenic evolution in A/H7N9 viruses isolated between 2013 and 2019. The A/H7 antigenic map and knowledge of the molecular determinants of their antigenic evolution add value to A/H7 influenza virus surveillance programs, the design of vaccines and vaccination strategies, and pandemic preparedness.
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Affiliation(s)
- Adinda Kok
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Rachel Scheuer
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Theo M. Bestebroer
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - David F. Burke
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Samuel H. Wilks
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Monique I. Spronken
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Dennis de Meulder
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Pascal Lexmond
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Mark Pronk
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Derek J. Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Sander Herfst
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ron A. M. Fouchier
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Mathilde Richard
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
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44
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Chardès V, Mazzolini A, Mora T, Walczak AM. Evolutionary stability of antigenically escaping viruses. Proc Natl Acad Sci U S A 2023; 120:e2307712120. [PMID: 37871216 PMCID: PMC10622963 DOI: 10.1073/pnas.2307712120] [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: 05/08/2023] [Accepted: 08/24/2023] [Indexed: 10/25/2023] Open
Abstract
Antigenic variation is the main immune escape mechanism for RNA viruses like influenza or SARS-CoV-2. While high mutation rates promote antigenic escape, they also induce large mutational loads and reduced fitness. It remains unclear how this cost-benefit trade-off selects the mutation rate of viruses. Using a traveling wave model for the coevolution of viruses and host immune systems in a finite population, we investigate how immunity affects the evolution of the mutation rate and other nonantigenic traits, such as virulence. We first show that the nature of the wave depends on how cross-reactive immune systems are, reconciling previous approaches. The immune-virus system behaves like a Fisher wave at low cross-reactivities, and like a fitness wave at high cross-reactivities. These regimes predict different outcomes for the evolution of nonantigenic traits. At low cross-reactivities, the evolutionarily stable strategy is to maximize the speed of the wave, implying a higher mutation rate and increased virulence. At large cross-reactivities, where our estimates place H3N2 influenza, the stable strategy is to increase the basic reproductive number, keeping the mutation rate to a minimum and virulence low.
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Affiliation(s)
- Victor Chardès
- Laboratoire de Physique de l’École Normale Supérieure, CNRS, Paris Sciences & Lettres University, Sorbonne Université, and Université Paris-Cité, 75005Paris, France
- Center for Computational Biology, Flatiron Institute, New York, NY10010
| | - Andrea Mazzolini
- Laboratoire de Physique de l’École Normale Supérieure, CNRS, Paris Sciences & Lettres University, Sorbonne Université, and Université Paris-Cité, 75005Paris, France
| | - Thierry Mora
- Laboratoire de Physique de l’École Normale Supérieure, CNRS, Paris Sciences & Lettres University, Sorbonne Université, and Université Paris-Cité, 75005Paris, France
| | - Aleksandra M. Walczak
- Laboratoire de Physique de l’École Normale Supérieure, CNRS, Paris Sciences & Lettres University, Sorbonne Université, and Université Paris-Cité, 75005Paris, France
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45
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Wang K, Hu X, Zhang J. Fast clonal family inference from large-scale B cell repertoire sequencing data. CELL REPORTS METHODS 2023; 3:100601. [PMID: 37788671 PMCID: PMC10626204 DOI: 10.1016/j.crmeth.2023.100601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/31/2023] [Accepted: 09/08/2023] [Indexed: 10/05/2023]
Abstract
Advances in high-throughput sequencing technologies have facilitated the large-scale characterization of B cell receptor (BCR) repertoires. However, the vast amount and high diversity of the BCR sequences pose challenges for efficient and biologically meaningful analysis. Here, we introduce fastBCR, an efficient computational approach for inferring B cell clonal families from massive BCR heavy chain sequences. We demonstrate that fastBCR substantially reduces the running time while ensuring high accuracy on simulated datasets with diverse numbers of B cell lineages and varying mutation rates. We apply fastBCR to real BCR sequencing data from peripheral blood samples of COVID-19 patients, showing that the inferred clonal families display disease-associated features, as well as corresponding antigen-binding specificity and affinity. Overall, our results demonstrate the advantages of fastBCR for analyzing BCR repertoire data, which will facilitate the identification of disease-associated antibodies and improve our understanding of the B cell immune response.
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Affiliation(s)
- Kaixuan Wang
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
| | - Xihao Hu
- GV20 Therapeutics, Cambridge, MA, USA
| | - Jian Zhang
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China.
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46
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Pliasas VC, Neasham PJ, Naskou MC, Neto R, Strate PG, North JF, Pedroza S, Chastain SD, Padykula I, Tompkins SM, Kyriakis CS. Heterologous prime-boost H1N1 vaccination exacerbates disease following challenge with a mismatched H1N2 influenza virus in the swine model. Front Immunol 2023; 14:1253626. [PMID: 37928521 PMCID: PMC10623127 DOI: 10.3389/fimmu.2023.1253626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/04/2023] [Indexed: 11/07/2023] Open
Abstract
Influenza A viruses (IAVs) pose a significant threat to both human and animal health. Developing IAV vaccine strategies able to elicit broad heterologous protection against antigenically diverse IAV strains is pivotal in effectively controlling the disease. The goal of this study was to examine the immunogenicity and protective efficacy of diverse H1N1 influenza vaccine strategies including monovalent, bivalent, and heterologous prime-boost vaccination regimens, against a mismatched H1N2 swine influenza virus. Five groups were homologous prime-boost vaccinated with either an oil-adjuvanted whole-inactivated virus (WIV) monovalent A/swine/Georgia/27480/2019 (GA19) H1N2 vaccine, a WIV monovalent A/sw/Minnesota/A02636116/2021 (MN21) H1N1 vaccine, a WIV monovalent A/California/07/2009 (CA09) H1N1, a WIV bivalent vaccine composed of CA09 and MN21, or adjuvant only (mock-vaccinated group). A sixth group was prime-vaccinated with CA09 WIV and boosted with MN21 WIV (heterologous prime-boost group). Four weeks post-boost pigs were intranasally and intratracheally challenged with A/swine/Georgia/27480/2019, an H1N2 swine IAV field isolate. Vaccine-induced protection was evaluated based on five critical parameters: (i) hemagglutination inhibiting (HAI) antibody responses, (ii) clinical scores, (iii) virus titers in nasal swabs and respiratory tissue homogenates, (iv) BALf cytology, and (v) pulmonary pathology. While all vaccination regimens induced seroprotective titers against homologous viruses, heterologous prime-boost vaccination failed to enhance HAI responses against the homologous vaccine strains compared to monovalent vaccine regimens and did not expand the scope of cross-reactive antibody responses against antigenically distinct swine and human IAVs. Mismatched vaccination regimens not only failed to confer clinical and virological protection post-challenge but also exacerbated disease and pathology. In particular, heterologous-boosted pigs showed prolonged clinical disease and increased pulmonary pathology compared to mock-vaccinated pigs. Our results demonstrated that H1-specific heterologous prime-boost vaccination, rather than enhancing cross-protection, worsened the clinical outcome and pathology after challenge with the antigenically distant A/swine/Georgia/27480/2019 strain.
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Affiliation(s)
- Vasilis C. Pliasas
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
- Emory-University of Georgia (UGA) Center of Excellence for Influenza Research and Surveillance (CEIRS), Atlanta, GA, United States
| | - Peter J. Neasham
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
- Emory-University of Georgia (UGA) Center of Excellence for Influenza Research and Surveillance (CEIRS), Atlanta, GA, United States
| | - Maria C. Naskou
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Rachel Neto
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Philip G. Strate
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - J. Fletcher North
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
- Emory-University of Georgia (UGA) Center of Excellence for Influenza Research and Surveillance (CEIRS), Atlanta, GA, United States
| | - Stephen Pedroza
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Strickland D. Chastain
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Ian Padykula
- Emory-University of Georgia (UGA) Center of Excellence for Influenza Research and Surveillance (CEIRS), Atlanta, GA, United States
- Center for Vaccines and Immunology, University of Georgia, Athens GA, United States
| | - S. Mark Tompkins
- Emory-University of Georgia (UGA) Center of Excellence for Influenza Research and Surveillance (CEIRS), Atlanta, GA, United States
- Center for Vaccines and Immunology, University of Georgia, Athens GA, United States
| | - Constantinos S. Kyriakis
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
- Emory-University of Georgia (UGA) Center of Excellence for Influenza Research and Surveillance (CEIRS), Atlanta, GA, United States
- Center for Vaccines and Immunology, University of Georgia, Athens GA, United States
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47
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Port JR, Morris DH, Riopelle JC, Yinda CK, Avanzato VA, Holbrook MG, Bushmaker T, Schulz JE, Saturday TA, Barbian K, Russell CA, Perry-Gottschalk R, Shaia CI, Martens C, Lloyd-Smith JO, Fischer RJ, Munster VJ. Host and viral determinants of airborne transmission of SARS-CoV-2 in the Syrian hamster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2022.08.15.504010. [PMID: 36032963 PMCID: PMC9413705 DOI: 10.1101/2022.08.15.504010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
It remains poorly understood how SARS-CoV-2 infection influences the physiological host factors important for aerosol transmission. We assessed breathing pattern, exhaled droplets, and infectious virus after infection with Alpha and Delta variants of concern (VOC) in the Syrian hamster. Both VOCs displayed a confined window of detectable airborne virus (24-48 h), shorter than compared to oropharyngeal swabs. The loss of airborne shedding was linked to airway constriction resulting in a decrease of fine aerosols (1-10μm) produced, which are suspected to be the major driver of airborne transmission. Male sex was associated with increased viral replication and virus shedding in the air. Next, we compared the transmission efficiency of both variants and found no significant differences. Transmission efficiency varied mostly among donors, 0-100% (including a superspreading event), and aerosol transmission over multiple chain links was representative of natural heterogeneity of exposure dose and downstream viral kinetics. Co-infection with VOCs only occurred when both viruses were shed by the same donor during an increased exposure timeframe (24-48 h). This highlights that assessment of host and virus factors resulting in a differential exhaled particle profile is critical for understanding airborne transmission.
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Affiliation(s)
- Julia R. Port
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Dylan H. Morris
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Jade C. Riopelle
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Claude Kwe Yinda
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Victoria A. Avanzato
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Myndi G. Holbrook
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Trenton Bushmaker
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Jonathan E. Schulz
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Taylor A. Saturday
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Kent Barbian
- Rocky Mountain Research and Technologies Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Colin A. Russell
- Department of Medical Microbiology | Amsterdam University Medical Center, University of Amsterdam
| | - Rose Perry-Gottschalk
- Rocky Mountain Visual and Medical Arts Unit, Research Technologies Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Carl I. Shaia
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Craig Martens
- Rocky Mountain Research and Technologies Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - James O. Lloyd-Smith
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Robert J. Fischer
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Vincent J. Munster
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
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48
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Jones RP, Ponomarenko A. COVID-19-Related Age Profiles for SARS-CoV-2 Variants in England and Wales and States of the USA (2020 to 2022): Impact on All-Cause Mortality. Infect Dis Rep 2023; 15:600-634. [PMID: 37888139 PMCID: PMC10606787 DOI: 10.3390/idr15050058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 09/07/2023] [Accepted: 09/07/2023] [Indexed: 10/28/2023] Open
Abstract
Since 2020, COVID-19 has caused serious mortality around the world. Given the ambiguity in establishing COVID-19 as the direct cause of death, we first investigate the effects of age and sex on all-cause mortality during 2020 and 2021 in England and Wales. Since infectious agents have their own unique age profile for death, we use a 9-year time series and several different methods to adjust single-year-of-age deaths in England and Wales during 2019 (the pre-COVID-19 base year) to a pathogen-neutral single-year-of-age baseline. This adjusted base year is then used to confirm the widely reported higher deaths in males for most ages above 43 in both 2020 and 2021. During 2020 (+COVID-19 but no vaccination), both male and female population-adjusted deaths significantly increased above age 35. A significant reduction in all-cause mortality among both males and females aged 75+ could be demonstrated in 2021 during the widespread COVID-19 vaccination period; however, deaths below age 75 progressively increased. This finding arises from a mix of vaccination coverage and year-of-age profiles of deaths for the different SARS-CoV-2 variants. In addition, specific effects of age around puberty were demonstrated, where females had higher deaths than males. There is evidence that year-of-birth cohorts may also be involved, indicating that immune priming to specific pathogen outbreaks in the past may have led to lower deaths for some birth cohorts. To specifically identify the age profile for the COVID-19 variants from 2020 to 2023, we employ the proportion of total deaths at each age that are potentially due to or 'with' COVID-19. The original Wuhan strain and the Alpha variant show somewhat limited divergence in the age profile, with the Alpha variant shifting to a moderately higher proportion of deaths below age 84. The Delta variant specifically targeted individuals below age 65. The Omicron variants showed a significantly lower proportion of overall mortality, with a markedly higher relative proportion of deaths above age 65, steeply increasing with age to a maximum around 100 years of age. A similar age profile for the variants can be seen in the age-banded deaths in US states, although they are slightly obscured by using age bands rather than single years of age. However, the US data shows that higher male deaths are greatly dependent on age and the COVID variant. Deaths assessed to be 'due to' COVID-19 (as opposed to 'involving' COVID-19) in England and Wales were especially overestimated in 2021 relative to the change in all-cause mortality. This arose as a by-product of an increase in COVID-19 testing capacity in late 2020. Potential structure-function mechanisms for the age-specificity of SARS-CoV-2 variants are discussed, along with potential roles for small noncoding RNAs (miRNAs). Using data from England, it is possible to show that the unvaccinated do indeed have a unique age profile for death from each variant and that vaccination alters the shape of the age profile in a manner dependent on age, sex, and the variant. The question is posed as to whether vaccines based on different variants carry a specific age profile.
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Affiliation(s)
| | - Andrey Ponomarenko
- Department of Biophysics, Informatics and Medical Instrumentation, Odessa National Medical University, Valikhovsky Lane 2, 65082 Odessa, Ukraine
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49
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Wilks SH, Mühlemann B, Shen X, Türeli S, LeGresley EB, Netzl A, Caniza MA, Chacaltana-Huarcaya JN, Corman VM, Daniell X, Datto MB, Dawood FS, Denny TN, Drosten C, Fouchier RAM, Garcia PJ, Halfmann PJ, Jassem A, Jeworowski LM, Jones TC, Kawaoka Y, Krammer F, McDanal C, Pajon R, Simon V, Stockwell MS, Tang H, van Bakel H, Veguilla V, Webby R, Montefiori DC, Smith DJ. Mapping SARS-CoV-2 antigenic relationships and serological responses. Science 2023; 382:eadj0070. [PMID: 37797027 DOI: 10.1126/science.adj0070] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/23/2023] [Indexed: 10/07/2023]
Abstract
During the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, multiple variants escaping preexisting immunity emerged, causing reinfections of previously exposed individuals. Here, we used antigenic cartography to analyze patterns of cross-reactivity among 21 variants and 15 groups of human sera obtained after primary infection with 10 different variants or after messenger RNA (mRNA)-1273 or mRNA-1273.351 vaccination. We found antigenic differences among pre-Omicron variants caused by substitutions at spike-protein positions 417, 452, 484, and 501. Quantifying changes in response breadth over time and with additional vaccine doses, our results show the largest increase between 4 weeks and >3 months after a second dose. We found changes in immunodominance of different spike regions, depending on the variant an individual was first exposed to, with implications for variant risk assessment and vaccine-strain selection.
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Affiliation(s)
- Samuel H Wilks
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Barbara Mühlemann
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | - Xiaoying Shen
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Sina Türeli
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Eric B LeGresley
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Antonia Netzl
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Miguela A Caniza
- Department of Global Pediatric Medicine, Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Victor M Corman
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | - Xiaoju Daniell
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Michael B Datto
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | | | - Thomas N Denny
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Christian Drosten
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | | | - Patricia J Garcia
- School of Public Health, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Peter J Halfmann
- Influenza Research Institute, Department of Pathobiological Science, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Agatha Jassem
- BC Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Lara M Jeworowski
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Terry C Jones
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Charité, 10117 Berlin, Germany
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Science, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
- Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), University of Tokyo, Tokyo, Japan
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Cellular and Molecular Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Charlene McDanal
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | | | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Cellular and Molecular Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa S Stockwell
- Division of Child and Adolescent Health, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, and Department of Population and Family Health, Mailman School of Public Health, New York, NY, USA
| | - Haili Tang
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vic Veguilla
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Richard Webby
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David C Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Derek J Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
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50
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Vinzón SE, Lopez MV, Cafferata EGA, Soto AS, Berguer PM, Vazquez L, Nusblat L, Pontoriero AV, Belotti EM, Salvetti NR, Viale DL, Vilardo AE, Avaro MM, Benedetti E, Russo ML, Dattero ME, Carobene M, Sánchez-Lamas M, Afonso J, Heitrich M, Cristófalo AE, Otero LH, Baumeister EG, Ortega HH, Edelstein A, Podhajcer OL. Cross-protection and cross-neutralization capacity of ancestral and VOC-matched SARS-CoV-2 adenoviral vector-based vaccines. NPJ Vaccines 2023; 8:149. [PMID: 37794010 PMCID: PMC10550992 DOI: 10.1038/s41541-023-00737-4] [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: 11/16/2022] [Accepted: 09/15/2023] [Indexed: 10/06/2023] Open
Abstract
COVID-19 vaccines were originally designed based on the ancestral Spike protein, but immune escape of emergent Variants of Concern (VOC) jeopardized their efficacy, warranting variant-proof vaccines. Here, we used preclinical rodent models to establish the cross-protective and cross-neutralizing capacity of adenoviral-vectored vaccines expressing VOC-matched Spike. CoroVaxG.3-D.FR, matched to Delta Plus Spike, displayed the highest levels of nAb to the matched VOC and mismatched variants. Cross-protection against viral infection in aged K18-hACE2 mice showed dramatic differences among the different vaccines. While Delta-targeted vaccines fully protected mice from a challenge with Gamma, a Gamma-based vaccine offered only partial protection to Delta challenge. Administration of CorovaxG.3-D.FR in a prime/boost regimen showed that a booster was able to increase the neutralizing capacity of the sera against all variants and fully protect aged K18-hACE2 mice against Omicron BA.1, as a BA.1-targeted vaccine did. The neutralizing capacity of the sera diminished in all cases against Omicron BA.2 and BA.5. Altogether, the data demonstrate that a booster with a vaccine based on an antigenically distant variant, such as Delta or BA.1, has the potential to protect from a wider range of SARS-CoV-2 lineages, although careful surveillance of breakthrough infections will help to evaluate combination vaccines targeting antigenically divergent variants yet to emerge.
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Affiliation(s)
- Sabrina E Vinzón
- Laboratorio de Terapia Molecular y Celular, Fundación Instituto Leloir-CONICET; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina
| | - María V Lopez
- Laboratorio de Terapia Molecular y Celular, Fundación Instituto Leloir-CONICET; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina
| | - Eduardo G A Cafferata
- Laboratorio de Terapia Molecular y Celular, Fundación Instituto Leloir-CONICET; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina
| | - Ariadna S Soto
- Laboratorio de Microbiología e Inmunología Molecular, Fundación Instituto Leloir-CONICET; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina
| | - Paula M Berguer
- Laboratorio de Microbiología e Inmunología Molecular, Fundación Instituto Leloir-CONICET; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina
| | - Luciana Vazquez
- Unidad Operativa Centro de Contención Biológica, ANLIS Dr. Carlos G. Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Leonora Nusblat
- Unidad Operativa Centro de Contención Biológica, ANLIS Dr. Carlos G. Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Andrea V Pontoriero
- Servicio Virosis Respiratorias, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales, Laboratorio Nacional de Referencia de SARS-CoV-2/COVID-19 OPS/OMS, INEI-ANLIS Dr Carlos G Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Eduardo M Belotti
- Centro de Medicina Comparada, ICiVet-Litoral, Universidad Nacional del Litoral-CONICET; Esperanza, Santa Fe, 3080, Argentina
| | - Natalia R Salvetti
- Centro de Medicina Comparada, ICiVet-Litoral, Universidad Nacional del Litoral-CONICET; Esperanza, Santa Fe, 3080, Argentina
| | - Diego L Viale
- Laboratorio de Terapia Molecular y Celular, Fundación Instituto Leloir-CONICET; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina
| | - Ariel E Vilardo
- Unidad Operativa Centro de Contención Biológica, ANLIS Dr. Carlos G. Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Martin M Avaro
- Servicio Virosis Respiratorias, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales, Laboratorio Nacional de Referencia de SARS-CoV-2/COVID-19 OPS/OMS, INEI-ANLIS Dr Carlos G Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Estefanía Benedetti
- Servicio Virosis Respiratorias, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales, Laboratorio Nacional de Referencia de SARS-CoV-2/COVID-19 OPS/OMS, INEI-ANLIS Dr Carlos G Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Mara L Russo
- Servicio Virosis Respiratorias, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales, Laboratorio Nacional de Referencia de SARS-CoV-2/COVID-19 OPS/OMS, INEI-ANLIS Dr Carlos G Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - María E Dattero
- Servicio Virosis Respiratorias, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales, Laboratorio Nacional de Referencia de SARS-CoV-2/COVID-19 OPS/OMS, INEI-ANLIS Dr Carlos G Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Mauricio Carobene
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (UBA-CONICET), Ciudad Autónoma de Buenos Aires, C1121ABG, Buenos Aires, Argentina
| | | | - Jimena Afonso
- Area de Bioterio, Fundación Instituto Leloir; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina
| | - Mauro Heitrich
- Laboratorio de Terapia Molecular y Celular, Fundación Instituto Leloir-CONICET; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina
| | - Alejandro E Cristófalo
- Centro de Re-diseño e Ingeniería de Proteínas (CRIP), Universidad Nacional de San Martín, San Martin, Buenos Aires, 1650, Argentina
| | - Lisandro H Otero
- Centro de Re-diseño e Ingeniería de Proteínas (CRIP), Universidad Nacional de San Martín, San Martin, Buenos Aires, 1650, Argentina
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Instituto de Biotecnología Ambiental y Salud, CONICET, Universidad Nacional de Río Cuarto, Córdoba, X5804BYA, Argentina
| | - Elsa G Baumeister
- Servicio Virosis Respiratorias, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales, Laboratorio Nacional de Referencia de SARS-CoV-2/COVID-19 OPS/OMS, INEI-ANLIS Dr Carlos G Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Hugo H Ortega
- Centro de Medicina Comparada, ICiVet-Litoral, Universidad Nacional del Litoral-CONICET; Esperanza, Santa Fe, 3080, Argentina
| | - Alexis Edelstein
- Unidad Operativa Centro de Contención Biológica, ANLIS Dr. Carlos G. Malbrán; Ciudad Autónoma de Buenos Aires, C1282AFF, Buenos Aires, Argentina
| | - Osvaldo L Podhajcer
- Laboratorio de Terapia Molecular y Celular, Fundación Instituto Leloir-CONICET; Ciudad Autónoma de Buenos Aires, C1405BWE, Buenos Aires, Argentina.
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