101
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Einav T, Kosikova M, Radvak P, Kuo YC, Kwon HJ, Xie H. Mapping the Antibody Repertoires in Ferrets with Repeated Influenza A/H3 Infections: Is Original Antigenic Sin Really "Sinful"? Viruses 2023; 15:374. [PMID: 36851590 PMCID: PMC9959794 DOI: 10.3390/v15020374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 01/20/2023] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
The influenza-specific antibody repertoire is continuously reshaped by infection and vaccination. The host immune response to contemporary viruses can be redirected to preferentially boost antibodies specific for viruses encountered early in life, a phenomenon called original antigenic sin (OAS) that is suggested to be responsible for diminished vaccine effectiveness after repeated seasonal vaccination. Using a new computational tool called Neutralization Landscapes, we tracked the progression of hemagglutination inhibition antibodies within ferret antisera elicited by repeated influenza A/H3 infections and deciphered the influence of prior exposures on the de novo antibody response to evolved viruses. The results indicate that a broadly neutralizing antibody signature can nevertheless be induced by repeated exposures despite OAS induction. Our study offers a new way to visualize how immune history shapes individual antibodies within a repertoire, which may help to inform future universal influenza vaccine design.
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Affiliation(s)
- Tal Einav
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Martina Kosikova
- Laboratory of Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Peter Radvak
- Laboratory of Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Yuan-Chia Kuo
- Laboratory of Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Hyung Joon Kwon
- Laboratory of Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Hang Xie
- Laboratory of Respiratory Viral Diseases, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
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102
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King SM, Bryan SP, Hilchey SP, Wang J, Zand MS. First Impressions Matter: Immune Imprinting and Antibody Cross-Reactivity in Influenza and SARS-CoV-2. Pathogens 2023; 12:169. [PMID: 36839441 PMCID: PMC9967769 DOI: 10.3390/pathogens12020169] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/24/2023] Open
Abstract
Many rigorous studies have shown that early childhood infections leave a lasting imprint on the immune system. The understanding of this phenomenon has expanded significantly since 1960, when Dr. Thomas Francis Jr first coined the term "original antigenic sin", to account for all previous pathogen exposures, rather than only the first. Now more commonly referred to as "immune imprinting", this effect most often focuses on how memory B-cell responses are shaped by prior antigen exposure, and the resultant antibodies produced after subsequent exposure to antigenically similar pathogens. Although imprinting was originally observed within the context of influenza viral infection, it has since been applied to the pandemic coronavirus SARS-CoV-2. To fully comprehend how imprinting affects the evolution of antibody responses, it is necessary to compare responses elicited by pathogenic strains that are both antigenically similar and dissimilar to strains encountered previously. To accomplish this, we must be able to measure the antigenic distance between strains, which can be easily accomplished using data from multidimensional immunological assays. The knowledge of imprinting, combined with antigenic distance measures, may allow for improvements in vaccine design and development for both influenza and SARS-CoV-2 viruses.
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Affiliation(s)
- Samantha M. King
- Department of Medicine, Division of Nephrology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Shane P. Bryan
- Department of Medicine, Division of Nephrology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Shannon P. Hilchey
- Department of Medicine, Division of Nephrology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Jiong Wang
- Department of Medicine, Division of Nephrology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Martin S. Zand
- Department of Medicine, Division of Nephrology, University of Rochester Medical Center, Rochester, NY 14642, USA
- Clinical and Translational Science Institute, University of Rochester Medical Center, Rochester, NY 14618, USA
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103
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Chiba S, Hatta M, Pattinson D, Yasuhara A, Neumann G, Kawaoka Y. Ferret model to mimic the sequential exposure of humans to historical H3N2 influenza viruses. Vaccine 2023; 41:590-597. [PMID: 36517323 DOI: 10.1016/j.vaccine.2022.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/04/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022]
Abstract
Mutations accumulate in influenza A virus proteins, especially in the main epitopes on the virus surface glycoprotein hemagglutinin (HA). For influenza A(H3N2) viruses, in particular, the antigenicity of their HA has altered since their emergence in 1968, requiring changes of vaccine strains every few years. Most adults have been exposed to several antigenically divergent H3N2 viruses through infection and/or vaccination, and those exposures affect the immune responses of those individuals. However, animal models reflecting this 'immune history' in humans are lacking and naïve animals are generally used for vaccination and virus challenge studies. Here, we describe a ferret model to mimic the serial exposure of humans to antigenically different historical H3HA proteins. In this model, ferrets were sequentially immunized with adjuvanted recombinant H3HA proteins from two or three different H3HA antigenic clusters in chronological order, and serum neutralizing antibody titers were examined against the homologous virus and viruses from different antigenic clusters. For ferrets immunized with a single HA antigen, serum neutralizing antibody titers were elevated specifically against the homologous virus. However, after immunization with the second or third antigenically distinct HA antigen in chronological order, the ferrets showed an increase in more broadly cross-reactive neutralizing titers against the antigenically distinct viruses and against the homologous virus. Sequentially immunized animals challenged with an antigenically advanced H3N2 virus showed attenuated virus growth and less body temperature increase compared with naïve animals. These results suggest that sequential exposure to antigenically different HAs elicits broader neutralizing activity in sera and enhances immune responses against more antigenically distinct viruses Our findings may partly explain why adults who have been exposed to antigenically divergent HAs are less likely to be infected with influenza virus and have severe symptoms than children.
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Affiliation(s)
- Shiho Chiba
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, WI 53711, USA
| | - Masato Hatta
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, WI 53711, USA
| | - David Pattinson
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, WI 53711, USA
| | - Atsuhiro Yasuhara
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Gabriele Neumann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, WI 53711, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, WI 53711, USA; Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan; The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan.
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104
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Aguilar-Bretones M, Fouchier RA, Koopmans MP, van Nierop GP. Impact of antigenic evolution and original antigenic sin on SARS-CoV-2 immunity. J Clin Invest 2023; 133:e162192. [PMID: 36594464 PMCID: PMC9797340 DOI: 10.1172/jci162192] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and vaccinations targeting the spike protein (S) offer protective immunity against coronavirus disease 2019 (COVID-19). This immunity may further be shaped by cross-reactivity with common cold coronaviruses. Mutations arising in S that are associated with altered intrinsic virus properties and immune escape result in the continued circulation of SARS-CoV-2 variants. Potentially, vaccine updates will be required to protect against future variants of concern, as for influenza. To offer potent protection against future variants, these second-generation vaccines may need to redirect immunity to epitopes associated with immune escape and not merely boost immunity toward conserved domains in preimmune individuals. For influenza, efficacy of repeated vaccination is hampered by original antigenic sin, an attribute of immune memory that leads to greater induction of antibodies specific to the first-encountered variant of an immunogen compared with subsequent variants. In this Review, recent findings on original antigenic sin are discussed in the context of SARS-CoV-2 evolution. Unanswered questions and future directions are highlighted, with an emphasis on the impact on disease outcome and vaccine design.
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105
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Vandoorn E, Stadejek W, Leroux-Roels I, Leroux-Roels G, Parys A, Van Reeth K. Human Immunity and Susceptibility to Influenza A(H3) Viruses of Avian, Equine, and Swine Origin. Emerg Infect Dis 2023; 29:98-109. [PMID: 36573615 PMCID: PMC9796212 DOI: 10.3201/eid2901.220943] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Influenza A viruses (IAVs) of subtype H3 that infect humans are antigenically divergent from those of birds, horses, and swine. Human immunity against these viruses might be limited, implying potential pandemic risk. To determine human risk, we selected 4 avian, 1 equine, and 3 swine IAVs representing major H3 lineages. We tested serum collected during 2017-2018 from 286 persons in Belgium for hemagglutination inhibiting antibodies and virus neutralizing antibodies against those animal-origin IAVs and tested replication in human airway epithelia. Seroprevalence rates for circulating IAVs from swine in North America were >51%, swine in Europe 7%-37%, and birds and equids ≤12%. Replication was efficient for cluster IV-A IAVs from swine in North America and IAVs from swine in Europe, intermediate for IAVs from horses and poultry, and absent for IAVs from wild birds and a novel human-like swine IAV in North America. Public health risk may be highest for swine H3 IAVs.
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106
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Jones-Gray E, Robinson EJ, Kucharski AJ, Fox A, Sullivan SG. Does repeated influenza vaccination attenuate effectiveness? A systematic review and meta-analysis. THE LANCET. RESPIRATORY MEDICINE 2023; 11:27-44. [PMID: 36152673 PMCID: PMC9780123 DOI: 10.1016/s2213-2600(22)00266-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/13/2022] [Accepted: 07/13/2022] [Indexed: 01/11/2023]
Abstract
BACKGROUND Influenza vaccines require annual readministration; however, several reports have suggested that repeated vaccination might attenuate the vaccine's effectiveness. We aimed to estimate the reduction in vaccine effectiveness associated with repeated influenza vaccination. METHODS In this systematic review and meta-analysis, we searched MEDLINE, EMBASE, and CINAHL Complete databases for articles published from Jan 1, 2016, to June 13, 2022, and Web of Science for studies published from database inception to June 13, 2022. For studies published before Jan 1, 2016, we consulted published systematic reviews. Two reviewers (EJ-G and EJR) independently screened, extracted data using a data collection form, assessed studies' risk of bias using the Risk Of Bias In Non-Randomized Studies of Interventions (ROBINS-I) and evaluated the weight of evidence by Grading of Recommendations Assessment, Development, and Evaluation (GRADE). We included observational studies and randomised controlled trials that reported vaccine effectiveness against influenza A(H1N1)pdm09, influenza A(H3N2), or influenza B using four vaccination groups: current season; previous season; current and previous seasons; and neither season (reference). For each study, we calculated the absolute difference in vaccine effectiveness (ΔVE) for current season only and previous season only versus current and previous season vaccination to estimate attenuation associated with repeated vaccination. Pooled vaccine effectiveness and ∆VE were calculated by season, age group, and overall. This study is registered with PROSPERO, CRD42021260242. FINDINGS We identified 4979 publications, selected 681 for full review, and included 83 in the systematic review and 41 in meta-analyses. ΔVE for vaccination in both seasons compared with the current season was -9% (95% CI -16 to -1, I2=0%; low certainty) for influenza A(H1N1)pdm09, -18% (-26 to -11, I2=7%; low certainty) for influenza A(H3N2), and -7% (-14 to 0, I2=0%; low certainty) for influenza B, indicating lower protection with consecutive vaccination. However, for all types, A subtypes and B lineages, vaccination in both seasons afforded better protection than not being vaccinated. INTERPRETATION Our estimates suggest that, although vaccination in the previous year attenuates vaccine effectiveness, vaccination in two consecutive years provides better protection than does no vaccination. The estimated effects of vaccination in the previous year are concerning and warrant additional investigation, but are not consistent or severe enough to support an alternative vaccination regimen at this time. FUNDING WHO and the US National Institutes of Health.
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Affiliation(s)
- Elenor Jones-Gray
- Department of Infectious Diseases, University of Melbourne, Melbourne, VIC, Australia
| | - Elizabeth J Robinson
- Department of Infectious Diseases, University of Melbourne, Melbourne, VIC, Australia
| | - Adam J Kucharski
- Centre for the Mathematical Modelling of Infectious Diseases (CMMID), London School of Hygiene and Tropical Medicine, London, UK
| | - Annette Fox
- Department of Infectious Diseases, University of Melbourne, Melbourne, VIC, Australia; WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Sheena G Sullivan
- Department of Infectious Diseases, University of Melbourne, Melbourne, VIC, Australia; WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Epidemiology, University of California, Los Angeles, CA, USA.
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107
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Kuraoka M, Curtis NC, Watanabe A, Tanno H, Shin S, Ye K, Macdonald E, Lavidor O, Kong S, Von Holle T, Windsor I, Ippolito GC, Georgiou G, Walter EB, Kelsoe G, Harrison SC, Moody MA, Bajic G, Lee J. Infant Antibody Repertoires during the First Two Years of Influenza Vaccination. mBio 2022; 13:e0254622. [PMID: 36314798 PMCID: PMC9765176 DOI: 10.1128/mbio.02546-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 09/19/2022] [Indexed: 01/11/2023] Open
Abstract
The first encounter with influenza virus biases later immune responses. This "immune imprinting," formerly from infection within a few years of birth, is in the United States now largely from immunization with a quadrivalent, split vaccine (IIV4 [quadrivalent inactivated influenza vaccine]). In a pilot study of IIV4 imprinting, we used single-cell cultures, next-generation sequencing, and plasma antibody proteomics to characterize the primary antibody responses to influenza in two infants during their first 2 years of seasonal influenza vaccination. One infant, who received only a single vaccination in year 1, contracted an influenza B virus (IBV) infection between the 2 years, allowing us to compare imprinting by infection and vaccination. That infant had a shift in hemagglutinin (HA)-reactive B cell specificity from largely influenza A virus (IAV) specific in year 1 to IBV specific in year 2, both before and after the year 2 vaccination. HA-reactive B cells from the other infant maintained a more evenly distributed specificity. In year 2, class-switched HA-specific B cell IGHV somatic hypermutation (SHM) levels reached the average levels seen in adults. The HA-reactive plasma antibody repertoires of both infants comprised a relatively small number of antibody clonotypes, with one or two very abundant clonotypes. Thus, after the year 2 boost, both infants had overall B cell profiles that resembled those of adult controls. IMPORTANCE Influenza virus is a moving target for the immune system. Variants emerge that escape protection from antibodies elicited by a previously circulating variant ("antigenic drift"). The immune system usually responds to a drifted influenza virus by mutating existing antibodies rather than by producing entirely new ones. Thus, immune memory of the earliest influenza virus exposure has a major influence on later responses to infection or vaccination ("immune imprinting"). In the many studies of influenza immunity in adult subjects, imprinting has been from an early infection, since only in the past 2 decades have infants received influenza immunizations. The work reported in this paper is a pilot study of imprinting by the flu vaccine in two infants, who received the vaccine before experiencing an influenza virus infection. The results suggest that a quadrivalent (four-subtype) vaccine may provide an immune imprint less dominated by one subtype than does a monovalent infection.
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Affiliation(s)
- Masayuki Kuraoka
- Department of Immunology, Duke University, Durham, North Carolina, USA
| | - Nicholas C. Curtis
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA
| | - Akiko Watanabe
- Department of Immunology, Duke University, Durham, North Carolina, USA
| | - Hidetaka Tanno
- Department of Chemical Engineering, University of Texas, Austin, Texas, USA
- Department of Molecular Biosciences, University of Texas, Austin, Texas, USA
- Department of Biomedical Engineering, University of Texas, Austin, Texas, USA
- Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas, USA
| | - Seungmin Shin
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA
| | - Kevin Ye
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA
| | - Elizabeth Macdonald
- Laboratory of Molecular Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Olivia Lavidor
- Laboratory of Molecular Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Susan Kong
- Laboratory of Molecular Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Tarra Von Holle
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
| | - Ian Windsor
- Laboratory of Molecular Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Gregory C. Ippolito
- Department of Molecular Biosciences, University of Texas, Austin, Texas, USA
- Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas, USA
| | - George Georgiou
- Department of Chemical Engineering, University of Texas, Austin, Texas, USA
- Department of Molecular Biosciences, University of Texas, Austin, Texas, USA
- Department of Biomedical Engineering, University of Texas, Austin, Texas, USA
- Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas, USA
| | - Emmanuel B. Walter
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
| | - Garnett Kelsoe
- Department of Immunology, Duke University, Durham, North Carolina, USA
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - Stephen C. Harrison
- Laboratory of Molecular Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - M. Anthony Moody
- Department of Immunology, Duke University, Durham, North Carolina, USA
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
| | - Goran Bajic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jiwon Lee
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA
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108
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Wang W, Lusvarghi S, Subramanian R, Epsi NJ, Wang R, Goguet E, Fries AC, Echegaray F, Vassell R, Coggins SA, Richard SA, Lindholm DA, Mende K, Ewers EC, Larson DT, Colombo RE, Colombo CJ, Joseph JO, Rozman JS, Smith A, Lalani T, Berjohn CM, Maves RC, Jones MU, Mody R, Huprikar N, Livezey J, Saunders D, Hollis-Perry M, Wang G, Ganesan A, Simons MP, Broder CC, Tribble DR, Laing ED, Agan BK, Burgess TH, Mitre E, Pollett SD, Katzelnick LC, Weiss CD. Antigenic cartography of well-characterized human sera shows SARS-CoV-2 neutralization differences based on infection and vaccination history. Cell Host Microbe 2022; 30:1745-1758.e7. [PMID: 36356586 PMCID: PMC9584854 DOI: 10.1016/j.chom.2022.10.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/31/2022] [Accepted: 10/18/2022] [Indexed: 01/26/2023]
Abstract
The rapid emergence of SARS-CoV-2 variants challenges vaccination strategies. Here, we collected 201 serum samples from persons with a single infection or multiple vaccine exposures, or both. We measured their neutralization titers against 15 natural variants and 7 variants with engineered spike mutations and analyzed antigenic diversity. Antigenic maps of primary infection sera showed that Omicron sublineages BA.2, BA.4/BA.5, and BA.2.12.1 are distinct from BA.1 and more similar to Beta/Gamma/Mu variants. Three mRNA COVID-19 vaccinations increased neutralization of BA.1 more than BA.4/BA.5 or BA.2.12.1. BA.1 post-vaccination infection elicited higher neutralization titers to all variants than three vaccinations alone, although with less neutralization to BA.2.12.1 and BA.4/BA.5. Those with BA.1 infection after two or three vaccinations had similar neutralization titer magnitude and antigenic recognition. Accounting for antigenic differences among variants when interpreting neutralization titers can aid the understanding of complex patterns in humoral immunity that informs the selection of future COVID-19 vaccine strains.
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Affiliation(s)
- Wei Wang
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Sabrina Lusvarghi
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 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, USA
| | - Nusrat J Epsi
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Richard Wang
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Emilie Goguet
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA; Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Anthony C Fries
- U.S. Air Force School of Aerospace Medicine, Wright-Patterson Air Force Base, Fairborn, OH, USA
| | - Fernando Echegaray
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Russell Vassell
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Si'Ana A Coggins
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA; Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Stephanie A Richard
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - David A Lindholm
- Brooke Army Medical Center, Joint Base San Antonio-Fort Sam Houston, San Antonio, TX, USA; Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Katrin Mende
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Evan C Ewers
- Fort Belvoir Community Hospital, Fort Belvoir, VA, USA
| | | | - Rhonda E Colombo
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA; Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Madigan Army Medical Center, Tacoma, WA, USA
| | - Christopher J Colombo
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Madigan Army Medical Center, Tacoma, WA, USA
| | - Janet O Joseph
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Julia S Rozman
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Alfred Smith
- Naval Medical Center Portsmouth, Portsmouth, VA, USA
| | - Tahaniyat Lalani
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA; Naval Medical Center Portsmouth, Portsmouth, VA, USA
| | - Catherine M Berjohn
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Naval Medical Center San Diego, San Diego, CA, USA
| | - Ryan C Maves
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Section of Infectious Diseases, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | | | - Rupal Mody
- William Beaumont Army Medical Center, El Paso, TX, USA
| | - Nikhil Huprikar
- Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Jeffrey Livezey
- Department of Pediatrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - David Saunders
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Monique Hollis-Perry
- Clinical Trials Center, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, MD, USA
| | - Gregory Wang
- General Dynamics Information Technology, Falls Church, VA, USA
| | - Anuradha Ganesan
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA; Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Mark P Simons
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Christopher C Broder
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - David R Tribble
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Eric D Laing
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Brian K Agan
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Timothy H Burgess
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Edward Mitre
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Simon D Pollett
- Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA.
| | - 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, USA.
| | - Carol D Weiss
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA.
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Rössler A, Netzl A, Knabl L, Schäfer H, Wilks SH, Bante D, Falkensammer B, Borena W, von Laer D, Smith DJ, Kimpel J. BA.2 and BA.5 omicron differ immunologically from both BA.1 omicron and pre-omicron variants. Nat Commun 2022; 13:7701. [PMID: 36513653 PMCID: PMC9745279 DOI: 10.1038/s41467-022-35312-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
Several studies have shown that SARS-CoV-2 BA.1 omicron is an immune escape variant. Meanwhile, however, omicron BA.2 and BA.5 became dominant in many countries and replaced BA.1. As both have several mutations compared to BA.1, we analyzed whether BA.2 and BA.5 show further immune escape relative to BA.1. Here, we characterized neutralization profiles against the BA.2 and BA.5 omicron sub-variants in plasma samples from individuals with different history of exposures to infection/vaccination and found that unvaccinated individuals after a single exposure to BA.2 had limited cross-neutralizing antibodies to pre-omicron variants and to BA.1. Consequently, our antigenic map including all Variants of Concern and BA.1, BA.2 and BA.5 omicron sub-variants, showed that all omicron sub-variants are distinct to pre-omicron variants, but that the three omicron variants are also antigenically distinct from each other. The antibody landscapes illustrate that cross-neutralizing antibodies against the current antigenic space, as described in our maps, are generated only after three or more exposures to antigenically close variants but also after two exposures to antigenically distant variants. Here, we describe the antigenic space inhabited by the relevant SARS-CoV-2 variants, the understanding of which will have important implications for further vaccine strain adaptations.
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Affiliation(s)
- Annika Rössler
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020, Innsbruck, Austria
| | - Antonia Netzl
- University of Cambridge, Center for Pathogen Evolution, Department of Zoology, Cambridge, UK
| | - Ludwig Knabl
- Tyrolpath Obrist Brunhuber GmbH, Hauptplatz 4, 6511, Zams, Austria
| | - Helena Schäfer
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020, Innsbruck, Austria
| | - Samuel H Wilks
- University of Cambridge, Center for Pathogen Evolution, Department of Zoology, Cambridge, UK
| | - David Bante
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020, Innsbruck, Austria
| | - Barbara Falkensammer
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020, Innsbruck, Austria
| | - Wegene Borena
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020, Innsbruck, Austria
| | - Dorothee von Laer
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020, Innsbruck, Austria
| | - Derek J Smith
- University of Cambridge, Center for Pathogen Evolution, Department of Zoology, Cambridge, UK.
| | - Janine Kimpel
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Peter-Mayr-Str. 4b, 6020, Innsbruck, Austria.
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110
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Yang B, García-Carreras B, Lessler J, Read JM, Zhu H, Metcalf CJE, Hay JA, Kwok KO, Shen R, Jiang CQ, Guan Y, Riley S, Cummings DA. Long term intrinsic cycling in human life course antibody responses to influenza A(H3N2): an observational and modeling study. eLife 2022; 11:81457. [PMID: 36458815 PMCID: PMC9757834 DOI: 10.7554/elife.81457] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 12/01/2022] [Indexed: 12/05/2022] Open
Abstract
Background Over a life course, human adaptive immunity to antigenically mutable pathogens exhibits competitive and facilitative interactions. We hypothesize that such interactions may lead to cyclic dynamics in immune responses over a lifetime. Methods To investigate the cyclic behavior, we analyzed hemagglutination inhibition titers against 21 historical influenza A(H3N2) strains spanning 47 years from a cohort in Guangzhou, China, and applied Fourier spectrum analysis. To investigate possible biological mechanisms, we simulated individual antibody profiles encompassing known feedbacks and interactions due to generally recognized immunological mechanisms. Results We demonstrated a long-term periodicity (about 24 years) in individual antibody responses. The reported cycles were robust to analytic and sampling approaches. Simulations suggested that individual-level cross-reaction between antigenically similar strains likely explains the reported cycle. We showed that the reported cycles are predictable at both individual and birth cohort level and that cohorts show a diversity of phases of these cycles. Phase of cycle was associated with the risk of seroconversion to circulating strains, after accounting for age and pre-existing titers of the circulating strains. Conclusions Our findings reveal the existence of long-term periodicities in individual antibody responses to A(H3N2). We hypothesize that these cycles are driven by preexisting antibody responses blunting responses to antigenically similar pathogens (by preventing infection and/or robust antibody responses upon infection), leading to reductions in antigen-specific responses over time until individual's increasing risk leads to an infection with an antigenically distant enough virus to generate a robust immune response. These findings could help disentangle cohort effects from individual-level exposure histories, improve our understanding of observed heterogeneous antibody responses to immunizations, and inform targeted vaccine strategy. Funding This study was supported by grants from the NIH R56AG048075 (DATC, JL), NIH R01AI114703 (DATC, BY), the Wellcome Trust 200861/Z/16/Z (SR), and 200187/Z/15/Z (SR). This work was also supported by research grants from Guangdong Government HZQB-KCZYZ-2021014 and 2019B121205009 (YG and HZ). DATC, JMR and SR acknowledge support from the National Institutes of Health Fogarty Institute (R01TW0008246). JMR acknowledges support from the Medical Research Council (MR/S004793/1) and the Engineering and Physical Sciences Research Council (EP/N014499/1). The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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Affiliation(s)
- Bingyi Yang
- Department of Biology, University of FloridaGainesvilleUnited States
- Emerging Pathogens Institute, University of FloridaGainesvilleUnited States
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong KongHong KongChina
| | - Bernardo García-Carreras
- Department of Biology, University of FloridaGainesvilleUnited States
- Emerging Pathogens Institute, University of FloridaGainesvilleUnited States
| | - Justin Lessler
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
- Department of Epidemiology, UNC Gillings School of Global Public HealthChapel HillUnited States
- UNC Carolina Population CenterChapel HillUnited States
| | - Jonathan M Read
- Centre for Health Informatics Computing and Statistics, Lancaster UniversityLancasterUnited Kingdom
| | - Huachen Zhu
- Guangdong‐Hong Kong Joint Laboratory of Emerging Infectious Diseases/MOE Joint Laboratory for International Collaboration in Virology and Emerging Infectious Diseases, Joint Institute of Virology (Shantou University/The University of Hong Kong), Shantou UniversityShantouChina
- State Key Laboratory of Emerging Infectious Diseases / World Health Organization Influenza Reference Laboratory, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong KongHong KongChina
- EKIH (Gewuzhikang) Pathogen Research InstituteGuangdongChina
| | - C Jessica E Metcalf
- Department of Ecology and Evolutionary Biology, Princeton UniversityPrincetonUnited States
| | - James A Hay
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College LondonLondonUnited Kingdom
- Center for Communicable Disease Dynamics, Harvard TH Chan School of Public HealthBostonUnited States
| | - Kin O Kwok
- The Jockey Club School of Public Health and Primary Care, Chinese University of Hong KongHong KongChina
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong KongHong KongChina
- Shenzhen Research Institute of The Chinese University of Hong KongGuangdongChina
| | - Ruiyun Shen
- Guangzhou No.12 Hospital, GuangzhouGuangdongChina
| | - Chao Q Jiang
- Guangzhou No.12 Hospital, GuangzhouGuangdongChina
| | - Yi Guan
- Guangdong‐Hong Kong Joint Laboratory of Emerging Infectious Diseases/MOE Joint Laboratory for International Collaboration in Virology and Emerging Infectious Diseases, Joint Institute of Virology (Shantou University/The University of Hong Kong), Shantou UniversityShantouChina
- State Key Laboratory of Emerging Infectious Diseases / World Health Organization Influenza Reference Laboratory, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong KongHong KongChina
- EKIH (Gewuzhikang) Pathogen Research InstituteGuangdongChina
| | - Steven Riley
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College LondonLondonUnited Kingdom
| | - Derek A Cummings
- Department of Biology, University of FloridaGainesvilleUnited States
- Emerging Pathogens Institute, University of FloridaGainesvilleUnited States
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Chen Y, Hilchey SP, Wang J, Garigen J, Zand MS, Huang J. Anamnestic broadly reactive antibodies induced by H7N9 virus more efficiently bind to seasonal H3N2 strains. Hum Vaccin Immunother 2022; 18:2128014. [PMID: 36197079 DOI: 10.1080/21645515.2022.2128014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The very first influenza virus exposure in a human during infancy is known to imprint the host immune system. However, it is unclear how the memory B cells that first target virus epitopes affect antibody response to the stalk of hemagglutinin (HA) domain of influenza virus. Our study is designed to measure the cross-reactivity of antibodies induced by inactivated H7N9 virus using isolated human peripheral blood B cells. Most of the participants displayed higher levels of plasma IgG against the seasonal strains A/Vic11 and A/Cali09 than those binding to historical outbreak A/HK68 and A/PR8. H3 stalk-binding antibodies were detected in plasma at a 1:5000 dilution in 12 of 13 donors, H1 stalk-binding antibodies in all donors, indicating the existence of H3 and H1 stalk-reactive memory B cells. A moderate to high level of broadly cross-reactive antibodies was induced in memory B cells from all donors after in vitro stimulation of B cells with H7N9 virus. H3 stalk-binding antibodies were also detected in most subjects, with cross-reactivity to H1 and H7 stalk domains. The stalk-reactive antibodies bound to five H3 strains spanning 45 years and different H1, H2, H3, H5, H6, H7, H9 and B strains. Interestingly, H1- and H3-reactive IgG were much higher than H7-binding antibodies after 6 days of H7N9 stimulation. Our results demonstrate that HA stalk-reactive antibodies induced by H7N9 viruses more efficiently bound to yearly circulating both H3N2 and H1N1 strains than the boosting strain, indicating that HA stalk immunological imprint can be extended across currently circulating strains or vaccines.
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Affiliation(s)
- Yao Chen
- Department of Blood Transfusion, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Shannon P Hilchey
- Department of Medicine, Division of Nephrology, University of Rochester Medical Center, Rochester, NY, USA
| | - Jiong Wang
- Department of Medicine, Division of Nephrology, University of Rochester Medical Center, Rochester, NY, USA
| | - Jessica Garigen
- Department of Medicine, Division of Nephrology, University of Rochester Medical Center, Rochester, NY, USA
| | - Martin S Zand
- Department of Medicine, Division of Nephrology, University of Rochester Medical Center, Rochester, NY, USA
| | - Junqiong Huang
- Department of Blood Transfusion, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
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112
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de Jong SPJ, Felix Garza ZC, Gibson JC, Han AX, 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, de Jong MD, Russell CA. Potential impacts of prolonged absence of influenza virus circulation on subsequent epidemics. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.02.05.22270494. [PMID: 36415458 PMCID: PMC9681055 DOI: 10.1101/2022.02.05.22270494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Background During the first two years of the COVID-19 pandemic, the circulation of seasonal influenza viruses was unprecedentedly low. This led to concerns that the lack of immune stimulation to influenza viruses combined with waning antibody titres could lead to increased susceptibility to influenza in subsequent seasons, resulting in larger and more severe epidemics. Methods We analyzed historical influenza virus epidemiological data from 2003-2019 to assess the historical frequency of near-absence of seasonal influenza virus circulation and its impact on the size and severity of subsequent epidemics. Additionally, we measured haemagglutination inhibition-based antibody titres against seasonal influenza viruses using longitudinal serum samples from 165 healthy adults, collected before and during the COVID-19 pandemic, and estimated how antibody titres against seasonal influenza waned during the first two years of the pandemic. Findings Low country-level prevalence of influenza virus (sub)types over one or more years occurred frequently before the COVID-19 pandemic and had relatively small impacts on subsequent epidemic size and severity. Additionally, antibody titres against seasonal influenza viruses waned negligibly during the first two years of the pandemic. Interpretation The commonly held notion that lulls in influenza virus circulation, as observed during the COVID-19 pandemic, will lead to larger and/or more severe subsequent epidemics might not be fully warranted, and it is likely that post-lull seasons will be similar in size and severity to pre-lull seasons. Funding European Research Council, Netherlands Organization for Scientific Research, Royal Dutch Academy of Sciences, Public Health Service of Amsterdam. Research in context Evidence before this study: During the first years of the COVID-19 pandemic, the incidence of seasonal influenza was unusually low, leading to widespread concerns of exceptionally large and/or severe influenza epidemics in the coming years. We searched PubMed and Google Scholar using a combination of search terms (i.e., "seasonal influenza", "SARS-CoV-2", "COVID-19", "low incidence", "waning rates", "immune protection") and critically considered published articles and preprints that studied or reviewed the low incidence of seasonal influenza viruses since the start of the COVID-19 pandemic and its potential impact on future seasonal influenza epidemics. We found a substantial body of work describing how influenza virus circulation was reduced during the COVID-19 pandemic, and a number of studies projecting the size of future epidemics, each positing that post-pandemic epidemics are likely to be larger than those observed pre-pandemic. However, it remains unclear to what extent the assumed relationship between accumulated susceptibility and subsequent epidemic size holds, and it remains unknown to what extent antibody levels have waned during the COVID-19 pandemic. Both are potentially crucial for accurate prediction of post-pandemic epidemic sizes.Added value of this study: We find that the relationship between epidemic size and severity and the magnitude of circulation in the preceding season(s) is decidedly more complex than assumed, with the magnitude of influenza circulation in preceding seasons having only limited effects on subsequent epidemic size and severity. Rather, epidemic size and severity are dominated by season-specific effects unrelated to the magnitude of circulation in the preceding season(s). Similarly, we find that antibody levels waned only modestly during the COVID-19 pandemic.Implications of all the available evidence: The lack of changes observed in the patterns of measured antibody titres against seasonal influenza viruses in adults and nearly two decades of epidemiological data suggest that post-pandemic epidemic sizes will likely be similar to those observed pre-pandemic, and challenge the commonly held notion that the widespread concern that the near-absence of seasonal influenza virus circulation during the COVID-19 pandemic, or potential future lulls, are likely to result in larger influenza epidemics in subsequent years.
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113
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Caradonna TM, Ronsard L, Yousif AS, Windsor IW, Hecht R, Bracamonte-Moreno T, Roffler AA, Maron MJ, Maurer DP, Feldman J, Marchiori E, Barnes RM, Rohrer D, Lonberg N, Oguin TH, Sempowski GD, Kepler TB, Kuraoka M, Lingwood D, Schmidt AG. An epitope-enriched immunogen expands responses to a conserved viral site. Cell Rep 2022; 41:111628. [PMID: 36351401 PMCID: PMC9883670 DOI: 10.1016/j.celrep.2022.111628] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 08/22/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022] Open
Abstract
Pathogens evade host humoral responses by accumulating mutations in surface antigens. While variable, there are conserved regions that cannot mutate without compromising fitness. Antibodies targeting these conserved epitopes are often broadly protective but remain minor components of the repertoire. Rational immunogen design leverages a structural understanding of viral antigens to modulate humoral responses to favor these responses. Here, we report an epitope-enriched immunogen presenting a higher copy number of the influenza hemagglutinin (HA) receptor-binding site (RBS) epitope relative to other B cell epitopes. Immunization in a partially humanized murine model imprinted with an H1 influenza shows H1-specific serum and >99% H1-specific B cells being RBS-directed. Single B cell analyses show a genetically restricted response that structural analysis defines as RBS-directed antibodies engaging the RBS with germline-encoded contacts. These data show how epitope enrichment expands B cell responses toward conserved epitopes and advances immunogen design approaches for next-generation viral vaccines.
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Affiliation(s)
| | - Larance Ronsard
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ashraf S Yousif
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Rachel Hecht
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Anne A Roffler
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Max J Maron
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Daniel P Maurer
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Elisa Marchiori
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ralston M Barnes
- Bristol-Myers Squibb, 700 Bay Road, Redwood City, CA 94063-2478, USA
| | - Daniel Rohrer
- Bristol-Myers Squibb, 700 Bay Road, Redwood City, CA 94063-2478, USA
| | - Nils Lonberg
- Bristol-Myers Squibb, 700 Bay Road, Redwood City, CA 94063-2478, USA
| | - Thomas H Oguin
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham NC 27703, USA
| | - Gregory D Sempowski
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham NC 27703, USA
| | - Thomas B Kepler
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Masayuki Kuraoka
- Department of Immunology, Duke University, Durham, NC 27710, USA
| | - Daniel Lingwood
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
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Ali ST, Lau YC, Shan S, Ryu S, Du Z, Wang L, Xu XK, Chen D, Xiong J, Tae J, Tsang TK, Wu P, Lau EHY, Cowling BJ. Prediction of upcoming global infection burden of influenza seasons after relaxation of public health and social measures during the COVID-19 pandemic: a modelling study. THE LANCET GLOBAL HEALTH 2022; 10:e1612-e1622. [PMID: 36240828 PMCID: PMC9573849 DOI: 10.1016/s2214-109x(22)00358-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 08/01/2022] [Accepted: 08/04/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The transmission dynamics of influenza were affected by public health and social measures (PHSMs) implemented globally since early 2020 to mitigate the COVID-19 pandemic. We aimed to assess the effect of COVID-19 PHSMs on the transmissibility of influenza viruses and to predict upcoming influenza epidemics. METHODS For this modelling study, we used surveillance data on influenza virus activity for 11 different locations and countries in 2017-22. We implemented a data-driven mechanistic predictive modelling framework to predict future influenza seasons on the basis of pre-COVID-19 dynamics and the effect of PHSMs during the COVID-19 pandemic. We simulated the potential excess burden of upcoming influenza epidemics in terms of fold rise in peak magnitude and epidemic size compared with pre-COVID-19 levels. We also examined how a proactive influenza vaccination programme could mitigate this effect. FINDINGS We estimated that COVID-19 PHSMs reduced influenza transmissibility by a maximum of 17·3% (95% CI 13·3-21·4) to 40·6% (35·2-45·9) and attack rate by 5·1% (1·5-7·2) to 24·8% (20·8-27·5) in the 2019-20 influenza season. We estimated a 10-60% increase in the population susceptibility for influenza, which might lead to a maximum of 1-5-fold rise in peak magnitude and 1-4-fold rise in epidemic size for the upcoming 2022-23 influenza season across locations, with a significantly higher fold rise in Singapore and Taiwan. The infection burden could be mitigated by additional proactive one-off influenza vaccination programmes. INTERPRETATION Our results suggest the potential for substantial increases in infection burden in upcoming influenza seasons across the globe. Strengthening influenza vaccination programmes is the best preventive measure to reduce the effect of influenza virus infections in the community. FUNDING Health and Medical Research Fund, Hong Kong.
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Affiliation(s)
- Sheikh Taslim Ali
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China,Laboratory of Data Discovery for Health, Hong Kong Science Park, New Territories, Hong Kong Special Administrative Region, China
| | - Yiu Chung Lau
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China,Laboratory of Data Discovery for Health, Hong Kong Science Park, New Territories, Hong Kong Special Administrative Region, China
| | - Songwei Shan
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China,Laboratory of Data Discovery for Health, Hong Kong Science Park, New Territories, Hong Kong Special Administrative Region, China
| | - Sukhyun Ryu
- Department of Preventive Medicine, Konyang University College of Medicine, Daejeon, South Korea
| | - Zhanwei Du
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China,Laboratory of Data Discovery for Health, Hong Kong Science Park, New Territories, Hong Kong Special Administrative Region, China
| | - Lin Wang
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Xiao-Ke Xu
- College of Information and Communication Engineering, Dalian Minzu University, Dalian, China
| | - Dongxuan Chen
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China,Laboratory of Data Discovery for Health, Hong Kong Science Park, New Territories, Hong Kong Special Administrative Region, China
| | - Jiaming Xiong
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China,Laboratory of Data Discovery for Health, Hong Kong Science Park, New Territories, Hong Kong Special Administrative Region, China
| | - Jungyeon Tae
- Department of Preventive Medicine, Konyang University College of Medicine, Daejeon, South Korea
| | - Tim K Tsang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Peng Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China,Laboratory of Data Discovery for Health, Hong Kong Science Park, New Territories, Hong Kong Special Administrative Region, China
| | - Eric H Y Lau
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China,Laboratory of Data Discovery for Health, Hong Kong Science Park, New Territories, Hong Kong Special Administrative Region, China
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China,Laboratory of Data Discovery for Health, Hong Kong Science Park, New Territories, Hong Kong Special Administrative Region, China,Correspondence to: Prof Benjamin J Cowling, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
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115
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Jaago M, Rähni A, Pupina N, Pihlak A, Sadam H, Tuvikene J, Avarlaid A, Planken A, Planken M, Haring L, Vasar E, Baćević M, Lambert F, Kalso E, Pussinen P, Tienari PJ, Vaheri A, Lindholm D, Timmusk T, Ghaemmaghami AM, Palm K. Differential patterns of cross-reactive antibody response against SARS-CoV-2 spike protein detected for chronically ill and healthy COVID-19 naïve individuals. Sci Rep 2022; 12:16817. [PMID: 36207326 PMCID: PMC9540097 DOI: 10.1038/s41598-022-20849-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 09/20/2022] [Indexed: 11/18/2022] Open
Abstract
Immunity to previously encountered viruses can alter response to unrelated pathogens. We reasoned that similar mechanism may also involve SARS-CoV-2 and thereby affect the specificity and the quality of the immune response against the virus. Here, we employed high-throughput next generation phage display method to explore the link between antibody immune response to previously encountered antigens and spike (S) glycoprotein. By profiling the antibody response in COVID-19 naïve individuals with a diverse clinical history (including cardiovascular, neurological, or oncological diseases), we identified 15 highly antigenic epitopes on spike protein that showed cross-reactivity with antigens of seasonal, persistent, latent or chronic infections from common human viruses. We observed varying degrees of cross-reactivity of different viral antigens with S in an epitope-specific manner. The data show that pre-existing SARS-CoV-2 S1 and S2 cross-reactive serum antibody is readily detectable in pre-pandemic cohort. In the severe COVID-19 cases, we found differential antibody response to the 15 defined antigenic and cross-reactive epitopes on spike. We also noted that despite the high mutation rates of Omicron (B.1.1.529) variants of SARS-CoV-2, some of the epitopes overlapped with the described mutations. Finally, we propose that the resolved epitopes on spike if targeted by re-called antibody response from SARS-CoV-2 infections or vaccinations can function in chronically ill COVID-19 naïve/unvaccinated individuals as immunogenic targets to boost antibodies augmenting the chronic conditions. Understanding the relationships between prior antigen exposure at the antibody epitope level and the immune response to subsequent infections with viruses from a different strain is paramount to guiding strategies to exit the COVID-19 pandemic.
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Affiliation(s)
- Mariliis Jaago
- Protobios LLC, Tallinn, Estonia
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Annika Rähni
- Protobios LLC, Tallinn, Estonia
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | | | | | - Helle Sadam
- Protobios LLC, Tallinn, Estonia
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Jürgen Tuvikene
- Protobios LLC, Tallinn, Estonia
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
- DXLabs LLC, Tallinn, Estonia
| | - Annela Avarlaid
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Anu Planken
- North Estonia Medical Centre Foundation, Tallinn, Estonia
| | - Margus Planken
- North Estonia Medical Centre Foundation, Tallinn, Estonia
| | - Liina Haring
- Institute of Clinical Medicine, Psychiatry Clinic of Tartu University Hospital, University of Tartu, Tartu, Estonia
| | - Eero Vasar
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
- Center of Excellence for Genomics and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Miljana Baćević
- Dental Biomaterial Research Unit (d-BRU), Faculty of Medicine, University of Liege, Liege, Belgium
| | - France Lambert
- Department of Periodontology and Oral Surgery, Faculty of Medicine, University of Liege, Liege, Belgium
| | - Eija Kalso
- Department of Anaesthesiology, Intensive Care and Pain Medicine, Helsinki University Hospital, Helsinki, Finland
- SleepWell Research Programme, Department of Pharmacology, University of Helsinki, Helsinki, Finland
| | - Pirkko Pussinen
- Oral and Maxillofacial Diseases, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Pentti J Tienari
- Translational Immunology Research Program, Department of Neurology, Neurocenter, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Antti Vaheri
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland
| | - Dan Lindholm
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Tõnis Timmusk
- Protobios LLC, Tallinn, Estonia
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Amir M Ghaemmaghami
- Immunology and Immuno-Bioengineering Group, School of Life Science, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, United Kingdom
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116
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Desikan R, Linderman SL, Davis C, Zarnitsyna VI, Ahmed H, Antia R. Vaccine models predict rules for updating vaccines against evolving pathogens such as SARS-CoV-2 and influenza in the context of pre-existing immunity. Front Immunol 2022; 13:985478. [PMID: 36263031 PMCID: PMC9574365 DOI: 10.3389/fimmu.2022.985478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 09/16/2022] [Indexed: 11/13/2022] Open
Abstract
Currently, vaccines for SARS-CoV-2 and influenza viruses are updated if the new vaccine induces higher antibody-titers to circulating variants than current vaccines. This approach does not account for complex dynamics of how prior immunity skews recall responses to the updated vaccine. We: (i) use computational models to mechanistically dissect how prior immunity influences recall responses; (ii) explore how this affects the rules for evaluating and deploying updated vaccines; and (iii) apply this to SARS-CoV-2. Our analysis of existing data suggests that there is a strong benefit to updating the current SARS-CoV-2 vaccines to match the currently circulating variants. We propose a general two-dose strategy for determining if vaccines need updating as well as for vaccinating high-risk individuals. Finally, we directly validate our model by reanalysis of earlier human H5N1 influenza vaccine studies.
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Affiliation(s)
- Rajat Desikan
- Clinical Pharmacology Modeling & Simulation, GlaxoSmithKline (GSK), Stevenage, Hertfordshire, United Kingdom
| | - Susanne L. Linderman
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, United States
| | - Carl Davis
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, United States
| | | | - Hasan Ahmed
- Department of Biology, Emory University, Atlanta, GA, United States
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA, United States
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117
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van der Straten K, Guerra D, van Gils MJ, Bontjer I, Caniels TG, van Willigen HDG, Wynberg E, Poniman M, Burger JA, Bouhuijs JH, van Rijswijk J, Olijhoek W, Liesdek MH, Lavell AHA, Appelman B, Sikkens JJ, Bomers MK, Han AX, Nichols BE, Prins M, Vennema H, Reusken C, de Jong MD, de Bree GJ, Russell CA, Eggink D, Sanders RW. Antigenic cartography using sera from sequence-confirmed SARS-CoV-2 variants of concern infections reveals antigenic divergence of Omicron. Immunity 2022; 55:1725-1731.e4. [PMID: 35973428 PMCID: PMC9353602 DOI: 10.1016/j.immuni.2022.07.018] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 05/26/2022] [Accepted: 07/26/2022] [Indexed: 11/26/2022]
Abstract
Large-scale vaccination campaigns have prevented countless hospitalizations and deaths due to COVID-19. However, the emergence of SARS-CoV-2 variants that escape from immunity challenges the effectiveness of current vaccines. Given this continuing evolution, an important question is when and how to update SARS-CoV-2 vaccines to antigenically match circulating variants, similarly to seasonal influenza viruses where antigenic drift necessitates periodic vaccine updates. Here, we studied SARS-CoV-2 antigenic drift by assessing neutralizing activity against variants of concern (VOCs) in a set of sera from patients infected with viral sequence-confirmed VOCs. Infections with D614G or Alpha strains induced the broadest immunity, whereas individuals infected with other VOCs had more strain-specific responses. Omicron BA.1 and BA.2 were substantially resistant to neutralization by sera elicited by all other variants. Antigenic cartography revealed that Omicron BA.1 and BA.2 were antigenically most distinct from D614G, associated with immune escape, and possibly will require vaccine updates to ensure vaccine effectiveness.
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Affiliation(s)
- Karlijn van der Straten
- Amsterdam UMC Location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands; Amsterdam UMC Location University of Amsterdam, Department of Internal Medicine, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Denise Guerra
- Amsterdam UMC Location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Marit J van Gils
- Amsterdam UMC Location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Ilja Bontjer
- Amsterdam UMC Location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Tom G Caniels
- Amsterdam UMC Location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Hugo D G van Willigen
- Amsterdam UMC Location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Elke Wynberg
- Amsterdam UMC Location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands; Department of Infectious Diseases, Public Health Service of Amsterdam, GGD, 1018 WT Amsterdam, the Netherlands
| | - Meliawati Poniman
- Amsterdam UMC Location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Judith A Burger
- Amsterdam UMC Location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Joey H Bouhuijs
- Amsterdam UMC Location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Jacqueline van Rijswijk
- Amsterdam UMC Location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Wouter Olijhoek
- Amsterdam UMC Location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Marinus H Liesdek
- Amsterdam UMC Location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands; Amsterdam UMC Location University of Amsterdam, Department of Internal Medicine, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - A H Ayesha Lavell
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands; Amsterdam UMC Location VU University Amsterdam, Department of Internal Medicine, Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Brent Appelman
- Amsterdam UMC Location University of Amsterdam, Center for Experimental and Molecular Medicine, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Jonne J Sikkens
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands; Amsterdam UMC Location VU University Amsterdam, Department of Internal Medicine, Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Marije K Bomers
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands; Amsterdam UMC Location VU University Amsterdam, Department of Internal Medicine, Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Alvin X Han
- Amsterdam UMC Location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Brooke E Nichols
- Amsterdam UMC Location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands; Department of Global Health, Boston University School of Public Health, Boston, MA, USA
| | - Maria Prins
- Amsterdam UMC Location University of Amsterdam, Department of Internal Medicine, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Department of Infectious Diseases, Public Health Service of Amsterdam, GGD, 1018 WT Amsterdam, the Netherlands
| | - Harry Vennema
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3721 MA Bilthoven, the Netherlands
| | - Chantal Reusken
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3721 MA Bilthoven, the Netherlands
| | - Menno D de Jong
- Amsterdam UMC Location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands
| | - Godelieve J de Bree
- Amsterdam UMC Location University of Amsterdam, Department of Internal Medicine, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Colin A Russell
- Amsterdam UMC Location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands.
| | - Dirk Eggink
- Amsterdam UMC Location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands; Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3721 MA Bilthoven, the Netherlands.
| | - Rogier W Sanders
- Amsterdam UMC Location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, the Netherlands; Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10065, USA.
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118
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Sicca F, Sakorafa E, de Jonge A, de Vries-Idema J, Zhou F, Cox RJ, Huckriede A. The evolution of humoral immune responses to past and novel influenza virus strains gives evidence for antigenic seniority. Front Immunol 2022; 13:987984. [PMID: 36119111 PMCID: PMC9478913 DOI: 10.3389/fimmu.2022.987984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/17/2022] [Indexed: 11/18/2022] Open
Abstract
The high genetic and antigenic variability of influenza virus and the repeated exposures of individuals to the virus over time account for the human immune responses toward this pathogen to continuously evolve during the lifespan of an individual. Influenza-specific immune memory to past strains has been shown to affect the immune responses to subsequent influenza strains and in turn to be changed itself through the new virus encounter. However, exactly how and to what extent this happens remains unclear. Here we studied pre-existing immunity against influenza A virus (IAV) by assessing IAV binding (IgG), neutralizing, and neuraminidase-specific antibodies to 5 different IAV strains in 180 subjects from 3 different age cohorts, adolescents, adults, and elderly, over a 5-year time span. In each age cohort, the highest neutralizing antibody titers were seen for a virus strain that circulated early in their life but the highest increase in titer was found for the most recent virus strains. In contrast, the highest IgG titers were seen against recent virus strains but the biggest increase in titer occurred against older strains. Significant increases in neutralizing antibody titers against a newly encountered virus strain were observed in all age cohorts demonstrating that pre-existing immunity did not hamper antibody induction. Our results indicate that the evolution of influenza-specific humoral immunity differs for rather cross-reactive virus-binding antibodies and more strain-specific neutralizing antibodies. Nevertheless, in general, our observations lend support to the antigenic seniority theory according to which the antibody response to influenza is broadened with each virus encounter, with the earliest encountered strain taking in the most senior and thus dominant position.
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Affiliation(s)
- Federica Sicca
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Eleni Sakorafa
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Anouk de Jonge
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Jacqueline de Vries-Idema
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Fan Zhou
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Rebecca Jane Cox
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Anke Huckriede
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- *Correspondence: Anke Huckriede,
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119
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Williams BJM, Ogbunugafor CB, Althouse BM, Hébert-Dufresne L. Immunity-induced criticality of the genotype network of influenza A (H3N2) hemagglutinin. PNAS NEXUS 2022; 1:pgac143. [PMID: 36060623 PMCID: PMC9434636 DOI: 10.1093/pnasnexus/pgac143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 07/22/2022] [Indexed: 11/17/2022]
Abstract
Seasonal influenza kills hundreds of thousands every year, with multiple constantly changing strains in circulation at any given time. A high mutation rate enables the influenza virus to evade recognition by the human immune system, including immunity acquired through past infection and vaccination. Here, we capture the genetic similarity of influenza strains and their evolutionary dynamics with genotype networks. We show that the genotype networks of influenza A (H3N2) hemagglutinin are characterized by heavy-tailed distributions of module sizes and connectivity indicative of critical behavior. We argue that (i) genotype networks are driven by mutation and host immunity to explore a subspace of networks predictable in structure and (ii) genotype networks provide an underlying structure necessary to capture the rich dynamics of multistrain epidemic models. In particular, inclusion of strain-transcending immunity in epidemic models is dependent upon the structure of an underlying genotype network. This interplay is consistent with self-organized criticality where the epidemic dynamics of influenza locates critical regions of its genotype network. We conclude that this interplay between disease dynamics and network structure might be key for future network analysis of pathogen evolution and realistic multistrain epidemic models.
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Affiliation(s)
- Blake J M Williams
- Vermont Complex Systems Center, University of Vermont , Burlington, VT 05405, USA
| | - C Brandon Ogbunugafor
- Vermont Complex Systems Center, University of Vermont , Burlington, VT 05405, USA
- Department of Ecology and Evolutionary Biology, Yale University , New Haven, CT 06511, USA
- Santa Fe Institute , Santa Fe, NM 87501, USA
- Public Health Modeling Unit, Yale School of Public Health , New Haven, CT 06510, USA
| | - Benjamin M Althouse
- Institute for Disease Modeling, Global Health, Bill & Melinda Gates Foundation , Seattle, WA 98109, USA
- Information School, University of Washington , Seattle, WA 98195, USA
- Department of Biology, New Mexico State University , Las Cruces, NM 88003, USA
| | - Laurent Hébert-Dufresne
- Vermont Complex Systems Center, University of Vermont , Burlington, VT 05405, USA
- Department of Computer Science, University of Vermont , Burlington VT 05405, USA
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120
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Abstract
SARS CoV 2 S-glycoproteins play a crucial role in the entry steps of viral particles. Due to their surface location, they are the main target for host immune responses and the focus of most vaccine strategies. The D614G mutation identified in late January became dominant during March 2020, rendering SARS-CoV-2 more infectious. In April 2020, the Alpha, Beta and Gamma variants emerged simultaneously in Asia, South Africa, and South America, respectively. They were 1.6 to 2 times more transmissible than the ancestral strain. The currently dominant Omicron variant (BA.2) is not a direct descendant from the D614G lineage, but rather emerged from the BA.1 variant (as did BA.4 and BA.5). It is substantially different from all the other variants. It presents significantly reduced susceptibility to antibody neutralization: after 2 doses of mRNA-vaccine, neutralizing titers to Omicron are 41 to 84 times lower than neutralization titers to D614G. That said, a booster dose of mRNA-vaccine increases Omicron neutralization titers and reduces the risk of severe infection.
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Affiliation(s)
- B Lina
- Laboratoire de virologie, Institut des Agents Infectieux, CHU Lyon, Lyon, France
| | - J Bauer
- Service Universitaire des Maladies Infectieuses et du Voyageurs, CH Dron, 59200 Tourcoing, France.
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121
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Windsor IW, Tong P, Lavidor O, Sanjari Moghaddam A, McKay LG, Gautam A, Chen Y, MacDonald EA, Yoo DK, Griffiths A, Wesemann DR, Harrison SC. Antibodies induced by an ancestral SARS-CoV-2 strain that cross-neutralize variants from Alpha to Omicron BA.1. Sci Immunol 2022; 7:eabo3425. [PMID: 35536154 PMCID: PMC9097876 DOI: 10.1126/sciimmunol.abo3425] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/03/2022] [Indexed: 12/21/2022]
Abstract
Neutralizing antibodies that recognize the SARS-CoV-2 spike glycoprotein are the principal host defense against viral invasion. Variants of SARS-CoV-2 bear mutations that allow escape from neutralization by many human antibodies, especially those in widely distributed ("public") classes. Identifying antibodies that neutralize these variants of concern and determining their prevalence are important goals for understanding immune protection. To determine the Delta and Omicron BA.1 variant specificity of B cell repertoires established by an initial Wuhan strain infection, we measured neutralization potencies of 73 antibodies from an unbiased survey of the early memory B cell response. Antibodies recognizing each of three previously defined epitopic regions on the spike receptor binding domain (RBD) varied in neutralization potency and variant-escape resistance. The ACE2 binding surface ("RBD-2") harbored the binding sites of neutralizing antibodies with the highest potency but with the greatest sensitivity to viral escape; two other epitopic regions on the RBD ("RBD-1" and "RBD-3") bound antibodies of more modest potency but greater breadth. The structures of several Fab:spike complexes that neutralized all five variants of concern tested, including one Fab each from the RBD-1, -2, and -3 clusters, illustrated the determinants of broad neutralization and showed that B cell repertoires can have specificities that avoid immune escape driven by public antibodies. The structure of the RBD-2 binding, broad neutralizer shows why it retains neutralizing activity for Omicron BA.1, unlike most others in the same public class. Our results correlate with real-world data on vaccine efficacy, which indicate mitigation of disease caused by Omicron BA.1.
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Affiliation(s)
- Ian W. Windsor
- Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Pei Tong
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Olivia Lavidor
- Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Ali Sanjari Moghaddam
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Lindsay G.A. McKay
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02115
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02115
| | - Avneesh Gautam
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yuezhou Chen
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Elizabeth A. MacDonald
- Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Duck Kyun Yoo
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Anthony Griffiths
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02115
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02115
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
| | - Duane R. Wesemann
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
| | - Stephen C. Harrison
- Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston, MA 02115, USA
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122
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van Doremalen N, Schulz JE, Adney DR, Saturday TA, Fischer RJ, Yinda CK, Thakur N, Newman J, Ulaszewska M, Belij-Rammerstorfer S, Saturday G, Spencer AJ, Bailey D, Russell CA, Gilbert SC, Lambe T, Munster VJ. ChAdOx1 nCoV-19 (AZD1222) or nCoV-19-Beta (AZD2816) protect Syrian hamsters against Beta Delta and Omicron variants. Nat Commun 2022; 13:4610. [PMID: 35941149 PMCID: PMC9358389 DOI: 10.1038/s41467-022-32248-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 07/22/2022] [Indexed: 01/09/2023] Open
Abstract
ChAdOx1 nCoV-19 (AZD1222) is a replication-deficient simian adenovirus-vectored vaccine encoding the spike (S) protein of SARS-CoV-2, based on the first published full-length sequence (Wuhan-1). AZD1222 has been shown to have 74% vaccine efficacy against symptomatic disease in clinical trials. However, variants of concern (VoCs) have been detected, with substitutions that are associated with a reduction in virus neutralizing antibody titer. Updating vaccines to include S proteins of VoCs may be beneficial, even though current real-world data is suggesting good efficacy following boosting with vaccines encoding the ancestral S protein. Using the Syrian hamster model, we evaluate the effect of a single dose of AZD2816, encoding the S protein of the Beta VoC, and efficacy of AZD1222/AZD2816 as a heterologous primary series against challenge with the Beta or Delta variant. Minimal to no viral sgRNA could be detected in lungs of vaccinated animals obtained at 3- or 5- days post inoculation, in contrast to lungs of control animals. In Omicron-challenged hamsters, a single dose of AZD2816 or AZD1222 reduced virus shedding. Thus, these vaccination regimens are protective against the Beta, Delta, and Omicron VoCs in the hamster model.
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Affiliation(s)
- Neeltje van Doremalen
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA.
| | - Jonathan E Schulz
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Danielle R Adney
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
- Lovelace Biomedical Research Institute, Department of Comparative Medicine, Albuquerque, NM, USA
| | - Taylor A Saturday
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Robert J Fischer
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Claude Kwe Yinda
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Nazia Thakur
- Viral Glycoproteins Group, The Pirbright Institute, Pirbright, Woking, UK
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Joseph Newman
- Viral Glycoproteins Group, The Pirbright Institute, Pirbright, Woking, UK
| | - Marta Ulaszewska
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Greg Saturday
- Rocky Mountain Veterinary Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Alexandra J Spencer
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Dalan Bailey
- Viral Glycoproteins Group, The Pirbright Institute, Pirbright, Woking, UK
| | - Colin A Russell
- Laboratory of Applied Evolutionary Biology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Sarah C Gilbert
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Teresa Lambe
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Vincent J Munster
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA.
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123
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Nguyen DC, Lamothe PA, Woodruff MC, Saini AS, Faliti CE, Sanz I, Lee FE. COVID-19 and plasma cells: Is there long-lived protection? Immunol Rev 2022; 309:40-63. [PMID: 35801537 PMCID: PMC9350162 DOI: 10.1111/imr.13115] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Infection with SARS-CoV-2, the etiology of the ongoing COVID-19 pandemic, has resulted in over 450 million cases with more than 6 million deaths worldwide, causing global disruptions since early 2020. Memory B cells and durable antibody protection from long-lived plasma cells (LLPC) are the mainstay of most effective vaccines. However, ending the pandemic has been hampered by the lack of long-lived immunity after infection or vaccination. Although immunizations offer protection from severe disease and hospitalization, breakthrough infections still occur, most likely due to new mutant viruses and the overall decline of neutralizing antibodies after 6 months. Here, we review the current knowledge of B cells, from extrafollicular to memory populations, with a focus on distinct plasma cell subsets, such as early-minted blood antibody-secreting cells and the bone marrow LLPC, and how these humoral compartments contribute to protection after SARS-CoV-2 infection and immunization.
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Affiliation(s)
- Doan C. Nguyen
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of MedicineEmory UniversityAtlantaGeorgiaUSA
| | - Pedro A. Lamothe
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of MedicineEmory UniversityAtlantaGeorgiaUSA
| | - Matthew C. Woodruff
- Division of Rheumatology, Department of MedicineEmory UniversityAtlantaGeorgiaUSA
- Emory Autoimmunity Center of ExcellenceEmory UniversityAtlantaGeorgiaUSA
- Lowance Center for Human ImmunologyEmory UniversityAtlantaGeorgiaUSA
| | - Ankur S. Saini
- Division of Rheumatology, Department of MedicineEmory UniversityAtlantaGeorgiaUSA
- Emory Autoimmunity Center of ExcellenceEmory UniversityAtlantaGeorgiaUSA
- Lowance Center for Human ImmunologyEmory UniversityAtlantaGeorgiaUSA
| | - Caterina E. Faliti
- Division of Rheumatology, Department of MedicineEmory UniversityAtlantaGeorgiaUSA
- Lowance Center for Human ImmunologyEmory UniversityAtlantaGeorgiaUSA
| | - Ignacio Sanz
- Division of Rheumatology, Department of MedicineEmory UniversityAtlantaGeorgiaUSA
- Emory Autoimmunity Center of ExcellenceEmory UniversityAtlantaGeorgiaUSA
- Lowance Center for Human ImmunologyEmory UniversityAtlantaGeorgiaUSA
| | - Frances Eun‐Hyung Lee
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of MedicineEmory UniversityAtlantaGeorgiaUSA
- Lowance Center for Human ImmunologyEmory UniversityAtlantaGeorgiaUSA
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124
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Extrapolating missing antibody-virus measurements across serological studies. Cell Syst 2022; 13:561-573.e5. [PMID: 35798005 DOI: 10.1016/j.cels.2022.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 05/03/2022] [Accepted: 06/10/2022] [Indexed: 01/25/2023]
Abstract
The development of new vaccines, as well as our understanding of key processes that shape viral evolution and host antibody repertoires, relies on measuring multiple antibody responses against large panels of viruses. Given the enormous diversity of circulating virus strains and antibody responses, comprehensively testing all antibody-virus interactions is infeasible. Even within individual studies with limited panels, exhaustive testing is not always performed, and there is no common framework for combining information across studies with partially overlapping panels, especially when the assay type or host species differ. Prior studies have demonstrated that antibody-virus interactions can be characterized in a vastly simpler and lower dimensional space, suggesting that relatively few measurements could predict unmeasured antibody-virus interactions. Here, we apply matrix completion to several large-scale influenza and HIV-1 studies. We explore how prediction accuracy evolves as the number of measurements changes and approximates the number of additional measurements necessary in several highly incomplete datasets (suggesting ∼250,000 measurements could be saved). In addition, we show how the method can combine disparate datasets, even when the number of available measurements is below the theoretical limit that guarantees successful prediction. This approach can be readily generalized to other viruses or more broadly to other low-dimensional biological datasets.
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125
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Branche AR, Rouphael NG, Diemert DJ, Falsey AR, Losada C, Baden LR, Frey SE, Whitaker JA, Little SJ, Anderson EJ, Walter EB, Novak RM, Rupp R, Jackson LA, Babu TM, Kottkamp AC, Luetkemeyer AF, Immergluck LC, Presti RM, Bäcker M, Winokur PL, Mahgoub SM, Goepfert PA, Fusco DN, Malkin E, Bethony JM, Walsh EE, Graciaa DS, Samaha H, Sherman AC, Walsh SR, Abate G, Oikonomopoulou Z, El Sahly HM, Martin TCS, Rostad CA, Smith MJ, Ladner BG, Porterfield L, Dunstan M, Wald A, Davis T, Atmar RL, Mulligan MJ, Lyke KE, Posavad CM, Meagher MA, Stephens DS, Neuzil KM, Abebe K, Hill H, Albert J, Lewis TC, Giebeig LA, Eaton A, Netzl A, Wilks SH, Türeli S, Makhene M, Crandon S, Lee M, Nayak SU, Montefiori DC, Makowski M, Smith DJ, Roberts PC, Beigel JH. SARS-CoV-2 Variant Vaccine Boosters Trial: Preliminary Analyses. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.07.12.22277336. [PMID: 35898343 PMCID: PMC9327623 DOI: 10.1101/2022.07.12.22277336] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Background Protection from SARS-CoV-2 vaccines wanes over time and is compounded by emerging variants including Omicron subvariants. This study evaluated safety and immunogenicity of SARS-CoV-2 variant vaccines. Methods This phase 2 open-label, randomized trial enrolled healthy adults previously vaccinated with a SARS-CoV-2 primary series and a single boost. Eligible participants were randomized to one of six Moderna COVID19 mRNA vaccine arms (50µg dose): Prototype (mRNA-1273), Omicron BA.1+Beta (1 or 2 doses), Omicron BA.1+Delta, Omicron BA.1 monovalent, and Omicron BA.1+Prototype. Neutralization antibody titers (ID 50 ) were assessed for D614G, Delta, Beta and Omicron BA.1 variants and Omicron BA.2.12.1 and BA.4/BA.5 subvariants 15 days after vaccination. Results From March 30 to May 6, 2022, 597 participants were randomized and vaccinated. Median age was 53 years, and 20% had a prior SARS-CoV-2 infection. All vaccines were safe and well-tolerated. Day 15 geometric mean titers (GMT) against D614G were similar across arms and ages, and higher with prior infection. For uninfected participants, Day 15 Omicron BA.1 GMTs were similar across Omicron-containing vaccine arms (3724-4561) and higher than Prototype (1,997 [95%CI:1,482-2,692]). The Omicron BA.1 monovalent and Omicron BA.1+Prototype vaccines induced a geometric mean ratio (GMR) to Prototype for Omicron BA.1 of 2.03 (97.5%CI:1.37-3.00) and 1.56 (97.5%CI:1.06-2.31), respectively. A subset of samples from uninfected participants in four arms were also tested in a different laboratory at Day 15 for neutralizing antibody titers to D614G and Omicron subvariants BA.1, BA.2.12.2 and BA.4/BA.5. Omicron BA.4/BA.5 GMTs were approximately one third BA.1 GMTs (Prototype 517 [95%CI:324-826] vs. 1503 [95%CI:949-2381]; Omicron BA.1+Beta 628 [95%CI:367-1,074] vs. 2125 [95%CI:1139-3965]; Omicron BA.1+Delta 765 [95%CI:443-1,322] vs. 2242 [95%CI:1218-4128] and Omicron BA.1+Prototype 635 [95%CI:447-903] vs. 1972 [95%CI:1337-2907). Conclusions Higher Omicron BA.1 titers were observed with Omicron-containing vaccines compared to Prototype vaccine and titers against Omicron BA.4/BA.5 were lower than against BA.1 for all candidate vaccines. Clinicaltrialsgov NCT05289037.
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126
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Torresi J, Edeling MA, Nolan T, Godfrey DI. A Complementary Union of SARS-CoV2 Natural and Vaccine Induced Immune Responses. Front Immunol 2022; 13:914167. [PMID: 35911696 PMCID: PMC9326230 DOI: 10.3389/fimmu.2022.914167] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/13/2022] [Indexed: 12/27/2022] Open
Abstract
Our understanding of the immune responses that follow SARS-CoV-2 infection and vaccination has progressed considerably since the COVID-19 pandemic was first declared on the 11th of March in 2020. Recovery from infection is associated with the development of protective immune responses, although over time these become less effective against new emerging SARS-CoV-2 variants. Consequently, reinfection with SARS-CoV-2 variants is not infrequent and has contributed to the ongoing pandemic. COVID-19 vaccines have had a tremendous impact on reducing infection and particularly the number of deaths associated with SARS-CoV-2 infection. However, waning of vaccine induced immunity plus the emergence of new variants has necessitated the use of boosters to maintain the benefits of vaccination in reducing COVID-19 associated deaths. Boosting is also beneficial for individuals who have recovered from COVID-19 and developed natural immunity, also enhancing responses immune responses to SARS-CoV-2 variants. This review summarizes our understanding of the immune responses that follow SARS-CoV-2 infection and vaccination, the risks of reinfection with emerging variants and the very important protective role vaccine boosting plays in both vaccinated and previously infected individuals.
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Affiliation(s)
- Joseph Torresi
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Melissa A. Edeling
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Terry Nolan
- Department of Infectious Diseases, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | - Dale I. Godfrey
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
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Otani N, Nakajima K, Ishikawa K, Ichiki K, Yoda Y, Ueda T, Takesue Y, Yamamoto T, Tanimura S, Shima M, Okuno T. Comparison of the Hemagglutination Inhibition Titers against Influenza Vaccine Strains in Japan from the 2017/2018 to 2021/2022 Seasons Using a Single Set of Serum Samples. Viruses 2022; 14:v14071455. [PMID: 35891435 PMCID: PMC9323423 DOI: 10.3390/v14071455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 06/28/2022] [Accepted: 06/28/2022] [Indexed: 12/10/2022] Open
Abstract
In Japan, inactivated influenza vaccines are used. We measured titers of antibodies to vaccine strains of three influenza types—influenza A (H1N1), influenza A (H3N2), and influenza B/Victoria—from the 2017/2018 to 2021/2022 seasons, but not for influenza A (H3N2) from the 2018/2019 season, using a single set of serum samples from 34 healthy volunteers, and assessed the consistency in antibody positivity between seasons. The antibody titers in the 2017/2018 season were used as a reference. The influenza A (H1N1) antibody titer in 2019/2020 did not differ significantly from that in the 2017/2018 season, but the titers varied in the two subsequent seasons. The influenza A (H3N2) antibody titers toward the 2019/2020, 2020/2021, and 2021/2022 seasonal viruses differed significantly from that in the 2017/2018 season. The influenza B/Victoria antibody titer toward the 2019/2020 seasonal antigen differed from that in the 2017/2018 season, and the antibody positivity was inconsistent between seasons; however, the antibody titer in the 2020/2021 season did not differ significantly from those in the prior two seasons, and the antibody positivity was consistent between seasons. Antibody titers and their consistency can be used to evaluate cross-immunity of antibodies.
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Affiliation(s)
- Naruhito Otani
- Department of Public Health, Hyogo Medical University, Nishinomiya 663-8501, Japan; (Y.Y.); (M.S.)
- Correspondence: ; Tel.: +81-798-45-6566; Fax: +81-798-45-6567
| | - Kazuhiko Nakajima
- Department of Infection Control and Prevention, Hyogo Medical University, Nishinomiya 663-8501, Japan; (K.N.); (K.I.); (K.I.); (T.U.); (Y.T.)
| | - Kaori Ishikawa
- Department of Infection Control and Prevention, Hyogo Medical University, Nishinomiya 663-8501, Japan; (K.N.); (K.I.); (K.I.); (T.U.); (Y.T.)
| | - Kaoru Ichiki
- Department of Infection Control and Prevention, Hyogo Medical University, Nishinomiya 663-8501, Japan; (K.N.); (K.I.); (K.I.); (T.U.); (Y.T.)
| | - Yoshiko Yoda
- Department of Public Health, Hyogo Medical University, Nishinomiya 663-8501, Japan; (Y.Y.); (M.S.)
| | - Takashi Ueda
- Department of Infection Control and Prevention, Hyogo Medical University, Nishinomiya 663-8501, Japan; (K.N.); (K.I.); (K.I.); (T.U.); (Y.T.)
| | - Yoshio Takesue
- Department of Infection Control and Prevention, Hyogo Medical University, Nishinomiya 663-8501, Japan; (K.N.); (K.I.); (K.I.); (T.U.); (Y.T.)
| | - Takuma Yamamoto
- Department of Legal Medicine, Hyogo Medical University, Nishinomiya 663-8501, Japan;
| | - Susumu Tanimura
- Department of Public Health Nursing, Mie University Graduate School of Medicine, Tsu 514-0001, Japan;
| | - Masayuki Shima
- Department of Public Health, Hyogo Medical University, Nishinomiya 663-8501, Japan; (Y.Y.); (M.S.)
| | - Toshiomi Okuno
- Department of Microbiology, Hyogo Medical University, Nishinomiya 663-8501, Japan;
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Ertesvåg NU, Cox RJ, Lartey SL, Mohn KGI, Brokstad KA, Trieu MC. Seasonal influenza vaccination expands hemagglutinin-specific antibody breadth to older and future A/H3N2 viruses. NPJ Vaccines 2022; 7:67. [PMID: 35750781 PMCID: PMC9232600 DOI: 10.1038/s41541-022-00490-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 05/13/2022] [Indexed: 11/09/2022] Open
Abstract
History of influenza A/H3N2 exposure, especially childhood infection, shape antibody responses after influenza vaccination and infection, but have not been extensively studied. We investigated the breadth and durability of influenza A/H3N2-specific hemagglutinin-inhibition antibodies after live-attenuated influenza vaccine in children (aged 3-17 years, n = 42), and after inactivated influenza vaccine or infection in adults (aged 22-61 years, n = 42) using 14 antigenically distinct A/H3N2 viruses circulating from 1968 to 2018. We found that vaccination and infection elicited cross-reactive antibody responses, predominantly directed against newer or future strains. Childhood H3-priming increased the breadth and magnitude of back-boosted A/H3N2-specific antibodies in adults. Broader and more durable A/H3N2-specific antibodies were observed in repeatedly vaccinated adults than in children and previously unvaccinated adults. Our findings suggest that early A/H3N2 exposure and frequent seasonal vaccination could increase the breadth and seropositivity of antibody responses, which may improve vaccine protection against future viruses.
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Affiliation(s)
- Nina Urke Ertesvåg
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway.
| | - Rebecca Jane Cox
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Sarah Larteley Lartey
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Kristin G-I Mohn
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Karl Albert Brokstad
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Mai-Chi Trieu
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway.
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129
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Cohen LE, Spiro DJ, Viboud C. Projecting the SARS-CoV-2 transition from pandemicity to endemicity: Epidemiological and immunological considerations. PLoS Pathog 2022; 18:e1010591. [PMID: 35771775 PMCID: PMC9246171 DOI: 10.1371/journal.ppat.1010591] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
In this review, we discuss the epidemiological dynamics of different viral infections to project how the transition from a pandemic to endemic Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) might take shape. Drawing from theories of disease invasion and transmission dynamics, waning immunity in the face of viral evolution and antigenic drift, and empirical data from influenza, dengue, and seasonal coronaviruses, we discuss the putative periodicity, severity, and age dynamics of SARS-CoV-2 as it becomes endemic. We review recent studies on SARS-CoV-2 epidemiology, immunology, and evolution that are particularly useful in projecting the transition to endemicity and highlight gaps that warrant further research.
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Affiliation(s)
- Lily E. Cohen
- Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - David J. Spiro
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
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130
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Desikan R, Linderman SL, Davis C, Zarnitsyna V, Ahmed H, Antia R. Modeling suggests that multiple immunizations or infections will reveal the benefits of updating SARS-CoV-2 vaccines. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.05.21.492928. [PMID: 35665010 PMCID: PMC9164442 DOI: 10.1101/2022.05.21.492928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
When should vaccines to evolving pathogens such as SARS-CoV-2 be updated? Our computational models address this focusing on updating SARS-CoV-2 vaccines to the currently circulating Omicron variant. Current studies typically compare the antibody titers to the new variant following a single dose of the original-vaccine versus the updated-vaccine in previously immunized individuals. These studies find that the updated-vaccine does not induce higher titers to the vaccine-variant compared with the original-vaccine, suggesting that updating may not be needed. Our models recapitulate this observation but suggest that vaccination with the updated-vaccine generates qualitatively different humoral immunity, a small fraction of which is specific for unique epitopes to the new variant. Our simulations suggest that these new variant-specific responses could dominate following subsequent vaccination or infection with either the currently circulating or future variants. We suggest a two-dose strategy for determining if the vaccine needs updating and for vaccinating high-risk individuals.
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Affiliation(s)
- Rajat Desikan
- Clinical Pharmacology Modeling & Simulation, GlaxoSmithKline (GSK), Gunnels Wood Rd, Stevenage, Hertfordshire, SG1 2NY, United Kingdom
- These authors contributed equally
| | - Susanne L. Linderman
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Carl Davis
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Veronika Zarnitsyna
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Hasan Ahmed
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA 30322, USA
- These authors contributed equally
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131
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Minter A, Hoschler K, Jagne YJ, Sallah H, Armitage E, Lindsey B, Hay JA, Riley S, de Silva TI, Kucharski AJ. Estimation of Seasonal Influenza Attack Rates and Antibody Dynamics in Children Using Cross-Sectional Serological Data. J Infect Dis 2022; 225:1750-1754. [PMID: 32556290 PMCID: PMC9113438 DOI: 10.1093/infdis/jiaa338] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 06/13/2020] [Indexed: 11/14/2022] Open
Abstract
Directly measuring evidence of influenza infections is difficult, especially in low-surveillance settings such as sub-Saharan Africa. Using a Bayesian model, we estimated unobserved infection times and underlying antibody responses to influenza A/H3N2, using cross-sectional serum antibody responses to 4 strains in children aged 24-60 months. Among the 242 individuals, we estimated a variable seasonal attack rate and found that most children had ≥1 infection before 2 years of age. Our results are consistent with previously published high attack rates in children. The modeling approach highlights how cross-sectional serological data can be used to estimate epidemiological dynamics.
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Affiliation(s)
- Amanda Minter
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Katja Hoschler
- Respiratory Virus Reference Department, Public Health England, London, United Kingdom
| | - Ya Jankey Jagne
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Hadijatou Sallah
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Edwin Armitage
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Benjamin Lindsey
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - James A Hay
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Steven Riley
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Thushan I de Silva
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
- The Florey Institute, Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Adam J Kucharski
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Correspondence: Adam Kucharski, London School of Hygiene & Tropical Medicine, Keppel Street, Bloomsbury, London WC1E 7HT, United Kingdom ()
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132
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DeGrace MM, Ghedin E, Frieman MB, Krammer F, Grifoni A, Alisoltani A, Alter G, Amara RR, Baric RS, Barouch DH, Bloom JD, Bloyet LM, Bonenfant G, Boon ACM, Boritz EA, Bratt DL, Bricker TL, Brown L, Buchser WJ, Carreño JM, Cohen-Lavi L, Darling TL, Davis-Gardner ME, Dearlove BL, Di H, Dittmann M, Doria-Rose NA, Douek DC, Drosten C, Edara VV, Ellebedy A, Fabrizio TP, Ferrari G, Fischer WM, Florence WC, Fouchier RAM, Franks J, García-Sastre A, Godzik A, Gonzalez-Reiche AS, Gordon A, Haagmans BL, Halfmann PJ, Ho DD, Holbrook MR, Huang Y, James SL, Jaroszewski L, Jeevan T, Johnson RM, Jones TC, Joshi A, Kawaoka Y, Kercher L, Koopmans MPG, Korber B, Koren E, Koup RA, LeGresley EB, Lemieux JE, Liebeskind MJ, Liu Z, Livingston B, Logue JP, Luo Y, McDermott AB, McElrath MJ, Meliopoulos VA, Menachery VD, Montefiori DC, Mühlemann B, Munster VJ, Munt JE, Nair MS, Netzl A, Niewiadomska AM, O'Dell S, Pekosz A, Perlman S, Pontelli MC, Rockx B, Rolland M, Rothlauf PW, Sacharen S, Scheuermann RH, Schmidt SD, Schotsaert M, Schultz-Cherry S, Seder RA, Sedova M, Sette A, Shabman RS, Shen X, Shi PY, Shukla M, Simon V, Stumpf S, Sullivan NJ, Thackray LB, Theiler J, et alDeGrace MM, Ghedin E, Frieman MB, Krammer F, Grifoni A, Alisoltani A, Alter G, Amara RR, Baric RS, Barouch DH, Bloom JD, Bloyet LM, Bonenfant G, Boon ACM, Boritz EA, Bratt DL, Bricker TL, Brown L, Buchser WJ, Carreño JM, Cohen-Lavi L, Darling TL, Davis-Gardner ME, Dearlove BL, Di H, Dittmann M, Doria-Rose NA, Douek DC, Drosten C, Edara VV, Ellebedy A, Fabrizio TP, Ferrari G, Fischer WM, Florence WC, Fouchier RAM, Franks J, García-Sastre A, Godzik A, Gonzalez-Reiche AS, Gordon A, Haagmans BL, Halfmann PJ, Ho DD, Holbrook MR, Huang Y, James SL, Jaroszewski L, Jeevan T, Johnson RM, Jones TC, Joshi A, Kawaoka Y, Kercher L, Koopmans MPG, Korber B, Koren E, Koup RA, LeGresley EB, Lemieux JE, Liebeskind MJ, Liu Z, Livingston B, Logue JP, Luo Y, McDermott AB, McElrath MJ, Meliopoulos VA, Menachery VD, Montefiori DC, Mühlemann B, Munster VJ, Munt JE, Nair MS, Netzl A, Niewiadomska AM, O'Dell S, Pekosz A, Perlman S, Pontelli MC, Rockx B, Rolland M, Rothlauf PW, Sacharen S, Scheuermann RH, Schmidt SD, Schotsaert M, Schultz-Cherry S, Seder RA, Sedova M, Sette A, Shabman RS, Shen X, Shi PY, Shukla M, Simon V, Stumpf S, Sullivan NJ, Thackray LB, Theiler J, Thomas PG, Trifkovic S, Türeli S, Turner SA, Vakaki MA, van Bakel H, VanBlargan LA, Vincent LR, Wallace ZS, Wang L, Wang M, Wang P, Wang W, Weaver SC, Webby RJ, Weiss CD, Wentworth DE, Weston SM, Whelan SPJ, Whitener BM, Wilks SH, Xie X, Ying B, Yoon H, Zhou B, Hertz T, Smith DJ, Diamond MS, Post DJ, Suthar MS. Defining the risk of SARS-CoV-2 variants on immune protection. Nature 2022; 605:640-652. [PMID: 35361968 PMCID: PMC9345323 DOI: 10.1038/s41586-022-04690-5] [Show More Authors] [Citation(s) in RCA: 122] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/24/2022] [Indexed: 11/09/2022]
Abstract
The global emergence of many severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants jeopardizes the protective antiviral immunity induced after infection or vaccination. To address the public health threat caused by the increasing SARS-CoV-2 genomic diversity, the National Institute of Allergy and Infectious Diseases within the National Institutes of Health established the SARS-CoV-2 Assessment of Viral Evolution (SAVE) programme. This effort was designed to provide a real-time risk assessment of SARS-CoV-2 variants that could potentially affect the transmission, virulence, and resistance to infection- and vaccine-induced immunity. The SAVE programme is a critical data-generating component of the US Government SARS-CoV-2 Interagency Group to assess implications of SARS-CoV-2 variants on diagnostics, vaccines and therapeutics, and for communicating public health risk. Here we describe the coordinated approach used to identify and curate data about emerging variants, their impact on immunity and effects on vaccine protection using animal models. We report the development of reagents, methodologies, models and notable findings facilitated by this collaborative approach and identify future challenges. This programme is a template for the response to rapidly evolving pathogens with pandemic potential by monitoring viral evolution in the human population to identify variants that could reduce the effectiveness of countermeasures.
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Affiliation(s)
- Marciela M DeGrace
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Elodie Ghedin
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institutes of Health, Rockville, MD, USA
| | - Matthew B Frieman
- Center for Pathogen Research, Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, MD, USA
| | - Florian Krammer
- Department of Microbiology, 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.
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Boston, MA, USA
| | - Rama R Amara
- Department of Microbiology and Immunology, Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jesse D Bloom
- Fred Hutch Cancer Center, Howard Hughes Medical Institute, Seattle, WA, USA
| | - Louis-Marie Bloyet
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Gaston Bonenfant
- CDC COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Adrianus C M Boon
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Eli A Boritz
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Debbie L Bratt
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- CAMRIS, Contractor for NIAID, Bethesda, MD, USA
| | - Traci L Bricker
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Liliana Brown
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - William J Buchser
- High Throughput Screening Center, Washington University School of Medicine, St Louis, MO, USA
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Liel Cohen-Lavi
- National Institute for Biotechnology in the Negev, Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
| | - Tamarand L Darling
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Meredith E Davis-Gardner
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Bethany L Dearlove
- US Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Han Di
- CDC COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Meike Dittmann
- Microbiology Department, New York University Grossman School of Medicine, New York, NY, USA
| | - Nicole A Doria-Rose
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Daniel C Douek
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin and German Center for Infection Research (DZIF), Berlin, Germany
| | - Venkata-Viswanadh Edara
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Ali Ellebedy
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Thomas P Fabrizio
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Guido Ferrari
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Will M Fischer
- Los Alamos National Laboratory, New Mexico Consortium, Los Alamos, NM, USA
| | - William C Florence
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | | | - John Franks
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Adolfo García-Sastre
- Department of Microbiology, 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
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adam Godzik
- University of California Riverside School of Medicine, Riverside, CA, USA
| | - Ana Silvia Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aubree Gordon
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Bart L Haagmans
- Department Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Peter J Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Michael R Holbrook
- National Institute of Allergy and Infectious Diseases Integrated Research Facility, Frederick, MD, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Sarah L James
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Lukasz Jaroszewski
- University of California Riverside School of Medicine, Riverside, CA, USA
| | - Trushar Jeevan
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Robert M Johnson
- Center for Pathogen Research, Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, MD, USA
| | - Terry C Jones
- Institute of Virology, Charité-Universitätsmedizin and German Center for Infection Research (DZIF), Berlin, Germany
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Astha Joshi
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, Tokyo, Japan
| | - Lisa Kercher
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Bette Korber
- Los Alamos National Laboratory, New Mexico Consortium, Los Alamos, NM, USA
| | - Eilay Koren
- National Institute for Biotechnology in the Negev, Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
- The Shraga Segal Department of Microbiology and Immunology, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Richard A Koup
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Eric B LeGresley
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | | | - Mariel J Liebeskind
- High Throughput Screening Center, Washington University School of Medicine, St Louis, MO, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Brandi Livingston
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - James P Logue
- Center for Pathogen Research, Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, MD, USA
| | - Yang Luo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Adrian B McDermott
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | | | - Victoria A Meliopoulos
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Vineet D Menachery
- Department of Microbiology and Immunology, Institute for Human Infection and Immunity, World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | | | - Barbara Mühlemann
- Institute of Virology, Charité-Universitätsmedizin and German Center for Infection Research (DZIF), Berlin, Germany
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Vincent J Munster
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Jenny E Munt
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Manoj S Nair
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Antonia Netzl
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | | | - Sijy O'Dell
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Andrew Pekosz
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Marjorie C Pontelli
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Barry Rockx
- Department Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Morgane Rolland
- US Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Paul W Rothlauf
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Sinai Sacharen
- National Institute for Biotechnology in the Negev, Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
- The Shraga Segal Department of Microbiology and Immunology, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | | | - Stephen D Schmidt
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Robert A Seder
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Mayya Sedova
- University of California Riverside School of Medicine, Riverside, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Reed S Shabman
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Xiaoying Shen
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Maulik Shukla
- University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Data Science and Learning Division, Argonne National Laboratory, Argonne, IL, USA
| | - Viviana Simon
- Department of Microbiology, 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
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Spencer Stumpf
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Nancy J Sullivan
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Larissa B Thackray
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - James Theiler
- Los Alamos National Laboratory, New Mexico Consortium, Los Alamos, NM, USA
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Sanja Trifkovic
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Sina Türeli
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Samuel A Turner
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Maria A Vakaki
- High Throughput Screening Center, Washington University School of Medicine, St Louis, MO, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura A VanBlargan
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Leah R Vincent
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Zachary S Wallace
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Li Wang
- CDC COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Maple Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Pengfei Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Wei Wang
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Scott C Weaver
- Department of Microbiology and Immunology, Institute for Human Infection and Immunity, World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Richard J Webby
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Carol D Weiss
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - David E Wentworth
- CDC COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Stuart M Weston
- Center for Pathogen Research, Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Bradley M Whitener
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Samuel H Wilks
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Baoling Ying
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Hyejin Yoon
- Los Alamos National Laboratory, New Mexico Consortium, Los Alamos, NM, USA
| | - Bin Zhou
- CDC COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Tomer Hertz
- Department of Microbiology, Immunology and Genetics Faculty of Health Sciences Ben-Gurion University of the Negev, Be'er Sheva, Israel.
| | - Derek J Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK.
| | - Michael S Diamond
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA.
- Department of Pathology & Immunology, Washington University School of Medicine, St Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA.
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA.
| | - Diane J Post
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.
| | - Mehul S Suthar
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA.
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Gagne M, Moliva JI, Foulds KE, Andrew SF, Flynn BJ, Werner AP, Wagner DA, Teng IT, Lin BC, Moore C, Jean-Baptiste N, Carroll R, Foster SL, Patel M, Ellis M, Edara VV, Maldonado NV, Minai M, McCormick L, Honeycutt CC, Nagata BM, Bock KW, Dulan CNM, Cordon J, Flebbe DR, Todd JPM, McCarthy E, Pessaint L, Van Ry A, Narvaez B, Valentin D, Cook A, Dodson A, Steingrebe K, Nurmukhambetova ST, Godbole S, Henry AR, Laboune F, Roberts-Torres J, Lorang CG, Amin S, Trost J, Naisan M, Basappa M, Willis J, Wang L, Shi W, Doria-Rose NA, Zhang Y, Yang ES, Leung K, O'Dell S, Schmidt SD, Olia AS, Liu C, Harris DR, Chuang GY, Stewart-Jones G, Renzi I, Lai YT, Malinowski A, Wu K, Mascola JR, Carfi A, Kwong PD, Edwards DK, Lewis MG, Andersen H, Corbett KS, Nason MC, McDermott AB, Suthar MS, Moore IN, Roederer M, Sullivan NJ, Douek DC, Seder RA. mRNA-1273 or mRNA-Omicron boost in vaccinated macaques elicits similar B cell expansion, neutralizing responses, and protection from Omicron. Cell 2022; 185:1556-1571.e18. [PMID: 35447072 PMCID: PMC8947944 DOI: 10.1016/j.cell.2022.03.038] [Citation(s) in RCA: 152] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/11/2022] [Accepted: 03/23/2022] [Indexed: 01/06/2023]
Abstract
SARS-CoV-2 Omicron is highly transmissible and has substantial resistance to neutralization following immunization with ancestral spike-matched vaccines. It is unclear whether boosting with Omicron-matched vaccines would enhance protection. Here, nonhuman primates that received mRNA-1273 at weeks 0 and 4 were boosted at week 41 with mRNA-1273 or mRNA-Omicron. Neutralizing titers against D614G were 4,760 and 270 reciprocal ID50 at week 6 (peak) and week 41 (preboost), respectively, and 320 and 110 for Omicron. 2 weeks after the boost, titers against D614G and Omicron increased to 5,360 and 2,980 for mRNA-1273 boost and 2,670 and 1,930 for mRNA-Omicron, respectively. Similar increases against BA.2 were observed. Following either boost, 70%-80% of spike-specific B cells were cross-reactive against WA1 and Omicron. Equivalent control of virus replication in lower airways was observed following Omicron challenge 1 month after either boost. These data show that mRNA-1273 and mRNA-Omicron elicit comparable immunity and protection shortly after the boost.
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Affiliation(s)
- Matthew Gagne
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Juan I Moliva
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kathryn E Foulds
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shayne F Andrew
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Barbara J Flynn
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anne P Werner
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Danielle A Wagner
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bob C Lin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christopher Moore
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nazaire Jean-Baptiste
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robin Carroll
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephanie L Foster
- Department of Pediatrics, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Mit Patel
- Department of Pediatrics, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Madison Ellis
- Department of Pediatrics, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Venkata-Viswanadh Edara
- Department of Pediatrics, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nahara Vargas Maldonado
- Department of Pediatrics, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Mahnaz Minai
- Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20892, USA
| | - Lauren McCormick
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christopher Cole Honeycutt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bianca M Nagata
- Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20892, USA
| | - Kevin W Bock
- Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20892, USA
| | - Caitlyn N M Dulan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jamilet Cordon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dillon R Flebbe
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John-Paul M Todd
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elizabeth McCarthy
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | | | | | | | | | | | - Saule T Nurmukhambetova
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sucheta Godbole
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy R Henry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Farida Laboune
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jesmine Roberts-Torres
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cynthia G Lorang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shivani Amin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jessica Trost
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mursal Naisan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Manjula Basappa
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jacquelyn Willis
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wei Shi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kwanyee Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sijy O'Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephen D Schmidt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cuiping Liu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Darcy R Harris
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | | | | | | | - Kai Wu
- Moderna Inc., Cambridge, MA 02139, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | | | - Kizzmekia S Corbett
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Martha C Nason
- Biostatistics Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adrian B McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mehul S Suthar
- Department of Pediatrics, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ian N Moore
- Division of Pathology, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nancy J Sullivan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Robert A Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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134
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Barman S, Soni D, Brook B, Nanishi E, Dowling DJ. Precision Vaccine Development: Cues From Natural Immunity. Front Immunol 2022; 12:662218. [PMID: 35222350 PMCID: PMC8866702 DOI: 10.3389/fimmu.2021.662218] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 12/21/2021] [Indexed: 12/31/2022] Open
Abstract
Traditional vaccine development against infectious diseases has been guided by the overarching aim to generate efficacious vaccines normally indicated by an antibody and/or cellular response that correlates with protection. However, this approach has been shown to be only a partially effective measure, since vaccine- and pathogen-specific immunity may not perfectly overlap. Thus, some vaccine development strategies, normally focused on targeted generation of both antigen specific antibody and T cell responses, resulting in a long-lived heterogenous and stable pool of memory lymphocytes, may benefit from better mimicking the immune response of a natural infection. However, challenges to achieving this goal remain unattended, due to gaps in our understanding of human immunity and full elucidation of infectious pathogenesis. In this review, we describe recent advances in the development of effective vaccines, focusing on how understanding the differences in the immunizing and non-immunizing immune responses to natural infections and corresponding shifts in immune ontogeny are crucial to inform the next generation of infectious disease vaccines.
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Affiliation(s)
- Soumik Barman
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Dheeraj Soni
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Byron Brook
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Etsuro Nanishi
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - David J Dowling
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, United States.,Department of Pediatrics, Harvard Medical School, Boston, MA, United States
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135
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Ge J, Lin X, Guo J, Liu L, Li Z, Lan Y, Liu L, Guo J, Lu J, Huang W, Xin L, Wang D, Qin K, Xu C, Zhou J. The Antibody Response Against Neuraminidase in Human Influenza A (H3N2) Virus Infections During 2018/2019 Flu Season: Focusing on the Epitopes of 329- N-Glycosylation and E344 in N2. Front Microbiol 2022; 13:845088. [PMID: 35387078 PMCID: PMC8978628 DOI: 10.3389/fmicb.2022.845088] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 02/10/2022] [Indexed: 11/13/2022] Open
Abstract
Seasonal influenza A (H3N2) virus has been a concern since its first introduction in humans in 1968. Accumulating antigenic changes in viral hemagglutinin (HA), particularly recent cocirculations of multiple HA genetic clades, allow H3N2 virus evade into humans annually. From 2010, the binding of neuraminidase (NA) to sialic acid made the traditional assay for HA inhibition antibodies (Abs) unsuitable for antigenicity characterization. Here, we investigated the serum anti-NA response in a cohort with a seroconversion of microneutralizing (MN) Abs targeting the circulating strain, A/Singapore/INFIMH-16-0019/2016 (H3N2, 3C.2a1)-like, a virus during 2018/2019 flu seasons. We discovered that MN Ab titers show no difference between children and adults. Nevertheless, higher titers of Abs with NA activity inhibition (NI) activity of 129 and seroconversion rate of 68.42% are presented in children aged 7-17 years (n = 19) and 73.47 and 41.17% in adults aged 21-59 years (n = 17), respectively. The MN Abs generated in children display direct correlations with HA- and NA-binding Abs or NI Abs. The NI activity exhibited cross-reactivity to N2 of H3N2 viruses of 2007 and 2013, commonly with 329-N-glycosylation and E344 in N2, a characteristic of earlier 3C.2a H3N2 virus in 2014. The percentage of such viruses pronouncedly decreased and was even replaced by those dominant H3N2 viruses with E344K and 329 non-glycosylation, which have a significantly low activity to the tested antisera. Our findings suggest that NI assay is a testable assay applied in H3N2 infection in children, and the antigenic drift of current N2 should be considered for vaccine selection.
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Affiliation(s)
- Jing Ge
- Key Laboratory for Medical Virology, National Health, and Family Planning Commission, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Xiaojing Lin
- Key Laboratory for Medical Virology, National Health, and Family Planning Commission, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Jinlei Guo
- The Disease Control and Prevention of Qinhuai District, Nanjing, China
| | - Ling Liu
- Qinhuai District Center for Disease Control and Prevention, Nanjing, China
| | - Zi Li
- Key Laboratory for Medical Virology, National Health, and Family Planning Commission, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Yu Lan
- Key Laboratory for Medical Virology, National Health, and Family Planning Commission, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Liqi Liu
- Key Laboratory for Medical Virology, National Health, and Family Planning Commission, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Junfeng Guo
- Key Laboratory for Medical Virology, National Health, and Family Planning Commission, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Jian Lu
- Key Laboratory for Medical Virology, National Health, and Family Planning Commission, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Weijuan Huang
- Key Laboratory for Medical Virology, National Health, and Family Planning Commission, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Li Xin
- Key Laboratory for Medical Virology, National Health, and Family Planning Commission, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Dayan Wang
- Key Laboratory for Medical Virology, National Health, and Family Planning Commission, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Kun Qin
- Key Laboratory for Medical Virology, National Health, and Family Planning Commission, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Cuiling Xu
- Key Laboratory for Medical Virology, National Health, and Family Planning Commission, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Jianfang Zhou
- Key Laboratory for Medical Virology, National Health, and Family Planning Commission, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
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136
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Wang Y, Tang CY, Wan XF. Antigenic characterization of influenza and SARS-CoV-2 viruses. Anal Bioanal Chem 2022; 414:2841-2881. [PMID: 34905077 PMCID: PMC8669429 DOI: 10.1007/s00216-021-03806-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/21/2021] [Accepted: 11/24/2021] [Indexed: 12/24/2022]
Abstract
Antigenic characterization of emerging and re-emerging viruses is necessary for the prevention of and response to outbreaks, evaluation of infection mechanisms, understanding of virus evolution, and selection of strains for vaccine development. Primary analytic methods, including enzyme-linked immunosorbent/lectin assays, hemagglutination inhibition, neuraminidase inhibition, micro-neutralization assays, and antigenic cartography, have been widely used in the field of influenza research. These techniques have been improved upon over time for increased analytical capacity, and some have been mobilized for the rapid characterization of the SARS-CoV-2 virus as well as its variants, facilitating the development of highly effective vaccines within 1 year of the initially reported outbreak. While great strides have been made for evaluating the antigenic properties of these viruses, multiple challenges prevent efficient vaccine strain selection and accurate assessment. For influenza, these barriers include the requirement for a large virus quantity to perform the assays, more than what can typically be provided by the clinical samples alone, cell- or egg-adapted mutations that can cause antigenic mismatch between the vaccine strain and circulating viruses, and up to a 6-month duration of vaccine development after vaccine strain selection, which allows viruses to continue evolving with potential for antigenic drift and, thus, antigenic mismatch between the vaccine strain and the emerging epidemic strain. SARS-CoV-2 characterization has faced similar challenges with the additional barrier of the need for facilities with high biosafety levels due to its infectious nature. In this study, we review the primary analytic methods used for antigenic characterization of influenza and SARS-CoV-2 and discuss the barriers of these methods and current developments for addressing these challenges.
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Affiliation(s)
- Yang Wang
- MU Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Cynthia Y Tang
- MU Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Xiu-Feng Wan
- MU Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia, MO, USA.
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA.
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA.
- Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, MO, USA.
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137
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Abstract
Although the need for a universal influenza vaccine has long been recognized, only a handful of candidates have been identified so far, with even fewer advancing in the clinical pipeline. The 24–amino acid ectodomain of M2 protein (M2e) has been developed over the past two decades. However, M2e-based vaccine candidates have shortcomings, including the need for several administrations and the lack of sustained antibody titers over time. We report here a vaccine targeting strategy that has the potential to confer sustained and strong protection upon a single shot of a small amount of M2e antigen. The current COVID-19 pandemic has highlighted the importance of developing versatile, powerful platforms for the rapid deployment of vaccines against any incoming threat. Influenza, commonly referred to as “flu,” is a major global public health concern and a huge economic burden to societies. Current influenza vaccines need to be updated annually to match circulating strains, resulting in low take-up rates and poor coverage due to inaccurate prediction. Broadly protective universal flu vaccines that do not need to be updated annually have therefore been pursued. The highly conserved 24–amino acid ectodomain of M2 protein (M2e) is a leading candidate, but its poor immunogenicity has been a major roadblock in its clinical development. Here, we report a targeting strategy that shuttles M2e to a specific dendritic cell subset (cDC1) by engineering a recombinant anti-Clec9A monoclonal antibody fused at each of its heavy chains with three copies of M2e. Single administration in mice of 2 µg of the Clec9A–M2e construct triggered an exceptionally sustained anti-M2e antibody response and resulted in a strong anamnestic protective response upon influenza challenge. Furthermore, and importantly, Clec9A–M2e immunization significantly boosted preexisting anti-M2e titers from prior flu exposure. Thus, the Clec9A-targeting strategy allows antigen and dose sparing, addressing the shortcomings of current M2e vaccine candidates. As the cDC1 subset exists in humans, translation to humans is an exciting and realistic avenue.
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138
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Crowley AR, Natarajan H, Hederman AP, Bobak CA, Weiner JA, Wieland-Alter W, Lee J, Bloch EM, Tobian AAR, Redd AD, Blankson JN, Wolf D, Goetghebuer T, Marchant A, Connor RI, Wright PF, Ackerman ME. Boosting of cross-reactive antibodies to endemic coronaviruses by SARS-CoV-2 infection but not vaccination with stabilized spike. eLife 2022; 11:e75228. [PMID: 35289271 PMCID: PMC8923670 DOI: 10.7554/elife.75228] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 02/23/2022] [Indexed: 12/12/2022] Open
Abstract
Preexisting antibodies to endemic coronaviruses (CoV) that cross-react with SARS-CoV-2 have the potential to influence the antibody response to COVID-19 vaccination and infection for better or worse. In this observational study of mucosal and systemic humoral immunity in acutely infected, convalescent, and vaccinated subjects, we tested for cross-reactivity against endemic CoV spike (S) protein at subdomain resolution. Elevated responses, particularly to the β-CoV OC43, were observed in all natural infection cohorts tested and were correlated with the response to SARS-CoV-2. The kinetics of this response and isotypes involved suggest that infection boosts preexisting antibody lineages raised against prior endemic CoV exposure that cross-react. While further research is needed to discern whether this recalled response is desirable or detrimental, the boosted antibodies principally targeted the better-conserved S2 subdomain of the viral spike and were not associated with neutralization activity. In contrast, vaccination with a stabilized spike mRNA vaccine did not robustly boost cross-reactive antibodies, suggesting differing antigenicity and immunogenicity. In sum, this study provides evidence that antibodies targeting endemic CoV are robustly boosted in response to SARS-CoV-2 infection but not to vaccination with stabilized S, and that depending on conformation or other factors, the S2 subdomain of the spike protein triggers a rapidly recalled, IgG-dominated response that lacks neutralization activity.
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Affiliation(s)
- Andrew R Crowley
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Dartmouth CollegeHanoverUnited States
| | - Harini Natarajan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Dartmouth CollegeHanoverUnited States
| | | | - Carly A Bobak
- Biomedical Data Science, Dartmouth CollegeHanoverUnited States
| | - Joshua A Weiner
- Thayer School of Engineering, Dartmouth CollegeHanoverUnited States
| | - Wendy Wieland-Alter
- Department of Pediatrics, Geisel School of Medicine at Dartmouth, Dartmouth-Hitchcock Medical CenterLebanonUnited States
| | - Jiwon Lee
- Thayer School of Engineering, Dartmouth CollegeHanoverUnited States
| | - Evan M Bloch
- Department of Pathology, Johns Hopkins School of MedicineBaltimoreUnited States
| | - Aaron AR Tobian
- Department of Pathology, Johns Hopkins School of MedicineBaltimoreUnited States
| | - Andrew D Redd
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of MedicineBaltimoreUnited States
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Joel N Blankson
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of MedicineBaltimoreUnited States
| | - Dana Wolf
- Hadassah University Medical CenterJerusalemIsrael
| | - Tessa Goetghebuer
- Institute for Medical Immunology, Université libre de BruxellesCharleroiBelgium
- Pediatric Department, CHU St PierreBrusselsBelgium
| | - Arnaud Marchant
- Institute for Medical Immunology, Université libre de BruxellesCharleroiBelgium
| | - Ruth I Connor
- Department of Pediatrics, Geisel School of Medicine at Dartmouth, Dartmouth-Hitchcock Medical CenterLebanonUnited States
| | - Peter F Wright
- Department of Pediatrics, Geisel School of Medicine at Dartmouth, Dartmouth-Hitchcock Medical CenterLebanonUnited States
| | - Margaret E Ackerman
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Dartmouth CollegeHanoverUnited States
- Thayer School of Engineering, Dartmouth CollegeHanoverUnited States
- Biomedical Data Science, Dartmouth CollegeHanoverUnited States
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139
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Fox A, Carolan L, Leung V, Phuong HVM, Khvorov A, Auladell M, Tseng YY, Thai PQ, Barr I, Subbarao K, Mai LTQ, van Doorn HR, Sullivan SG. Opposing Effects of Prior Infection versus Prior Vaccination on Vaccine Immunogenicity against Influenza A(H3N2) Viruses. Viruses 2022; 14:470. [PMID: 35336877 PMCID: PMC8949461 DOI: 10.3390/v14030470] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/10/2021] [Accepted: 11/28/2021] [Indexed: 02/05/2023] Open
Abstract
Prior vaccination can alternately enhance or attenuate influenza vaccine immunogenicity and effectiveness. Analogously, we found that vaccine immunogenicity was enhanced by prior A(H3N2) virus infection among participants of the Ha Nam Cohort, Viet Nam, but was attenuated by prior vaccination among Australian Health Care Workers (HCWs) vaccinated in the same year. Here, we combined these studies to directly compare antibody titers against 35 A(H3N2) viruses spanning 1968-2018. Participants received licensed inactivated vaccines containing A/HongKong/4801/2014 (H3N2). The analysis was limited to participants aged 18-65 Y, and compared those exposed to A(H3N2) viruses circulating since 2009 by infection (Ha Nam) or vaccination (HCWs) to a reference group who had no recent A(H3N2) infection or vaccination (Ha Nam). Antibody responses were compared by fitting titer/titer-rise landscapes across strains, and by estimating titer ratios to the reference group of 2009-2018 viruses. Pre-vaccination, titers were lowest against 2009-2014 viruses among the reference (no recent exposure) group. Post-vaccination, titers were, on average, two-fold higher among participants with prior infection and two-fold lower among participants with 3-5 prior vaccinations compared to the reference group. Titer rise was negligible among participants with 3-5 prior vaccinations, poor among participants with 1-2 prior vaccinations, and equivalent or better among those with prior infection compared to the reference group. The enhancing effect of prior infection versus the incrementally attenuating effect of prior vaccinations suggests that these exposures may alternately promote and constrain the generation of memory that can be recalled by a new vaccine strain.
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Affiliation(s)
- Annette Fox
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (L.C.); (V.L.); (I.B.); (K.S.); (S.G.S.)
- Department of Infectious Diseases, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (A.K.); (Y.-Y.T.)
| | - Louise Carolan
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (L.C.); (V.L.); (I.B.); (K.S.); (S.G.S.)
| | - Vivian Leung
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (L.C.); (V.L.); (I.B.); (K.S.); (S.G.S.)
| | - Hoang Vu Mai Phuong
- National Institute of Hygiene and Epidemiology, Ha Noi 100000, Vietnam; (H.V.M.P.); (P.Q.T.); (L.T.Q.M.)
| | - Arseniy Khvorov
- Department of Infectious Diseases, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (A.K.); (Y.-Y.T.)
| | - Maria Auladell
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia;
| | - Yeu-Yang Tseng
- Department of Infectious Diseases, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (A.K.); (Y.-Y.T.)
| | - Pham Quang Thai
- National Institute of Hygiene and Epidemiology, Ha Noi 100000, Vietnam; (H.V.M.P.); (P.Q.T.); (L.T.Q.M.)
| | - Ian Barr
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (L.C.); (V.L.); (I.B.); (K.S.); (S.G.S.)
| | - Kanta Subbarao
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (L.C.); (V.L.); (I.B.); (K.S.); (S.G.S.)
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia;
| | - Le Thi Quynh Mai
- National Institute of Hygiene and Epidemiology, Ha Noi 100000, Vietnam; (H.V.M.P.); (P.Q.T.); (L.T.Q.M.)
| | - H. Rogier van Doorn
- Oxford University Clinical Research Unit, Wellcome Africa Asia Programme, National Hospital of Tropical Diseases, Ha Noi 100000, Vietnam;
- Centre of Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7LG, UK
| | - Sheena G. Sullivan
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (L.C.); (V.L.); (I.B.); (K.S.); (S.G.S.)
- Department of Infectious Diseases, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; (A.K.); (Y.-Y.T.)
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140
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Asamoah-Boaheng M, Goldfarb DM, Barakauskas V, Kirkham TL, Demers PA, Karim ME, Lavoie PM, Marquez AC, Jassem AN, Jenneson S, MacDonald C, Grunau B. Evaluation of the Performance of a Multiplexed Serological Assay in the Detection of SARS-CoV-2 Infections in a Predominantly Vaccinated Population. Microbiol Spectr 2022; 10:e0145421. [PMID: 35196794 PMCID: PMC8865468 DOI: 10.1128/spectrum.01454-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/21/2022] [Indexed: 11/20/2022] Open
Abstract
SARS-CoV-2 seroprevalence studies may be complicated by vaccination efforts. It is important to characterize the ability of serology methods to correctly distinguish prior infection from postvaccination seroreactivity. We report the performance of the Meso Scale Discovery (MSD) V-PLEX COVID-19 Coronavirus Panel 2 IgG assay. Using serum samples from a prospective cohort of paramedics, we calculated the performance of the V-PLEX nucleocapsid ("N") assay to classify prior SARS-CoV-2 infections, defined as a (i) history of a positive SARS-CoV-2 PCR test or (ii) positive serology results using the Roche Elecsys total nucleocapsid anti-SARS-Cov-2 assay. We calculated sensitivity and specificity at the optimal threshold (defined by the highest Youden index). We compared subgroups based on vaccination status, and between models that excluded prior infections 3 to 12 months before sample collection. Of 1119 participants, 914 (81.7%) were vaccinated and 60 (5.4%) had evidence of a preceding SARS-CoV-2 infection. Overall and within vaccinated and unvaccinated subgroups, the optimal thresholds were 828 AU/mL, 827 AU/mL, and 1324 AU/mL; with sensitivities of 0.95 (95% CI: 0.94 to 0.96), 0.95 (0.94 to 0.96), 0.94 (0.92 to 0.96) and specificities of 0.88 (0.86 to 0.90), 0.87 (0.85 to 0.89), and 0.94 (0.89 to 0.98), respectively. N-assay specificity was significantly better in unvaccinated (versus vaccinated) individuals (P = 0.005). Overall optimal thresholds based on the AUC values were higher for samples from unvaccinated participants, especially when examining infections within the preceding 9 months (5855 versus 1704 AU/mL). Overall, V-PLEX nucleocapsid assay cutoff values were higher among unvaccinated individuals. Specificity was also significantly higher among unvaccinated individuals. Different thresholds were required to achieve optimal test performance, especially for detecting SARS-CoV-2 infections within the preceding 9 months. IMPORTANCE Among a cohort of adult paramedics in Canada, we investigated the performance of nucleocapsid (N) antibody detection (measured with a V-PLEX assay) to identify previous COVID-19 infections and compared differences among vaccinated and unvaccinated. Our data indicate that vaccinated and unvaccinated groups require different thresholds to achieve optimal test performance, especially for detecting COVID-19 within the preceding 9 months. Overall, specificity was significantly higher among unvaccinated, compared to vaccinated individuals.
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Affiliation(s)
- Michael Asamoah-Boaheng
- Faculty of Medicine, Clinical Epidemiology, Memorial University of Newfoundland, Newfoundland and Labrador, Canada
- Department of Emergency Medicine, University of British Columbia and St. Paul’s Hospital, Vancouver, British Columbia, Canada
| | - David M. Goldfarb
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Vilte Barakauskas
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tracy L. Kirkham
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Occupational Cancer Research Centre, Ontario Health, Toronto, Ontario, Canada
| | - Paul A. Demers
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Occupational Cancer Research Centre, Ontario Health, Toronto, Ontario, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mohammad Ehsanul Karim
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Health Evaluation & Outcome Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Pascal M. Lavoie
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ana Citlali Marquez
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Agatha N. Jassem
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sandra Jenneson
- Department of Emergency Medicine, University of British Columbia and St. Paul’s Hospital, Vancouver, British Columbia, Canada
- British Columbia Emergency Health Services, Vancouver, British Columbia, Canada
| | - Christopher MacDonald
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Occupational Cancer Research Centre, Ontario Health, Toronto, Ontario, Canada
| | - Brian Grunau
- Department of Emergency Medicine, University of British Columbia and St. Paul’s Hospital, Vancouver, British Columbia, Canada
- Centre for Health Evaluation & Outcome Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- British Columbia Emergency Health Services, Vancouver, British Columbia, Canada
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141
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Brouwer AF, Balmaseda A, Gresh L, Patel M, Ojeda S, Schiller AJ, Lopez R, Webby RJ, Nelson MI, Kuan G, Gordon A. Birth cohort relative to an influenza A virus's antigenic cluster introduction drives patterns of children's antibody titers. PLoS Pathog 2022; 18:e1010317. [PMID: 35192673 PMCID: PMC8896668 DOI: 10.1371/journal.ppat.1010317] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 03/04/2022] [Accepted: 01/27/2022] [Indexed: 11/18/2022] Open
Abstract
An individual's antibody titers to influenza A strains are a result of the complicated interplay between infection history, cross-reactivity, immune waning, and other factors. It has been challenging to disentangle how population-level patterns of humoral immunity change as a function of age, calendar year, and birth cohort from cross-sectional data alone. We analyzed 1,589 longitudinal sera samples from 260 children across three studies in Nicaragua, 2006-16. Hemagglutination inhibition (HAI) titers were determined against four H3N2 strains, one H1N1 strain, and two H1N1pdm strains. We assessed temporal patterns of HAI titers using an age-period-cohort modeling framework. We found that titers against a given virus depended on calendar year of serum collection and birth cohort but not on age. Titer cohort patterns were better described by participants' ages relative to year of likely introduction of the virus's antigenic cluster than by age relative to year of strain introduction or by year of birth. These cohort effects may be driven by a decreasing likelihood of early-life infection after cluster introduction and by more broadly reactive antibodies at a young age. H3N2 and H1N1 viruses had qualitatively distinct cohort patterns, with cohort patterns of titers to specific H3N2 strains reaching their peak in children born 3 years prior to that virus's antigenic cluster introduction and with titers to H1N1 and H1N1pdm strains peaking for children born 1-2 years prior to cluster introduction but not being dramatically lower for older children. Ultimately, specific patterns of strain circulation and antigenic cluster introduction may drive population-level antibody titer patterns in children.
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Affiliation(s)
- Andrew F. Brouwer
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail: (AFB); (AG)
| | - Angel Balmaseda
- Sócrates Flores Vivas Health Center, Ministry of Health, Managua, Nicaragua
- Sustainable Sciences Institute, Managua, Nicaragua
| | - Lionel Gresh
- Sustainable Sciences Institute, Managua, Nicaragua
| | - Mayuri Patel
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Sergio Ojeda
- Sustainable Sciences Institute, Managua, Nicaragua
| | - Amy J. Schiller
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Roger Lopez
- Sócrates Flores Vivas Health Center, Ministry of Health, Managua, Nicaragua
- Sustainable Sciences Institute, Managua, Nicaragua
| | - Richard J. Webby
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Martha I. Nelson
- Laboratory of Parasitic Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Guillermina Kuan
- Sustainable Sciences Institute, Managua, Nicaragua
- Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
| | - Aubree Gordon
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail: (AFB); (AG)
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142
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Auladell M, Phuong HVM, Mai LTQ, Tseng YY, Carolan L, Wilks S, Thai PQ, Price D, Duong NT, Hang NLK, Thanh LT, Thuong NTH, Huong TTK, Diep NTN, Bich VTN, Khvorov A, Hensen L, Duong TN, Kedzierska K, Anh DD, Wertheim H, Boyd SD, Good-Jacobson KL, Smith D, Barr I, Sullivan S, van Doorn HR, Fox A. Influenza virus infection history shapes antibody responses to influenza vaccination. Nat Med 2022; 28:363-372. [PMID: 35177857 DOI: 10.1038/s41591-022-01690-w] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 01/10/2022] [Indexed: 02/06/2023]
Abstract
Studies of successive vaccination suggest that immunological memory against past influenza viruses may limit responses to vaccines containing current strains. The impact of memory induced by prior infection is rarely considered and is difficult to ascertain, because infections are often subclinical. This study investigated influenza vaccination among adults from the Ha Nam cohort (Vietnam), who were purposefully selected to include 72 with and 28 without documented influenza A(H3N2) infection during the preceding 9 years (Australian New Zealand Clinical Trials Registry 12621000110886). The primary outcome was the effect of prior influenza A(H3N2) infection on hemagglutinin-inhibiting antibody responses induced by a locally available influenza vaccine administered in November 2016. Baseline and postvaccination sera were titrated against 40 influenza A(H3N2) strains spanning 1968-2018. At each time point (baseline, day 14 and day 280), geometric mean antibody titers against 2008-2018 strains were higher among participants with recent infection (34 (29-40), 187 (154-227) and 86 (72-103)) than among participants without recent infection (19 (17-22), 91 (64-130) and 38 (30-49)). On days 14 and 280, mean titer rises against 2014-2018 strains were 6.1-fold (5.0- to 7.4-fold) and 2.6-fold (2.2- to 3.1-fold) for participants with recent infection versus 4.8-fold (3.5- to 6.7-fold) and 1.9-fold (1.5- to 2.3-fold) for those without. One of 72 vaccinees with recent infection versus 4 of 28 without developed symptomatic A(H3N2) infection in the season after vaccination (P = 0.021). The range of A(H3N2) viruses recognized by vaccine-induced antibodies was associated with the prior infection strain. These results suggest that recall of immunological memory induced by prior infection enhances antibody responses to inactivated influenza vaccine and is important to attain protective antibody titers.
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Affiliation(s)
- Maria Auladell
- Department of Microbiology and Immunology, University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | | | | | - Yeu-Yang Tseng
- 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
| | - Louise Carolan
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Sam Wilks
- Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Pham Quang Thai
- National Institute of Hygiene and Epidemiology, Ha Noi, Vietnam
| | - David Price
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia.,Victorian Infectious Diseases Reference Laboratory Epidemiology Unit and The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | | | | | - Le Thi Thanh
- National Institute of Hygiene and Epidemiology, Ha Noi, Vietnam
| | - Nguyen Thi Hong Thuong
- Oxford University Clinical Research Unit, Wellcome Africa Asia Programme, National Hospital of Tropical Diseases, Ha Noi, Vietnam
| | - Tran Thi Kieu Huong
- Oxford University Clinical Research Unit, Wellcome Africa Asia Programme, National Hospital of Tropical Diseases, Ha Noi, Vietnam
| | - Nguyen Thi Ngoc Diep
- Oxford University Clinical Research Unit, Wellcome Africa Asia Programme, National Hospital of Tropical Diseases, Ha Noi, Vietnam
| | - Vu Thi Ngoc Bich
- Oxford University Clinical Research Unit, Wellcome Africa Asia Programme, National Hospital of Tropical Diseases, Ha Noi, Vietnam
| | - Arseniy Khvorov
- 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
| | - Luca Hensen
- Department of Microbiology and Immunology, University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Tran Nhu Duong
- National Institute of Hygiene and Epidemiology, Ha Noi, Vietnam
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Dang Duc Anh
- National Institute of Hygiene and Epidemiology, Ha Noi, Vietnam
| | - Heiman Wertheim
- Oxford University Clinical Research Unit, Wellcome Africa Asia Programme, National Hospital of Tropical Diseases, Ha Noi, Vietnam.,Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Scott D Boyd
- Stanford University Medical Centre, Stanford University, Stanford, CA, USA
| | - Kim L Good-Jacobson
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.,Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Derek Smith
- Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Ian Barr
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Sheena Sullivan
- 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
| | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Wellcome Africa Asia Programme, National Hospital of Tropical Diseases, Ha Noi, Vietnam.,Centre of Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Annette Fox
- Department of Microbiology and Immunology, University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, 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. .,Department of Infectious Diseases, University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
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143
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Ionov S, Lee J. An Immunoproteomic Survey of the Antibody Landscape: Insights and Opportunities Revealed by Serological Repertoire Profiling. Front Immunol 2022; 13:832533. [PMID: 35178051 PMCID: PMC8843944 DOI: 10.3389/fimmu.2022.832533] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/14/2022] [Indexed: 12/12/2022] Open
Abstract
Immunoproteomics has emerged as a versatile tool for analyzing the antibody repertoire in various disease contexts. Until recently, characterization of antibody molecules in biological fluids was limited to bulk serology, which identifies clinically relevant features of polyclonal antibody responses. The past decade, however, has seen the rise of mass-spectrometry-enabled proteomics methods that have allowed profiling of the antibody response at the molecular level, with the disease-specific serological repertoire elucidated in unprecedented detail. In this review, we present an up-to-date survey of insights into the disease-specific immunological repertoire by examining how quantitative proteomics-based approaches have shed light on the humoral immune response to infection and vaccination in pathogenic illnesses, the molecular basis of autoimmune disease, and the tumor-specific repertoire in cancer. We address limitations of this technology with a focus on emerging potential solutions and discuss the promise of high-resolution immunoproteomics in therapeutic discovery and novel vaccine design.
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Affiliation(s)
| | - Jiwon Lee
- Thayer School of Engineering, Dartmouth College, Hanover, NH, United States
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144
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Lin CY, Wolf J, Brice DC, Sun Y, Locke M, Cherry S, Castellaw AH, Wehenkel M, Crawford JC, Zarnitsyna VI, Duque D, Allison KJ, Allen EK, Brown SA, Mandarano AH, Estepp JH, Taylor C, Molina-Paris C, Schultz-Cherry S, Tang L, Thomas PG, McGargill MA. Pre-existing humoral immunity to human common cold coronaviruses negatively impacts the protective SARS-CoV-2 antibody response. Cell Host Microbe 2022; 30:83-96.e4. [PMID: 34965382 PMCID: PMC8648673 DOI: 10.1016/j.chom.2021.12.005] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/05/2021] [Accepted: 11/30/2021] [Indexed: 11/03/2022]
Abstract
SARS-CoV-2 infection causes diverse outcomes ranging from asymptomatic infection to respiratory distress and death. A major unresolved question is whether prior immunity to endemic, human common cold coronaviruses (hCCCoVs) impacts susceptibility to SARS-CoV-2 infection or immunity following infection and vaccination. Therefore, we analyzed samples from the same individuals before and after SARS-CoV-2 infection or vaccination. We found hCCCoV antibody levels increase after SARS-CoV-2 exposure, demonstrating cross-reactivity. However, a case-control study indicates that baseline hCCCoV antibody levels are not associated with protection against SARS-CoV-2 infection. Rather, higher magnitudes of pre-existing betacoronavirus antibodies correlate with more SARS-CoV-2 antibodies following infection, an indicator of greater disease severity. Additionally, immunization with hCCCoV spike proteins before SARS-CoV-2 immunization impedes the generation of SARS-CoV-2-neutralizing antibodies in mice. Together, these data suggest that pre-existing hCCCoV antibodies hinder SARS-CoV-2 antibody-based immunity following infection and provide insight on how pre-existing coronavirus immunity impacts SARS-CoV-2 infection, which is critical considering emerging variants.
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Affiliation(s)
- Chun-Yang Lin
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA; Integrated Biomedical Sciences Program, University of Tennessee Health Science, Memphis, TN, USA
| | - Joshua Wolf
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David C Brice
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yilun Sun
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Sean Cherry
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ashley H Castellaw
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Marie Wehenkel
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Veronika I Zarnitsyna
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Daniel Duque
- School of Mathematics, University of Leeds, Leeds, UK
| | - Kim J Allison
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - E Kaitlynn Allen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Scott A Brown
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Jeremie H Estepp
- Department of Global Pediatric Medicine, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Carmen Molina-Paris
- School of Mathematics, University of Leeds, Leeds, UK; T-6, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Li Tang
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Maureen A McGargill
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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145
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Wen FT, Malani A, Cobey S. The Potential Beneficial Effects of Vaccination on Antigenically Evolving Pathogens. Am Nat 2022; 199:223-237. [DOI: 10.1086/717410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Frank T. Wen
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637
| | - Anup Malani
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637
- University of Chicago Law School, Chicago, Illinois 60637; and University of Chicago Pritzker School of Medicine, Chicago, Illinois 60637
| | - Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637
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146
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Kok A, Fouchier RAM, Richard M. Cross-Reactivity Conferred by Homologous and Heterologous Prime-Boost A/H5 Influenza Vaccination Strategies in Humans: A Literature Review. Vaccines (Basel) 2021; 9:vaccines9121465. [PMID: 34960210 PMCID: PMC8708856 DOI: 10.3390/vaccines9121465] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/28/2021] [Accepted: 11/30/2021] [Indexed: 11/16/2022] Open
Abstract
Avian influenza viruses from the A/H5 A/goose/Guangdong/1/1996 (GsGd) lineage pose a continuing threat to animal and human health. Since their emergence in 1997, these viruses have spread across multiple continents and have become enzootic in poultry. Additionally, over 800 cases of human infection with A/H5 GsGd viruses have been reported to date, which raises concerns about the potential for a new influenza virus pandemic. The continuous circulation of A/H5 GsGd viruses for over 20 years has resulted in the genetic and antigenic diversification of their hemagglutinin (HA) surface glycoprotein, which poses a serious challenge to pandemic preparedness and vaccine design. In the present article, clinical studies on A/H5 influenza vaccination strategies were reviewed to evaluate the breadth of antibody responses induced upon homologous and heterologous prime-boost vaccination strategies. Clinical data on immunological endpoints were extracted from studies and compiled into a dataset, which was used for the visualization and analysis of the height and breadth of humoral immune responses. Several aspects leading to high immunogenicity and/or cross-reactivity were identified, although the analysis was limited by the heterogeneity in study design and vaccine type used in the included studies. Consequently, crucial questions remain to be addressed in future studies on A/H5 GsGd vaccination strategies.
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147
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Immune-mediated attenuation of influenza illness after infection: opportunities and challenges. THE LANCET MICROBE 2021; 2:e715-e725. [DOI: 10.1016/s2666-5247(21)00180-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 06/01/2021] [Accepted: 07/01/2021] [Indexed: 01/04/2023] Open
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148
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Oidtman RJ, Arevalo P, Bi Q, McGough L, Russo CJ, Vera Cruz D, Costa Vieira M, Gostic KM. Influenza immune escape under heterogeneous host immune histories. Trends Microbiol 2021; 29:1072-1082. [PMID: 34218981 PMCID: PMC8578193 DOI: 10.1016/j.tim.2021.05.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 11/30/2022]
Abstract
In a pattern called immune imprinting, individuals gain the strongest immune protection against the influenza strains encountered earliest in life. In many recent examples, differences in early infection history can explain birth year-associated differences in susceptibility (cohort effects). Susceptibility shapes strain fitness, but without a clear conceptual model linking host susceptibility to the identity and order of past infections general conclusions on the evolutionary and epidemic implications of cohort effects are not possible. Failure to differentiate between cohort effects caused by differences in the set, rather than the order (path), of past infections is a current source of confusion. We review and refine hypotheses for path-dependent cohort effects, which include imprinting. We highlight strategies to measure their underlying causes and emergent consequences.
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Affiliation(s)
- Rachel J Oidtman
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Philip Arevalo
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Qifang Bi
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Lauren McGough
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | | | - Diana Vera Cruz
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Marcos Costa Vieira
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Katelyn M Gostic
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.
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149
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Vinh DN, Nhat NTD, de Bruin E, Vy NHT, Thao TTN, Phuong HT, Anh PH, Todd S, Quan TM, Thanh NTL, Lien NTN, Ha NTH, Hong TTK, Thai PQ, Choisy M, Nguyen TD, Simmons CP, Thwaites GE, Clapham HE, Chau NVV, Koopmans M, Boni MF. Age-seroprevalence curves for the multi-strain structure of influenza A virus. Nat Commun 2021; 12:6680. [PMID: 34795239 PMCID: PMC8602397 DOI: 10.1038/s41467-021-26948-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 10/27/2021] [Indexed: 11/21/2022] Open
Abstract
The relationship between age and seroprevalence can be used to estimate the annual attack rate of an infectious disease. For pathogens with multiple serologically distinct strains, there is a need to describe composite exposure to an antigenically variable group of pathogens. In this study, we assay 24,402 general-population serum samples, collected in Vietnam between 2009 to 2015, for antibodies to eleven human influenza A strains. We report that a principal components decomposition of antibody titer data gives the first principal component as an appropriate surrogate for seroprevalence; this results in annual attack rate estimates of 25.6% (95% CI: 24.1% - 27.1%) for subtype H3 and 16.0% (95% CI: 14.7% - 17.3%) for subtype H1. The remaining principal components separate the strains by serological similarity and associate birth cohorts with their particular influenza histories. Our work shows that dimensionality reduction can be used on human antibody profiles to construct an age-seroprevalence relationship for antigenically variable pathogens.
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MESH Headings
- Algorithms
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Geography
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Humans
- Immunoglobulin G/blood
- Immunoglobulin G/immunology
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza A Virus, H1N1 Subtype/physiology
- Influenza A Virus, H3N2 Subtype/immunology
- Influenza A Virus, H3N2 Subtype/physiology
- Influenza A virus/classification
- Influenza A virus/immunology
- Influenza A virus/physiology
- Influenza, Human/epidemiology
- Influenza, Human/immunology
- Influenza, Human/virology
- Models, Theoretical
- Seroepidemiologic Studies
- Time Factors
- Vietnam/epidemiology
- Virus Replication/immunology
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Affiliation(s)
- Dao Nguyen Vinh
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Nguyen Thi Duy Nhat
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Erwin de Bruin
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, Netherlands
| | - Nguyen Ha Thao Vy
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Tran Thi Nhu Thao
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Huynh Thi Phuong
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Pham Hong Anh
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Stacy Todd
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
- Liverpool School of Tropical Medicine, Liverpool, UK
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, England
| | - Tran Minh Quan
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Nguyen Thi Le Thanh
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | | | | | | | - Pham Quang Thai
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Marc Choisy
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tran Dang Nguyen
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Cameron P Simmons
- Institute of Vector Borne Disease, Monash University, Melbourne, VIC, Australia
| | - Guy E Thwaites
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Hannah E Clapham
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | | | - Marion Koopmans
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, Netherlands
| | - Maciej F Boni
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA.
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150
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Antigenic distance between North American swine and human seasonal H3N2 influenza A viruses as an indication of zoonotic risk to humans. J Virol 2021; 96:e0137421. [PMID: 34757846 DOI: 10.1128/jvi.01374-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Human-to-swine transmission of influenza A virus (IAV) repeatedly occurs, leading to sustained transmission and increased diversity in swine; human seasonal H3N2 introductions occurred in the 1990s and 2010s and were maintained in North American swine. Swine H3N2 were subsequently associated with zoonotic infections, highlighting the need to understand the risk of endemic swine IAV to humans. We quantified antigenic distances between swine H3N2 and human seasonal vaccine strains from 1973 to 2014 using a panel of monovalent antisera raised in pigs in hemagglutination inhibition (HI) assays. Swine H3N2 lineages retained closest antigenic similarity to human vaccine strains from the decade of incursion. Swine lineages from the 1990s were antigenically more similar to human vaccine strains of the mid-1990s but had substantial distance from recent human vaccine strains. In contrast, lineages from the 2010s were closer to human vaccine strains from 2011 and 2014 and most antigenically distant from human vaccine strains prior to 2007. HI assays using ferret antisera demonstrated that swine lineages from the 1990s and 2010s had significant fold-reduction compared with the homologous HI titer of the nearest pandemic preparedness candidate vaccine virus (CVV) or seasonal vaccine strain. The assessment of post-infection and post-vaccination human sera cohorts demonstrated limited cross-reactivity to swine H3N2 from the 1990s, especially in older adults born before 1970s. We identified swine strains to which humans are likely to lack population immunity or are not protected against by a current human seasonal vaccine or CVV to use in prioritizing future human CVV strain selection. IMPORTANCE Human H3N2 influenza A viruses spread to pigs in North America in the 1990s and more recently in the 2010s. These cross-species events led to sustained circulation and increased H3N2 diversity in pig populations. Evolution of H3N2 in swine led to a reduced similarity with human seasonal H3N2 and the vaccine strains used to protect human populations. We quantified the antigenic phenotypes and found that North American swine H3N2 lineages retained more antigenic similarity to historical human vaccine strains from the decade of incursion but had substantial difference compared with recent human vaccine strains. Additionally, pandemic preparedness vaccine strains demonstrated a loss in similarity with contemporary swine strains. Lastly, human sera revealed that although these adults had antibodies against human H3N2 strains, many had limited immunity to swine H3N2, especially older adults born before 1970. Antigenic assessment of swine H3N2 provides critical information for pandemic preparedness and candidate vaccine development.
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