1
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Girard B, Baum-Jones E, Best RL, Campbell TW, Coupart J, Dangerfield K, Dhal A, Jhatro M, Martinez B, Reifert J, Shon J, Zhang M, Waitz R, Chalkias S, Edwards DK, Maglinao M, Paris R, Pajon R. Profiling antibody epitopes induced by mRNA-1273 vaccination and boosters. Front Immunol 2024; 15:1285278. [PMID: 38562934 PMCID: PMC10983613 DOI: 10.3389/fimmu.2024.1285278] [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: 08/29/2023] [Accepted: 02/27/2024] [Indexed: 04/04/2024] Open
Abstract
Background Characterizing the antibody epitope profiles of messenger RNA (mRNA)-based vaccines against SARS-CoV-2 can aid in elucidating the mechanisms underlying the antibody-mediated immune responses elicited by these vaccines. Methods This study investigated the distinct antibody epitopes toward the SARS-CoV-2 spike (S) protein targeted after a two-dose primary series of mRNA-1273 followed by a booster dose of mRNA-1273 or a variant-updated vaccine among serum samples from clinical trial adult participants. Results Multiple S-specific epitopes were targeted after primary vaccination; while signal decreased over time, a booster dose after >6 months largely revived waning antibody signals. Epitope identity also changed after booster vaccination in some subjects, with four new S-specific epitopes detected with stronger signals after boosting than with primary vaccination. Notably, the strength of antibody responses after booster vaccination differed by the exact vaccine formulation, with variant-updated mRNA-1273.211 and mRNA-1273.617.2 booster formulations inducing significantly stronger S-specific signals than a mRNA-1273 booster. Conclusion Overall, these results identify key S-specific epitopes targeted by antibodies induced by mRNA-1273 primary and variant-updated booster vaccination.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - John Shon
- Serimmune, Goleta, CA, United States
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2
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Klein J, Wood J, Jaycox JR, Dhodapkar RM, Lu P, Gehlhausen JR, Tabachnikova A, Greene K, Tabacof L, Malik AA, Silva Monteiro V, Silva J, Kamath K, Zhang M, Dhal A, Ott IM, Valle G, Peña-Hernández M, Mao T, Bhattacharjee B, Takahashi T, Lucas C, Song E, McCarthy D, Breyman E, Tosto-Mancuso J, Dai Y, Perotti E, Akduman K, Tzeng TJ, Xu L, Geraghty AC, Monje M, Yildirim I, Shon J, Medzhitov R, Lutchmansingh D, Possick JD, Kaminski N, Omer SB, Krumholz HM, Guan L, Dela Cruz CS, van Dijk D, Ring AM, Putrino D, Iwasaki A. Distinguishing features of long COVID identified through immune profiling. Nature 2023; 623:139-148. [PMID: 37748514 PMCID: PMC10620090 DOI: 10.1038/s41586-023-06651-y] [Citation(s) in RCA: 90] [Impact Index Per Article: 90.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/18/2023] [Indexed: 09/27/2023]
Abstract
Post-acute infection syndromes may develop after acute viral disease1. Infection with SARS-CoV-2 can result in the development of a post-acute infection syndrome known as long COVID. Individuals with long COVID frequently report unremitting fatigue, post-exertional malaise, and a variety of cognitive and autonomic dysfunctions2-4. However, the biological processes that are associated with the development and persistence of these symptoms are unclear. Here 275 individuals with or without long COVID were enrolled in a cross-sectional study that included multidimensional immune phenotyping and unbiased machine learning methods to identify biological features associated with long COVID. Marked differences were noted in circulating myeloid and lymphocyte populations relative to the matched controls, as well as evidence of exaggerated humoral responses directed against SARS-CoV-2 among participants with long COVID. Furthermore, higher antibody responses directed against non-SARS-CoV-2 viral pathogens were observed among individuals with long COVID, particularly Epstein-Barr virus. Levels of soluble immune mediators and hormones varied among groups, with cortisol levels being lower among participants with long COVID. Integration of immune phenotyping data into unbiased machine learning models identified the key features that are most strongly associated with long COVID status. Collectively, these findings may help to guide future studies into the pathobiology of long COVID and help with developing relevant biomarkers.
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Affiliation(s)
- Jon Klein
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Jamie Wood
- Abilities Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jillian R Jaycox
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Rahul M Dhodapkar
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Ophthalmology, USC Keck School of Medicine, Los Angeles, CA, USA
| | - Peiwen Lu
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Jeff R Gehlhausen
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Dermatology, Yale School of Medicine, New Haven, CT, USA
| | | | - Kerrie Greene
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Laura Tabacof
- Abilities Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amyn A Malik
- Yale Institute for Global Health, Yale School of Public Health, New Haven, CT, USA
| | | | - Julio Silva
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | | | | | | | - Isabel M Ott
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Gabrielee Valle
- Department of Internal Medicine (Pulmonary, Critical Care and Sleep Medicine), Yale School of Medicine, New Haven, CT, USA
| | - Mario Peña-Hernández
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Microbiology, Yale School of Medicine, New Haven, CT, USA
| | - Tianyang Mao
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | | | - Takehiro Takahashi
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Carolina Lucas
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Center for Infection and Immunity, Yale School of Medicine, New Haven, CT, USA
| | - Eric Song
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Dayna McCarthy
- Abilities Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Erica Breyman
- Abilities Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jenna Tosto-Mancuso
- Abilities Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yile Dai
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Emily Perotti
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Koray Akduman
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Tiffany J Tzeng
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Lan Xu
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Anna C Geraghty
- Department of Neurology and Neurological Sciences, Stanford University, Palo Alto, CA, USA
| | - Michelle Monje
- Department of Neurology and Neurological Sciences, Stanford University, Palo Alto, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Inci Yildirim
- Yale Institute for Global Health, Yale School of Public Health, New Haven, CT, USA
- Center for Infection and Immunity, Yale School of Medicine, New Haven, CT, USA
- Department of Pediatrics (Infectious Diseases), Yale New Haven Hospital, New Haven, CT, USA
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | | | - Ruslan Medzhitov
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Center for Infection and Immunity, Yale School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Denyse Lutchmansingh
- Department of Internal Medicine (Pulmonary, Critical Care and Sleep Medicine), Yale School of Medicine, New Haven, CT, USA
| | - Jennifer D Possick
- Department of Internal Medicine (Pulmonary, Critical Care and Sleep Medicine), Yale School of Medicine, New Haven, CT, USA
| | - Naftali Kaminski
- Department of Internal Medicine (Pulmonary, Critical Care and Sleep Medicine), Yale School of Medicine, New Haven, CT, USA
| | - Saad B Omer
- Yale Institute for Global Health, Yale School of Public Health, New Haven, CT, USA
- Center for Infection and Immunity, Yale School of Medicine, New Haven, CT, USA
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Internal Medicine (Infectious Diseases), Yale School of Medicine, New Haven, CT, USA
| | - Harlan M Krumholz
- Center for Infection and Immunity, Yale School of Medicine, New Haven, CT, USA
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
- Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Health Policy and Management, Yale School of Public Health, New Haven, CT, USA
| | - Leying Guan
- Center for Infection and Immunity, Yale School of Medicine, New Haven, CT, USA
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Charles S Dela Cruz
- Department of Internal Medicine (Pulmonary, Critical Care and Sleep Medicine), Yale School of Medicine, New Haven, CT, USA
- Center for Infection and Immunity, Yale School of Medicine, New Haven, CT, USA
| | - David van Dijk
- Center for Infection and Immunity, Yale School of Medicine, New Haven, CT, USA.
- Department of Computer Science, Yale University, New Haven, CT, USA.
- Department of Internal Medicine (Cardiology), Yale School of Medicine, New Haven, CT, USA.
| | - Aaron M Ring
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.
- Center for Infection and Immunity, Yale School of Medicine, New Haven, CT, USA.
| | - David Putrino
- Abilities Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Rehabilitation and Human Performance, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Akiko Iwasaki
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.
- Center for Infection and Immunity, Yale School of Medicine, New Haven, CT, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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3
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Szardenings M, Delaroque N, Kern K, Ramirez-Caballero L, Puder M, Ehrentreich-Förster E, Beige J, Zürner S, Popp G, Wolf J, Borte S. Detection of Antibodies against Endemic and SARS-CoV-2 Coronaviruses with Short Peptide Epitopes. Vaccines (Basel) 2023; 11:1403. [PMID: 37766081 PMCID: PMC10535424 DOI: 10.3390/vaccines11091403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/08/2023] [Accepted: 08/17/2023] [Indexed: 09/29/2023] Open
Abstract
(1) Background: Coronavirus proteins are quite conserved amongst endemic strains (eCoV) and SARS-CoV-2. We aimed to evaluate whether peptide epitopes might serve as useful diagnostic biomarkers to stratify previous infections and COVID-19. (2) Methods: Peptide epitopes were identified at an amino acid resolution that applied a novel statistical approach to generate data sets of potential antibody binding peptides. (3) Results: Data sets from more than 120 COVID-19 or eCoV-infected patients, as well as vaccinated persons, have been used to generate data sets that have been used to search in silico for potential epitopes in proteins of SARS-CoV-2 and eCoV. Peptide epitopes were validated with >300 serum samples in synthetic peptide micro arrays and epitopes specific for different viruses, in addition to the identified cross reactive epitopes. (4) Conclusions: Most patients develop antibodies against non-structural proteins, which are useful general markers for recent infections. However, there are differences in the epitope patterns of COVID-19, and eCoV, and the S-protein vaccine, which can only be explained by a high degree of cross-reactivity between the viruses, a pre-existing immune response against some epitopes, and even an alternate processing of the vaccine proteins.
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Affiliation(s)
- Michael Szardenings
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Perlickstr. 1, 04103 Leipzig, Germany; (N.D.); (K.K.); (S.Z.); (G.P.)
- epitopic GmbH, Deutscher Platz 5e, 04103 Leipzig, Germany;
| | - Nicolas Delaroque
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Perlickstr. 1, 04103 Leipzig, Germany; (N.D.); (K.K.); (S.Z.); (G.P.)
| | - Karolin Kern
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Perlickstr. 1, 04103 Leipzig, Germany; (N.D.); (K.K.); (S.Z.); (G.P.)
- epitopic GmbH, Deutscher Platz 5e, 04103 Leipzig, Germany;
| | - Lisbeth Ramirez-Caballero
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Perlickstr. 1, 04103 Leipzig, Germany; (N.D.); (K.K.); (S.Z.); (G.P.)
| | - Marcus Puder
- epitopic GmbH, Deutscher Platz 5e, 04103 Leipzig, Germany;
| | - Eva Ehrentreich-Förster
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses IZI-BB, Am Mühlenberg 13, 14476 Potsdam, Germany;
| | - Joachim Beige
- Martin-Luther-University Halle/Wittenberg, Medical Clinic 2, 06112 Halle, Germany;
| | - Sebastian Zürner
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Perlickstr. 1, 04103 Leipzig, Germany; (N.D.); (K.K.); (S.Z.); (G.P.)
- WINF/Informationsmanagement, University Leipzig, Grimmaische Straße 12, 04109 Leipzig, Germany
| | - Georg Popp
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Perlickstr. 1, 04103 Leipzig, Germany; (N.D.); (K.K.); (S.Z.); (G.P.)
| | - Johannes Wolf
- Department of Laboratory Medicine, Hospital St. Georg, Delitzscher Strasse 141, 04129 Leipzig, Germany; (J.W.); (S.B.)
- ImmunoDeficiencyCenter Leipzig (IDCL), Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiency Diseases, Hospital St. Georg, Delitzscher Strasse 141, 04129 Leipzig, Germany
| | - Stephan Borte
- Department of Laboratory Medicine, Hospital St. Georg, Delitzscher Strasse 141, 04129 Leipzig, Germany; (J.W.); (S.B.)
- ImmunoDeficiencyCenter Leipzig (IDCL), Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiency Diseases, Hospital St. Georg, Delitzscher Strasse 141, 04129 Leipzig, Germany
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4
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Chowdhury R, Taguchi AT, Kelbauskas L, Stafford P, Diehnelt C, Zhao ZG, Williamson PC, Green V, Woodbury NW. Modeling the sequence dependence of differential antibody binding in the immune response to infectious disease. PLoS Comput Biol 2023; 19:e1010773. [PMID: 37339137 DOI: 10.1371/journal.pcbi.1010773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 05/15/2023] [Indexed: 06/22/2023] Open
Abstract
Past studies have shown that incubation of human serum samples on high density peptide arrays followed by measurement of total antibody bound to each peptide sequence allows detection and discrimination of humoral immune responses to a variety of infectious diseases. This is true even though these arrays consist of peptides with near-random amino acid sequences that were not designed to mimic biological antigens. This "immunosignature" approach, is based on a statistical evaluation of the binding pattern for each sample but it ignores the information contained in the amino acid sequences that the antibodies are binding to. Here, similar array-based antibody profiles are instead used to train a neural network to model the sequence dependence of molecular recognition involved in the immune response of each sample. The binding profiles used resulted from incubating serum from 5 infectious disease cohorts (Hepatitis B and C, Dengue Fever, West Nile Virus and Chagas disease) and an uninfected cohort with 122,926 peptide sequences on an array. These sequences were selected quasi-randomly to represent an even but sparse sample of the entire possible combinatorial sequence space (~1012). This very sparse sampling of combinatorial sequence space was sufficient to capture a statistically accurate representation of the humoral immune response across the entire space. Processing array data using the neural network not only captures the disease-specific sequence-binding information but aggregates binding information with respect to sequence, removing sequence-independent noise and improving the accuracy of array-based classification of disease compared with the raw binding data. Because the neural network model is trained on all samples simultaneously, a highly condensed representation of the differential information between samples resides in the output layer of the model, and the column vectors from this layer can be used to represent each sample for classification or unsupervised clustering applications.
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Affiliation(s)
- Robayet Chowdhury
- Center for Innovations in Medicine, Biodesign Institute, Arizona State University, Tempe, fsupArizona, United States of America
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, United States of America
| | | | - Laimonas Kelbauskas
- Center for Innovations in Medicine, Biodesign Institute, Arizona State University, Tempe, fsupArizona, United States of America
| | - Phillip Stafford
- Center for Innovations in Medicine, Biodesign Institute, Arizona State University, Tempe, fsupArizona, United States of America
| | - Chris Diehnelt
- Center for Innovations in Medicine, Biodesign Institute, Arizona State University, Tempe, fsupArizona, United States of America
| | - Zhan-Gong Zhao
- Center for Innovations in Medicine, Biodesign Institute, Arizona State University, Tempe, fsupArizona, United States of America
| | | | - Valerie Green
- Creative Testing Solutions, Tempe, Arizona, United States of America
| | - Neal W Woodbury
- Center for Innovations in Medicine, Biodesign Institute, Arizona State University, Tempe, fsupArizona, United States of America
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, United States of America
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5
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Lapidus S, Liu F, Casanovas-Massana A, Dai Y, Huck JD, Lucas C, Klein J, Filler RB, Strine MS, Sy M, Deme AB, Badiane AS, Dieye B, Ndiaye IM, Diedhiou Y, Mbaye AM, Diagne CT, Vigan-Womas I, Mbengue A, Sadio BD, Diagne MM, Moore AJ, Mangou K, Diallo F, Sene SD, Pouye MN, Faye R, Diouf B, Nery N, Costa F, Reis MG, Muenker MC, Hodson DZ, Mbarga Y, Katz BZ, Andrews JR, Campbell M, Srivathsan A, Kamath K, Baum-Jones E, Faye O, Sall AA, Vélez JCQ, Cappello M, Wilson M, Ben-Mamoun C, Tedder R, McClure M, Cherepanov P, Somé FA, Dabiré RK, Moukoko CEE, Ouédraogo JB, Boum Y, Shon J, Ndiaye D, Wisnewski A, Parikh S, Iwasaki A, Wilen CB, Ko AI, Ring AM, Bei AK. Plasmodium infection is associated with cross-reactive antibodies to carbohydrate epitopes on the SARS-CoV-2 Spike protein. Sci Rep 2022; 12:22175. [PMID: 36550362 PMCID: PMC9778468 DOI: 10.1038/s41598-022-26709-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Sero-surveillance can monitor and project disease burden and risk. However, SARS-CoV-2 antibody test results can produce false positive results, limiting their efficacy as a sero-surveillance tool. False positive SARS-CoV-2 antibody results are associated with malaria exposure, and understanding this association is essential to interpret sero-surveillance results from malaria-endemic countries. Here, pre-pandemic samples from eight malaria endemic and non-endemic countries and four continents were tested by ELISA to measure SARS-CoV-2 Spike S1 subunit reactivity. Individuals with acute malaria infection generated substantial SARS-CoV-2 reactivity. Cross-reactivity was not associated with reactivity to other human coronaviruses or other SARS-CoV-2 proteins, as measured by peptide and protein arrays. ELISAs with deglycosylated and desialated Spike S1 subunits revealed that cross-reactive antibodies target sialic acid on N-linked glycans of the Spike protein. The functional activity of cross-reactive antibodies measured by neutralization assays showed that cross-reactive antibodies did not neutralize SARS-CoV-2 in vitro. Since routine use of glycosylated or sialated assays could result in false positive SARS-CoV-2 antibody results in malaria endemic regions, which could overestimate exposure and population-level immunity, we explored methods to increase specificity by reducing cross-reactivity. Overestimating population-level exposure to SARS-CoV-2 could lead to underestimates of risk of continued COVID-19 transmission in sub-Saharan Africa.
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Affiliation(s)
- Sarah Lapidus
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Feimei Liu
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Arnau Casanovas-Massana
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Yile Dai
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, 06510, USA
| | - John D Huck
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Carolina Lucas
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Jon Klein
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Renata B Filler
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, 06510, USA
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Madison S Strine
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, 06510, USA
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Mouhamad Sy
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
- Laboratory of Parasitology and Mycology, Aristide le Dantec Hospital, Cheikh Anta Diop University, Dakar, Senegal
| | - Awa B Deme
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
- Laboratory of Parasitology and Mycology, Aristide le Dantec Hospital, Cheikh Anta Diop University, Dakar, Senegal
| | - Aida S Badiane
- Laboratory of Parasitology and Mycology, Aristide le Dantec Hospital, Cheikh Anta Diop University, Dakar, Senegal
| | - Baba Dieye
- Laboratory of Parasitology and Mycology, Aristide le Dantec Hospital, Cheikh Anta Diop University, Dakar, Senegal
| | - Ibrahima Mbaye Ndiaye
- Laboratory of Parasitology and Mycology, Aristide le Dantec Hospital, Cheikh Anta Diop University, Dakar, Senegal
| | - Younous Diedhiou
- Laboratory of Parasitology and Mycology, Aristide le Dantec Hospital, Cheikh Anta Diop University, Dakar, Senegal
| | - Amadou Moctar Mbaye
- Laboratory of Parasitology and Mycology, Aristide le Dantec Hospital, Cheikh Anta Diop University, Dakar, Senegal
| | - Cheikh Tidiane Diagne
- DiaTROPIX Rapid Diagnostic Tests Facility, Institut Pasteur de Dakar, Dakar, Senegal
| | - Inés Vigan-Womas
- Pôle Immunophysiopathologie et Maladies Infectieuses, Institut Pasteur de Dakar, Dakar, Senegal
| | - Alassane Mbengue
- G4-Malaria Experimental Genetic Approaches and Vaccines, Pôle Immunophysiopathologie et Maladies Infectieuses, Institut Pasteur de Dakar, Dakar, Senegal
| | - Bacary D Sadio
- Pôle Virologie, Institut Pasteur de Dakar, Dakar, Senegal
| | | | - Adam J Moore
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Khadidiatou Mangou
- G4-Malaria Experimental Genetic Approaches and Vaccines, Pôle Immunophysiopathologie et Maladies Infectieuses, Institut Pasteur de Dakar, Dakar, Senegal
| | - Fatoumata Diallo
- G4-Malaria Experimental Genetic Approaches and Vaccines, Pôle Immunophysiopathologie et Maladies Infectieuses, Institut Pasteur de Dakar, Dakar, Senegal
| | - Seynabou D Sene
- G4-Malaria Experimental Genetic Approaches and Vaccines, Pôle Immunophysiopathologie et Maladies Infectieuses, Institut Pasteur de Dakar, Dakar, Senegal
| | - Mariama N Pouye
- G4-Malaria Experimental Genetic Approaches and Vaccines, Pôle Immunophysiopathologie et Maladies Infectieuses, Institut Pasteur de Dakar, Dakar, Senegal
| | - Rokhaya Faye
- Pôle Immunophysiopathologie et Maladies Infectieuses, Institut Pasteur de Dakar, Dakar, Senegal
| | - Babacar Diouf
- Pôle Immunophysiopathologie et Maladies Infectieuses, Institut Pasteur de Dakar, Dakar, Senegal
| | - Nivison Nery
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, BA, Brazil
- Department of Internal Medicine, Yale Occupational and Environmental Medicine Program, Yale School of Medicine, New Haven, CT, USA
| | - Federico Costa
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, BA, Brazil
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, BA, Brazil
| | - Mitermayer G Reis
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, BA, Brazil
- Faculty of Medicine, Federal University of Bahia, Salvador, Brazil
| | - M Catherine Muenker
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Daniel Z Hodson
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | | | - Ben Z Katz
- Division of Infectious Diseases, Department of Pediatrics, Northwestern University Feinberg School of Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, USA
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, School of Medicine, Stanford University, Stanford, CA, USA
| | - Melissa Campbell
- Yale Center for Clinical Investigation, Yale School of Medicine, New Haven, CT, USA
| | - Ariktha Srivathsan
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | | | | | - Ousmane Faye
- Pôle Virologie, Institut Pasteur de Dakar, Dakar, Senegal
| | | | - Juan Carlos Quintero Vélez
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
- Grupo de Investigación Ciencias Veterinarias Centauro, University of Antioquia, Medellín, Colombia
- Grupo de Investigación Microbiología Básica y Aplicada, University of Antioquia, Medellín, Colombia
| | - Michael Cappello
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - Michael Wilson
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Choukri Ben-Mamoun
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Richard Tedder
- Department of Infectious Disease, Imperial College London, St Mary's Campus, London, W2 1PG, UK
- South London Specialist Virology Centre, Kings College Hospital NHS Foundation Trust, London, UK
| | - Myra McClure
- Department of Infectious Disease, Imperial College London, St Mary's Campus, London, W2 1PG, UK
| | - Peter Cherepanov
- Department of Infectious Disease, Imperial College London, St Mary's Campus, London, W2 1PG, UK
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
- Crick COVID19 Consortium, Francis Crick Institute, London, NW1 1AT, UK
| | - Fabrice A Somé
- Institut de Recherche en Sciences de La Santé (IRSS)/Centre Muraz, Bobo-Dioulasso, Burkina Faso
| | - Roch K Dabiré
- Institut de Recherche en Sciences de La Santé (IRSS)/Centre Muraz, Bobo-Dioulasso, Burkina Faso
| | - Carole Else Eboumbou Moukoko
- Department of Biological Sciences, Faculty of Medicine and Pharmaceutical Sciences, University of Douala, Douala, 2701, BP, Cameroon
- Malaria Research Unit, Center Pasteur Cameroon, Yaoundé, Cameroon
| | - Jean Bosco Ouédraogo
- Institut de Recherche en Sciences de La Santé (IRSS)/Centre Muraz, Bobo-Dioulasso, Burkina Faso
| | - Yap Boum
- Médecins Sans Frontières, University of Yaoundé and Epicentre, Yaoundé, Cameroon
| | | | - Daouda Ndiaye
- Laboratory of Parasitology and Mycology, Aristide le Dantec Hospital, Cheikh Anta Diop University, Dakar, Senegal
| | - Adam Wisnewski
- Department of Internal Medicine, Yale Occupational and Environmental Medicine Program, Yale School of Medicine, New Haven, CT, USA
| | - Sunil Parikh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Akiko Iwasaki
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, 06510, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Craig B Wilen
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Albert I Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, BA, Brazil
| | - Aaron M Ring
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Amy K Bei
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA.
- Laboratory of Parasitology and Mycology, Aristide le Dantec Hospital, Cheikh Anta Diop University, Dakar, Senegal.
- G4-Malaria Experimental Genetic Approaches and Vaccines, Pôle Immunophysiopathologie et Maladies Infectieuses, Institut Pasteur de Dakar, Dakar, Senegal.
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6
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Klein J, Wood J, Jaycox J, Lu P, Dhodapkar RM, Gehlhausen JR, Tabachnikova A, Tabacof L, Malik AA, Kamath K, Greene K, Monteiro VS, Peña-Hernandez M, Mao T, Bhattacharjee B, Takahashi T, Lucas C, Silva J, Mccarthy D, Breyman E, Tosto-Mancuso J, Dai Y, Perotti E, Akduman K, Tzeng TJ, Xu L, Yildirim I, Krumholz HM, Shon J, Medzhitov R, Omer SB, van Dijk D, Ring AM, Putrino D, Iwasaki A. Distinguishing features of Long COVID identified through immune profiling. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.08.09.22278592. [PMID: 35982667 PMCID: PMC9387160 DOI: 10.1101/2022.08.09.22278592] [Citation(s) in RCA: 92] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
SARS-CoV-2 infection can result in the development of a constellation of persistent sequelae following acute disease called post-acute sequelae of COVID-19 (PASC) or Long COVID 1-3 . Individuals diagnosed with Long COVID frequently report unremitting fatigue, post-exertional malaise, and a variety of cognitive and autonomic dysfunctions 1-3 ; however, the basic biological mechanisms responsible for these debilitating symptoms are unclear. Here, 215 individuals were included in an exploratory, cross-sectional study to perform multi-dimensional immune phenotyping in conjunction with machine learning methods to identify key immunological features distinguishing Long COVID. Marked differences were noted in specific circulating myeloid and lymphocyte populations relative to matched control groups, as well as evidence of elevated humoral responses directed against SARS-CoV-2 among participants with Long COVID. Further, unexpected increases were observed in antibody responses directed against non-SARS-CoV-2 viral pathogens, particularly Epstein-Barr virus. Analysis of circulating immune mediators and various hormones also revealed pronounced differences, with levels of cortisol being uniformly lower among participants with Long COVID relative to matched control groups. Integration of immune phenotyping data into unbiased machine learning models identified significant distinguishing features critical in accurate classification of Long COVID, with decreased levels of cortisol being the most significant individual predictor. These findings will help guide additional studies into the pathobiology of Long COVID and may aid in the future development of objective biomarkers for Long COVID.
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7
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Haynes WA, Kamath K, Bozekowski J, Baum-Jones E, Campbell M, Casanovas-Massana A, Daugherty PS, Dela Cruz CS, Dhal A, Farhadian SF, Fitzgibbons L, Fournier J, Jhatro M, Jordan G, Klein J, Lucas C, Kessler D, Luchsinger LL, Martinez B, Catherine Muenker M, Pischel L, Reifert J, Sawyer JR, Waitz R, Wunder EA, Zhang M, Iwasaki A, Ko A, Shon JC. High-resolution epitope mapping and characterization of SARS-CoV-2 antibodies in large cohorts of subjects with COVID-19. Commun Biol 2021; 4:1317. [PMID: 34811480 PMCID: PMC8608966 DOI: 10.1038/s42003-021-02835-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 10/22/2021] [Indexed: 12/12/2022] Open
Abstract
As Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to spread, characterization of its antibody epitopes, emerging strains, related coronaviruses, and even the human proteome in naturally infected patients can guide the development of effective vaccines and therapies. Since traditional epitope identification tools are dependent upon pre-defined peptide sequences, they are not readily adaptable to diverse viral proteomes. The Serum Epitope Repertoire Analysis (SERA) platform leverages a high diversity random bacterial display library to identify proteome-independent epitope binding specificities which are then analyzed in the context of organisms of interest. When evaluating immune response in the context of SARS-CoV-2, we identify dominant epitope regions and motifs which demonstrate potential to classify mild from severe disease and relate to neutralization activity. We highlight SARS-CoV-2 epitopes that are cross-reactive with other coronaviruses and demonstrate decreased epitope signal for mutant SARS-CoV-2 strains. Collectively, the evolution of SARS-CoV-2 mutants towards reduced antibody response highlight the importance of data-driven development of the vaccines and therapies to treat COVID-19.
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Affiliation(s)
| | | | | | | | - Melissa Campbell
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Arnau Casanovas-Massana
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | | | - Charles S Dela Cruz
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, Yale University School of Medicine, New Haven, CT, USA
| | | | - Shelli F Farhadian
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | | | - John Fournier
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | | | | | - Jon Klein
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Carolina Lucas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | | | | | | | - M Catherine Muenker
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Lauren Pischel
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | | | | | | | - Elsio A Wunder
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | | | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Albert Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
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8
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Klein J, Brito AF, Trubin P, Lu P, Wong P, Alpert T, Peña-Hernández MA, Haynes W, Kamath K, Liu F, Vogels CBF, Fauver JR, Lucas C, Oh J, Mao T, Silva J, Wyllie AL, Muenker MC, Casanovas-Massana A, Moore AJ, Petrone ME, Kalinich CC, Dela Cruz C, Farhadian S, Ring A, Shon J, Ko AI, Grubaugh ND, Israelow B, Iwasaki A, Azar MM. Longitudinal immune profiling of a SARS-CoV-2 reinfection in a solid organ transplant recipient. J Infect Dis 2021; 225:374-384. [PMID: 34718647 DOI: 10.1093/infdis/jiab553] [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: 07/09/2021] [Accepted: 10/28/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The underlying immunologic deficiencies enabling SARS-CoV-2 reinfection are currently unknown. We describe deep longitudinal immune profiling of a transplant recipient hospitalized twice for COVID-19. METHODS A 66-year-old male renal transplant recipient was hospitalized with COVID-19 March 2020 then readmitted to the hospital with COVID-19 233 days after initial diagnosis. Virologic and immunologic investigation were performed on samples from the primary and secondary infections. RESULTS Whole viral genome sequencing and phylogenic analysis revealed that viruses causing both infections were caused by distinct genetic lineages without evidence of immune escape mutations. Longitudinal comparison of cellular and humoral responses during primary SARS-CoV-2 infection revealed that this patient responded to the primary infection with low neutralization titer anti-SARS-CoV-2 antibodies that were likely present at the time of reinfection. DISCUSSION The development of neutralizing antibodies and humoral memory responses in this patient failed to confer protection against reinfection, suggesting that they were below a neutralizing titer threshold or that additional factors may be required for efficient prevention of SARS-CoV-2 reinfection. Development of poorly neutralizing antibodies may have been due to profound and relatively specific reduction in naïve CD4 T-cell pools. Seropositivity alone may not be a perfect correlate of protection in immunocompromised patients.
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Affiliation(s)
- Jonathan Klein
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Anderson F Brito
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Paul Trubin
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Peiwen Lu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Patrick Wong
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Tara Alpert
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mario A Peña-Hernández
- Department of Biological and Biomedical Sciences, Yale University School of Medicine, New Haven, CT, USA
| | | | | | - Feimei Liu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Joseph R Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Carolina Lucas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Jieun Oh
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Tianyang Mao
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Julio Silva
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - M Catherine Muenker
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Arnau Casanovas-Massana
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Adam J Moore
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mary E Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Chaney C Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Charles Dela Cruz
- Department of Medicine, Section of Pulmonary and Critical Care Medicine; Yale University School of Medicine, New Haven, CT, USA
| | - Shelli Farhadian
- Department of Internal Medicine, Section General Medicine; Yale University School of Medicine, New Haven, CT, USA
| | - Aaron Ring
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Albert I Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.,Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.,Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Benjamin Israelow
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.,Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Marwan M Azar
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
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9
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Wisnewski AV, Redlich CA, Liu J, Kamath K, Abad QA, Smith RF, Fazen L, Santiago R, Campillo Luna J, Martinez B, Baum-Jones E, Waitz R, Haynes WA, Shon JC. Immunogenic amino acid motifs and linear epitopes of COVID-19 mRNA vaccines. PLoS One 2021; 16:e0252849. [PMID: 34499652 PMCID: PMC8428655 DOI: 10.1371/journal.pone.0252849] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/18/2021] [Indexed: 12/12/2022] Open
Abstract
Reverse vaccinology is an evolving approach for improving vaccine effectiveness and minimizing adverse responses by limiting immunizations to critical epitopes. Towards this goal, we sought to identify immunogenic amino acid motifs and linear epitopes of the SARS-CoV-2 spike protein that elicit IgG in COVID-19 mRNA vaccine recipients. Paired pre/post vaccination samples from N = 20 healthy adults, and post-vaccine samples from an additional N = 13 individuals were used to immunoprecipitate IgG targets expressed by a bacterial display random peptide library, and preferentially recognized peptides were mapped to the spike primary sequence. The data identify several distinct amino acid motifs recognized by vaccine-induced IgG, a subset of those targeted by IgG from natural infection, which may mimic 3-dimensional conformation (mimotopes). Dominant linear epitopes were identified in the C-terminal domains of the S1 and S2 subunits (aa 558-569, 627-638, and 1148-1159) which have been previously associated with SARS-CoV-2 neutralization in vitro and demonstrate identity to bat coronavirus and SARS-CoV, but limited homology to non-pathogenic human coronavirus. The identified COVID-19 mRNA vaccine epitopes should be considered in the context of variants, immune escape and vaccine and therapy design moving forward.
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Affiliation(s)
- Adam V. Wisnewski
- Department of Medicine, Yale University School of Medicine, New Haven, CT, United States of America
| | - Carrie A. Redlich
- Department of Medicine, Yale University School of Medicine, New Haven, CT, United States of America
| | - Jian Liu
- Department of Medicine, Yale University School of Medicine, New Haven, CT, United States of America
| | - Kathy Kamath
- Serimmune, Inc., Goleta, CA, United States of America
| | - Queenie-Ann Abad
- Department of Medicine, Yale University School of Medicine, New Haven, CT, United States of America
| | - Richard F. Smith
- Department of Medicine, Yale University School of Medicine, New Haven, CT, United States of America
| | - Louis Fazen
- Department of Medicine, Yale University School of Medicine, New Haven, CT, United States of America
| | - Romero Santiago
- Department of Medicine, Yale University School of Medicine, New Haven, CT, United States of America
| | - Julian Campillo Luna
- Department of Medicine, Yale University School of Medicine, New Haven, CT, United States of America
| | | | | | - Rebecca Waitz
- Serimmune, Inc., Goleta, CA, United States of America
| | | | - John C. Shon
- Serimmune, Inc., Goleta, CA, United States of America
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10
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Dorff T, Hirasawa Y, Acoba J, Pagano I, Tamura D, Pal S, Zhang M, Waitz R, Dhal A, Haynes W, Shon J, Scholz M, Furuya H, Chan OTM, Huang J, Rosser C. Phase Ib study of patients with metastatic castrate-resistant prostate cancer treated with different sequencing regimens of atezolizumab and sipuleucel-T. J Immunother Cancer 2021; 9:jitc-2021-002931. [PMID: 34376554 PMCID: PMC8356194 DOI: 10.1136/jitc-2021-002931] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2021] [Indexed: 12/15/2022] Open
Abstract
Background Combining an immune checkpoint inhibitor with a tumor vaccine may modulate the immune system to leverage complementary mechanisms of action that lead to sustained T-cell activation and a potent prolonged immunotherapeutic response in metastatic castration resistant prostate cancer (mCRPC). Methods Subjects with asymptomatic or minimally symptomatic mCRPC were randomly assigned in a 1:1 ratio to receive either atezolizumab followed by sipuleucel-T (Arm 1) or sipuleucel-T followed by atezolizumab (Arm 2). The primary endpoint was safety, while secondary endpoints included preliminary clinical activity such as objective tumor response and systemic immune responses that could identify key molecular and immunological changes associated with sequential administration of atezolizumab and sipuleucel-T. Results A total of 37 subjects were enrolled. The median age was 75.0 years, median prostate specific antigen (PSA) was 21.9 ng/mL, and subjects had a median number of three prior treatments. Most subjects (83.8%) had at least one treatment-related adverse event. There were no grade 4 or 5 toxicities attributed to either study drug. Immune-related adverse events and infusion reactions occurred in 13.5% of subjects, and all of which were grade 1 or 2. Of 23 subjects with Response Evaluation Criteria in Solid Tumors measurable disease, only one subject in Arm 2 had a partial response (PR) and four subjects overall had stable disease (SD) at 6 months reflecting an objective response rate of 4.3% and a disease control rate of 21.7%. T-cell receptor diversity was higher in subjects with a response, including SD. Immune response to three novel putative antigens (SIK3, KDM1A/LSD1, and PIK3R6) appeared to increase with treatment. Conclusions Overall, regardless of the order in which they were administered, the combination of atezolizumab with sipuleucel-T appears to be safe and well tolerated with a comparable safety profile to each agent administered as monotherapy. Correlative immune studies may suggest the combination to be beneficial; however, further studies are needed. Trial registration number NCT03024216.
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Affiliation(s)
- Tanya Dorff
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California, USA
| | - Yosuke Hirasawa
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Jared Acoba
- University of Hawaii Cancer Center, Honolulu, Hawaii, USA
| | - Ian Pagano
- University of Hawaii Cancer Center, Honolulu, Hawaii, USA
| | - David Tamura
- University of Hawaii Cancer Center, Honolulu, Hawaii, USA
| | - Sumanta Pal
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California, USA
| | | | | | | | | | | | - Mark Scholz
- Prostate Oncology Specialists, Marina del Rey, California, USA
| | - Hideki Furuya
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Owen T M Chan
- University of Hawaii Cancer Center, Honolulu, Hawaii, USA
| | - Jeffrey Huang
- University of Hawaii Cancer Center, Honolulu, Hawaii, USA
| | - Charles Rosser
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
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11
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Lapidus S, Liu F, Casanovas-Massana A, Dai Y, Huck JD, Lucas C, Klein J, Filler RB, Strine MS, Sy M, Deme AB, Badiane AS, Dieye B, Ndiaye IM, Diedhiou Y, Mbaye AM, Diagne CT, Vigan-Womas I, Mbengue A, Sadio BD, Diagne MM, Moore AJ, Mangou K, Diallo F, Sene SD, Pouye MN, Faye R, Diouf B, Nery N, Costa F, Reis M, Muenker MC, Hodson DZ, Mbarga Y, Katz BZ, Andrews JR, Campbell M, Srivathsan A, Kamath K, Baum-Jones E, Faye O, Sall AA, Quintero Vélez JC, Cappello M, Wilson M, Ben-Mamoun C, Somé FA, Dabiré RK, Moukoko CEE, Ouédraogo JB, Boum Y, Shon J, Ndiaye D, Wisnewski A, Parikh S, Iwasaki A, Wilen CB, Ko AI, Ring AM, Bei AK. Plasmodium infection induces cross-reactive antibodies to carbohydrate epitopes on the SARS-CoV-2 Spike protein. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.05.10.21256855. [PMID: 34013301 PMCID: PMC8132281 DOI: 10.1101/2021.05.10.21256855] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Individuals with acute malaria infection generated high levels of antibodies that cross-react with the SARS-CoV-2 Spike protein. Cross-reactive antibodies specifically recognized the sialic acid moiety on N-linked glycans of the Spike protein and do not neutralize in vitro SARS-CoV-2. Sero-surveillance is critical for monitoring and projecting disease burden and risk during the pandemic; however, routine use of Spike protein-based assays may overestimate SARS-CoV-2 exposure and population-level immunity in malaria-endemic countries.
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Affiliation(s)
- Sarah Lapidus
- Yale School of Public Health, Department of Epidemiology of Microbial Diseases, New Haven, CT, 06510, USA
| | - Feimei Liu
- Yale School of Medicine, Department of Immunobiology, New Haven, CT, 06510, USA
| | - Arnau Casanovas-Massana
- Yale School of Public Health, Department of Epidemiology of Microbial Diseases, New Haven, CT, 06510, USA
| | - Yile Dai
- Yale School of Medicine, Department of Immunobiology, New Haven, CT, 06510, USA
| | - John D. Huck
- Yale School of Medicine, Department of Immunobiology, New Haven, CT, 06510, USA
| | - Carolina Lucas
- Yale School of Medicine, Department of Immunobiology, New Haven, CT, 06510, USA
| | - Jon Klein
- Yale School of Medicine, Department of Immunobiology, New Haven, CT, 06510, USA
| | - Renata B. Filler
- Yale School of Medicine, Department of Immunobiology, New Haven, CT, 06510, USA,Yale School of Medicine, Department of Laboratory Medicine, New Haven, CT, 06510, USA
| | - Madison S. Strine
- Yale School of Medicine, Department of Immunobiology, New Haven, CT, 06510, USA,Yale School of Medicine, Department of Laboratory Medicine, New Haven, CT, 06510, USA
| | - Mouhamad Sy
- Cheikh Anta Diop University, Aristide le Dantec Hospital, Laboratory of Parasitology and Mycology, Dakar, Senegal
| | - Awa B. Deme
- Cheikh Anta Diop University, Aristide le Dantec Hospital, Laboratory of Parasitology and Mycology, Dakar, Senegal
| | - Aida S. Badiane
- Cheikh Anta Diop University, Aristide le Dantec Hospital, Laboratory of Parasitology and Mycology, Dakar, Senegal
| | - Baba Dieye
- Cheikh Anta Diop University, Aristide le Dantec Hospital, Laboratory of Parasitology and Mycology, Dakar, Senegal
| | - Ibrahima Mbaye Ndiaye
- Cheikh Anta Diop University, Aristide le Dantec Hospital, Laboratory of Parasitology and Mycology, Dakar, Senegal
| | - Younous Diedhiou
- Cheikh Anta Diop University, Aristide le Dantec Hospital, Laboratory of Parasitology and Mycology, Dakar, Senegal
| | - Amadou Moctar Mbaye
- Cheikh Anta Diop University, Aristide le Dantec Hospital, Laboratory of Parasitology and Mycology, Dakar, Senegal
| | - Cheikh Tidiane Diagne
- DiaTROPIX Rapid Diagnostic Tests Facility, Institut Pasteur de Dakar, Dakar, Senegal
| | - Inés Vigan-Womas
- Pôle Immunophysiopathologie et Maladies Infectieuses, Institut Pasteur de Dakar, Dakar, Senegal
| | - Alassane Mbengue
- G4 - Malaria Experimental Genetic Approaches & Vaccines, Pôle Immunophysiopathologie et Maladies Infectieuses, Institut Pasteur de Dakar, Dakar, Senegal
| | | | | | - Adam J. Moore
- Yale School of Public Health, Department of Epidemiology of Microbial Diseases, New Haven, CT, 06510, USA
| | - Khadidiatou Mangou
- G4 - Malaria Experimental Genetic Approaches & Vaccines, Pôle Immunophysiopathologie et Maladies Infectieuses, Institut Pasteur de Dakar, Dakar, Senegal
| | - Fatoumata Diallo
- G4 - Malaria Experimental Genetic Approaches & Vaccines, Pôle Immunophysiopathologie et Maladies Infectieuses, Institut Pasteur de Dakar, Dakar, Senegal
| | - Seynabou D. Sene
- G4 - Malaria Experimental Genetic Approaches & Vaccines, Pôle Immunophysiopathologie et Maladies Infectieuses, Institut Pasteur de Dakar, Dakar, Senegal
| | - Mariama N. Pouye
- G4 - Malaria Experimental Genetic Approaches & Vaccines, Pôle Immunophysiopathologie et Maladies Infectieuses, Institut Pasteur de Dakar, Dakar, Senegal
| | - Rokhaya Faye
- Pôle Immunophysiopathologie et Maladies Infectieuses, Institut Pasteur de Dakar, Dakar, Senegal
| | - Babacar Diouf
- Pôle Immunophysiopathologie et Maladies Infectieuses, Institut Pasteur de Dakar, Dakar, Senegal
| | - Nivison Nery
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, BA, Brazil,Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, BA, Brazil
| | - Federico Costa
- Yale School of Public Health, Department of Epidemiology of Microbial Diseases, New Haven, CT, 06510, USA,Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, BA, Brazil,Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, BA, Brazil
| | - Mitermayer Reis
- Yale School of Public Health, Department of Epidemiology of Microbial Diseases, New Haven, CT, 06510, USA,Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, BA, Brazil,Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, BA, Brazil
| | - M. Catherine Muenker
- Yale School of Public Health, Department of Epidemiology of Microbial Diseases, New Haven, CT, 06510, USA
| | - Daniel Z. Hodson
- Yale School of Public Health, Department of Epidemiology of Microbial Diseases, New Haven, CT, 06510, USA
| | | | - Ben Z. Katz
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Division of Infectious Diseases, Ann & Robert H. Lurie Children’s Hospital of Chicago
| | - Jason R. Andrews
- Division of Infectious Diseases and Geographic Medicine, School of Medicine, Stanford University, Stanford, CA, USA
| | - Melissa Campbell
- Yale Center for Clinical Investigation, Yale School of Medicine, New Haven, Connecticut, USA
| | - Ariktha Srivathsan
- Yale School of Public Health, Department of Epidemiology of Microbial Diseases, New Haven, CT, 06510, USA
| | | | | | - Ousmane Faye
- Pôle Virologie, Institut Pasteur de Dakar, Dakar, Senegal
| | | | - Juan Carlos Quintero Vélez
- Grupo de Investigación Ciencias Veterinarias Centauro, Universidad de Antioquia, Medellin, Colombia,Grupo de Investigación Ciencias Veterinarias Centauro, University of Antioquia, Medellín, Colombia,Grupo de Investigación Microbiología Básica y Aplicada, University of Antioquia, Medellín, Colombia
| | - Michael Cappello
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - Michael Wilson
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Choukri Ben-Mamoun
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | - Fabrice A. Somé
- Institut de Recherche en Sciences de La Santé (IRSS)/Centre Muraz, Bobo-Dioulasso, Burkina Faso
| | - Roch K. Dabiré
- Institut de Recherche en Sciences de La Santé (IRSS)/Centre Muraz, Bobo-Dioulasso, Burkina Faso
| | - Carole Else Eboumbou Moukoko
- Department of Biological Sciences, Faculty of Medicine and Pharmaceutical Sciences, University of Douala, BP 2701 Douala, Cameroon,Malaria Research Unit, Center Pasteur Cameroon, Yaoundé, Cameroon
| | - Jean Bosco Ouédraogo
- Institut de Recherche en Sciences de La Santé (IRSS)/Centre Muraz, Bobo-Dioulasso, Burkina Faso
| | - Yap Boum
- University of Yaoundé and Epicentre, Médecins Sans Frontières
| | | | - Daouda Ndiaye
- Cheikh Anta Diop University, Aristide le Dantec Hospital, Laboratory of Parasitology and Mycology, Dakar, Senegal
| | - Adam Wisnewski
- Yale Occupational and Environmental Medicine Program, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Sunil Parikh
- Yale School of Public Health, Department of Epidemiology of Microbial Diseases, New Haven, CT, 06510, USA
| | - Akiko Iwasaki
- Yale School of Medicine, Department of Immunobiology, New Haven, CT, 06510, USA
| | - Craig B. Wilen
- Yale School of Medicine, Department of Immunobiology, New Haven, CT, 06510, USA
| | - Albert I. Ko
- Yale School of Public Health, Department of Epidemiology of Microbial Diseases, New Haven, CT, 06510, USA,Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, BA, Brazil
| | - Aaron M. Ring
- Yale School of Medicine, Department of Immunobiology, New Haven, CT, 06510, USA
| | - Amy K. Bei
- Yale School of Public Health, Department of Epidemiology of Microbial Diseases, New Haven, CT, 06510, USA,Cheikh Anta Diop University, Aristide le Dantec Hospital, Laboratory of Parasitology and Mycology, Dakar, Senegal,G4 - Malaria Experimental Genetic Approaches & Vaccines, Pôle Immunophysiopathologie et Maladies Infectieuses, Institut Pasteur de Dakar, Dakar, Senegal,
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12
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Klein J, Brito A, Trubin P, Lu P, Wong P, Alpert T, Pena-Hernandez M, Haynes W, Kamath K, Liu F, Vogels C, Fauver J, Lucas C, Oh JE, Mao T, Silva J, Wyllie A, Muenker MC, Casanovas-Massana A, Moore A, Petrone M, Kalinich C, Cruz CD, Farhadian S, Ring A, Shon J, Ko A, Grubaugh N, Goldman-Israelow B, Iwasaki A, Azar M. Longitudinal immune profiling of a SARS-CoV-2 reinfection in a solid organ transplant recipient. RESEARCH SQUARE 2021:rs.3.rs-405958. [PMID: 34013255 PMCID: PMC8132249 DOI: 10.21203/rs.3.rs-405958/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The underlying immunologic deficiencies enabling SARS-CoV-2 reinfections are currently unknown. Here we describe a renal-transplant recipient who developed recurrent, symptomatic SARS-CoV-2 infection 7 months after primary infection. To elucidate the immunological mechanisms responsible for reinfection, we performed longitudinal profiling of cellular and humoral responses during both primary and recurrent SARS-CoV-2 infection. We found that the patient responded to the primary infection with transient, poor-quality adaptive immune responses that was further compromised by intervening treatment for acute rejection of the renal allograft prior to reinfection. Importantly, we identified the development of neutralizing antibodies and humoral memory responses prior to SARS-CoV-2 reinfection. However, these neutralizing antibodies failed to confer protection against reinfection, suggesting that additional factors are required for efficient prevention of SARS-CoV-2 reinfection. Further, we found no evidence supporting viral evasion of primary adaptive immune responses, suggesting that susceptibility to reinfection may be determined by host factors rather than pathogen adaptation.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Ji Eun Oh
- Korea Advanced Institute of Science and Technology
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