51
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Wang M, Chang W, Zhang L, Zhang Y. Pyroptotic cell death in SARS-CoV-2 infection: revealing its roles during the immunopathogenesis of COVID-19. Int J Biol Sci 2022; 18:5827-5848. [PMID: 36263178 PMCID: PMC9576507 DOI: 10.7150/ijbs.77561] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/10/2022] [Indexed: 01/12/2023] Open
Abstract
The rapid dissemination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), remains a global public health emergency. The host immune response to SARS-CoV-2 plays a key role in COVID-19 pathogenesis. SARS-CoV-2 can induce aberrant and excessive immune responses, leading to cytokine storm syndrome, autoimmunity, lymphopenia, neutrophilia and dysfunction of monocytes and macrophages. Pyroptosis, a proinflammatory form of programmed cell death, acts as a host defense mechanism against infections. Pyroptosis deprives the replicative niche of SARS-CoV-2 by inducing the lysis of infected cells and exposing the virus to extracellular immune attack. Notably, SARS-CoV-2 has evolved sophisticated mechanisms to hijack this cell death mode for its own survival, propagation and shedding. SARS-CoV-2-encoded viral products act to modulate various key components in the pyroptosis pathways, including inflammasomes, caspases and gasdermins. SARS-CoV-2-induced pyroptosis contriubtes to the development of COVID-19-associated immunopathologies through leakage of intracellular contents, disruption of immune system homeostasis or exacerbation of inflammation. Therefore, pyroptosis has emerged as an important mechanism involved in COVID-19 immunopathogenesis. However, the entangled links between pyroptosis and SARS-CoV-2 pathogenesis lack systematic clarification. In this review, we briefly summarize the characteristics of SARS-CoV-2 and COVID-19-related immunopathologies. Moreover, we present an overview of the interplay between SARS-CoV-2 infection and pyroptosis and highlight recent research advances in the understanding of the mechanisms responsible for the implication of the pyroptosis pathways in COVID-19 pathogenesis, which will provide informative inspirations and new directions for further investigation and clinical practice. Finally, we discuss the potential value of pyroptosis as a therapeutic target in COVID-19. An in-depth discussion of the underlying mechanisms of COVID-19 pathogenesis will be conducive to the identification of potential therapeutic targets and the exploration of effective treatment measures aimed at conquering SARS-CoV-2-induced COVID-19.
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Affiliation(s)
- Man Wang
- ✉ Corresponding author: Man Wang, Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 38 Dengzhou Road, Qingdao 266021, China. Tel.: +86-532-82991791; E-mail address:
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52
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Waltari E, Nafees S, McCutcheon KM, Wong J, Pak JE. AIRRscape: An interactive tool for exploring B-cell receptor repertoires and antibody responses. PLoS Comput Biol 2022; 18:e1010052. [PMID: 36126074 PMCID: PMC9524643 DOI: 10.1371/journal.pcbi.1010052] [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: 03/23/2022] [Revised: 09/30/2022] [Accepted: 09/04/2022] [Indexed: 11/18/2022] Open
Abstract
The sequencing of antibody repertoires of B-cells at increasing coverage and depth has led to the identification of vast numbers of immunoglobulin heavy and light chains. However, the size and complexity of these Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) datasets makes it difficult to perform exploratory analyses. To aid in data exploration, we have developed AIRRscape, an R Shiny-based interactive web browser application that enables B-cell receptor (BCR) and antibody feature discovery through comparisons among multiple repertoires. Using AIRR-seq data as input, AIRRscape starts by aggregating and sorting repertoires into interactive and explorable bins of germline V-gene, germline J-gene, and CDR3 length, providing a high-level view of the entire repertoire. Interesting subsets of repertoires can be quickly identified and selected, and then network topologies of CDR3 motifs can be generated for further exploration. Here we demonstrate AIRRscape using patient BCR repertoires and sequences of published monoclonal antibodies to investigate patterns of humoral immunity to three viral pathogens: SARS-CoV-2, HIV-1, and DENV (dengue virus). AIRRscape reveals convergent antibody sequences among datasets for all three pathogens, although HIV-1 antibody datasets display limited convergence and idiosyncratic responses. We have made AIRRscape available as a web-based Shiny application, along with code on GitHub to encourage its open development and use by immuno-informaticians, virologists, immunologists, vaccine developers, and other scientists that are interested in exploring and comparing multiple immune receptor repertoires.
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Affiliation(s)
- Eric Waltari
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- * E-mail: (EW); (JEP)
| | - Saba Nafees
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | | | - Joan Wong
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - John E. Pak
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- * E-mail: (EW); (JEP)
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53
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Mikelov AI, Alekseeva EI, Komech EA, Staroverov DB, Turchaninova MA, Shugay M, Chudakov DM, Bazykin GA, Zvyagin IV. Memory persistence and differentiation into antibody-secreting cells accompanied by positive selection in longitudinal BCR repertoires. eLife 2022; 11:79254. [PMID: 36107479 PMCID: PMC9525062 DOI: 10.7554/elife.79254] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 09/11/2022] [Indexed: 11/18/2022] Open
Abstract
The stability and plasticity of B cell-mediated immune memory ensures the ability to respond to the repeated challenges. We have analyzed the longitudinal dynamics of immunoglobulin heavy chain repertoires from memory B cells, plasmablasts, and plasma cells from the peripheral blood of generally healthy volunteers. We reveal a high degree of clonal persistence in individual memory B cell subsets, with inter-individual convergence in memory and antibody-secreting cells (ASCs). ASC clonotypes demonstrate clonal relatedness to memory B cells, and are transient in peripheral blood. We identify two clusters of expanded clonal lineages with differing prevalence of memory B cells, isotypes, and persistence. Phylogenetic analysis revealed signs of reactivation of persisting memory B cell-enriched clonal lineages, accompanied by new rounds of affinity maturation during proliferation and differentiation into ASCs. Negative selection contributes to both persisting and reactivated lineages, preserving the functionality and specificity of B cell receptors (BCRs) to protect against current and future pathogens.
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Affiliation(s)
| | | | | | | | | | | | | | - Georgii A Bazykin
- Institute of Translational Medicine, Pirogov Russian National Research Medical University
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Gruell H, Vanshylla K, Korenkov M, Tober-Lau P, Zehner M, Münn F, Janicki H, Augustin M, Schommers P, Sander LE, Kurth F, Kreer C, Klein F. SARS-CoV-2 Omicron sublineages exhibit distinct antibody escape patterns. Cell Host Microbe 2022; 30:1231-1241.e6. [PMID: 35921836 PMCID: PMC9260412 DOI: 10.1016/j.chom.2022.07.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/02/2022] [Accepted: 06/30/2022] [Indexed: 11/12/2022]
Abstract
SARS-CoV-2 neutralizing antibodies play a critical role in COVID-19 prevention and treatment but are challenged by viral evolution and the emergence of novel escape variants. Importantly, the recently identified Omicron sublineages BA.2.12.1 and BA.4/5 are rapidly becoming predominant in various countries. By determining polyclonal serum activity of 50 convalescent or vaccinated individuals against BA.1, BA.1.1, BA.2, BA.2.12.1, and BA.4/5, we reveal a further reduction in BA.4/5 susceptibility to vaccinee sera. Most notably, delineation of sensitivity to an extended 163-antibody panel demonstrates pronounced antigenic differences with distinct escape patterns among Omicron sublineages. Antigenic distance and/or higher resistance may therefore favor immune-escape-mediated BA.4/5 expansion after the first Omicron wave. Finally, while most clinical-stage monoclonal antibodies are inactive against Omicron sublineages, we identify promising antibodies with high pan-SARS-CoV-2 neutralizing potency. Our study provides a detailed understanding of Omicron-sublineage antibody escape that can inform on effective strategies against COVID-19.
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Affiliation(s)
- Henning Gruell
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Kanika Vanshylla
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Michael Korenkov
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Pinkus Tober-Lau
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
| | - Matthias Zehner
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Friederike Münn
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
| | - Hanna Janicki
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Max Augustin
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Philipp Schommers
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Leif Erik Sander
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
| | - Florian Kurth
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany; Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine and Department of Medicine I, University Medical Center Hamburg-Eppendorf, 20359 Hamburg, Germany
| | - Christoph Kreer
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; German Center for Infection Research (DZIF), Partner site Bonn-Cologne, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany.
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55
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Fraley ER, Khanal S, Pierce SH, LeMaster CA, McLennan R, Pastinen T, Bradley T. Effects of Prior Infection with SARS-CoV-2 on B Cell Receptor Repertoire Response during Vaccination. Vaccines (Basel) 2022; 10:1477. [PMID: 36146555 PMCID: PMC9506540 DOI: 10.3390/vaccines10091477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/24/2022] [Accepted: 08/29/2022] [Indexed: 11/24/2022] Open
Abstract
Understanding the B cell response to SARS-CoV-2 vaccines is a high priority. High-throughput sequencing of the B cell receptor (BCR) repertoire allows for dynamic characterization of B cell response. Here, we sequenced the BCR repertoire of individuals vaccinated by the Pfizer SARS-CoV-2 mRNA vaccine. We compared BCR repertoires of individuals with previous COVID-19 infection (seropositive) to individuals without previous infection (seronegative). We discovered that vaccine-induced expanded IgG clonotypes had shorter heavy-chain complementarity determining region 3 (HCDR3), and for seropositive individuals, these expanded clonotypes had higher somatic hypermutation (SHM) than seronegative individuals. We uncovered shared clonotypes present in multiple individuals, including 28 clonotypes present across all individuals. These 28 shared clonotypes had higher SHM and shorter HCDR3 lengths compared to the rest of the BCR repertoire. Shared clonotypes were present across both serotypes, indicating convergent evolution due to SARS-CoV-2 vaccination independent of prior viral exposure.
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Affiliation(s)
- Elizabeth R. Fraley
- Genomic Medicine Center, Children’s Mercy Research Institute, Children’s Mercy Kansas City, Kansas City, MO 64108, USA
| | - Santosh Khanal
- Genomic Medicine Center, Children’s Mercy Research Institute, Children’s Mercy Kansas City, Kansas City, MO 64108, USA
| | - Stephen H. Pierce
- Genomic Medicine Center, Children’s Mercy Research Institute, Children’s Mercy Kansas City, Kansas City, MO 64108, USA
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Cas A. LeMaster
- Genomic Medicine Center, Children’s Mercy Research Institute, Children’s Mercy Kansas City, Kansas City, MO 64108, USA
| | - Rebecca McLennan
- Genomic Medicine Center, Children’s Mercy Research Institute, Children’s Mercy Kansas City, Kansas City, MO 64108, USA
| | - Tomi Pastinen
- Genomic Medicine Center, Children’s Mercy Research Institute, Children’s Mercy Kansas City, Kansas City, MO 64108, USA
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
| | - Todd Bradley
- Genomic Medicine Center, Children’s Mercy Research Institute, Children’s Mercy Kansas City, Kansas City, MO 64108, USA
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
- Department of Pediatrics, University of Kansas Medical Center, Kansas City, KS 66160, USA
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56
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de Souza MO, Madan B, Teng IT, Huang A, Liu L, Fahad AS, Lopez Acevedo SN, Pan X, Sastry M, Gutierrez-Gonzalez M, Yin MT, Zhou T, Ho DD, Kwong PD, DeKosky BJ. Mapping monoclonal anti-SARS-CoV-2 antibody repertoires against diverse coronavirus antigens. Front Immunol 2022; 13:977064. [PMID: 36119018 PMCID: PMC9478573 DOI: 10.3389/fimmu.2022.977064] [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: 06/24/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have emerged continuously, challenging the effectiveness of vaccines, diagnostics, and treatments. Moreover, the possibility of the appearance of a new betacoronavirus with high transmissibility and high fatality is reason for concern. In this study, we used a natively paired yeast display technology, combined with next-generation sequencing (NGS) and massive bioinformatic analysis to perform a comprehensive study of subdomain specificity of natural human antibodies from two convalescent donors. Using this screening technology, we mapped the cross-reactive responses of antibodies generated by the two donors against SARS-CoV-2 variants and other betacoronaviruses. We tested the neutralization potency of a set of the cross-reactive antibodies generated in this study and observed that most of the antibodies produced by these patients were non-neutralizing. We performed a comparison of the specific and non-specific antibodies by somatic hypermutation in a repertoire-scale for the two individuals and observed that the degree of somatic hypermutation was unique for each patient. The data from this study provide functional insights into cross-reactive antibodies that can assist in the development of strategies against emerging SARS-CoV-2 variants and divergent betacoronaviruses.
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Affiliation(s)
- Matheus Oliveira de Souza
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States
| | - Bharat Madan
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | - Aric Huang
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
| | - Lihong Liu
- Aaron Diamond acquired immunodeficiency syndrome (AIDS) Research Center, Columbia University Irving Medical Center, New York, NY, United States
| | - Ahmed S. Fahad
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
| | - Sheila N. Lopez Acevedo
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
| | - Xiaoli Pan
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
| | - Mallika Sastry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | - Matias Gutierrez-Gonzalez
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States
| | - Michael T. Yin
- Department of Medicine , Division of Infectious Diseases, Columbia University Irving Medical Center, New York, NY, United States
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | - David D. Ho
- Aaron Diamond acquired immunodeficiency syndrome (AIDS) Research Center, Columbia University Irving Medical Center, New York, NY, United States
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States
| | - Brandon J. DeKosky
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States
- Department of Chemical Engineering, The University of Kansas, Lawrence, KS, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
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57
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Novel skewed usage of B-cell receptors in COVID-19 patients with various clinical presentations. Immunol Lett 2022; 249:23-32. [PMID: 36055412 PMCID: PMC9428335 DOI: 10.1016/j.imlet.2022.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 08/07/2022] [Accepted: 08/30/2022] [Indexed: 01/13/2023]
Abstract
B cell-mediated immune responses play important roles in controlling SARS-CoV infection. Here, we performed the single-cell B cell receptor sequencing (scBCR-seq) of the PBMC samples from eleven healthy controls, five asymptomatic subjects and 33 symptomatic COVID-19 patients with various clinical presentations, and subsequently analyzed the abundance and diversity of the BCR repertoires in different groups, respectively. We revealed the skewed usage of the IGHV, IGLV and IGKV genes and identified a number of heavy or light chain VDJ gene pairs and combinational preference in each group, such as IGKV3-7 and IGKV2-24 enriched in the asymptomatic subjects, whereas IGHV3-13, IGHV3-23-IGHJ4, IGHV1-18-IGLV3-19, IGHV1-18-IGLV3-21, and IGHV1-18-IGLV3-25 enriched in the recovery patients with severe diseases. We also observed the differential expression of IGHV3-23 in various B cell clusters by analysis of the scRNA-seq data. Additional dock analysis indicated that IGHV3-13 could bind to the spike protein of SARS-CoV-2. These findings may advance our understanding of the humoral immune responses in COVID-19 patients and help develop novel vaccine candidates as well as therapeutical antibodies against SASR-CoV-2 infections.
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58
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Dysregulated naïve B cells and de novo autoreactivity in severe COVID-19. Nature 2022; 611:139-147. [PMID: 36044993 PMCID: PMC9630115 DOI: 10.1038/s41586-022-05273-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 08/24/2022] [Indexed: 12/15/2022]
Abstract
Severe SARS-CoV-2 infection1 has been associated with highly inflammatory immune activation since the earliest days of the COVID-19 pandemic2–5. More recently, these responses have been associated with the emergence of self-reactive antibodies with pathologic potential6–10, although their origins and resolution have remained unclear11. Previously, we and others have identified extrafollicular B cell activation, a pathway associated with the formation of new autoreactive antibodies in chronic autoimmunity12,13, as a dominant feature of severe and critical COVID-19 (refs. 14–18). Here, using single-cell B cell repertoire analysis of patients with mild and severe disease, we identify the expansion of a naive-derived, low-mutation IgG1 population of antibody-secreting cells (ASCs) reflecting features of low selective pressure. These features correlate with progressive, broad, clinically relevant autoreactivity, particularly directed against nuclear antigens and carbamylated proteins, emerging 10–15 days after the onset of symptoms. Detailed analysis of the low-selection compartment shows a high frequency of clonotypes specific for both SARS-CoV-2 and autoantigens, including pathogenic autoantibodies against the glomerular basement membrane. We further identify the contraction of this pathway on recovery, re-establishment of tolerance standards and concomitant loss of acute-derived ASCs irrespective of antigen specificity. However, serological autoreactivity persists in a subset of patients with postacute sequelae, raising important questions as to the contribution of emerging autoreactivity to continuing symptomology on recovery. In summary, this study demonstrates the origins, breadth and resolution of autoreactivity in severe COVID-19, with implications for early intervention and the treatment of patients with post-COVID sequelae. Single-cell B cell repertoire analysis identifies the expansion of a naive-derived population of antibody-secreting cells contributing to de novo autoreactivity in patients with severe COVID-19 and those with post-COVID symptoms.
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A key F27I substitution within HCDR1 facilitates the rapid maturation of P2C-1F11-like neutralizing antibodies in a SARS-CoV-2-infected donor. Cell Rep 2022; 40:111335. [PMID: 36057256 PMCID: PMC9395280 DOI: 10.1016/j.celrep.2022.111335] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/20/2022] [Accepted: 08/18/2022] [Indexed: 11/23/2022] Open
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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: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [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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61
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Lee H, Yoo DK, Han J, Kim KH, Noh J, Lee Y, Lee E, Kwon S, Chung J. Optimization of peripheral blood volume for in silico reconstitution of the human B cell receptor repertoire. FEBS Open Bio 2022; 12:1634-1643. [PMID: 35866358 PMCID: PMC9433817 DOI: 10.1002/2211-5463.13467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/08/2022] [Accepted: 07/20/2022] [Indexed: 11/30/2022] Open
Abstract
B cells recognize antigens via membrane‐expressed B‐cell receptors (BCR) and antibodies. Similar human BCR sequences are frequently found at a significantly higher frequency than that theoretically calculated. Patients infected with SARS‐CoV2 and HIV or with autoimmune diseases share very similar BCRs. Therefore, in silico reconstitution of BCR repertoires and identification of stereotypical BCR sequences related to human pathology have diagnostic potential. Furthermore, monitoring changes of clinically significant BCR sequences and isotype conversion has prognostic potential. For BCR repertoire analysis, peripheral blood (PB) is the most convenient source. However, the optimal human PB volume for in silico reconstitution of the BCR repertoire has not been studied in detail. Here, we sampled 5, 10, and 20 mL PB from the left arm and 40 mL PB from the right arm of two volunteers, reconstituted in silico PB BCR repertoires, and compared their composition. In both volunteers, PB sampling over 20 mL resulted in slight increases in functional unique sequences (FUSs) or almost no increase in repertoire diversity. All FUSs with a frequency above 0.08% or 0.03% in the 40 mL PB BCR repertoire were detected even in the 5 mL PB BCR repertoire from each volunteer. FUSs with a higher frequency were more likely to be found in BCR repertoires from reduced PB volume, and those coexisting in two repertoires showed a statistically significant correlation in frequency irrespective of sampled anatomical site. The correlation was more significant in higher‐frequency FUSs. These observations support the potential of BCR repertoire analysis for diagnosis.
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Affiliation(s)
- Hyunho Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Korea
| | - Duck Kyun Yoo
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 03080, Korea.,Department of Biomedical Science, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Jerome Han
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 03080, Korea.,Department of Biomedical Science, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Ki Hyun Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 03080, Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Jinsung Noh
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Korea
| | - Yonghee Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Korea
| | - Eunjae Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 03080, Korea.,Department of Biomedical Science, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Korea.,Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Korea.,BK21+ Creative Research Engineer Development for IT, Seoul National University, Seoul, 08826, Korea.,Bio-MAX Institute, Seoul National University, Seoul, 08826, Korea
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 03080, Korea.,Department of Biomedical Science, Seoul National University College of Medicine, Seoul, 03080, Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080, Korea
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62
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Lee T, Kim Y, Kim HJ, Ha NY, Lee S, Chin B, Cho NH. Acute Surge of Atypical Memory and Plasma B-Cell Subsets Driven by an Extrafollicular Response in Severe COVID-19. Front Cell Infect Microbiol 2022; 12:909218. [PMID: 35899045 PMCID: PMC9309264 DOI: 10.3389/fcimb.2022.909218] [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: 03/31/2022] [Accepted: 06/13/2022] [Indexed: 11/20/2022] Open
Abstract
Background Despite the use of vaccines and therapeutics against the coronavirus disease 2019 (COVID-19) pandemic, this severe disease has been a critical burden on public health, whereas the pathogenic mechanism remains elusive. Recently, accumulating evidence underscores the potential role of the aberrant B-cell response and humoral immunity in disease progression, especially in high-risk groups. Methods Using single-cell RNA (scRNA) sequencing analysis, we investigated transcriptional features of B-cell population in peripheral blood from COVID-19 patients and compared them, according to clinical severity and disease course, against a public B-cell dataset. Results We confirmed that acute B cells differentiate into plasma cells, particularly in severe patients, potentially through enhanced extrafollicular (EF) differentiation. In severe groups, the elevated plasma B-cell response displayed increased B-cell receptor (BCR) diversity, as well as higher levels of anti–severe acute respiratory syndrome coronavirus 2 (anti–SARS-CoV-2) spike antibodies in plasma, than those in moderate cases, suggesting more robust and heterogeneous plasma cell response in severe COVID-19 patients. Trajectory analysis identified a differentiation pathway for the EF B-cell response from active naïve to atypical memory B cells (AM2), in addition to the emergence of an aberrant plasma cell subset (PC2), which was associated with COVID-19 progression and severity. The AM2 and PC2 subsets surged in the acute phase of the severe disease and presented multiple inflammatory features, including higher cytokine expression and humoral effector function, respectively. These features differ from other B-cell subsets, suggesting a pathogenic potential for disease progression. Conclusion The acute surge of AM2 and PC2 subsets with lower somatic hypermutation and higher inflammatory features may be driven by the EF B-cell response during the acute phase of severe COVID-19 and may represent one of the critical drivers in disease severity.
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Affiliation(s)
- Taeseob Lee
- Department of Digital Health, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, South Korea
- Discovery department, Biomarker Laboratory, Geninus Inc., Seoul, South Korea
| | - Yuri Kim
- Institute of Endemic Diseases, Medical Research Center, Seoul National University, Seoul, South Korea
| | - Hyun Je Kim
- College of Medicine, Genome Medicine Institute, Seoul National University, Seoul, South Korea
| | - Na-Young Ha
- Institute of Endemic Diseases, Medical Research Center, Seoul National University, Seoul, South Korea
- School of Medicine, Biomedical Research Institute, Chungnam National University, Daejeon, South Korea
| | - Siyoung Lee
- Discovery department, Biomarker Laboratory, Geninus Inc., Seoul, South Korea
| | - BumSik Chin
- Department of Internal Medicine, National Medical Center, Seoul, South Korea
- *Correspondence: Nam-Hyuk Cho, ; BumSik Chin,
| | - Nam-Hyuk Cho
- Institute of Endemic Diseases, Medical Research Center, Seoul National University, Seoul, South Korea
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul, South Korea
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, South Korea
- Bundang Hospital, Seoul National University, Seongnam, South Korea
- Wide River Institute of Immunology, Seoul National University, Hongcheon, South Korea
- *Correspondence: Nam-Hyuk Cho, ; BumSik Chin,
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63
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Planchais C, Fernández I, Bruel T, de Melo GD, Prot M, Beretta M, Guardado-Calvo P, Dufloo J, Molinos-Albert LM, Backovic M, Chiaravalli J, Giraud E, Vesin B, Conquet L, Grzelak L, Planas D, Staropoli I, Guivel-Benhassine F, Hieu T, Boullé M, Cervantes-Gonzalez M, Ungeheuer MN, Charneau P, van der Werf S, Agou F, Dimitrov JD, Simon-Lorière E, Bourhy H, Montagutelli X, Rey FA, Schwartz O, Mouquet H. Potent human broadly SARS-CoV-2-neutralizing IgA and IgG antibodies effective against Omicron BA.1 and BA.2. J Exp Med 2022; 219:e20220638. [PMID: 35704748 PMCID: PMC9206116 DOI: 10.1084/jem.20220638] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 12/11/2022] Open
Abstract
Memory B-cell and antibody responses to the SARS-CoV-2 spike protein contribute to long-term immune protection against severe COVID-19, which can also be prevented by antibody-based interventions. Here, wide SARS-CoV-2 immunoprofiling in Wuhan COVID-19 convalescents combining serological, cellular, and monoclonal antibody explorations revealed humoral immunity coordination. Detailed characterization of a hundred SARS-CoV-2 spike memory B-cell monoclonal antibodies uncovered diversity in their repertoire and antiviral functions. The latter were influenced by the targeted spike region with strong Fc-dependent effectors to the S2 subunit and potent neutralizers to the receptor-binding domain. Amongst those, Cv2.1169 and Cv2.3194 antibodies cross-neutralized SARS-CoV-2 variants of concern, including Omicron BA.1 and BA.2. Cv2.1169, isolated from a mucosa-derived IgA memory B cell demonstrated potency boost as IgA dimers and therapeutic efficacy as IgG antibodies in animal models. Structural data provided mechanistic clues to Cv2.1169 potency and breadth. Thus, potent broadly neutralizing IgA antibodies elicited in mucosal tissues can stem SARS-CoV-2 infection, and Cv2.1169 and Cv2.3194 are prime candidates for COVID-19 prevention and treatment.
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Affiliation(s)
- Cyril Planchais
- Institut Pasteur, Université Paris Cité, Laboratory of Humoral Immunology, Paris, France
- INSERM U1222, Paris, France
| | - Ignacio Fernández
- Institut Pasteur, Université Paris Cité, Structural Virology Unit, Paris, France
- CNRS UMR3569, Paris, France
| | - Timothée Bruel
- CNRS UMR3569, Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, Paris, France
| | - Guilherme Dias de Melo
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, Paris, France
| | - Matthieu Prot
- Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, Paris, France
| | - Maxime Beretta
- Institut Pasteur, Université Paris Cité, Laboratory of Humoral Immunology, Paris, France
- INSERM U1222, Paris, France
| | - Pablo Guardado-Calvo
- Institut Pasteur, Université Paris Cité, Structural Virology Unit, Paris, France
- CNRS UMR3569, Paris, France
| | - Jérémy Dufloo
- CNRS UMR3569, Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, Paris, France
| | - Luis M. Molinos-Albert
- Institut Pasteur, Université Paris Cité, Laboratory of Humoral Immunology, Paris, France
- INSERM U1222, Paris, France
| | - Marija Backovic
- Institut Pasteur, Université Paris Cité, Structural Virology Unit, Paris, France
- CNRS UMR3569, Paris, France
| | - Jeanne Chiaravalli
- Institut Pasteur, Université Paris Cité, Chemogenomic and Biological Screening Core Facility, C2RT, Paris, France
| | - Emilie Giraud
- Institut Pasteur, Université Paris Cité, Chemogenomic and Biological Screening Core Facility, C2RT, Paris, France
| | - Benjamin Vesin
- Pasteur-TheraVectys, Paris, France
- Institut Pasteur, Université Paris Cité, Molecular Virology & Vaccinology Unit, Paris, France
| | - Laurine Conquet
- Institut Pasteur, Université Paris Cité, Mouse Genetics Laboratory, Paris, France
| | - Ludivine Grzelak
- CNRS UMR3569, Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, Paris, France
| | - Delphine Planas
- CNRS UMR3569, Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, Paris, France
| | - Isabelle Staropoli
- CNRS UMR3569, Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, Paris, France
| | - Florence Guivel-Benhassine
- CNRS UMR3569, Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, Paris, France
| | - Thierry Hieu
- Institut Pasteur, Université Paris Cité, Functional Genetics of Infectious Diseases Unit, Paris, France
| | - Mikaël Boullé
- Institut Pasteur, Université Paris Cité, Chemogenomic and Biological Screening Core Facility, C2RT, Paris, France
| | - Minerva Cervantes-Gonzalez
- Department of Epidemiology, Biostatistics and Clinical Research, Assistance Publique-Hôpitaux de Paris, Bichat Claude Bernard University Hospital, INSERM CIC-EC 1425, Paris, France
| | - Marie-Noëlle Ungeheuer
- Institut Pasteur, Université Paris Cité, Investigation Clinique et Accès aux Ressources Biologiques, Center for Translational Research, Paris, France
| | - Pierre Charneau
- Pasteur-TheraVectys, Paris, France
- Institut Pasteur, Université Paris Cité, Molecular Virology & Vaccinology Unit, Paris, France
| | - Sylvie van der Werf
- CNRS UMR3569, Paris, France
- Institut Pasteur, Université Paris Cité, Molecular Genetics of RNA Viruses, Paris, France
- Université de Paris, Paris, France
| | - Fabrice Agou
- Institut Pasteur, Université Paris Cité, Chemogenomic and Biological Screening Core Facility, C2RT, Paris, France
| | - Jordan D. Dimitrov
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Paris, France
| | - Etienne Simon-Lorière
- Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, Paris, France
| | - Hervé Bourhy
- Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, Paris, France
| | - Xavier Montagutelli
- Institut Pasteur, Université Paris Cité, Mouse Genetics Laboratory, Paris, France
| | - Félix A. Rey
- Institut Pasteur, Université Paris Cité, Structural Virology Unit, Paris, France
- CNRS UMR3569, Paris, France
| | - Olivier Schwartz
- CNRS UMR3569, Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, Paris, France
| | - Hugo Mouquet
- Institut Pasteur, Université Paris Cité, Laboratory of Humoral Immunology, Paris, France
- INSERM U1222, Paris, France
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Leem J, Mitchell LS, Farmery JH, Barton J, Galson JD. Deciphering the language of antibodies using self-supervised learning. PATTERNS 2022; 3:100513. [PMID: 35845836 PMCID: PMC9278498 DOI: 10.1016/j.patter.2022.100513] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/01/2022] [Accepted: 04/26/2022] [Indexed: 11/17/2022]
Abstract
An individual’s B cell receptor (BCR) repertoire encodes information about past immune responses and potential for future disease protection. Deciphering the information stored in BCR sequence datasets will transform our understanding of disease and enable discovery of novel diagnostics and antibody therapeutics. A key challenge of BCR sequence analysis is the prediction of BCR properties from their amino acid sequence alone. Here, we present an antibody-specific language model, Antibody-specific Bidirectional Encoder Representation from Transformers (AntiBERTa), which provides a contextualized representation of BCR sequences. Following pre-training, we show that AntiBERTa embeddings capture biologically relevant information, generalizable to a range of applications. As a case study, we fine-tune AntiBERTa to predict paratope positions from an antibody sequence, outperforming public tools across multiple metrics. To our knowledge, AntiBERTa is the deepest protein-family-specific language model, providing a rich representation of BCRs. AntiBERTa embeddings are primed for multiple downstream tasks and can improve our understanding of the language of antibodies. AntiBERTa is an antibody-specific transformer model for representation learning AntiBERTa embeddings capture aspects of antibody function Attention maps of AntiBERTa correspond to structural contacts and binding sites AntiBERTa can be fine-tuned for state-of-the-art paratope prediction
Understanding antibody function is critical for deciphering the biology of disease and for the discovery of novel therapeutic antibodies. The challenge is the vast diversity of antibody variants compared with the limited labeled data available. We overcome this challenge by using self-supervised learning to train a large antibody-specific language model, followed by transfer learning, to fine-tune the model for predicting information related to antibody function. We initially demonstrate the success of the model by providing leading results in antibody binding site prediction. The model is amenable to further fine-tuning for diverse applications to improve our understanding of antibody function.
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Affiliation(s)
- Jinwoo Leem
- Alchemab Therapeutics, Ltd., East Side, Office 1.02, Kings Cross, London N1C 4AX, UK
- Corresponding author
| | - Laura S. Mitchell
- Alchemab Therapeutics, Ltd., East Side, Office 1.02, Kings Cross, London N1C 4AX, UK
| | - James H.R. Farmery
- Alchemab Therapeutics, Ltd., East Side, Office 1.02, Kings Cross, London N1C 4AX, UK
| | - Justin Barton
- Alchemab Therapeutics, Ltd., East Side, Office 1.02, Kings Cross, London N1C 4AX, UK
| | - Jacob D. Galson
- Alchemab Therapeutics, Ltd., East Side, Office 1.02, Kings Cross, London N1C 4AX, UK
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65
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Clonal structure, stability and dynamics of human memory B cells and circulating plasmablasts. Nat Immunol 2022; 23:1076-1085. [PMID: 35761085 PMCID: PMC9276532 DOI: 10.1038/s41590-022-01230-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/26/2022] [Indexed: 12/22/2022]
Abstract
Memory B cells persist for a lifetime and rapidly differentiate into antibody-producing plasmablasts and plasma cells upon antigen re-encounter. The clonal relationship and evolution of memory B cells and circulating plasmablasts is not well understood. Using single-cell sequencing combined with isolation of specific antibodies, we found that in two healthy donors, the memory B cell repertoire was dominated by large IgM, IgA and IgG2 clonal families, whereas IgG1 families, including those specific for recall antigens, were of small size. Analysis of multiyear samples demonstrated stability of memory B cell clonal families and revealed that a large fraction of recently generated plasmablasts was derived from long-term memory B cell families and was found recurrently. Collectively, this study provides a systematic description of the structure, stability and dynamics of the human memory B cell pool and suggests that memory B cells may be active at any time point in the generation of plasmablasts.
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66
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Chen Y, Ye Z, Zhang Y, Xie W, Chen Q, Lan C, Yang X, Zeng H, Zhu Y, Ma C, Tang H, Wang Q, Guan J, Chen S, Li F, Yang W, Yan H, Yu X, Zhang Z. A Deep Learning Model for Accurate Diagnosis of Infection Using Antibody Repertoires. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:2675-2685. [PMID: 35606050 DOI: 10.4049/jimmunol.2200063] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/11/2022] [Indexed: 06/15/2023]
Abstract
The adaptive immune receptor repertoire consists of the entire set of an individual's BCRs and TCRs and is believed to contain a record of prior immune responses and the potential for future immunity. Analyses of TCR repertoires via deep learning (DL) methods have successfully diagnosed cancers and infectious diseases, including coronavirus disease 2019. However, few studies have used DL to analyze BCR repertoires. In this study, we collected IgG H chain Ab repertoires from 276 healthy control subjects and 326 patients with various infections. We then extracted a comprehensive feature set consisting of 10 subsets of repertoire-level features and 160 sequence-level features and tested whether these features can distinguish between infected individuals and healthy control subjects. Finally, we developed an ensemble DL model, namely, DL method for infection diagnosis (https://github.com/chenyuan0510/DeepID), and used this model to differentiate between the infected and healthy individuals. Four subsets of repertoire-level features and four sequence-level features were selected because of their excellent predictive performance. The DL method for infection diagnosis outperformed traditional machine learning methods in distinguishing between healthy and infected samples (area under the curve = 0.9883) and achieved a multiclassification accuracy of 0.9104. We also observed differences between the healthy and infected groups in V genes usage, clonal expansion, the complexity of reads within clone, the physical properties in the α region, and the local flexibility of the CDR3 amino acid sequence. Our results suggest that the Ab repertoire is a promising biomarker for the diagnosis of various infections.
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Affiliation(s)
- Yuan Chen
- Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Zhiming Ye
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Division of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yanfang Zhang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Wenxi Xie
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Qingyun Chen
- Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Chunhong Lan
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xiujia Yang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Huikun Zeng
- Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yan Zhu
- Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Cuiyu Ma
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Haipei Tang
- Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Qilong Wang
- Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Junjie Guan
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Sen Chen
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Fenxiang Li
- Department of Infectious Disease Control and Prevention, Center for Disease Control and Prevention of Southern Theatre Command, Guangzhou, China
| | - Wei Yang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Huacheng Yan
- Department of Infectious Disease Control and Prevention, Center for Disease Control and Prevention of Southern Theatre Command, Guangzhou, China
| | - Xueqing Yu
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China;
- Division of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Zhenhai Zhang
- Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China;
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- State Key Laboratory of Organ Failure Research, Division of Nephrology, Southern Medical University, Guangzhou, China; and
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou, China
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67
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Wang Y, Abolhassani H, Hammarström L, Pan-Hammarström Q. SARS-CoV-2 infection in patients with inborn errors of immunity due to DNA repair defects. Acta Biochim Biophys Sin (Shanghai) 2022; 54:836-846. [PMID: 35713311 PMCID: PMC9827799 DOI: 10.3724/abbs.2022071] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Clinical information on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in patients with inborn errors of immunity (IEI) during the current Coronavirus disease 2019 (COVID-19) pandemic is still limited. Proper DNA repair machinery is required for the development of the adaptive immune system, which provides specific and long-term protection against SARS-CoV-2. This review highlights the impact of SARS-CoV-2 infections on IEI patients with DNA repair disorders and summarizes susceptibility risk factors, pathogenic mechanisms, clinical manifestations and management strategies of COVID-19 in this special patient population.
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68
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Li Q, Wang Y, Sun Q, Knopf J, Herrmann M, Lin L, Jiang J, Shao C, Li P, He X, Hua F, Niu Z, Ma C, Zhu Y, Ippolito G, Piacentini M, Estaquier J, Melino S, Weiss FD, Andreano E, Latz E, Schultze JL, Rappuoli R, Mantovani A, Mak TW, Melino G, Shi Y. Immune response in COVID-19: what is next? Cell Death Differ 2022; 29:1107-1122. [PMID: 35581387 PMCID: PMC9110941 DOI: 10.1038/s41418-022-01015-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 04/16/2022] [Accepted: 04/26/2022] [Indexed: 12/18/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) has been a global pandemic for more than 2 years and it still impacts our daily lifestyle and quality in unprecedented ways. A better understanding of immunity and its regulation in response to SARS-CoV-2 infection is urgently needed. Based on the current literature, we review here the various virus mutations and the evolving disease manifestations along with the alterations of immune responses with specific focuses on the innate immune response, neutrophil extracellular traps, humoral immunity, and cellular immunity. Different types of vaccines were compared and analyzed based on their unique properties to elicit specific immunity. Various therapeutic strategies such as antibody, anti-viral medications and inflammation control were discussed. We predict that with the available and continuously emerging new technologies, more powerful vaccines and administration schedules, more effective medications and better public health measures, the COVID-19 pandemic will be under control in the near future. ![]()
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Affiliation(s)
- Qing Li
- The Third Affiliated Hospital of Soochow University/The First People's Hospital of Changzhou, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine of Soochow University, Medical College, Suzhou, China
| | - Ying Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences/Shanghai Jiao Tong University School of Medicine, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qiang Sun
- Beijing Institute of Biotechnology, Research Unit of Cell Death Mechanism, Chinese Academy of Medical Sciences, 2021RU008, 20 Dongda Street, 100071, Beijing, China
| | - Jasmin Knopf
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany.,Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Martin Herrmann
- Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany.,Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Liangyu Lin
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences/Shanghai Jiao Tong University School of Medicine, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jingting Jiang
- The Third Affiliated Hospital of Soochow University/The First People's Hospital of Changzhou, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine of Soochow University, Medical College, Suzhou, China
| | - Changshun Shao
- The Third Affiliated Hospital of Soochow University/The First People's Hospital of Changzhou, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine of Soochow University, Medical College, Suzhou, China
| | - Peishan Li
- The Third Affiliated Hospital of Soochow University/The First People's Hospital of Changzhou, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine of Soochow University, Medical College, Suzhou, China
| | - Xiaozhou He
- The Third Affiliated Hospital of Soochow University/The First People's Hospital of Changzhou, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine of Soochow University, Medical College, Suzhou, China
| | - Fei Hua
- The Third Affiliated Hospital of Soochow University/The First People's Hospital of Changzhou, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine of Soochow University, Medical College, Suzhou, China
| | - Zubiao Niu
- Beijing Institute of Biotechnology, Research Unit of Cell Death Mechanism, Chinese Academy of Medical Sciences, 2021RU008, 20 Dongda Street, 100071, Beijing, China
| | - Chaobing Ma
- Beijing Institute of Biotechnology, Research Unit of Cell Death Mechanism, Chinese Academy of Medical Sciences, 2021RU008, 20 Dongda Street, 100071, Beijing, China
| | - Yichao Zhu
- Beijing Institute of Biotechnology, Research Unit of Cell Death Mechanism, Chinese Academy of Medical Sciences, 2021RU008, 20 Dongda Street, 100071, Beijing, China
| | | | - Mauro Piacentini
- Department of Biology, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Jerome Estaquier
- INSERM-U1124, Université Paris, Paris, France.,CHU de Québec - Université Laval Research Center, Québec City, QC, Canada
| | - Sonia Melino
- Department of Biology, TOR, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Felix Daniel Weiss
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, 53127, Bonn, Germany
| | - Emanuele Andreano
- Research and Development Center, GlaxoSmithKline (GSK), Siena, Italy
| | - Eicke Latz
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, 53127, Bonn, Germany.,Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - Joachim L Schultze
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.,Genomics & Immunoregulation, LIMES-Institute, University of Bonn, Bonn, Germany
| | - Rino Rappuoli
- Research and Development Center, GlaxoSmithKline (GSK), Siena, Italy
| | - Alberto Mantovani
- Department of Biomedical Sciences, Humanitas University, via Rita Levi Montalcini 4, Pieve Emanuele, 20072, Milan, Italy.,IRCCS Humanitas Clinical Research Hospital, via Manzoni 56, Rozzano, 20089, Milan, Italy.,William Harvey Research Institute, Queen Mary University, London, UK
| | - Tak Wah Mak
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Toronto, ON, M5G 2M9, Canada.,Department of Pathology, University of Hong Kong, Hong Kong, Pok Fu Lam, 999077, Hong Kong
| | - Gerry Melino
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany. .,Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy.
| | - Yufang Shi
- The Third Affiliated Hospital of Soochow University/The First People's Hospital of Changzhou, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine of Soochow University, Medical College, Suzhou, China. .,CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences/Shanghai Jiao Tong University School of Medicine, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China. .,Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133, Rome, Italy.
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69
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Paschold L, Klee B, Gottschick C, Willscher E, Diexer S, Schultheiß C, Simnica D, Sedding D, Girndt M, Gekle M, Mikolajczyk R, Binder M. Rapid Hypermutation B Cell Trajectory Recruits Previously Primed B Cells Upon Third SARS-Cov-2 mRNA Vaccination. Front Immunol 2022; 13:876306. [PMID: 35615365 PMCID: PMC9126551 DOI: 10.3389/fimmu.2022.876306] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/14/2022] [Indexed: 12/14/2022] Open
Abstract
The COVID-19 pandemic shows that vaccination strategies building on an ancestral viral strain need to be optimized for the control of potentially emerging viral variants. Therefore, aiming at strong B cell somatic hypermutation to increase antibody affinity to the ancestral strain - not only at high antibody titers - is a priority when utilizing vaccines that are not targeted at individual variants since high affinity may offer some flexibility to compensate for strain-individual mutations. Here, we developed a next-generation sequencing based SARS-CoV-2 B cell tracking protocol to rapidly determine the level of immunoglobulin somatic hypermutation at distinct points during the immunization period. The percentage of somatically hypermutated B cells in the SARS-CoV-2 specific repertoire was low after the primary vaccination series, evolved further over months and increased steeply after boosting. The third vaccination mobilized not only naïve, but also antigen-experienced B cell clones into further rapid somatic hypermutation trajectories indicating increased affinity. Together, the strongly mutated post-booster repertoires and antibodies deriving from this may explain why the third, but not the primary vaccination series, offers some protection against immune-escape variants such as Omicron B.1.1.529.
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Affiliation(s)
- Lisa Paschold
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Bianca Klee
- Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Center for Health Sciences, Medical School of the Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Cornelia Gottschick
- Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Center for Health Sciences, Medical School of the Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Edith Willscher
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Sophie Diexer
- Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Center for Health Sciences, Medical School of the Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Christoph Schultheiß
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Donjete Simnica
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Daniel Sedding
- Mid-German Heart Center, Department of Cardiology and Intensive Care Medicine, University Hospital, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Matthias Girndt
- Department of Internal Medicine II, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Michael Gekle
- Julius Bernstein-Institute of Physiology, Faculty of Medicine, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Rafael Mikolajczyk
- Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Center for Health Sciences, Medical School of the Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Mascha Binder
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
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70
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Lai YC, Cheng YW, Chao CH, Chang YY, Chen CD, Tsai WJ, Wang S, Lin YS, Chang CP, Chuang WJ, Chen LY, Wang YR, Chang SY, Huang W, Wang JR, Tseng CK, Lin CK, Chuang YC, Yeh TM. Antigenic Cross-Reactivity Between SARS-CoV-2 S1-RBD and Its Receptor ACE2. Front Immunol 2022; 13:868724. [PMID: 35603169 PMCID: PMC9114768 DOI: 10.3389/fimmu.2022.868724] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 04/07/2022] [Indexed: 11/27/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging virus responsible for the ongoing COVID-19 pandemic. SARS-CoV-2 binds to the human cell receptor angiotensin-converting enzyme 2 (ACE2) through its receptor-binding domain in the S1 subunit of the spike protein (S1-RBD). The serum levels of autoantibodies against ACE2 are significantly higher in patients with COVID-19 than in controls and are associated with disease severity. However, the mechanisms through which these anti-ACE2 antibodies are induced during SARS-CoV-2 infection are unclear. In this study, we confirmed the increase in antibodies against ACE2 in patients with COVID-19 and found a positive correlation between the amounts of antibodies against ACE2 and S1-RBD. Moreover, antibody binding to ACE2 was significantly decreased in the sera of some COVID-19 patients after preadsorption of the sera with S1-RBD, which indicated that antibodies against S1-RBD can cross-react with ACE2. To confirm this possibility, two monoclonal antibodies (mAbs 127 and 150) which could bind to both S1-RBD and ACE2 were isolated from S1-RBD-immunized mice. Measurement of the binding affinities by Biacore showed these two mAbs bind to ACE2 much weaker than binding to S1-RBD. Epitope mapping using synthetic overlapping peptides and hydrogen deuterium exchange mass spectrometry (HDX-MS) revealed that the amino acid residues P463, F464, E465, R466, D467 and E471 of S1-RBD are critical for the recognition by mAbs 127 and 150. In addition, Western blotting analysis showed that these mAbs could recognize ACE2 only in native but not denatured form, indicating the ACE2 epitopes recognized by these mAbs were conformation-dependent. The protein-protein interaction between ACE2 and the higher affinity mAb 127 was analyzed by HDX-MS and visualized by negative-stain transmission electron microscopy imaging combined with antigen-antibody docking. Together, our results suggest that ACE2-cross-reactive anti-S1-RBD antibodies can be induced during SARS-CoV-2 infection due to potential antigenic cross-reactivity between S1-RBD and its receptor ACE2.
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Affiliation(s)
- Yen-Chung Lai
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Leadgene Biomedical, Inc., Tainan, Taiwan
| | - Yu-Wei Cheng
- Leadgene Biomedical, Inc., Tainan, Taiwan
- The Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chiao-Hsuan Chao
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | | | | | - Wei-Jiun Tsai
- The Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shuying Wang
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yee-Shin Lin
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chih-Peng Chang
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Woei-Jer Chuang
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | | | | | - Sui-Yuan Chang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Wenya Huang
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Jen-Ren Wang
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | | | | | - Yung-Chun Chuang
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Leadgene Biomedical, Inc., Tainan, Taiwan
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
| | - Trai-Ming Yeh
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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71
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Stewart A, Sinclair E, Ng JCF, O’Hare JS, Page A, Serangeli I, Margreitter C, Orsenigo F, Longman K, Frampas C, Costa C, Lewis HM, Kasar N, Wu B, Kipling D, Openshaw PJM, Chiu C, Baillie JK, Scott JT, Semple MG, Bailey MJ, Fraternali F, Dunn-Walters DK. Pandemic, Epidemic, Endemic: B Cell Repertoire Analysis Reveals Unique Anti-Viral Responses to SARS-CoV-2, Ebola and Respiratory Syncytial Virus. Front Immunol 2022; 13:807104. [PMID: 35592326 PMCID: PMC9111746 DOI: 10.3389/fimmu.2022.807104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/15/2022] [Indexed: 11/17/2022] Open
Abstract
Immunoglobulin gene heterogeneity reflects the diversity and focus of the humoral immune response towards different infections, enabling inference of B cell development processes. Detailed compositional and lineage analysis of long read IGH repertoire sequencing, combining examples of pandemic, epidemic and endemic viral infections with control and vaccination samples, demonstrates general responses including increased use of IGHV4-39 in both Zaire Ebolavirus (EBOV) and COVID-19 patient cohorts. We also show unique characteristics absent in Respiratory Syncytial Virus or yellow fever vaccine samples: EBOV survivors show unprecedented high levels of class switching events while COVID-19 repertoires from acute disease appear underdeveloped. Despite the high levels of clonal expansion in COVID-19 IgG1 repertoires there is a striking lack of evidence of germinal centre mutation and selection. Given the differences in COVID-19 morbidity and mortality with age, it is also pertinent that we find significant differences in repertoire characteristics between young and old patients. Our data supports the hypothesis that a primary viral challenge can result in a strong but immature humoral response where failures in selection of the repertoire risk off-target effects.
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Affiliation(s)
- Alexander Stewart
- School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Emma Sinclair
- School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Joseph Chi-Fung Ng
- Randall Centre for Cell & Molecular Biophysics, King’s College London, London, United Kingdom
| | - Joselli Silva O’Hare
- School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
- Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Audrey Page
- Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Ilaria Serangeli
- Dipartimento di Biologia e Biotecnologie Charles Darwin, Sapienza Università di Roma, Rome, Italy
| | | | - Federica Orsenigo
- School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
- Department of Biotechnology and Biosciences, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Katherine Longman
- Department of Chemistry, University of Surrey, Guildford, United Kingdom
| | - Cecile Frampas
- Department of Chemistry, University of Surrey, Guildford, United Kingdom
| | - Catia Costa
- Department of Chemistry, University of Surrey, Guildford, United Kingdom
| | - Holly-May Lewis
- Department of Chemistry, University of Surrey, Guildford, United Kingdom
| | - Nora Kasar
- School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Bryan Wu
- Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - David Kipling
- School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Peter JM Openshaw
- Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Christopher Chiu
- Faculty of Medicine, Imperial College London, London, United Kingdom
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Janet T. Scott
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Malcolm G. Semple
- Faculty of Health & Life Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Melanie J. Bailey
- Department of Chemistry, University of Surrey, Guildford, United Kingdom
| | - Franca Fraternali
- Randall Centre for Cell & Molecular Biophysics, King’s College London, London, United Kingdom
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72
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Mehboob S, Rehman A, Haq M, Rajab H, Haq M, Haq H, Ahmad J, Ahmad S, Abbas M, Anwar S, Haq N. Incidence of SARS-CoV-2 re-infection in anti-nucleocapsid IgG-positive healthcare workers: a prospective cohort study. Ir J Med Sci 2022; 192:915-918. [PMID: 35412213 PMCID: PMC9001818 DOI: 10.1007/s11845-022-02997-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 03/09/2022] [Indexed: 11/30/2022]
Abstract
Background Since the pandemic of SARS-CoV-2 began, our understanding of the pathogenesis and immune responses to this virus has continued to evolve. It has been shown that this infection produces natural detectable immune responses in many cases. However, the duration and durability of immunity and its effect on the severity of the illness are still under investigation. Moreover, the protective effects of antibodies against new SARS-CoV-2 variants still remain unclear. Objectives To assess the incidence and associated demographic features of SARS-CoV-2 infection in anti-nucleocapsid IgG-positive and anti-nucleocapsid IgG-negative healthcare workers. Material and methods This prospective longitudinal cohort study was conducted in Peshawar Medical College group of hospitals of Prime Foundation. Anti-nucleocapsid IgG sero-positive and anti-nucleocapsid IgG sero-negative healthcare workers were followed for a period of 6 months (from 1 Aug 2020 to 31 Jan 2021), and the incidence of SARS-CoV-2 was confirmed by RT-PCR. Results A total number of 555 cohorts were followed for a period of 6 months; of them 365 (65.7%) were anti-nucleocapsid-negative (group A) and 190 (34.3%) were anti-nucleocapsid-positive (group B) healthcare workers. The mean age of the study cohort was 33.85 ± 9.80 (anti-N (–), 34.2 ± 10.58; anti-N ( +), 33.5 ± 9.50). The median antibody level in anti-nucleocapsid-positive HCWs was 15.95 (IQR: 5.24–53.4). Male gender was the majority in both groups (group A, 246 (67%), group B, 143 (48%)) with statistically significant difference (P < 0.05). Majority of the HCWs were blood group B in both groups (34% each). None of the 190 anti-nucleocapsid-positive HCWs developed subsequent SARS-CoV-2 re-infection, while 17% (n = 65) HCWs developed infection in anti-nucleocapsid-negative group during the 6-month follow-up period. Conclusion In conclusion, none of the anti-nucleocapsid-positive HCWs developed SARS-CoV-2 re-infection in this study, and the presence of IgG anti-nucleocapsid antibodies substantially reduce the risk of re-infection for a period of 6 months. Supplementary information The online version contains supplementary material available at 10.1007/s11845-022-02997-w.
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Affiliation(s)
- Saima Mehboob
- Department of Medicine, Peshawar Medical College, Riphah International University, Islamabad, Pakistan.
| | - Asif Rehman
- Department of Community Health Sciences, Peshawar Medical College, Riphah International University, Islamabad, Pakistan
| | - Mohsina Haq
- Department of Pathology, Peshawar Medical College, Riphah International University, Islamabad, Pakistan
| | - Hala Rajab
- Department of Pathology, Peshawar Medical College, Riphah International University, Islamabad, Pakistan
| | - Momina Haq
- Department of Pathology, Peshawar Medical College, Riphah International University, Islamabad, Pakistan
| | - Hala Haq
- Department of Pathology, Fazaia Medical College, Air University, Islamabad, Pakistan
| | - Jawad Ahmad
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Sajjad Ahmad
- Department of Pathology, Peshawar Medical College, Riphah International University, Islamabad, Pakistan
| | - Mohammed Abbas
- Department of Pathology, Peshawar Medical College, Riphah International University, Islamabad, Pakistan
| | - Saeed Anwar
- Department of Community Health Sciences, Peshawar Medical College, Riphah International University, Islamabad, Pakistan
| | - NajibUl Haq
- Department of Medicine, Peshawar Medical College, Riphah International University, Islamabad, Pakistan
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73
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Woodruff MC, Nguyen DC, Faliti CE, Saini AS, Lee FEH, Sanz I. Response under pressure: deploying emerging technologies to understand B-cell-mediated immunity in COVID-19. Nat Methods 2022; 19:387-391. [PMID: 35396475 DOI: 10.1038/s41592-022-01450-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Matthew C Woodruff
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA.,Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA
| | - Doan C Nguyen
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Emory University, Atlanta, GA, USA
| | - Caterina E Faliti
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA.,Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA
| | - Ankur Singh Saini
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA.,Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA
| | - F Eun-Hyung Lee
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Emory University, Atlanta, GA, USA
| | - Ignacio Sanz
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA. .,Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA.
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74
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Willcox AC, Sung K, Garrett ME, Galloway JG, Erasmus JH, Logue JK, Hawman DW, Chu HY, Hasenkrug KJ, Fuller DH, Matsen IV FA, Overbaugh J. Detailed analysis of antibody responses to SARS-CoV-2 vaccination and infection in macaques. PLoS Pathog 2022; 18:e1010155. [PMID: 35404959 PMCID: PMC9022802 DOI: 10.1371/journal.ppat.1010155] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 04/21/2022] [Accepted: 03/21/2022] [Indexed: 02/02/2023] Open
Abstract
Macaques are a commonly used model for studying immunity to human viruses, including for studies of SARS-CoV-2 infection and vaccination. However, it is unknown whether macaque antibody responses resemble the response in humans. To answer this question, we employed a phage-based deep mutational scanning approach (Phage-DMS) to compare which linear epitopes are targeted on the SARS-CoV-2 Spike protein in convalescent humans, convalescent (re-infected) rhesus macaques, mRNA-vaccinated humans, and repRNA-vaccinated pigtail macaques. We also used Phage-DMS to determine antibody escape pathways within each epitope, enabling a granular comparison of antibody binding specificities at the locus level. Overall, we identified some common epitope targets in both macaques and humans, including in the fusion peptide (FP) and stem helix-heptad repeat 2 (SH-H) regions. Differences between groups included a response to epitopes in the N-terminal domain (NTD) and C-terminal domain (CTD) in vaccinated humans but not vaccinated macaques, as well as recognition of a CTD epitope and epitopes flanking the FP in convalescent macaques but not convalescent humans. There was also considerable variability in the escape pathways among individuals within each group. Sera from convalescent macaques showed the least variability in escape overall and converged on a common response with vaccinated humans in the SH-H epitope region, suggesting highly similar antibodies were elicited. Collectively, these findings suggest that the antibody response to SARS-CoV-2 in macaques shares many features with humans, but with substantial differences in the recognition of certain epitopes and considerable individual variability in antibody escape profiles, suggesting a diverse repertoire of antibodies that can respond to major epitopes in both humans and macaques. Differences in macaque species and exposure type may also contribute to these findings.
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Affiliation(s)
- Alexandra C. Willcox
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Medical Scientist Training Program, University of Washington, Seattle, Washington, United States of America
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, United States of America
| | - Kevin Sung
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Meghan E. Garrett
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, United States of America
| | - Jared G. Galloway
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Jesse H. Erasmus
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- HDT Bio, Seattle, Washington, United States of America
| | - Jennifer K. Logue
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - David W. Hawman
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Helen Y. Chu
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Kim J. Hasenkrug
- Laboratory of Persistent Viral Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Deborah H. Fuller
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- Infectious Diseases and Translational Medicine, Washington National Primate Research Center, Seattle, Washington, United States of America
- Center for Innate Immunity and Immune Disease, University of Washington, Seattle, Washington, United States of America
| | - Frederick A. Matsen IV
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Julie Overbaugh
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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75
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Wong MK, Liu JT, Budylowksi P, Yue FY, Li Z, Rini JM, Carlyle JR, Zia A, Ostrowski M, Martin A. Convergent CDR3 homology amongst Spike-specific antibody responses in convalescent COVID-19 subjects receiving the BNT162b2 vaccine. Clin Immunol 2022; 237:108963. [PMID: 35259543 PMCID: PMC8897198 DOI: 10.1016/j.clim.2022.108963] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/25/2022] [Accepted: 03/01/2022] [Indexed: 01/04/2023]
Abstract
Convalescent coronavirus disease 2019 (COVID-19) subjects who receive BNT162b2 develop robust antibody responses against SARS-CoV-2. However, our understanding of the clonal B cell response pre- and post-vaccination in such individuals is limited. Here we characterized B cell phenotypes and the BCR repertoire after BNT162b2 immunization in two convalescent COVID-19 subjects. BNT162b2 stimulated many B cell clones that were under-represented during SARS-CoV-2 infection. In addition, the vaccine generated B cell clusters with >65% similarity in CDR3 VH and VL region consensus sequences both within and between subjects. This result suggests that the CDR3 region plays a dominant role adjacent to heavy and light chain V/J pairing in the recognition of the SARS-CoV-2 spike protein. Antigen-specific B cell populations with homology to published SARS-CoV-2 antibody sequences from the CoV-AbDab database were observed in both subjects. These results point towards the development of convergent antibody responses against the virus in different individuals.
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Affiliation(s)
- Matthew K Wong
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Jun T Liu
- Department of Laboratory Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Patrick Budylowksi
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Feng Yun Yue
- Department of Laboratory Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Zhijie Li
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - James M Rini
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - James R Carlyle
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Amin Zia
- dYcode Bio, Toronto, Ontario, Canada
| | - Mario Ostrowski
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada; Department of Medicine, University of Toronto; Toronto, ON, Canada; Keenan Research Centre for Biomedical Science of St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada.
| | - Alberto Martin
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada.
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76
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Shafqat A, Shafqat S, Salameh SA, Kashir J, Alkattan K, Yaqinuddin A. Mechanistic Insights Into the Immune Pathophysiology of COVID-19; An In-Depth Review. Front Immunol 2022; 13:835104. [PMID: 35401519 PMCID: PMC8989408 DOI: 10.3389/fimmu.2022.835104] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/02/2022] [Indexed: 12/15/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), which causes coronavirus-19 (COVID-19), has caused significant morbidity and mortality globally. In addition to the respiratory manifestations seen in severe cases, multi-organ pathologies also occur, making management a much-debated issue. In addition, the emergence of new variants can potentially render vaccines with a relatively limited utility. Many investigators have attempted to elucidate the precise pathophysiological mechanisms causing COVID-19 respiratory and systemic disease. Spillover of lung-derived cytokines causing a cytokine storm is considered the cause of systemic disease. However, recent studies have provided contradictory evidence, whereby the extent of cytokine storm is insufficient to cause severe illness. These issues are highly relevant, as management approaches considering COVID-19 a classic form of acute respiratory distress syndrome with a cytokine storm could translate to unfounded clinical decisions, detrimental to patient trajectory. Additionally, the precise immune cell signatures that characterize disease of varying severity remain contentious. We provide an up-to-date review on the immune dysregulation caused by COVID-19 and highlight pertinent discussions in the scientific community. The response from the scientific community has been unprecedented regarding the development of highly effective vaccines and cutting-edge research on novel therapies. We hope that this review furthers the conversations held by scientists and informs the aims of future research projects, which will potentially further our understanding of COVID-19 and its immune pathogenesis.
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Affiliation(s)
- Areez Shafqat
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | | | | | - Junaid Kashir
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Center of Comparative Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Khaled Alkattan
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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77
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Chen L, Pang P, Qi H, Yan K, Ren Y, Ma M, Cao R, Li H, Hu C, Li Y, Xia J, Lai D, Dong Y, Jiang H, Zhang H, Shan H, Tao S, Liu S. Evaluation of Spike Protein Epitopes by Assessing the Dynamics of Humoral Immune Responses in Moderate COVID-19. Front Immunol 2022; 13:770982. [PMID: 35371042 PMCID: PMC8971992 DOI: 10.3389/fimmu.2022.770982] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 02/15/2022] [Indexed: 12/11/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is caused by a novel coronavirus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The spike protein (S) of SARS-CoV-2 is a major target for diagnosis and vaccine development because of its essential role in viral infection and host immunity. Currently, time-dependent responses of humoral immune system against various S protein epitopes are poorly understood. In this study, enzyme-linked immunosorbent assay (ELISA), peptide microarray, and antibody binding epitope mapping (AbMap) techniques were used to systematically analyze the dynamic changes of humoral immune responses against the S protein in a small cohort of moderate COVID-19 patients who were hospitalized for approximately two months after symptom onset. Recombinant truncated S proteins, target S peptides, and random peptides were used as antigens in the analyses. The assays demonstrated the dynamic IgM- and IgG recognition and reactivity against various S protein epitopes with patient-dependent patterns. Comprehensive analysis of epitope distribution along the spike gene sequence and spatial structure of the homotrimer S protein demonstrated that most IgM- and IgG-reactive peptides were clustered into similar genomic regions and were located at accessible domains. Seven S peptides were generally recognized by IgG antibodies derived from serum samples of all COVID-19 patients. The dynamic immune recognition signals from these seven S peptides were comparable to those of the entire S protein or truncated S1 protein. This suggested that the humoral immune system recognized few conserved S protein epitopes in most COVID-19 patients during the entire duration of humoral immune response after symptom onset. Furthermore, in this cohort, individual patients demonstrated stable immune recognition to certain S protein epitopes throughout their hospitalization period. Therefore, the dynamic characteristics of humoral immune responses to S protein have provided valuable information for accurate diagnosis and immunotherapy of COVID-19 patients.
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Affiliation(s)
- Lingyun Chen
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- Department of Proteomics, Beijing Genomics Institution, Shenzhen, China
| | - Pengfei Pang
- Center for Interventional Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Huan Qi
- Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
| | - Keqiang Yan
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- Department of Proteomics, Beijing Genomics Institution, Shenzhen, China
| | - Yan Ren
- Department of Proteomics, Beijing Genomics Institution, Shenzhen, China
| | - Mingliang Ma
- Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
| | - Ruyin Cao
- Department of Proteomics, Beijing Genomics Institution, Shenzhen, China
| | - Hua Li
- State Key laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Chuansheng Hu
- State Key laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yang Li
- Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
| | - Jun Xia
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- Department of Proteomics, Beijing Genomics Institution, Shenzhen, China
| | - Danyun Lai
- Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
| | - Yuliang Dong
- Department of Proteomics, Beijing Genomics Institution, Shenzhen, China
| | - Hewei Jiang
- Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
| | - Hainan Zhang
- Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
| | - Hong Shan
- Center for Interventional Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
- *Correspondence: Siqi Liu, ; Shengce Tao, ; Hong Shan,
| | - Shengce Tao
- Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
- *Correspondence: Siqi Liu, ; Shengce Tao, ; Hong Shan,
| | - Siqi Liu
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- Department of Proteomics, Beijing Genomics Institution, Shenzhen, China
- *Correspondence: Siqi Liu, ; Shengce Tao, ; Hong Shan,
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78
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Nairz M, Sahanic S, Pizzini A, Böhm A, Tymoszuk P, Mitterstiller AM, von Raffay L, Grubwieser P, Bellmann-Weiler R, Koppelstätter S, Schroll A, Haschka D, Zimmermann M, Blunder S, Trattnig K, Naschberger H, Klotz W, Theurl I, Petzer V, Gehrer C, Mindur JE, Luger A, Schwabl C, Widmann G, Weiss G, Löffler-Ragg J, Tancevski I, Sonnweber T. Quantity of IgG response to SARS-CoV-2 spike glycoprotein predicts pulmonary recovery from COVID-19. Sci Rep 2022; 12:3677. [PMID: 35256646 PMCID: PMC8901626 DOI: 10.1038/s41598-022-07489-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 02/16/2022] [Indexed: 02/06/2023] Open
Abstract
The CovILD study is a prospective, multicenter, observational cohort study to systematically follow up patients after coronavirus disease-2019 (COVID-19). We extensively evaluated 145 COVID-19 patients at 3 follow-up visits scheduled for 60, 100, and 180 days after initial confirmed diagnosis based on typical symptoms and a positive reverse transcription-polymerase chain reaction (RT-PCR) for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). We employed comprehensive pulmonary function and laboratory tests, including serum concentrations of IgG against the viral spike (S) glycoprotein, and compared the results to clinical data and chest computed tomography (CT). We found that at the 60 day follow-up, 131 of 145 (90.3%) participants displayed S-specific serum IgG levels above the cut-off threshold. Notably, the highly elevated IgG levels against S glycoprotein positively correlated with biomarkers of immune activation and negatively correlated with pulmonary function and the extent of pulmonary CT abnormalities. Based on the association between serum S glycoprotein-specific IgG and clinical outcome, we generated an S-specific IgG-based recovery score that, when applied in the early convalescent phase, accurately predicted delayed pulmonary recovery after COVID-19. Therefore, we propose that S-specific IgG levels serve as a useful immunological surrogate marker for identifying at-risk individuals with persistent pulmonary injury who may require intensive follow-up care after COVID-19.
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Affiliation(s)
- Manfred Nairz
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria.
| | - Sabina Sahanic
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Alex Pizzini
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Anna Böhm
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Piotr Tymoszuk
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Laura von Raffay
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Philipp Grubwieser
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Rosa Bellmann-Weiler
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Sabine Koppelstätter
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Andrea Schroll
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - David Haschka
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Martina Zimmermann
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Silvia Blunder
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Kristina Trattnig
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Helene Naschberger
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Werner Klotz
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Igor Theurl
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Verena Petzer
- Department of Internal Medicine V, Medical University of Innsbruck, Innsbruck, Austria
| | - Clemens Gehrer
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Anna Luger
- Department of Radiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Christoph Schwabl
- Department of Radiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Gerlig Widmann
- Department of Radiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Günter Weiss
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
- Christian Doppler Laboratory for Iron Metabolism and Anemia Research, Medical University of Innsbruck, Innsbruck, Austria
| | - Judith Löffler-Ragg
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Ivan Tancevski
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Thomas Sonnweber
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria.
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79
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Kotagiri P, Mescia F, Hanson AL, Turner L, Bergamaschi L, Peñalver A, Richoz N, Moore SD, Ortmann BM, Dunmore BJ, Morgan MD, Tuong ZK, Göttgens B, Toshner M, Hess C, Maxwell PH, Clatworthy MR, Nathan JA, Bradley JR, Lyons PA, Burrows N, Smith KGC. The impact of hypoxia on B cells in COVID-19. EBioMedicine 2022; 77:103878. [PMID: 35189575 PMCID: PMC8856886 DOI: 10.1016/j.ebiom.2022.103878] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/17/2021] [Accepted: 01/28/2022] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Prominent early features of COVID-19 include severe, often clinically silent, hypoxia and a pronounced reduction in B cells, the latter important in defence against SARS-CoV-2. This presentation resembles the phenotype of mice with VHL-deficient B cells, in which Hypoxia-Inducible Factors are constitutively active, suggesting hypoxia might drive B cell abnormalities in COVID-19. METHODS Detailed B cell phenotyping was undertaken by flow-cytometry on longitudinal samples from patients with COVID-19 across a range of severities (NIHR Cambridge BioResource). The impact of hypoxia on the transcriptome was assessed by single-cell and whole blood RNA sequencing analysis. The direct effect of hypoxia on B cells was determined through immunisation studies in genetically modified and hypoxia-exposed mice. FINDINGS We demonstrate the breadth of early and persistent defects in B cell subsets in moderate/severe COVID-19, including reduced marginal zone-like, memory and transitional B cells, changes also observed in B cell VHL-deficient mice. These findings were associated with hypoxia-related transcriptional changes in COVID-19 patient B cells, and similar B cell abnormalities were seen in mice kept in hypoxic conditions. INTERPRETATION Hypoxia may contribute to the pronounced and persistent B cell pathology observed in acute COVID-19 pneumonia. Assessment of the impact of early oxygen therapy on these immune defects should be considered, as their correction could contribute to improved outcomes. FUNDING Evelyn Trust, Addenbrooke's Charitable Trust, UKRI/NIHR, Wellcome Trust.
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Affiliation(s)
- Prasanti Kotagiri
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom
| | - Federica Mescia
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom
| | - Aimee L Hanson
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom
| | - Lorinda Turner
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom
| | - Laura Bergamaschi
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom
| | - Ana Peñalver
- Cambridge Institute for Medical Research, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Cambridge
| | - Nathan Richoz
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom; Cellular Genetics, Wellcome Sanger Institute, Hinxton. United Kingdom
| | - Stephen D Moore
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom
| | - Brian M Ortmann
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom
| | - Benjamin J Dunmore
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom
| | - Michael D Morgan
- Cancer Research UK - Cambridge Institute, Robinson Way, Cambridge CB2 0RE, United Kingdom; EMBL-EBI, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Zewen Kelvin Tuong
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom; Cellular Genetics, Wellcome Sanger Institute, Hinxton. United Kingdom
| | - Berthold Göttgens
- Department of Haematology, Wellcome & MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, United Kingdom
| | - Mark Toshner
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom; Heart and Lung Research Institute, Cambridge Biomedical Campus, Cambridge CB2 0QQ, United Kingdom
| | - Christoph Hess
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom
| | - Patrick H Maxwell
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom; Cambridge Institute for Medical Research, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Cambridge
| | - Menna R Clatworthy
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom; Cellular Genetics, Wellcome Sanger Institute, Hinxton. United Kingdom
| | - James A Nathan
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom
| | - John R Bradley
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom; NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge CB2 0QQ, United Kingdom
| | - Paul A Lyons
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom
| | - Natalie Burrows
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom; Cambridge Institute for Medical Research, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Cambridge.
| | - Kenneth G C Smith
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom.
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80
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Kotagiri P, Mescia F, Rae WM, Bergamaschi L, Tuong ZK, Turner L, Hunter K, Gerber PP, Hosmillo M, Hess C, Clatworthy MR, Goodfellow IG, Matheson NJ, McKinney EF, Wills MR, Gupta RK, Bradley JR, Bashford-Rogers RJM, Lyons PA, Smith KGC. B cell receptor repertoire kinetics after SARS-CoV-2 infection and vaccination. Cell Rep 2022; 38:110393. [PMID: 35143756 PMCID: PMC8801326 DOI: 10.1016/j.celrep.2022.110393] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/28/2021] [Accepted: 01/24/2022] [Indexed: 11/24/2022] Open
Abstract
B cells are important in immunity to both severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection and vaccination, but B cell receptor (BCR) repertoire development in these contexts has not been compared. We analyze serial samples from 171 SARS-CoV-2-infected individuals and 63 vaccine recipients and find the global BCR repertoire differs between them. Following infection, immunoglobulin (Ig)G1/3 and IgA1 BCRs increase, somatic hypermutation (SHM) decreases, and, in severe disease, IgM and IgA clones are expanded. In contrast, after vaccination, the proportion of IgD/M BCRs increase, SHM is unchanged, and expansion of IgG clones is prominent. VH1-24, which targets the N-terminal domain (NTD) and contributes to neutralization, is expanded post infection except in the most severe disease. Infection generates a broad distribution of SARS-CoV-2-specific clones predicted to target the spike protein, while a more focused response after vaccination mainly targets the spike's receptor-binding domain. Thus, the nature of SARS-CoV-2 exposure differentially affects BCR repertoire development, potentially informing vaccine strategies.
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Affiliation(s)
- Prasanti Kotagiri
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK.
| | - Federica Mescia
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - William M Rae
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Laura Bergamaschi
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Zewen K Tuong
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK; Cellular Genetics, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1RQ, UK
| | - Lorinda Turner
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Kelvin Hunter
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Pehuén P Gerber
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Myra Hosmillo
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Christoph Hess
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK; Department of Biomedicine, University and University Hospital Basel, Basel 4031, Switzerland; Botnar Research Centre for Child Health (BRCCH) University Basel and ETH Zurich, Basel 4059, Switzerland
| | - Menna R Clatworthy
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK; Cellular Genetics, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1RQ, UK
| | - Ian G Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Nicholas J Matheson
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK; NHS Blood and Transplant, Cambridge CB2 1PT, UK
| | - Eoin F McKinney
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Mark R Wills
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - John R Bradley
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK; NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | | | - Paul A Lyons
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK.
| | - Kenneth G C Smith
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK.
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81
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Xu G, Qi F, Wang H, Liu Y, Wang X, Zou R, Yuan J, Liao X, Liu Y, Zhang S, Zhang Z. The Transient IFN Response and the Delay of Adaptive Immunity Feature the Severity of COVID-19. Front Immunol 2022; 12:816745. [PMID: 35095917 PMCID: PMC8795972 DOI: 10.3389/fimmu.2021.816745] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/21/2021] [Indexed: 01/08/2023] Open
Abstract
COVID-19 patients show heterogeneous and dynamic immune features which determine the clinical outcome. Here, we built a single-cell RNA sequencing (scRNA-seq) dataset for dissecting these complicated immune responses through a longitudinal survey of COVID-19 patients with various categories of outcomes. The data reveals a highly fluctuating peripheral immune landscape in severe COVID-19, whereas the one in asymptomatic/mild COVID-19 is relatively steady. Then, the perturbed immune landscape in peripheral blood returned to normal state in those recovered from severe COVID-19. Importantly, the imbalance of the excessively strong innate immune response and delayed adaptive immunity in the early stage of viral infection accelerates the progression of the disease, indicated by a transient strong IFN response and weak T/B-cell specific response. The proportion of abnormal monocytes appeared early and rose further throughout the severe disease. Our data indicate that a dynamic immune landscape is associated with the progression and recovery of severe COVID-19, and have provided multiple immune biomarkers for early warning of severe COVID-19.
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Affiliation(s)
- Gang Xu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Furong Qi
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Haiyan Wang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Yu Liu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Xin Wang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Rongrong Zou
- Department for Infectious Diseases, Shenzhen Third People's Hospital, Shenzhen, China
| | - Jing Yuan
- Department for Infectious Diseases, Shenzhen Third People's Hospital, Shenzhen, China
| | - Xuejiao Liao
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Yang Liu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Shuye Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Zheng Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, China.,Shenzhen Research Center for Communicable Disease Diagnosis and Treatment of Chinese Academy of Medical Science, Shenzhen, China.,Guangdong Key Laboratory for Anti-Infection Drug Quality Evaluation, Shenzhen, China
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82
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Gusev E, Sarapultsev A, Solomatina L, Chereshnev V. SARS-CoV-2-Specific Immune Response and the Pathogenesis of COVID-19. Int J Mol Sci 2022; 23:1716. [PMID: 35163638 PMCID: PMC8835786 DOI: 10.3390/ijms23031716] [Citation(s) in RCA: 101] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 12/13/2022] Open
Abstract
The review aims to consolidate research findings on the molecular mechanisms and virulence and pathogenicity characteristics of coronavirus disease (COVID-19) causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and their relevance to four typical stages in the development of acute viral infection. These four stages are invasion; primary blockade of antiviral innate immunity; engagement of the virus's protection mechanisms against the factors of adaptive immunity; and acute, long-term complications of COVID-19. The invasion stage entails the recognition of the spike protein (S) of SARS-CoV-2 target cell receptors, namely, the main receptor (angiotensin-converting enzyme 2, ACE2), its coreceptors, and potential alternative receptors. The presence of a diverse repertoire of receptors allows SARS-CoV-2 to infect various types of cells, including those not expressing ACE2. During the second stage, the majority of the polyfunctional structural, non-structural, and extra proteins SARS-CoV-2 synthesizes in infected cells are involved in the primary blockage of antiviral innate immunity. A high degree of redundancy and systemic action characterizing these pathogenic factors allows SARS-CoV-2 to overcome antiviral mechanisms at the initial stages of invasion. The third stage includes passive and active protection of the virus from factors of adaptive immunity, overcoming of the barrier function at the focus of inflammation, and generalization of SARS-CoV-2 in the body. The fourth stage is associated with the deployment of variants of acute and long-term complications of COVID-19. SARS-CoV-2's ability to induce autoimmune and autoinflammatory pathways of tissue invasion and development of both immunosuppressive and hyperergic mechanisms of systemic inflammation is critical at this stage of infection.
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Affiliation(s)
- Evgenii Gusev
- Laboratory of Immunology of Inflammation, Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 620049 Ekaterinburg, Russia
| | - Alexey Sarapultsev
- Laboratory of Immunology of Inflammation, Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 620049 Ekaterinburg, Russia
- Russian-Chinese Education and Research Center of System Pathology, South Ural State University, 454080 Chelyabinsk, Russia
| | - Liliya Solomatina
- Laboratory of Immunology of Inflammation, Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 620049 Ekaterinburg, Russia
| | - Valeriy Chereshnev
- Laboratory of Immunology of Inflammation, Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 620049 Ekaterinburg, Russia
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83
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T cell apoptosis characterizes severe Covid-19 disease. Cell Death Differ 2022; 29:1486-1499. [PMID: 35066575 PMCID: PMC8782710 DOI: 10.1038/s41418-022-00936-x] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 01/06/2022] [Accepted: 01/10/2022] [Indexed: 02/02/2023] Open
Abstract
Severe SARS-CoV-2 infections are characterized by lymphopenia, but the mechanisms involved are still elusive. Based on our knowledge of HIV pathophysiology, we hypothesized that SARS-CoV-2 infection-mediated lymphopenia could also be related to T cell apoptosis. By comparing intensive care unit (ICU) and non-ICU COVID-19 patients with age-matched healthy donors, we found a strong positive correlation between plasma levels of soluble FasL (sFasL) and T cell surface expression of Fas/CD95 with the propensity of T cells to die and CD4 T cell counts. Plasma levels of sFasL and T cell death are correlated with CXCL10 which is part of the signature of 4 biomarkers of disease severity (ROC, 0.98). We also found that members of the Bcl-2 family had modulated in the T cells of COVID-19 patients. More importantly, we demonstrated that the pan-caspase inhibitor, Q-VD, prevents T cell death by apoptosis and enhances Th1 transcripts. Altogether, our results are compatible with a model in which T-cell apoptosis accounts for T lymphopenia in individuals with severe COVID-19. Therefore, a strategy aimed at blocking caspase activation could be beneficial for preventing immunodeficiency in COVID-19 patients.
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84
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Unterman A, Sumida TS, Nouri N, Yan X, Zhao AY, Gasque V, Schupp JC, Asashima H, Liu Y, Cosme C, Deng W, Chen M, Raredon MSB, Hoehn KB, Wang G, Wang Z, DeIuliis G, Ravindra NG, Li N, Castaldi C, Wong P, Fournier J, Bermejo S, Sharma L, Casanovas-Massana A, Vogels CBF, Wyllie AL, Grubaugh ND, Melillo A, Meng H, Stein Y, Minasyan M, Mohanty S, Ruff WE, Cohen I, Raddassi K, Niklason LE, Ko AI, Montgomery RR, Farhadian SF, Iwasaki A, Shaw AC, van Dijk D, Zhao H, Kleinstein SH, Hafler DA, Kaminski N, Dela Cruz CS. Single-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19. Nat Commun 2022; 13:440. [PMID: 35064122 PMCID: PMC8782894 DOI: 10.1038/s41467-021-27716-4] [Citation(s) in RCA: 79] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 12/03/2021] [Indexed: 02/06/2023] Open
Abstract
Dysregulated immune responses against the SARS-CoV-2 virus are instrumental in severe COVID-19. However, the immune signatures associated with immunopathology are poorly understood. Here we use multi-omics single-cell analysis to probe the dynamic immune responses in hospitalized patients with stable or progressive course of COVID-19, explore V(D)J repertoires, and assess the cellular effects of tocilizumab. Coordinated profiling of gene expression and cell lineage protein markers shows that S100Ahi/HLA-DRlo classical monocytes and activated LAG-3hi T cells are hallmarks of progressive disease and highlights the abnormal MHC-II/LAG-3 interaction on myeloid and T cells, respectively. We also find skewed T cell receptor repertories in expanded effector CD8+ clones, unmutated IGHG+ B cell clones, and mutated B cell clones with stable somatic hypermutation frequency over time. In conclusion, our in-depth immune profiling reveals dyssynchrony of the innate and adaptive immune interaction in progressive COVID-19.
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MESH Headings
- Adaptive Immunity/drug effects
- Adaptive Immunity/genetics
- Adaptive Immunity/immunology
- Aged
- Antibodies, Monoclonal, Humanized/therapeutic use
- CD4-Positive T-Lymphocytes/drug effects
- CD4-Positive T-Lymphocytes/immunology
- CD4-Positive T-Lymphocytes/metabolism
- CD8-Positive T-Lymphocytes/drug effects
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- COVID-19/genetics
- COVID-19/immunology
- Cells, Cultured
- Female
- Gene Expression Profiling/methods
- Gene Expression Regulation/drug effects
- Gene Expression Regulation/immunology
- Humans
- Immunity, Innate/drug effects
- Immunity, Innate/genetics
- Immunity, Innate/immunology
- Male
- RNA-Seq/methods
- Receptors, Antigen, B-Cell/genetics
- Receptors, Antigen, B-Cell/immunology
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- SARS-CoV-2/drug effects
- SARS-CoV-2/immunology
- SARS-CoV-2/physiology
- Single-Cell Analysis/methods
- COVID-19 Drug Treatment
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Affiliation(s)
- Avraham Unterman
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA.
- Pulmonary Institute, Tel Aviv Sourasky Medical Center, Tel Aviv University, Tel Aviv, Israel.
| | - Tomokazu S Sumida
- Department of Neurology, School of Medicine, Yale University, New Haven, CT, USA.
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA.
| | - Nima Nouri
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Center for Medical Informatics, Yale School of Medicine, New Haven, CT, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Xiting Yan
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Amy Y Zhao
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Victor Gasque
- Department of Computer Science, Yale University, New Haven, CT, USA
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jonas C Schupp
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
- Department of Respiratory Medicine, Hannover Medical School and Biomedical Research in End-stage and Obstructive Lung Disease Hannover, German Lung Research Center (DZL), Hannover, Germany
| | - Hiromitsu Asashima
- Department of Neurology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
| | - Yunqing Liu
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Carlos Cosme
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Wenxuan Deng
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Ming Chen
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Micha Sam Brickman Raredon
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Medical Scientist Training Program, Yale School of Medicine, New Haven, CT, USA
| | - Kenneth B Hoehn
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Guilin Wang
- Yale Center for Genome Analysis/Keck Biotechnology Resource Laboratory, Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, USA
| | - Zuoheng Wang
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Giuseppe DeIuliis
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Neal G Ravindra
- Department of Computer Science, Yale University, New Haven, CT, USA
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Ningshan Li
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
- SJTU-Yale Joint Center for Biostatistics and Data Science, Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | | | - Patrick Wong
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
| | - John Fournier
- School of Medicine, Yale University, New Haven, CT, USA
| | - Santos Bermejo
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Lokesh Sharma
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Arnau Casanovas-Massana
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Anthony Melillo
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Hailong Meng
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Yan Stein
- Pulmonary Institute, Tel Aviv Sourasky Medical Center, Tel Aviv University, Tel Aviv, Israel
| | - Maksym Minasyan
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Subhasis Mohanty
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - William E Ruff
- Department of Neurology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
| | - Inessa Cohen
- Department of Neurology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
| | - Khadir Raddassi
- Department of Neurology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
| | - Laura E Niklason
- Departments of Anesthesiology & Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Albert I Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Ruth R Montgomery
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Shelli F Farhadian
- Department of Neurology, School of Medicine, Yale University, New Haven, CT, USA
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Akiko Iwasaki
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Albert C Shaw
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - David van Dijk
- Department of Computer Science, Yale University, New Haven, CT, USA
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- SJTU-Yale Joint Center for Biostatistics and Data Science, Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Inter-Departmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Steven H Kleinstein
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Inter-Departmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - David A Hafler
- Department of Neurology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Charles S Dela Cruz
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
- West Haven Veterans Affair Medical Center, West Haven, CT, USA
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85
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Ehling RA, Weber CR, Mason DM, Friedensohn S, Wagner B, Bieberich F, Kapetanovic E, Vazquez-Lombardi R, Di Roberto RB, Hong KL, Wagner C, Pataia M, Overath MD, Sheward DJ, Murrell B, Yermanos A, Cuny AP, Savic M, Rudolf F, Reddy ST. SARS-CoV-2 reactive and neutralizing antibodies discovered by single-cell sequencing of plasma cells and mammalian display. Cell Rep 2022; 38:110242. [PMID: 34998467 PMCID: PMC8692065 DOI: 10.1016/j.celrep.2021.110242] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 09/22/2021] [Accepted: 12/20/2021] [Indexed: 01/05/2023] Open
Abstract
Characterization of COVID-19 antibodies has largely focused on memory B cells; however, it is the antibody-secreting plasma cells that are directly responsible for the production of serum antibodies, which play a critical role in resolving SARS-CoV-2 infection. Little is known about the specificity of plasma cells, largely because plasma cells lack surface antibody expression, thereby complicating their screening. Here, we describe a technology pipeline that integrates single-cell antibody repertoire sequencing and mammalian display to interrogate the specificity of plasma cells from 16 convalescent patients. Single-cell sequencing allows us to profile antibody repertoire features and identify expanded clonal lineages. Mammalian display screening is used to reveal that 43 antibodies (of 132 candidates) derived from expanded plasma cell lineages are specific to SARS-CoV-2 antigens, including antibodies with high affinity to the SARS-CoV-2 receptor-binding domain (RBD) that exhibit potent neutralization and broad binding to the RBD of SARS-CoV-2 variants (of concern/interest).
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Affiliation(s)
- Roy A Ehling
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Cédric R Weber
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; deepCDR Biologics AG, Basel, Switzerland
| | - Derek M Mason
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; deepCDR Biologics AG, Basel, Switzerland
| | - Simon Friedensohn
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; deepCDR Biologics AG, Basel, Switzerland
| | - Bastian Wagner
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Florian Bieberich
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Edo Kapetanovic
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Raphaël B Di Roberto
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Kai-Lin Hong
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Botnar Research Centre for Child Health, Basel, Switzerland
| | | | - Michele Pataia
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; deepCDR Biologics AG, Basel, Switzerland
| | - Max D Overath
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Alexander Yermanos
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Botnar Research Centre for Child Health, Basel, Switzerland; Institute of Microbiology and Immunology, Department of Biology, ETH Zurich, Zurich, Switzerland; Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Andreas P Cuny
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Swiss Institute of Bioinformatics, Mattenstr. 26, 4058 Basel, Switzerland
| | - Miodrag Savic
- Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland; Department of Surgery, Oral and Cranio-Maxillofacial Surgery, University Hospital Basel, Basel, Switzerland; Department of Health, Economics and Health Directorate, Canton Basel-Landschaft, Switzerland
| | - Fabian Rudolf
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Swiss Institute of Bioinformatics, Mattenstr. 26, 4058 Basel, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Botnar Research Centre for Child Health, Basel, Switzerland.
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86
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Vanshylla K, Fan C, Wunsch M, Poopalasingam N, Meijers M, Kreer C, Kleipass F, Ruchnewitz D, Ercanoglu MS, Gruell H, Münn F, Pohl K, Janicki H, Nolden T, Bartl S, Stein SC, Augustin M, Dewald F, Gieselmann L, Schommers P, Schulz TF, Sander LE, Koch M, Łuksza M, Lässig M, Bjorkman PJ, Klein F. Discovery of ultrapotent broadly neutralizing antibodies from SARS-CoV-2 elite neutralizers. Cell Host Microbe 2022; 30:69-82.e10. [PMID: 34973165 PMCID: PMC8683262 DOI: 10.1016/j.chom.2021.12.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/08/2021] [Accepted: 12/10/2021] [Indexed: 01/14/2023]
Abstract
A fraction of COVID-19 convalescent individuals mount a potent antibody response to SARS-CoV-2 with cross-reactivity to SARS-CoV-1. To uncover their humoral response in detail, we performed single B cell analysis from 10 SARS-CoV-2 elite neutralizers. We isolated and analyzed 126 monoclonal antibodies, many of which were sarbecovirus cross-reactive, with some displaying merbecovirus- and embecovirus-reactivity. Several isolated broadly neutralizing antibodies were effective against B.1.1.7, B.1.351, B.1.429, B.1.617, and B.1.617.2 variants and 19 prominent potential escape sites. Furthermore, assembly of 716,806 SARS-CoV-2 sequences predicted emerging escape variants, which were also effectively neutralized. One of these broadly neutralizing potent antibodies, R40-1G8, is a IGHV3-53 RBD-class-1 antibody. Remarkably, cryo-EM analysis revealed that R40-1G8 has a flexible binding mode, targeting both "up" and "down" conformations of the RBD. Given the threat of emerging SARS-CoV-2 variants, we demonstrate that elite neutralizers are a valuable source for isolating ultrapotent antibody candidates to prevent and treat SARS-CoV-2 infection.
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Affiliation(s)
- Kanika Vanshylla
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Chengcheng Fan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Marie Wunsch
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Nareshkumar Poopalasingam
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Matthijs Meijers
- Institute for Biological Physics, University of Cologne, 50937 Cologne, Germany
| | - Christoph Kreer
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Franziska Kleipass
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Denis Ruchnewitz
- Institute for Biological Physics, University of Cologne, 50937 Cologne, Germany
| | - Meryem S. Ercanoglu
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Henning Gruell
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Friederike Münn
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität Berlin, 13353 Berlin, Germany
| | - Kai Pohl
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität Berlin, 13353 Berlin, Germany
| | - Hanna Janicki
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | | | - Simone Bartl
- Vira Therapeutics GmbH, 6063 Rum, Austria,Boehringer Ingelheim International GmbH, Ingelheim, Germany
| | - Saskia C. Stein
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Max Augustin
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Felix Dewald
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Lutz Gieselmann
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Philipp Schommers
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany,German Center for Infection Research, Partner Site Bonn-Cologne, 50931 Cologne, Germany
| | - Thomas F. Schulz
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Leif Erik Sander
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität Berlin, 13353 Berlin, Germany
| | - Manuel Koch
- Institute for Dental Research and Oral Musculoskeletal Biology and Center for Biochemistry, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany,Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Marta Łuksza
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael Lässig
- Institute for Biological Physics, University of Cologne, 50937 Cologne, Germany
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Florian Klein
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany,German Center for Infection Research, Partner Site Bonn-Cologne, 50931 Cologne, Germany,Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany,Corresponding author
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87
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Abstract
Adaptive immune responses play critical roles in viral clearance and protection against re-infection, and SARS-CoV-2 is no exception. What is exceptional is the rapid characterization of the immune response to the virus performed by researchers during the first 20 months of the pandemic. This has given us a more detailed understanding of SARS-CoV-2 compared to many viruses that have been with us for a long time. Furthermore, effective COVID-19 vaccines were developed in record time, and their rollout worldwide is already making a significant difference, although major challenges remain in terms of equal access. The pandemic has engaged scientists and the public alike, and terms such as seroprevalence, neutralizing antibodies, antibody escape and vaccine certificates have become familiar to a broad community. Here, we review key findings concerning B cell and antibody (Ab) responses to SARS-CoV-2, focusing on non-severe cases and anti-spike (S) Ab responses in particular, the latter being central to protective immunity induced by infection or vaccination. The emergence of viral variants that have acquired mutations in S acutely highlights the need for continued characterization of both emerging variants and Ab responses against these during the evolving pathogen-immune system arms race.
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Affiliation(s)
- Xaquin Castro Dopico
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sebastian Ols
- Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Karin Loré
- Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
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88
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Abstract
The germinal centre (GC) response is critical for the generation of affinity-matured plasma cells and memory B cells capable of mediating long-term protective immunity. Understanding whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection or vaccination elicits a GC response has profound implications for the capacity of responding B cells to contribute to protection against infection. However, direct assessment of the GC response in humans remains a major challenge. Here we summarize emerging evidence for the importance of the GC response in the establishment of durable and broad immunity against SARS-CoV-2 and discuss new approaches to modulate the GC response to better protect against newly emerging SARS-CoV-2 variants. We also discuss new findings showing that the GC B cell response persists in the draining lymph nodes for at least 6 months in some individuals following vaccination with SARS-CoV-2 mRNA-based vaccines.
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Affiliation(s)
- Brian J Laidlaw
- Division of Allergy and Immunology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.
| | - Ali H Ellebedy
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
- The Andrew M. and Jane M. Bursky Center for Human Immunology & Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA.
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St Louis, MO, USA.
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89
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Tian Y, Carpp LN, Miller HER, Zager M, Newell EW, Gottardo R. Single-cell immunology of SARS-CoV-2 infection. Nat Biotechnol 2022; 40:30-41. [PMID: 34931002 PMCID: PMC9414121 DOI: 10.1038/s41587-021-01131-y] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 10/15/2021] [Indexed: 02/07/2023]
Abstract
Gaining a better understanding of the immune cell subsets and molecular factors associated with protective or pathological immunity against severe acute respiratory syndrome coronavirus (SARS-CoV)-2 could aid the development of vaccines and therapeutics for coronavirus disease 2019 (COVID-19). Single-cell technologies, such as flow cytometry, mass cytometry, single-cell transcriptomics and single-cell multi-omic profiling, offer considerable promise in dissecting the heterogeneity of immune responses among individual cells and uncovering the molecular mechanisms of COVID-19 pathogenesis. Single-cell immune-profiling studies reported to date have identified innate and adaptive immune cell subsets that correlate with COVID-19 disease severity, as well as immunological factors and pathways of potential relevance to the development of vaccines and treatments for COVID-19. For facilitation of integrative studies and meta-analyses into the immunology of SARS-CoV-2 infection, we provide standardized, download-ready versions of 21 published single-cell sequencing datasets (over 3.2 million cells in total) as well as an interactive visualization portal for data exploration.
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Affiliation(s)
- Yuan Tian
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Translational Data Science Integrated Research Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Lindsay N Carpp
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Helen E R Miller
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Michael Zager
- Center for Data Visualization, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Evan W Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Raphael Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Translational Data Science Integrated Research Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Biomedical Data Sciences, Lausanne University Hospital, Lausanne, Switzerland.
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90
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Marquez S, Babrak L, Greiff V, Hoehn KB, Lees WD, Luning Prak ET, Miho E, Rosenfeld AM, Schramm CA, Stervbo U. Adaptive Immune Receptor Repertoire (AIRR) Community Guide to Repertoire Analysis. Methods Mol Biol 2022; 2453:297-316. [PMID: 35622333 PMCID: PMC9761518 DOI: 10.1007/978-1-0716-2115-8_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Adaptive immune receptor repertoires (AIRRs) are rich with information that can be mined for insights into the workings of the immune system. Gene usage, CDR3 properties, clonal lineage structure, and sequence diversity are all capable of revealing the dynamic immune response to perturbation by disease, vaccination, or other interventions. Here we focus on a conceptual introduction to the many aspects of repertoire analysis and orient the reader toward the uses and advantages of each. Along the way, we note some of the many software tools that have been developed for these investigations and link the ideas discussed to chapters on methods provided elsewhere in this volume.
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Affiliation(s)
- Susanna Marquez
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Lmar Babrak
- Institute of Biomedical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz, Switzerland
| | - Victor Greiff
- Department of Immunology, University of Oslo, Oslo University Hospital, Oslo, Norway
| | - Kenneth B Hoehn
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - William D Lees
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Enkelejda Miho
- Institute of Biomedical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- aiNET GmbH, Basel, Switzerland
| | - Aaron M Rosenfeld
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Ulrik Stervbo
- Center for Translational Medicine, Immunology, and Transplantation, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany.
- Immundiagnostik, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany.
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91
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Robinson SA, Raybould MIJ, Schneider C, Wong WK, Marks C, Deane CM. Epitope profiling using computational structural modelling demonstrated on coronavirus-binding antibodies. PLoS Comput Biol 2021; 17:e1009675. [PMID: 34898603 PMCID: PMC8700021 DOI: 10.1371/journal.pcbi.1009675] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 12/23/2021] [Accepted: 11/22/2021] [Indexed: 12/30/2022] Open
Abstract
Identifying the epitope of an antibody is a key step in understanding its function and its potential as a therapeutic. Sequence-based clonal clustering can identify antibodies with similar epitope complementarity, however, antibodies from markedly different lineages but with similar structures can engage the same epitope. We describe a novel computational method for epitope profiling based on structural modelling and clustering. Using the method, we demonstrate that sequence dissimilar but functionally similar antibodies can be found across the Coronavirus Antibody Database, with high accuracy (92% of antibodies in multiple-occupancy structural clusters bind to consistent domains). Our approach functionally links antibodies with distinct genetic lineages, species origins, and coronavirus specificities. This indicates greater convergence exists in the immune responses to coronaviruses than is suggested by sequence-based approaches. Our results show that applying structural analytics to large class-specific antibody databases will enable high confidence structure-function relationships to be drawn, yielding new opportunities to identify functional convergence hitherto missed by sequence-only analysis. Antibodies are a key component of the immune system that combat pathogens by binding to a defined region of their molecular surface (known as an ‘epitope’). The ability to map which antibodies target the same epitopes is crucial when designing non-competing antibody therapeutics or predicting the influence of pathogen mutation on population immunity. While one can use laboratory experiments to deduce when pairs of antibodies engage the same epitope, such experiments are very expensive and time consuming if used to compare on the order of thousands of antibodies. In this work, we report a new computational algorithm (SPACE) that clusters antibodies that target the same epitope based on their predicted 3D structure, as binding site structure is a property often conserved between binders complementary to the same epitope. Unlike existing antibody epitope profiling tools which assume two antibodies must share a high sequence identity/similar genetic basis to engage the same region, our orthogonal method can detect broader patterns of convergent evolution across binders to different pathogen strains, and between antibodies with different genetic and even species origins.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/genetics
- Antibodies, Viral/chemistry
- Antibodies, Viral/genetics
- Antibodies, Viral/metabolism
- Antibody Specificity
- Antigen-Antibody Complex/chemistry
- Antigen-Antibody Complex/genetics
- Antigen-Antibody Reactions/genetics
- Antigen-Antibody Reactions/immunology
- Antigens, Viral/chemistry
- COVID-19/immunology
- COVID-19/virology
- Computational Biology
- Coronavirus/chemistry
- Coronavirus/genetics
- Coronavirus/immunology
- Databases, Chemical
- Epitope Mapping
- Epitopes, B-Lymphocyte/chemistry
- Epitopes, B-Lymphocyte/genetics
- Humans
- Mice
- Models, Molecular
- Pandemics
- SARS-CoV-2/chemistry
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Single-Domain Antibodies/immunology
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Affiliation(s)
- Sarah A Robinson
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, United Kingdom
| | - Matthew I J Raybould
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, United Kingdom
| | - Constantin Schneider
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, United Kingdom
| | - Wing Ki Wong
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, United Kingdom
| | - Claire Marks
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, United Kingdom
| | - Charlotte M Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, United Kingdom
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92
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Endothelial dysfunction contributes to severe COVID-19 in combination with dysregulated lymphocyte responses and cytokine networks. Signal Transduct Target Ther 2021; 6:418. [PMID: 34893580 PMCID: PMC8661333 DOI: 10.1038/s41392-021-00819-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/22/2021] [Accepted: 10/17/2021] [Indexed: 02/07/2023] Open
Abstract
The systemic processes involved in the manifestation of life-threatening COVID-19 and in disease recovery are still incompletely understood, despite investigations focusing on the dysregulation of immune responses after SARS-CoV-2 infection. To define hallmarks of severe COVID-19 in acute disease (n = 58) and in disease recovery in convalescent patients (n = 28) from Hannover Medical School, we used flow cytometry and proteomics data with unsupervised clustering analyses. In our observational study, we combined analyses of immune cells and cytokine/chemokine networks with endothelial activation and injury. ICU patients displayed an altered immune signature with prolonged lymphopenia but the expansion of granulocytes and plasmablasts along with activated and terminally differentiated T and NK cells and high levels of SARS-CoV-2-specific antibodies. The core signature of seven plasma proteins revealed a highly inflammatory microenvironment in addition to endothelial injury in severe COVID-19. Changes within this signature were associated with either disease progression or recovery. In summary, our data suggest that besides a strong inflammatory response, severe COVID-19 is driven by endothelial activation and barrier disruption, whereby recovery depends on the regeneration of the endothelial integrity.
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93
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Feldman J, Bals J, Altomare CG, St. Denis K, Lam EC, Hauser BM, Ronsard L, Sangesland M, Moreno TB, Okonkwo V, Hartojo N, Balazs AB, Bajic G, Lingwood D, Schmidt AG. Naive human B cells engage the receptor binding domain of SARS-CoV-2, variants of concern, and related sarbecoviruses. Sci Immunol 2021; 6:eabl5842. [PMID: 34648356 PMCID: PMC8720485 DOI: 10.1126/sciimmunol.abl5842] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Initial exposure to a pathogen elicits an adaptive immune response to control and eradicate the threat. Interrogating the abundance and specificity of the naive B cell repertoire drives understanding of how to mount protective responses. Here, we isolated naive B cells from eight seronegative human donors targeting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) receptor binding domain (RBD). Single-cell B cell receptor (BCR) sequencing identified diverse gene usage and no restriction on complementarity determining region length. A subset of recombinant antibodies produced by naive B cell precursors bound to SARS-CoV-2 RBD and engaged circulating variants including B.1.1.7, B.1.351, and B.1.617.2, as well as preemergent bat-derived coronaviruses RaTG13, SHC104, and WIV1. By structural characterization of a naive antibody in complex with SARS-CoV-2 spike, we identified a conserved mode of recognition shared with infection-induced antibodies. We found that representative naive antibodies could signal in a B cell activation assay, and by using directed evolution, we could select for a higher-affinity RBD interaction, conferred by a single amino acid change. The minimally mutated, affinity-matured antibodies also potently neutralized SARS-CoV-2. Understanding the SARS-CoV-2 RBD–specific naive repertoire may inform potential responses capable of recognizing future SARS-CoV-2 variants or emerging coronaviruses, enabling the development of pan-coronavirus vaccines aimed at engaging protective germline responses.
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Affiliation(s)
- Jared Feldman
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Julia Bals
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Clara G. Altomare
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Kerri St. Denis
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Evan C. Lam
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Blake M. Hauser
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Larance Ronsard
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Maya Sangesland
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | | | - Vintus Okonkwo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Nathania Hartojo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | | | - Goran Bajic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - 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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94
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Analysis of B cell receptor repertoires reveals key signatures of systemic B cell response after SARS-CoV-2 infection. J Virol 2021; 96:e0160021. [PMID: 34878902 PMCID: PMC8865482 DOI: 10.1128/jvi.01600-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
A comprehensive study of the B cell response against SARS-CoV-2 could be significant for understanding the immune response and developing therapeutical antibodies and vaccines. To define the dynamics and characteristics of the antibody repertoire following SARS-CoV-2 infection, we analyzed the mRNA transcripts of immunoglobulin heavy chain (IgH) repertoires of 24 peripheral blood samples collected between 3 and 111 days after symptom onset from 10 COVID-19 patients. Massive clonal expansion of naive B cells with limited somatic hypermutation (SHM) was observed in the second week after symptom onset. The proportion of low-SHM IgG clones strongly correlated with spike-specific IgG antibody titers, highlighting the significant activation of naive B cells in response to a novel virus infection. The antibody isotype switching landscape showed a transient IgA surge in the first week after symptom onset, followed by a sustained IgG elevation that lasted for at least 3 months. SARS-CoV-2 infection elicited poly-germ line reactive antibody responses. Interestingly, 17 different IGHV germ line genes recombined with IGHJ6 showed significant clonal expansion. By comparing the IgH repertoires that we sequenced with the 774 reported SARS-CoV-2–reactive monoclonal antibodies (MAbs), 13 shared spike-specific IgH clusters were found. These shared spike-specific IgH clusters are derived from the same lineage of several recently published neutralizing MAbs, including CC12.1, CC12.3, C102, REGN10977, and 4A8. Furthermore, identical spike-specific IgH sequences were found in different COVID-19 patients, suggesting a highly convergent antibody response to SARS-CoV-2. Our analysis based on sequencing antibody repertoires from different individuals revealed key signatures of the systemic B cell response induced by SARS-CoV-2 infection. IMPORTANCE Although the canonical delineation of serum antibody responses following SARS-CoV-2 infection has been well established, the dynamics of antibody repertoire at the mRNA transcriptional level has not been well understood, especially the correlation between serum antibody titers and the antibody mRNA transcripts. In this study, we analyzed the IgH transcripts and characterized the B cell clonal expansion and differentiation, isotype switching, and somatic hypermutation in COVID-19 patients. This study provided insights at the repertoire level for the B cell response after SARS-CoV-2 infection.
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95
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Willcox AC, Sung K, Garrett ME, Galloway JG, O’Connor MA, Erasmus JH, Logue JK, Hawman DW, Chu HY, Hasenkrug KJ, Fuller DH, Matsen FA, Overbaugh J. Macaque-human differences in SARS-CoV-2 Spike antibody response elicited by vaccination or infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.12.01.470697. [PMID: 34909774 PMCID: PMC8669841 DOI: 10.1101/2021.12.01.470697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Macaques are a commonly used model for studying immunity to human viruses, including for studies of SARS-CoV-2 infection and vaccination. However, it is unknown whether macaque antibody responses recapitulate, and thus appropriately model, the response in humans. To answer this question, we employed a phage-based deep mutational scanning approach (Phage-DMS) to compare which linear epitopes are targeted on the SARS-CoV-2 Spike protein in humans and macaques following either vaccination or infection. We also used Phage-DMS to determine antibody escape pathways within each epitope, enabling a granular comparison of antibody binding specificities at the locus level. Overall, we identified some common epitope targets in both macaques and humans, including in the fusion peptide (FP) and stem helix-heptad repeat 2 (SH-H) regions. Differences between groups included a response to epitopes in the N-terminal domain (NTD) and C-terminal domain (CTD) in vaccinated humans but not vaccinated macaques, as well as recognition of a CTD epitope and epitopes flanking the FP in convalescent macaques but not convalescent humans. There was also considerable variability in the escape pathways among individuals within each group. Sera from convalescent macaques showed the least variability in escape overall and converged on a common response with vaccinated humans in the SH-H epitope region, suggesting highly similar antibodies were elicited. Collectively, these findings suggest that the antibody response to SARS-CoV-2 in macaques shares many features with humans, but with substantial differences in the recognition of certain epitopes and considerable individual variability in antibody escape profiles, suggesting a diverse repertoire of antibodies that can respond to major epitopes in both humans and macaques.
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Affiliation(s)
- Alexandra C. Willcox
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Kevin Sung
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Meghan E. Garrett
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Jared G. Galloway
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Megan A. O’Connor
- Department of Microbiology, University of Washington, Seattle, WA, USA
- Infectious Diseases and Translational Medicine, Washington National Primate Research Center, Seattle, WA, USA
| | - Jesse H. Erasmus
- Department of Microbiology, University of Washington, Seattle, WA, USA
- HDT Bio, Seattle, WA, USA
| | | | - David W. Hawman
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Helen Y. Chu
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Kim J. Hasenkrug
- Laboratory of Persistent Viral Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Deborah H. Fuller
- Department of Microbiology, University of Washington, Seattle, WA, USA
- Infectious Diseases and Translational Medicine, Washington National Primate Research Center, Seattle, WA, USA
- Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA, USA
| | - Frederick A. Matsen
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Julie Overbaugh
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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96
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Wang L, Li G, Yuan C, Yang Y, Ling G, Zheng J, Zhou Y, Zhang T, Lin W, Lin Z. Progress in the Diagnosis and Treatment of COVID-19 in Children: A Review. Int J Gen Med 2021; 14:8097-8108. [PMID: 34795516 PMCID: PMC8594783 DOI: 10.2147/ijgm.s335888] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/27/2021] [Indexed: 12/14/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) has been circulating in many countries around the world, characterized by long incubation period, strong infectivity, strong variability, high population susceptibility and diversified transmission methods. Its causative agent is severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Compared with adult patients, the clinical manifestations of COVID-19 in children are often dominated by mild or asymptomatic infections, but children are also important virus carriers and play an important role in the transmission of the virus. In addition, some children will show excessive inflammatory response and experience serious complications such as multisystem inflammatory syndrome in children (MIS-C). At present, the research on COVID-19 in children is still imperfect. This article will review epidemiological characteristics, the mechanism of action, variant characteristics, clinical manifestations, auxiliary examinations and treatment of children with COVID-19, in order to provide help for the diagnosis, treatment and research of children with COVID-19.
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Affiliation(s)
- Libo Wang
- Department of Clinical Medicine, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, People's Republic of China
| | - Gan Li
- Department of Clinical Medicine, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, People's Republic of China
| | - Chang Yuan
- Department of Clinical Medicine, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, People's Republic of China
| | - Yuele Yang
- Department of Clinical Medicine, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, People's Republic of China
| | - Gongxia Ling
- Department of Clinical Medicine, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, People's Republic of China
| | - Jinyu Zheng
- Department of Clinical Medicine, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, People's Republic of China
| | - Yiyang Zhou
- Department of Clinical Medicine, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, People's Republic of China
| | - Tianlei Zhang
- Department of Clinical Medicine, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, People's Republic of China
| | - Wei Lin
- Department of Pediatrics, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, People's Republic of China
| | - Zhenlang Lin
- Department of Pediatrics, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, People's Republic of China
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97
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Perez-Saez J, Zaballa ME, Yerly S, Andrey DO, Meyer B, Eckerle I, Balavoine JF, Chappuis F, Pittet D, Trono D, Kherad O, Vuilleumier N, Kaiser L, Guessous I, Stringhini S, Azman AS. Persistence of anti-SARS-CoV-2 antibodies: immunoassay heterogeneity and implications for serosurveillance. Clin Microbiol Infect 2021; 27:1695.e7-1695.e12. [PMID: 34245905 PMCID: PMC8261139 DOI: 10.1016/j.cmi.2021.06.040] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/17/2021] [Accepted: 06/26/2021] [Indexed: 12/13/2022]
Abstract
OBJECTIVES Serological studies have been critical in tracking the evolution of the COVID-19 pandemic. Data on anti-SARS-CoV-2 antibodies persistence remain sparse, especially from infected individuals with few to no symptoms. The objective of the study was to quantify the sensitivity for detecting historic SARS-CoV-2 infections as a function of time since infection for three commercially available SARS-CoV-2 immunoassays and to explore the implications of decaying immunoassay sensitivity in estimating seroprevalence. METHODS We followed a cohort of mostly mild/asymptomatic SARS-CoV-2-infected individuals (n = 354) at least 8 months after their presumed infection date and tested their serum for anti-SARS-CoV-2 antibodies with three commercially available assays: Roche-N, Roche-RBD and EuroImmun-S1. We developed a latent class statistical model to infer the specificity and time-varying sensitivity of each assay and show through simulations how inappropriately accounting for test performance can lead to biased serosurvey estimates. RESULTS Antibodies were detected at follow-up in 74-100% of participants, depending on immunoassays. Both Roche assays maintain high sensitivity, with the EuroImmun assay missing 40% of infections after 9 months. Simulations reveal that without appropriate adjustment for time-varying assay sensitivity, seroprevalence surveys may underestimate infection rates. DISCUSSION Antibodies persist for at least 8 months after infection in a cohort of mildly infected individuals with detection depending on assay choice. Appropriate assay performance adjustment is important for the interpretation of serological studies in the case of diminishing sensitivity after infection.
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Affiliation(s)
- Javier Perez-Saez
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA; Institute of Global Health, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - María-Eugenia Zaballa
- Unit of Population Epidemiology, Division of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Sabine Yerly
- Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Diego O Andrey
- Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland; Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Benjamin Meyer
- Centre for Vaccinology, Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Isabella Eckerle
- Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland; Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland; Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | | | - François Chappuis
- Division and Department of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Didier Pittet
- Infection Control Program and World Health Organization Collaborating Center on Patient Safety, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Omar Kherad
- Division of Internal Medicine, Hôpital de la Tour and Faculty of Medicine, Geneva, Switzerland
| | - Nicolas Vuilleumier
- Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland; Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Laurent Kaiser
- Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland; Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland; Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Idris Guessous
- Division and Department of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland; Department of Health and Community Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Silvia Stringhini
- Unit of Population Epidemiology, Division of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland; Department of Health and Community Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland; University Center for General Medicine and Public Health, University of Lausanne, Lausanne, Switzerland
| | - Andrew S Azman
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA; Institute of Global Health, Faculty of Medicine, University of Geneva, Geneva, Switzerland; Unit of Population Epidemiology, Division of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland.
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98
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Bose P, Sunita P, Pattanayak SP. Molecular Insights into the Crosstalk Between Immune Inflammation Nexus and SARS-CoV-2 Virus. Curr Microbiol 2021; 78:3813-3828. [PMID: 34550435 PMCID: PMC8456397 DOI: 10.1007/s00284-021-02657-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 09/06/2021] [Indexed: 02/07/2023]
Abstract
COVID-19, a type of viral pneumonia caused by severe acute respiratory syndrome coronavirus 2 has challenged the world as global pandemic. It has marked the identification of third generation of extremely pathogenic zoonotic coronaviruses of twenty-first century posing threat to humans and mainly targeting the lower respiratory tract. In this review, we focused on not only the structure and virology of SARS-COV-2 but have discussed in detail the molecular immunopathogenesis of this novel virus highlighting its interaction with immune system and the role of compromised or dysregulated immune response towards disease severity. We attempted to correlate the crosstalk between unregulated inflammatory outcomes with disrupted host immunity which may play a potential role towards fatal acute respiratory distress syndrome that claims to be life-threatening in COVID-19. Exploration and investigation of molecular host-virus interactions will provide a better understanding on the mechanism of fatal COVID-19 infection and also enlighten the escape routes from the same.
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Affiliation(s)
- Pritha Bose
- Division of Pharmacology, Department of Pharmaceutical Sciences and Technology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Priyashree Sunita
- Government Pharmacy Institute, Govt. of Jharkhand, Bariatu, Ranchi, Jharkhand, 834009, India
| | - Shakti P Pattanayak
- Department of Pharmacy, School of Health Sciences, Central University of South Bihar, Govt. of India, Gaya, 824236, India.
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Burnett DL, Jackson KJL, Langley DB, Aggrawal A, Stella AO, Johansen MD, Balachandran H, Lenthall H, Rouet R, Walker G, Saunders BM, Singh M, Li H, Henry JY, Jackson J, Stewart AG, Witthauer F, Spence MA, Hansbro NG, Jackson C, Schofield P, Milthorpe C, Martinello M, Schulz SR, Roth E, Kelleher A, Emery S, Britton WJ, Rawlinson WD, Karl R, Schäfer S, Winkler TH, Brink R, Bull RA, Hansbro PM, Jäck HM, Turville S, Christ D, Goodnow CC. Immunizations with diverse sarbecovirus receptor-binding domains elicit SARS-CoV-2 neutralizing antibodies against a conserved site of vulnerability. Immunity 2021; 54:2908-2921.e6. [PMID: 34788600 PMCID: PMC8554075 DOI: 10.1016/j.immuni.2021.10.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/24/2021] [Accepted: 10/22/2021] [Indexed: 12/15/2022]
Abstract
Viral mutations are an emerging concern in reducing SARS-CoV-2 vaccination efficacy. Second-generation vaccines will need to elicit neutralizing antibodies against sites that are evolutionarily conserved across the sarbecovirus subgenus. Here, we immunized mice containing a human antibody repertoire with diverse sarbecovirus receptor-binding domains (RBDs) to identify antibodies targeting conserved sites of vulnerability. Antibodies with broad reactivity against diverse clade B RBDs targeting the conserved class 4 epitope, with recurring IGHV/IGKV pairs, were readily elicited but were non-neutralizing. However, rare class 4 antibodies binding this conserved RBD supersite showed potent neutralization of SARS-CoV-2 and all variants of concern. Structural analysis revealed that the neutralizing ability of cross-reactive antibodies was reserved only for those with an elongated CDRH3 that extends the antiparallel beta-sheet RBD core and orients the antibody light chain to obstruct ACE2-RBD interactions. These results identify a structurally defined pathway for vaccine strategies eliciting escape-resistant SARS-CoV-2 neutralizing antibodies.
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Affiliation(s)
- Deborah L Burnett
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia.
| | | | - David B Langley
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | | | | | - Matt D Johansen
- Center for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW 2006, Australia
| | | | - Helen Lenthall
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Romain Rouet
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia
| | - Gregory Walker
- UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia
| | - Bernadette M Saunders
- Center for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW 2006, Australia
| | - Mandeep Singh
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia
| | - Hui Li
- Kirby Institute, UNSW, Sydney, NSW 2052, Australia
| | - Jake Y Henry
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Jennifer Jackson
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Alastair G Stewart
- UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia; Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia
| | - Franka Witthauer
- Division of Molecular Immunology, University Hospital Erlangen, University of Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Matthew A Spence
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Nicole G Hansbro
- Center for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW 2006, Australia
| | - Colin Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Peter Schofield
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia
| | - Claire Milthorpe
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | | | - Sebastian R Schulz
- Division of Molecular Immunology, University Hospital Erlangen, University of Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Edith Roth
- Division of Molecular Immunology, University Hospital Erlangen, University of Erlangen-Nürnberg, Erlangen 91054, Germany
| | | | - Sean Emery
- Kirby Institute, UNSW, Sydney, NSW 2052, Australia
| | - Warwick J Britton
- Centenary Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - William D Rawlinson
- UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia; Serology and Virology Division (SAViD), NSW Health Pathology, SEALS Randwick, Sydney, NSW 2031, Australia
| | - Rudolfo Karl
- Division of Genetics, Department Biology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen 91054, Germany
| | - Simon Schäfer
- Division of Genetics, Department Biology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen 91054, Germany
| | - Thomas H Winkler
- Division of Genetics, Department Biology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen 91054, Germany
| | - Robert Brink
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia
| | - Rowena A Bull
- UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia; Kirby Institute, UNSW, Sydney, NSW 2052, Australia
| | - Philip M Hansbro
- Center for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW 2006, Australia
| | - Hans-Martin Jäck
- Division of Molecular Immunology, University Hospital Erlangen, University of Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Stuart Turville
- UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia; Kirby Institute, UNSW, Sydney, NSW 2052, Australia
| | - Daniel Christ
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia
| | - Christopher C Goodnow
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; Cellular Genomics Futures Institute, UNSW Sydney, Sydney, NSW 2052, Australia
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Dalle Carbonare L, Valenti MT, Bisoffi Z, Piubelli C, Pizzato M, Accordini S, Mariotto S, Ferrari S, Minoia A, Bertacco J, Li Vigni V, Dorelli G, Crisafulli E, Alberti D, Masin L, Tiberti N, Longoni SS, Lopalco L, Beretta A, Zipeto D. Serology study after BTN162b2 vaccination in participants previously infected with SARS-CoV-2 in two different waves versus naïve. COMMUNICATIONS MEDICINE 2021; 1:38. [PMID: 35602204 PMCID: PMC9053253 DOI: 10.1038/s43856-021-00039-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/22/2021] [Indexed: 12/13/2022] Open
Abstract
Background The antibody response to SARS-CoV-2 mRNA vaccines in individuals with waning immunity generated by a previous SARS-CoV-2 infection, as well as the patterns of IgA and IgM responses in previously infected and in naïve individuals are still poorly understood. Methods We performed a serology study in a cohort of BTN162b2 mRNA vaccine recipients who were immunologically naïve (N, n = 50) or had been previously infected with SARS-CoV-2 (P.I., n = 51) during the first (n = 25) or second (n = 26) pandemic waves in Italy, respectively. We measured IgG, IgM and IgA antibodies against the SARS-CoV-2 Spike (S) and IgG against the nucleocapsid (N) proteins, as well as the neutralizing activity of sera collected before vaccination, after the first and second dose of vaccine. Results Most P.I. individuals from the first pandemic wave who showed declining antibody titres responded to the first vaccine dose with IgG-S and pseudovirus neutralization titres that were significantly higher than those observed in N individuals after the second vaccine dose. In all recipients, a single dose of vaccine was sufficient to induce a potent IgA response that was not associated with serum neutralization titres. We observed an unconventional pattern of IgM responses that were elicited in only half of immunologically naïve subjects even after the second vaccine dose. Conclusions The response to a single dose of vaccine in P.I. individuals is more potent than that observed in N individuals after two doses. Vaccine-induced IgA are not associated with serum neutralization.
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Grants
- FUR 2020 Department of Excellence 2018-2022, MIUR, Italy, and the Brain Research Foundation Verona (D.Z.), the Italian Ministry of Health under “Fondi Ricerca Corrente – L1P5” and “Progetto COVID Ricerca Finalizzata 2020 12371675” to IRCCS Sacro Cuore Don Calabria Hospital (Z.B., C.P., N.T., S.L.), Fondazione VRT/CARITRO (M.P., S.A.), the COVID Research Projects 2020, Italian Ministry of Health, COVID2020-12371617 (L.L.).
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Affiliation(s)
| | | | - Zeno Bisoffi
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar (Verona), Italy
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Chiara Piubelli
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar (Verona), Italy
| | - Massimo Pizzato
- Department of Cellular, Computational and Integrative Biology, University of Trento, Povo (Trento), Italy
| | - Silvia Accordini
- Department of Cellular, Computational and Integrative Biology, University of Trento, Povo (Trento), Italy
| | - Sara Mariotto
- Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Sergio Ferrari
- Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Arianna Minoia
- Department of Medicine, University of Verona, Verona, Italy
| | | | | | | | | | - Daniela Alberti
- Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Laura Masin
- Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Natalia Tiberti
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar (Verona), Italy
| | - Silvia Stefania Longoni
- Department of Infectious, Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar (Verona), Italy
| | - Lucia Lopalco
- Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milan, Italy
| | | | - Donato Zipeto
- Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
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