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Martín-Martín C, del Riego ES, Castiñeira JRV, Zapico-Gonzalez MS, Rodríguez-Pérez M, Corte-Iglesias V, Saiz ML, Diaz-Bulnes P, Escudero D, Suárez-Alvarez B, López-Larrea C. Assessing Predictive Value of SARS-CoV-2 Epitope-Specific CD8 + T-Cell Response in Patients with Severe Symptoms. Vaccines (Basel) 2024; 12:679. [PMID: 38932408 PMCID: PMC11209605 DOI: 10.3390/vaccines12060679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/10/2024] [Accepted: 06/15/2024] [Indexed: 06/28/2024] Open
Abstract
Specific T cell responses against SARS-CoV-2 provided an overview of acquired immunity during the pandemic. Anti-SARS-CoV-2 immunity determines the severity of acute illness, but also might be related to the possible persistence of symptoms (long COVID). We retrospectively analyzed ex vivo longitudinal CD8+ T cell responses in 26 COVID-19 patients diagnosed with severe disease, initially (1 month) and long-term (10 months), and in a cohort of 32 vaccinated healthcare workers without previous SARS-CoV-2 infection. We used peptide-human leukocyte antigen (pHLA) dextramers recognizing 26 SARS-CoV-2-derived epitopes of viral and other non-structural proteins. Most patients responded to at least one of the peptides studied, mainly derived from non-structural ORF1ab proteins. After 10 months follow-up, CD8+ T cell responses were maintained at long term and reaction against certain epitopes (A*01:01-ORF1ab1637) was still detected and functional, showing a memory-like phenotype (CD127+ PD-1+). The total number of SARS-CoV-2-specific CD8+ T cells was significantly associated with protection against long COVID in these patients. Compared with vaccination, infected patients showed a less effective immune response to spike protein-derived peptides restricted by HLA. So, the A*01:01-S865 and A*24:02-S1208 dextramers were only recognized in vaccinated individuals. We conclude that initial SARS-CoV-2-specific CD8+ T cell response could be used as a marker to understand the evolution of severe disease and post-acute sequelae after SARS-CoV-2 infection.
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Affiliation(s)
- Cristina Martín-Martín
- Translational Immunology, Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011 Oviedo, Spain; (C.M.-M.); (J.R.V.C.); (V.C.-I.); (M.L.S.); (P.D.-B.)
| | - Estefanía Salgado del Riego
- Service of Intensive Medicine, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain; (E.S.d.R.); (D.E.)
- Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011 Oviedo, Spain
| | - Jose R. Vidal Castiñeira
- Translational Immunology, Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011 Oviedo, Spain; (C.M.-M.); (J.R.V.C.); (V.C.-I.); (M.L.S.); (P.D.-B.)
- Immunology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
| | | | - Mercedes Rodríguez-Pérez
- Microbiology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain; (M.S.Z.-G.); (M.R.-P.)
- Translational Microbiology, Health Research Institute of Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Viviana Corte-Iglesias
- Translational Immunology, Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011 Oviedo, Spain; (C.M.-M.); (J.R.V.C.); (V.C.-I.); (M.L.S.); (P.D.-B.)
- Immunology Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
| | - Maria Laura Saiz
- Translational Immunology, Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011 Oviedo, Spain; (C.M.-M.); (J.R.V.C.); (V.C.-I.); (M.L.S.); (P.D.-B.)
| | - Paula Diaz-Bulnes
- Translational Immunology, Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011 Oviedo, Spain; (C.M.-M.); (J.R.V.C.); (V.C.-I.); (M.L.S.); (P.D.-B.)
| | - Dolores Escudero
- Service of Intensive Medicine, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain; (E.S.d.R.); (D.E.)
- Translational Microbiology, Health Research Institute of Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Beatriz Suárez-Alvarez
- Translational Immunology, Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011 Oviedo, Spain; (C.M.-M.); (J.R.V.C.); (V.C.-I.); (M.L.S.); (P.D.-B.)
| | - Carlos López-Larrea
- Translational Immunology, Health Research Institute of the Principality of Asturias (ISPA), Avenida de Roma S/N, 33011 Oviedo, Spain; (C.M.-M.); (J.R.V.C.); (V.C.-I.); (M.L.S.); (P.D.-B.)
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Peluso MJ, Abdel-Mohsen M, Henrich TJ, Roan NR. Systems analysis of innate and adaptive immunity in Long COVID. Semin Immunol 2024; 72:101873. [PMID: 38460395 DOI: 10.1016/j.smim.2024.101873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/11/2024]
Abstract
Since the onset of the COVID-19 pandemic, significant progress has been made in developing effective preventive and therapeutic strategies against severe acute SARS-CoV-2 infection. However, the management of Long COVID (LC), an infection-associated chronic condition that has been estimated to affect 5-20% of individuals following SARS-CoV-2 infection, remains challenging due to our limited understanding of its mechanisms. Although LC is a heterogeneous disease that is likely to have several subtypes, immune system disturbances appear common across many cases. The extent to which these immune perturbations contribute to LC symptoms, however, is not entirely clear. Recent advancements in multi-omics technologies, capable of detailed, cell-level analysis, have provided valuable insights into the immune perturbations associated with LC. Although these studies are largely descriptive in nature, they are the crucial first step towards a deeper understanding of the condition and the immune system's role in its development, progression, and resolution. In this review, we summarize the current understanding of immune perturbations in LC, covering both innate and adaptive immune responses, and the cytokines and analytes involved. We explore whether these findings support or challenge the primary hypotheses about LC's underlying mechanisms. We also discuss the crosstalk between various immune system components and how it can be disrupted in LC. Finally, we emphasize the need for more tissue- and subtype-focused analyses of LC, and for enhanced collaborative efforts to analyze common specimens from large cohorts, including those undergoing therapeutic interventions. These collective efforts are vital to unravel the fundaments of this new disease, and could also shed light on the prevention and treatment of the larger family of chronic illnesses linked to other microbial infections.
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Affiliation(s)
- Michael J Peluso
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | | | - Timothy J Henrich
- Division of Experimental Medicine, University of California, San Francisco, USA
| | - Nadia R Roan
- Gladstone Institutes, University of California, San Francisco, USA; Department of Urology, University of California, San Francisco, USA.
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3
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Yin K, Peluso MJ, Luo X, Thomas R, Shin MG, Neidleman J, Andrew A, Young KC, Ma T, Hoh R, Anglin K, Huang B, Argueta U, Lopez M, Valdivieso D, Asare K, Deveau TM, Munter SE, Ibrahim R, Ständker L, Lu S, Goldberg SA, Lee SA, Lynch KL, Kelly JD, Martin JN, Münch J, Deeks SG, Henrich TJ, Roan NR. Long COVID manifests with T cell dysregulation, inflammation and an uncoordinated adaptive immune response to SARS-CoV-2. Nat Immunol 2024; 25:218-225. [PMID: 38212464 PMCID: PMC10834368 DOI: 10.1038/s41590-023-01724-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 11/29/2023] [Indexed: 01/13/2024]
Abstract
Long COVID (LC) occurs after at least 10% of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, yet its etiology remains poorly understood. We used 'omic" assays and serology to deeply characterize the global and SARS-CoV-2-specific immunity in the blood of individuals with clear LC and non-LC clinical trajectories, 8 months postinfection. We found that LC individuals exhibited systemic inflammation and immune dysregulation. This was evidenced by global differences in T cell subset distribution implying ongoing immune responses, as well as by sex-specific perturbations in cytolytic subsets. LC individuals displayed increased frequencies of CD4+ T cells poised to migrate to inflamed tissues and exhausted SARS-CoV-2-specific CD8+ T cells, higher levels of SARS-CoV-2 antibodies and a mis-coordination between their SARS-CoV-2-specific T and B cell responses. Our analysis suggested an improper crosstalk between the cellular and humoral adaptive immunity in LC, which can lead to immune dysregulation, inflammation and clinical symptoms associated with this debilitating condition.
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Affiliation(s)
- Kailin Yin
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Michael J Peluso
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Xiaoyu Luo
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Reuben Thomas
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA
| | - Min-Gyoung Shin
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA
| | - Jason Neidleman
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Alicer Andrew
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Kyrlia C Young
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Tongcui Ma
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Khamal Anglin
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Beatrice Huang
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Urania Argueta
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Monica Lopez
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Daisy Valdivieso
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Kofi Asare
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Tyler-Marie Deveau
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Sadie E Munter
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Rania Ibrahim
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Ludger Ständker
- Core Facility Functional Peptidomics, Ulm University Medical Center, Ulm, Germany
| | - Scott Lu
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Sarah A Goldberg
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Sulggi A Lee
- Zuckerberg San Francisco General Hospital and the University of California, San Francisco, San Francisco, CA, USA
| | - Kara L Lynch
- Division of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - J Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Jeffrey N Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Jan Münch
- Core Facility Functional Peptidomics, Ulm University Medical Center, Ulm, Germany
| | - Steven G Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Timothy J Henrich
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, USA.
| | - Nadia R Roan
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA.
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA.
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Soni J, Chattopadhyay P, Mehta P, Mohite R, Tardalkar K, Joshi M, Pandey R. Dynamics of Whole Transcriptome Analysis (WTA) and Surface markers expression (AbSeq) in Immune Cells of COVID-19 Patients and Recovered captured through Single Cell Genomics. Front Med (Lausanne) 2024; 11:1297001. [PMID: 38357647 PMCID: PMC10864604 DOI: 10.3389/fmed.2024.1297001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/15/2024] [Indexed: 02/16/2024] Open
Abstract
Introduction Single-cell multi-omics studies, such as multidimensional transcriptomics (whole transcriptomic analysis, WTA), and surface marker analysis (antibody sequencing, AbSeq), have turned out to be valuable techniques that offer inaccessible possibilities for single-cell profiling of mRNA, lncRNA, and proteins. Methods We used this technique to understand the dynamics of mRNA and protein-level differences in healthy, COVID-19-infected and recovered individuals using peripheral blood mononuclear cells (PBMCs). Our results demonstrate that compared to mRNA expression, protein abundance is a better indicator of the disease state. Results We demonstrate that compared to mRNA expression, protein abundance is a better indicator of the disease state. We observed high levels of cell identity and regulatory markers, CD3E, CD4, CD8A, CD5, CD7, GITR, and KLRB1 in healthy individuals, whereas markers related to cell activation, CD38, CD28, CD69, CD62L, CD14, and CD16 elevated in the SARS-CoV-2 infected patients at both WTA and AbSeq levels. Curiously, in recovered individuals, there was a high expression of cytokine and chemokine receptors (CCR5, CCR7, CCR4, CXCR3, and PTGRD2). We also observed variations in the expression of markers within cell populations under different states. Discussion Furthermore, our study emphasizes the significance of employing an oligo-based method (AbSeq) that can help in diagnosis, prognosis, and protection from disease/s by identifying cell surface markers that are unique to different cell types or states. It also allows simultaneous study of a vast array of markers, surpassing the constraints of techniques like FACS to query the vast repertoire of proteins.
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Affiliation(s)
- Jyoti Soni
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Partha Chattopadhyay
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Priyanka Mehta
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ramakant Mohite
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Kishore Tardalkar
- Department of Stem Cells & Regenerative Medicine, D. Y. Patil Education Society, Kolhapur, India
| | - Meghnad Joshi
- Department of Stem Cells & Regenerative Medicine, D. Y. Patil Education Society, Kolhapur, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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5
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Cojocaru E, Cojocaru T, Pînzariu GM, Vasiliu I, Armașu I, Cojocaru C. Perspectives on Post-COVID-19 Pulmonary Fibrosis Treatment. J Pers Med 2023; 14:51. [PMID: 38248752 PMCID: PMC10817460 DOI: 10.3390/jpm14010051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/19/2023] [Accepted: 12/26/2023] [Indexed: 01/23/2024] Open
Abstract
Pulmonary fibrosis, a critical outcome of chronic inflammatory diseases, has gained prominence in the context of post-coronavirus (post-COVID-19) complications. This review delves into the multifaceted landscape of post-COVID-19 pulmonary fibrosis, elucidating the intricate molecular mechanisms underlying its pathogenesis and highlighting promising therapeutic avenues. Examining the aftermath of severe acute respiratory syndrome-2 (SARS-CoV-2) infection, the review reveals key signaling pathways implicated in the fibrotic cascade. Drawing parallels with previous coronavirus outbreaks enhances our understanding of the distinctive features of post-COVID-19 fibrosis. Antifibrotic drugs, like pirfenidone and nintedanib, take center stage; their mechanisms of action and potential applications in post-COVID-19 cases are thoroughly explored. Beyond the established treatments, this review investigates emerging therapeutic modalities, including anti-interleukin agents, immunosuppressants, and experimental compounds, like buloxybutide, saracatinib, sirolimus, and resveratrol. Emphasizing the critical importance of early intervention, this review highlights the dynamic nature of post-COVID-19 pulmonary fibrosis research. In conclusion, the synthesis of current knowledge offers a foundation for advancing our approaches to the prevention and treatment of these consequential sequelae of COVID-19.
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Affiliation(s)
- Elena Cojocaru
- Morpho-Functional Sciences II Department, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania; (E.C.); (I.V.)
| | - Tudor Cojocaru
- Faculty of Medicine, University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania; (G.M.P.); (I.A.)
| | - Giulia Mihaela Pînzariu
- Faculty of Medicine, University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania; (G.M.P.); (I.A.)
| | - Ioana Vasiliu
- Morpho-Functional Sciences II Department, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania; (E.C.); (I.V.)
| | - Ioana Armașu
- Faculty of Medicine, University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania; (G.M.P.); (I.A.)
| | - Cristian Cojocaru
- Medical III Department, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania;
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Fraga-Silva TF, Cipriano UG, Fumagalli MJ, Correa GF, Fuzo CA, dos-Santos D, Mestriner FL, Becari C, Teixeira-Carvalho A, Coelho-dos-Reis J, Menegueti MG, Figueiredo LT, Cunha LD, Martins-Filho OA, Dias-Baruffi M, Auxiliadora-Martins M, Tostes RC, Bonato VL. Airway epithelial cells and macrophages trigger IL-6-CD95/CD95L axis and mediate initial immunopathology of COVID-19. iScience 2023; 26:108366. [PMID: 38047070 PMCID: PMC10692667 DOI: 10.1016/j.isci.2023.108366] [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: 10/07/2022] [Revised: 09/09/2023] [Accepted: 10/26/2023] [Indexed: 12/05/2023] Open
Abstract
Airway epithelial cells (AEC) infected with SARS-CoV-2 may drive the dysfunction of macrophages during COVID-19. We hypothesized that the direct interaction of AEC with macrophages mediated by CD95/CD95L or indirect interaction mediated by IL-6 signaling are key steps for the COVID-19 severe acute inflammation. The interaction of macrophages with apoptotic and infected AEC increased CD95 and CD163 expression, and induced macrophage death. Macrophages exposed to tracheal aspirate with high IL-6 levels from intubated patients with COVID-19 or to recombinant human IL-6 exhibited decreased HLA-DR expression, increased CD95 and CD163 expression and IL-1β production. IL-6 effects on macrophages were prevented by both CD95/CD95L antagonist and by IL-6 receptor antagonist and IL-6 or CD95 deficient mice showed significant reduction of acute pulmonary inflammation post-infection. Our findings show a non-canonical CD95L-CD95 pathway that simultaneously drives both macrophage activation and dysfunction and point to CD95/CD95L axis as therapeutic target.
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Affiliation(s)
- Thais F.C. Fraga-Silva
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo 14049-900, Brazil
| | - Ualter G. Cipriano
- Basic and Applied Immunology Program, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo 14049-900, Brazil
| | - Marcilio J. Fumagalli
- Basic and Applied Immunology Program, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo 14049-900, Brazil
| | - Giseli F. Correa
- Basic and Applied Immunology Program, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo 14049-900, Brazil
| | - Carlos A. Fuzo
- Department of Clinical Analysis, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo 14049-900, Brazil
| | - Douglas dos-Santos
- Department of Cell Biology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo 14049-900, Brazil
| | - Fabiola L.A.C. Mestriner
- Department of Surgery and Anatomy, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo 14049-900, Brazil
| | - Christiane Becari
- Department of Surgery and Anatomy, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo 14049-900, Brazil
| | - Andrea Teixeira-Carvalho
- René Rachou Institute, Oswaldo Cruz Foundation, FIOCRUZ-Minas, Belo Horizonte, Minas Gerais 30190-009, Brazil
| | - Jordana Coelho-dos-Reis
- Department of Microbiology, Biological Science Institute, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Mayra G. Menegueti
- Department of General and Specialized Nursing, Ribeirao Preto Nurse School, University of Sao Paulo, Ribeirao Preto, Sao Paulo 14049-900, Brazil
| | - Luiz T.M. Figueiredo
- Basic and Applied Immunology Program, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo 14049-900, Brazil
- Virology Research Center, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo 14049-900, Brazil
| | - Larissa Dias Cunha
- Department of Cell Biology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo 14049-900, Brazil
| | - Olindo A. Martins-Filho
- René Rachou Institute, Oswaldo Cruz Foundation, FIOCRUZ-Minas, Belo Horizonte, Minas Gerais 30190-009, Brazil
| | - Marcelo Dias-Baruffi
- Department of Clinical Analysis, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo 14049-900, Brazil
| | - Maria Auxiliadora-Martins
- Department of Surgery and Anatomy, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo 14049-900, Brazil
| | - Rita C. Tostes
- Department of Pharmacology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo 14049-900, Brazil
| | - Vania L.D. Bonato
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo 14049-900, Brazil
- Basic and Applied Immunology Program, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo 14049-900, Brazil
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7
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Markov NS, Ren Z, Senkow KJ, Grant RA, Gao CA, Malsin ES, Sichizya L, Kihshen H, Helmin KA, Jovisic M, Arnold JM, Pérez-Leonor XG, Abdala-Valencia H, Swaminathan S, Nwaezeapu J, Kang M, Rasmussen L, Ozer EA, Lorenzo-Redondo R, Hultquist JF, Simons LM, Rios-Guzman E, Misharin AV, Wunderink RG, Budinger GS, Singer BD, Morales-Nebreda L. A distinctive evolution of alveolar T cell responses is associated with clinical outcomes in unvaccinated patients with SARS-CoV-2 pneumonia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571479. [PMID: 38168346 PMCID: PMC10760069 DOI: 10.1101/2023.12.13.571479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Pathogen clearance and resolution of inflammation in patients with pneumonia require an effective local T cell response. Nevertheless, local T cell activation may drive lung injury, particularly during prolonged episodes of respiratory failure characteristic of severe SARS-CoV-2 pneumonia. While T cell responses in the peripheral blood are well described, the evolution of T cell phenotypes and molecular signatures in the distal lung of patients with severe pneumonia caused by SARS-CoV-2 or other pathogens is understudied. Accordingly, we serially obtained 432 bronchoalveolar lavage fluid samples from 273 patients with severe pneumonia and respiratory failure, including 74 unvaccinated patients with COVID-19, and performed flow cytometry, transcriptional, and T cell receptor profiling on sorted CD8+ and CD4+ T cell subsets. In patients with COVID-19 but not pneumonia secondary to other pathogens, we found that early and persistent enrichment in CD8+ and CD4+ T cell subsets correlated with survival to hospital discharge. Activation of interferon signaling pathways early after intubation for COVID-19 was associated with favorable outcomes, while activation of NF-κB-driven programs late in disease was associated with poor outcomes. Patients with SARS-CoV-2 pneumonia whose alveolar T cells preferentially targeted the Spike and Nucleocapsid proteins tended to experience more favorable outcomes than patients whose T cells predominantly targeted the ORF1ab polyprotein complex. These results suggest that in patients with severe SARS-CoV-2 pneumonia, alveolar T cell interferon responses targeting structural SARS-CoV-2 proteins characterize patients who recover, yet these responses progress to NF-κB activation against non-structural proteins in patients who go on to experience poor clinical outcomes.
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Affiliation(s)
- Nikolay S. Markov
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Ziyou Ren
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Karolina J. Senkow
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Rogan A. Grant
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Catherine A. Gao
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Elizabeth S. Malsin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Lango Sichizya
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Hermon Kihshen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Kathryn A. Helmin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Milica Jovisic
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Jason M. Arnold
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | | | - Hiam Abdala-Valencia
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Suchitra Swaminathan
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Julu Nwaezeapu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Mengjia Kang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Luke Rasmussen
- Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Egon A. Ozer
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Ramon Lorenzo-Redondo
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Judd F. Hultquist
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Lacy M. Simons
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Estefany Rios-Guzman
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Alexander V. Misharin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Richard G. Wunderink
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - G.R. Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Benjamin D. Singer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Luisa Morales-Nebreda
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
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8
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Cai C, Gao Y, Adamo S, Rivera-Ballesteros O, Hansson L, Österborg A, Bergman P, Sandberg JK, Ljunggren HG, Björkström NK, Strålin K, Llewellyn-Lacey S, Price DA, Qin C, Grifoni A, Weiskopf D, Wherry EJ, Sette A, Aleman S, Buggert M. SARS-CoV-2 vaccination enhances the effector qualities of spike-specific T cells induced by COVID-19. Sci Immunol 2023; 8:eadh0687. [PMID: 38064569 PMCID: PMC7615587 DOI: 10.1126/sciimmunol.adh0687] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 10/31/2023] [Indexed: 12/18/2023]
Abstract
T cells are critical for immune protection against severe COVID-19, but it has remained unclear whether repeated exposure to SARS-CoV-2 antigens delivered in the context of vaccination fuels T cell exhaustion or reshapes T cell functionality. Here, we sampled convalescent donors with a history of mild or severe COVID-19 before and after SARS-CoV-2 vaccination to profile the functional spectrum of hybrid T cell immunity. Using combined single-cell technologies and high-dimensional flow cytometry, we found that the frequencies and functional capabilities of spike-specific CD4+ and CD8+ T cells in previously infected individuals were enhanced by vaccination, despite concomitant increases in the expression of inhibitory receptors such as PD-1 and TIM3. In contrast, CD4+ and CD8+ T cells targeting non-spike proteins remained functionally static and waned over time, and only minimal effects were observed in healthy vaccinated donors experiencing breakthrough infections with SARS-CoV-2. Moreover, hybrid immunity was characterized by elevated expression of IFN-γ, which was linked with clonotype specificity in the CD8+ T cell lineage. Collectively, these findings identify a molecular hallmark of hybrid immunity and suggest that vaccination after infection is associated with cumulative immunological benefits over time, potentially conferring enhanced protection against subsequent episodes of COVID-19.
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Affiliation(s)
- Curtis Cai
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Yu Gao
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Sarah Adamo
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Olga Rivera-Ballesteros
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Lotta Hansson
- Department of Hematology, Karolinska University Hospital, Stockholm, Sweden
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Anders Österborg
- Department of Hematology, Karolinska University Hospital, Stockholm, Sweden
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Peter Bergman
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Johan K. Sandberg
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Hans-Gustaf Ljunggren
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Niklas K. Björkström
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Kristoffer Strålin
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Medicine Huddinge, Infectious Diseases, Karolinska Institutet, Stockholm, Sweden
| | - Sian Llewellyn-Lacey
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, UK
| | - David A. Price
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, UK
- Systems Immunity Research Institute, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, UK
| | - Chuan Qin
- Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing, China
- National Health Commission Key Laboratory of Human Disease Comparative Medicine, Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, California, USA
| | - E. John Wherry
- Institute for Immunology, Perelman School of Medicine at the University of Pennsylvania, Pennsylvania, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine at the University of Pennsylvania, Pennsylvania, USA
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine at the University of Pennsylvania, Pennsylvania, USA
| | - Alessandro Sette
- National Health Commission Key Laboratory of Human Disease Comparative Medicine, Comparative Medicine Center, Peking Union Medical College, Beijing, China
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, California, USA
| | - Soo Aleman
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Medicine Huddinge, Infectious Diseases, Karolinska Institutet, Stockholm, Sweden
| | - Marcus Buggert
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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9
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Chen DG, Xie J, Su Y, Heath JR. T cell receptor sequences are the dominant factor contributing to the phenotype of CD8 + T cells with specificities against immunogenic viral antigens. Cell Rep 2023; 42:113279. [PMID: 37883974 PMCID: PMC10729740 DOI: 10.1016/j.celrep.2023.113279] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 08/23/2023] [Accepted: 09/29/2023] [Indexed: 10/28/2023] Open
Abstract
Antigen-specific CD8+ T cells mediate pathogen clearance. T cell phenotype is influenced by T cell receptor (TCR) sequences and environmental signals. Quantitative comparisons of these factors in human disease, while challenging to obtain, can provide foundational insights into basic T cell biology. Here, we investigate the phenotype kinetics of 679 CD8+ T cell clonotypes, each with specificity against one of three immunogenic viral antigens. Data were collected from a longitudinal study of 68 COVID-19 patients with antigens from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), cytomegalovirus (CMV), and influenza. Each antigen is associated with a different type of immune activation during COVID-19. We find TCR sequence to be by far the most important factor in shaping T cell phenotype and persistence for populations specific to any of these antigens. Our work demonstrates the important relationship between TCR sequence and T cell phenotype and persistence and helps explain why T cell phenotype often appears to be determined early in an infection.
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Affiliation(s)
- Daniel G Chen
- Institute of Systems Biology, Seattle, WA 98109, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Clinical Research Division, Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jingyi Xie
- Institute of Systems Biology, Seattle, WA 98109, USA; Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA 98105, USA
| | - Yapeng Su
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Clinical Research Division, Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - James R Heath
- Institute of Systems Biology, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98105, USA.
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10
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Yusuf M, Destiarani W, Widayat W, Yosua Y, Gumilar G, Tanudireja AS, Rohmatulloh FG, Maulana FA, Baroroh U, Hardianto A, Maharani R, Nurainy N, Wijayadikusumah AR, Ristandi RB, Atmosukarto IIC, Subroto T. Coarse-grained molecular dynamics-guided immunoinformatics to explain the binder and non-binder classification of Cytotoxic T-cell epitope for SARS-CoV-2 peptide-based vaccine discovery. PLoS One 2023; 18:e0292156. [PMID: 37796941 PMCID: PMC10553366 DOI: 10.1371/journal.pone.0292156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/13/2023] [Indexed: 10/07/2023] Open
Abstract
Epitope-based peptide vaccine can elicit T-cell immunity against SARS-CoV-2 to clear the infection. However, finding the best epitope from the whole antigen is challenging. A peptide screening using immunoinformatics usually starts from MHC-binding peptide, immunogenicity, cross-reactivity with the human proteome, to toxicity analysis. This pipeline classified the peptides into three categories, i.e., strong-, weak-, and non-binder, without incorporating the structural aspect. For this reason, the molecular detail that discriminates the binders from non-binder is interesting to be investigated. In this study, five CTL epitopes against HLA-A*02:01 were identified from the coarse-grained molecular dynamics-guided immunoinformatics screening. The strong binder showed distinctive activities from the non-binder in terms of structural and energetic properties. Furthermore, the second residue from the nonameric peptide was most important in the interaction with HLA-A*02:01. By understanding the nature of MHC-peptide interaction, we hoped to improve the chance of finding the best epitope for a peptide vaccine candidate.
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Affiliation(s)
- Muhammad Yusuf
- Faculty of Mathematics and Natural Sciences, Department of Chemistry, Universitas Padjadjaran, Bandung, West Java, Indonesia
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, West Java, Indonesia
| | - Wanda Destiarani
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, West Java, Indonesia
| | - Wahyu Widayat
- Faculty of Pharmacy, Pharmaceutical Biology Science, Universitas Mulawarman, Samarinda, East Kalimantan, Indonesia
| | - Yosua Yosua
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, West Java, Indonesia
| | - Gilang Gumilar
- Research Center for Electronics, National Research and Innovation Agency Republic of Indonesia (BRIN), Bandung, West Java, Indonesia
| | - Angelica Shalfani Tanudireja
- Faculty of Mathematics and Natural Sciences, Department of Chemistry, Universitas Padjadjaran, Bandung, West Java, Indonesia
| | - Fauzian Giansyah Rohmatulloh
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, West Java, Indonesia
| | - Farhan Azhwin Maulana
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, West Java, Indonesia
| | - Umi Baroroh
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, West Java, Indonesia
- Department of Biotechnology, Indonesian School of Pharmacy, Bandung, West Java, Indonesia
| | - Ari Hardianto
- Faculty of Mathematics and Natural Sciences, Department of Chemistry, Universitas Padjadjaran, Bandung, West Java, Indonesia
| | - Rani Maharani
- Faculty of Mathematics and Natural Sciences, Department of Chemistry, Universitas Padjadjaran, Bandung, West Java, Indonesia
| | - Neni Nurainy
- Department of Research and Development, PT Bio Farma, Bandung, West Java, Indonesia
| | | | - Ryan B. Ristandi
- West Java Provincial Reference Laboratory, Bandung, West Java, Indonesia
| | | | - Toto Subroto
- Faculty of Mathematics and Natural Sciences, Department of Chemistry, Universitas Padjadjaran, Bandung, West Java, Indonesia
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, West Java, Indonesia
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11
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Ma T, Suryawanshi RK, Miller SR, Ly KK, Thomas R, Elphick N, Yin K, Luo X, Kaliss N, Chen IP, Montano M, Sreekumar B, Standker L, Münch J, Heath Damron F, Palop JJ, Ott M, Roan NR. Post-acute immunological and behavioral sequelae in mice after Omicron infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.543758. [PMID: 37333294 PMCID: PMC10274741 DOI: 10.1101/2023.06.05.543758] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Progress in understanding long COVID and developing effective therapeutics is hampered in part by the lack of suitable animal models. Here we used ACE2-transgenic mice recovered from Omicron (BA.1) infection to test for pulmonary and behavioral post-acute sequelae. Through in-depth phenotyping by CyTOF, we demonstrate that naïve mice experiencing a first Omicron infection exhibit profound immune perturbations in the lung after resolving acute infection. This is not observed if mice were first vaccinated with spike-encoding mRNA. The protective effects of vaccination against post-acute sequelae were associated with a highly polyfunctional SARS-CoV-2-specific T cell response that was recalled upon BA.1 breakthrough infection but not seen with BA.1 infection alone. Without vaccination, the chemokine receptor CXCR4 was uniquely upregulated on multiple pulmonary immune subsets in the BA.1 convalescent mice, a process previously connected to severe COVID-19. Taking advantage of recent developments in machine learning and computer vision, we demonstrate that BA.1 convalescent mice exhibited spontaneous behavioral changes, emotional alterations, and cognitive-related deficits in context habituation. Collectively, our data identify immunological and behavioral post-acute sequelae after Omicron infection and uncover a protective effect of vaccination against post-acute pulmonary immune perturbations.
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Affiliation(s)
- Tongcui Ma
- Gladstone Institutes of Virology, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, United States
| | | | - Stephanie R. Miller
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, CA 94158, USA
| | - Katie K. Ly
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, CA 94158, USA
| | - Reuben Thomas
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Natalie Elphick
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Kailin Yin
- Gladstone Institutes of Virology, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, United States
| | - Xiaoyu Luo
- Gladstone Institutes of Virology, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, United States
| | - Nick Kaliss
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, CA 94158, USA
| | - Irene P Chen
- Gladstone Institutes of Virology, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California San Francisco; San Francisco, CA, USA
- Department of Medicine, University of California San Francisco; San Francisco, CA, USA
- Core Facility Functional Peptidomics, Ulm University Medical Center, Meyerhofstrasse 1, Ulm, Germany
| | | | | | - Ludger Standker
- Core Facility Functional Peptidomics, Ulm University Medical Center, Meyerhofstrasse 1, Ulm, Germany
| | - Jan Münch
- Core Facility Functional Peptidomics, Ulm University Medical Center, Meyerhofstrasse 1, Ulm, Germany
| | - F. Heath Damron
- Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine, Morgantown WV, USA
| | - Jorge J. Palop
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, CA 94158, USA
| | - Melanie Ott
- Gladstone Institutes of Virology, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco; San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Nadia R. Roan
- Gladstone Institutes of Virology, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, United States
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12
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Burke B, Rocha SM, Zhan S, Eckley M, Reasoner C, Addetia A, Lewis J, Fagre A, Charley PA, Richt JA, Weiss SR, Tjalkens RB, Veesler D, Aboellail T, Schountz T. Regulatory T cell-like response to SARS-CoV-2 in Jamaican fruit bats (Artibeus jamaicensis) transduced with human ACE2. PLoS Pathog 2023; 19:e1011728. [PMID: 37856551 PMCID: PMC10617724 DOI: 10.1371/journal.ppat.1011728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 10/31/2023] [Accepted: 10/02/2023] [Indexed: 10/21/2023] Open
Abstract
Insectivorous Old World horseshoe bats (Rhinolophus spp.) are the likely source of the ancestral SARS-CoV-2 prior to its spillover into humans and causing the COVID-19 pandemic. Natural coronavirus infections of bats appear to be principally confined to the intestines, suggesting fecal-oral transmission; however, little is known about the biology of SARS-related coronaviruses in bats. Previous experimental challenges of Egyptian fruit bats (Rousettus aegyptiacus) resulted in limited infection restricted to the respiratory tract, whereas insectivorous North American big brown bats (Eptesicus fuscus) showed no evidence of infection. In the present study, we challenged Jamaican fruit bats (Artibeus jamaicensis) with SARS-CoV-2 to determine their susceptibility. Infection was confined to the intestine for only a few days with prominent viral nucleocapsid antigen in epithelial cells, and mononuclear cells of the lamina propria and Peyer's patches, but with no evidence of infection of other tissues; none of the bats showed visible signs of disease or seroconverted. Expression levels of ACE2 were low in the lungs, which may account for the lack of pulmonary infection. Bats were then intranasally inoculated with a replication-defective adenovirus encoding human ACE2 and 5 days later challenged with SARS-CoV-2. Viral antigen was prominent in lungs for up to 14 days, with loss of pulmonary cellularity during this time; however, the bats did not exhibit weight loss or visible signs of disease. From day 7, bats had low to moderate IgG antibody titers to spike protein by ELISA, and one bat on day 10 had low-titer neutralizing antibodies. CD4+ helper T cells became activated upon ex vivo recall stimulation with SARS-CoV-2 nucleocapsid peptide library and exhibited elevated mRNA expression of the regulatory T cell cytokines interleukin-10 and transforming growth factor-β, which may have limited inflammatory pathology. Collectively, these data show that Jamaican fruit bats are poorly susceptible to SARS-CoV-2 but that expression of human ACE2 in their lungs leads to robust infection and an adaptive immune response with low-titer antibodies and a regulatory T cell-like response that may explain the lack of prominent inflammation in the lungs. This model will allow for insight of how SARS-CoV-2 infects bats and how bat innate and adaptive immune responses engage the virus without overt clinical disease.
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Affiliation(s)
- Bradly Burke
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - Savannah M. Rocha
- Department of Environmental and Radiological Health Sciences, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - Shijun Zhan
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - Miles Eckley
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - Clara Reasoner
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - Amin Addetia
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Juliette Lewis
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - Anna Fagre
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - Phillida A. Charley
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - Juergen A. Richt
- Diagnostic Medicine/Pathobiology, Center of Excellence for Emerging and Zoonotic Animal Diseases, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, United States of America
| | - Susan R. Weiss
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ronald B. Tjalkens
- Department of Environmental and Radiological Health Sciences, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Tawfik Aboellail
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
| | - Tony Schountz
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine, Colorado State University, Fort Collins, Colorado, United States of America
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13
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Upadhyay V, Suryawanshi RK, Tasoff P, McCavitt-Malvido M, Kumar RG, Murray VW, Noecker C, Bisanz JE, Hswen Y, Ha CWY, Sreekumar B, Chen IP, Lynch SV, Ott M, Lee S, Turnbaugh PJ. Mild SARS-CoV-2 infection results in long-lasting microbiota instability. mBio 2023; 14:e0088923. [PMID: 37294090 PMCID: PMC10470529 DOI: 10.1128/mbio.00889-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 04/12/2023] [Indexed: 06/10/2023] Open
Abstract
Viruses targeting mammalian cells can indirectly alter the gut microbiota, potentially compounding their phenotypic effects. Multiple studies have observed a disrupted gut microbiota in severe cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection that require hospitalization. Yet, despite demographic shifts in disease severity resulting in a large and continuing burden of non-hospitalized infections, we still know very little about the impact of mild SARS-CoV-2 infection on the gut microbiota in the outpatient setting. To address this knowledge gap, we longitudinally sampled 14 SARS-CoV-2-positive subjects who remained outpatient and 4 household controls. SARS-CoV-2 cases exhibited a significantly less stable gut microbiota relative to controls. These results were confirmed and extended in the K18-humanized angiotensin-converting enzyme 2 mouse model, which is susceptible to SARS-CoV-2 infection. All of the tested SARS-CoV-2 variants significantly disrupted the mouse gut microbiota, including USA-WA1/2020 (the original variant detected in the USA), Delta, and Omicron. Surprisingly, despite the fact that the Omicron variant caused the least severe symptoms in mice, it destabilized the gut microbiota and led to a significant depletion in Akkermansia muciniphila. Furthermore, exposure of wild-type C57BL/6J mice to SARS-CoV-2 disrupted the gut microbiota in the absence of severe lung pathology. IMPORTANCE Taken together, our results demonstrate that even mild cases of SARS-CoV-2 can disrupt gut microbial ecology. Our findings in non-hospitalized individuals are consistent with studies of hospitalized patients, in that reproducible shifts in gut microbial taxonomic abundance in response to SARS-CoV-2 have been difficult to identify. Instead, we report a long-lasting instability in the gut microbiota. Surprisingly, our mouse experiments revealed an impact of the Omicron variant, despite producing the least severe symptoms in genetically susceptible mice, suggesting that despite the continued evolution of SARS-CoV-2, it has retained its ability to perturb the intestinal mucosa. These results will hopefully renew efforts to study the mechanisms through which Omicron and future SARS-CoV-2 variants alter gastrointestinal physiology, while also considering the potentially broad consequences of SARS-CoV-2-induced microbiota instability for host health and disease.
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Affiliation(s)
- Vaibhav Upadhyay
- Department of Microbiology and Immunology, G.W. Hooper Research Foundation, University of California, San Francisco, California, USA
- Department of Medicine, University of California San Francisco, University of California, San Francisco, California, USA
- Department of Medicine, Benioff Center for Microbiome Medicine, University of California, San Francisco, California, USA
| | | | - Preston Tasoff
- Department of Medicine, Benioff Center for Microbiome Medicine, University of California, San Francisco, California, USA
| | | | | | - Victoria Wong Murray
- Department of Medicine, University of California San Francisco, University of California, San Francisco, California, USA
| | - Cecilia Noecker
- Department of Microbiology and Immunology, G.W. Hooper Research Foundation, University of California, San Francisco, California, USA
- Department of Medicine, Benioff Center for Microbiome Medicine, University of California, San Francisco, California, USA
| | - Jordan E. Bisanz
- Department of Microbiology and Immunology, G.W. Hooper Research Foundation, University of California, San Francisco, California, USA
| | - Yulin Hswen
- Department of Epidemiology and Biostatistics and the Bakar Computational Health Institute, University of California San Francisco, San Francisco, California, USA
| | - Connie W. Y. Ha
- Department of Medicine, Benioff Center for Microbiome Medicine, University of California, San Francisco, California, USA
| | | | - Irene P. Chen
- Gladstone Institutes, San Francisco, California, USA
| | - Susan V. Lynch
- Department of Medicine, University of California San Francisco, University of California, San Francisco, California, USA
- Department of Medicine, Benioff Center for Microbiome Medicine, University of California, San Francisco, California, USA
- Department of Pediatrics, University of California San Francisco, University of California, San Francisco, California, USA
| | - Melanie Ott
- Department of Medicine, University of California San Francisco, University of California, San Francisco, California, USA
- Gladstone Institutes, San Francisco, California, USA
- Chan Zuckerberg Biohub-San Francisco, San Francisco, California, USA
| | - Sulggi Lee
- Department of Medicine, University of California San Francisco, University of California, San Francisco, California, USA
| | - Peter J. Turnbaugh
- Department of Microbiology and Immunology, G.W. Hooper Research Foundation, University of California, San Francisco, California, USA
- Department of Medicine, Benioff Center for Microbiome Medicine, University of California, San Francisco, California, USA
- Chan Zuckerberg Biohub-San Francisco, San Francisco, California, USA
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14
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Baird S, Ashley CL, Marsh‐Wakefield F, Alca S, Ashhurst TM, Ferguson AL, Lukeman H, Counoupas C, Post JJ, Konecny P, Bartlett A, Martinello M, Bull RA, Lloyd A, Grey A, Hutchings O, Palendira U, Britton WJ, Steain M, Triccas JA. A unique cytotoxic CD4 + T cell-signature defines critical COVID-19. Clin Transl Immunology 2023; 12:e1463. [PMID: 37645435 PMCID: PMC10461786 DOI: 10.1002/cti2.1463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/04/2023] [Accepted: 08/11/2023] [Indexed: 08/31/2023] Open
Abstract
Objectives SARS-CoV-2 infection causes a spectrum of clinical disease presentation, ranging from asymptomatic to fatal. While neutralising antibody (NAb) responses correlate with protection against symptomatic and severe infection, the contribution of the T-cell response to disease resolution or progression is still unclear. As newly emerging variants of concern have the capacity to partially escape NAb responses, defining the contribution of individual T-cell subsets to disease outcome is imperative to inform the development of next-generation COVID-19 vaccines. Methods Immunophenotyping of T-cell responses in unvaccinated individuals was performed, representing the full spectrum of COVID-19 clinical presentation. Computational and manual analyses were used to identify T-cell populations associated with distinct disease states. Results Critical SARS-CoV-2 infection was characterised by an increase in activated and cytotoxic CD4+ lymphocytes (CTL). These CD4+ CTLs were largely absent in asymptomatic to severe disease states. In contrast, non-critical COVID-19 was associated with high frequencies of naïve T cells and lack of activation marker expression. Conclusion Highly activated and cytotoxic CD4+ T-cell responses may contribute to cell-mediated host tissue damage and progression of COVID-19. Induction of these potentially detrimental T-cell responses should be considered when developing and implementing effective COVID-19 control strategies.
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Affiliation(s)
- Sarah Baird
- Sydney Infectious Diseases Institute, Faculty of Medicine and HealthThe University of SydneyNSWCamperdownAustralia
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
| | - Caroline L Ashley
- Sydney Infectious Diseases Institute, Faculty of Medicine and HealthThe University of SydneyNSWCamperdownAustralia
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
| | - Felix Marsh‐Wakefield
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
- Liver Injury and Cancer ProgramCentenary InstituteCamperdownNSWAustralia
- Human Cancer and Viral Immunology LaboratoryThe University of SydneyCamperdownNSWAustralia
| | - Sibel Alca
- Sydney Infectious Diseases Institute, Faculty of Medicine and HealthThe University of SydneyNSWCamperdownAustralia
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
| | - Thomas M Ashhurst
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
- Sydney Cytometry Core Research FacilityCharles Perkins Centre, Centenary Institute and The University of SydneyCamperdownNSWAustralia
| | - Angela L Ferguson
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
- Liver Injury and Cancer ProgramCentenary InstituteCamperdownNSWAustralia
| | - Hannah Lukeman
- Sydney Infectious Diseases Institute, Faculty of Medicine and HealthThe University of SydneyNSWCamperdownAustralia
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
| | - Claudio Counoupas
- Sydney Infectious Diseases Institute, Faculty of Medicine and HealthThe University of SydneyNSWCamperdownAustralia
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
- Tuberculosis Research ProgramCentenary InstituteSydneyNSWAustralia
| | - Jeffrey J Post
- Prince of Wales Clinical SchoolUNSWSydneyNSWAustralia
- School of Clinical Medicine, Medicine & HealthUNSWSydneyNSWAustralia
| | - Pamela Konecny
- Prince of Wales Clinical SchoolUNSWSydneyNSWAustralia
- St George HospitalSydneyNSWAustralia
| | - Adam Bartlett
- The Kirby Institute, UNSWSydneyNSWAustralia
- School of Biomedical Sciences, Medicine & HealthUNSWSydneyNSWAustralia
- Sydney Children's HospitalSydneyNSWAustralia
| | | | - Rowena A Bull
- The Kirby Institute, UNSWSydneyNSWAustralia
- School of Biomedical Sciences, Medicine & HealthUNSWSydneyNSWAustralia
| | - Andrew Lloyd
- The Kirby Institute, UNSWSydneyNSWAustralia
- School of Biomedical Sciences, Medicine & HealthUNSWSydneyNSWAustralia
| | - Alice Grey
- RPA Virtual Hospital, Sydney Local Health DistrictSydneyNSWAustralia
| | - Owen Hutchings
- RPA Virtual Hospital, Sydney Local Health DistrictSydneyNSWAustralia
| | - Umaimainthan Palendira
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
- Liver Injury and Cancer ProgramCentenary InstituteCamperdownNSWAustralia
| | - Warwick J Britton
- Tuberculosis Research ProgramCentenary InstituteSydneyNSWAustralia
- Department of Clinical ImmunologyRoyal Prince Alfred HospitalCamperdownNSWAustralia
| | - Megan Steain
- Sydney Infectious Diseases Institute, Faculty of Medicine and HealthThe University of SydneyNSWCamperdownAustralia
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
| | - James A Triccas
- Sydney Infectious Diseases Institute, Faculty of Medicine and HealthThe University of SydneyNSWCamperdownAustralia
- School of Medical Sciences and Charles Perkins CentreThe University of SydneyCamperdownNSWAustralia
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15
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Yin K, Peluso MJ, Luo X, Thomas R, Shin MG, Neidleman J, Andrew A, Young K, Ma T, Hoh R, Anglin K, Huang B, Argueta U, Lopez M, Valdivieso D, Asare K, Deveau TM, Munter SE, Ibrahim R, Ständker L, Lu S, Goldberg SA, Lee SA, Lynch KL, Kelly JD, Martin JN, Münch J, Deeks SG, Henrich TJ, Roan NR. Long COVID manifests with T cell dysregulation, inflammation, and an uncoordinated adaptive immune response to SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.09.527892. [PMID: 36798286 PMCID: PMC9934605 DOI: 10.1101/2023.02.09.527892] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Long COVID (LC), a type of post-acute sequelae of SARS-CoV-2 infection (PASC), occurs after at least 10% of SARS-CoV-2 infections, yet its etiology remains poorly understood. Here, we used multiple "omics" assays (CyTOF, RNAseq/scRNAseq, Olink) and serology to deeply characterize both global and SARS-CoV-2-specific immunity from blood of individuals with clear LC and non-LC clinical trajectories, 8 months following infection and prior to receipt of any SARS-CoV-2 vaccine. Our analysis focused on deep phenotyping of T cells, which play important roles in immunity against SARS-CoV-2 yet may also contribute to COVID-19 pathogenesis. Our findings demonstrate that individuals with LC exhibit systemic inflammation and immune dysregulation. This is evidenced by global differences in T cell subset distribution in ways that imply ongoing immune responses, as well as by sex-specific perturbations in cytolytic subsets. Individuals with LC harbored increased frequencies of CD4+ T cells poised to migrate to inflamed tissues, and exhausted SARS-CoV-2-specific CD8+ T cells. They also harbored significantly higher levels of SARS-CoV-2 antibodies, and in contrast to non-LC individuals, exhibited a mis-coordination between their SARS-CoV-2-specific T and B cell responses. RNAseq/scRNAseq and Olink analyses similarly revealed immune dysregulatory mechanisms, along with non-immune associated perturbations, in individuals with LC. Collectively, our data suggest that proper crosstalk between the humoral and cellular arms of adaptive immunity has broken down in LC, and that this, perhaps in the context of persistent virus, leads to the immune dysregulation, inflammation, and clinical symptoms associated with this debilitating condition.
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Affiliation(s)
- Kailin Yin
- Gladstone Institutes, University of California, San Francisco, USA
- Department of Urology, University of California, San Francisco, USA
| | - Michael J Peluso
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Xiaoyu Luo
- Gladstone Institutes, University of California, San Francisco, USA
- Department of Urology, University of California, San Francisco, USA
| | - Reuben Thomas
- Gladstone Institutes, University of California, San Francisco, USA
| | - Min-Gyoung Shin
- Gladstone Institutes, University of California, San Francisco, USA
| | - Jason Neidleman
- Gladstone Institutes, University of California, San Francisco, USA
- Department of Urology, University of California, San Francisco, USA
| | - Alicer Andrew
- Gladstone Institutes, University of California, San Francisco, USA
- Department of Urology, University of California, San Francisco, USA
| | - Kyrlia Young
- Gladstone Institutes, University of California, San Francisco, USA
- Department of Urology, University of California, San Francisco, USA
| | - Tongcui Ma
- Gladstone Institutes, University of California, San Francisco, USA
- Department of Urology, University of California, San Francisco, USA
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Khamal Anglin
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Beatrice Huang
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Urania Argueta
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Monica Lopez
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Daisy Valdivieso
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Kofi Asare
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Tyler-Marie Deveau
- Division of Experimental Medicine, University of California, San Francisco, USA
| | - Sadie E Munter
- Division of Experimental Medicine, University of California, San Francisco, USA
| | - Rania Ibrahim
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Ludger Ständker
- Core Facility Functional Peptidomics, Ulm University Medical Center, Meyerhofstrasse 1, Ulm, Germany
| | - Scott Lu
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
| | - Sarah A Goldberg
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
| | - Sulggi A Lee
- Zuckerberg San Francisco General Hospital and the University of California, San Francisco, USA
| | - Kara L Lynch
- Division of Laboratory Medicine, University of California, San Francisco, USA
| | - J Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
| | - Jeffrey N Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
| | - Jan Münch
- Core Facility Functional Peptidomics, Ulm University Medical Center, Meyerhofstrasse 1, Ulm, Germany
| | - Steven G Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Timothy J Henrich
- Division of Experimental Medicine, University of California, San Francisco, USA
| | - Nadia R Roan
- Gladstone Institutes, University of California, San Francisco, USA
- Department of Urology, University of California, San Francisco, USA
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16
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Hoffman TW, Leavis HL, Smits BM, van der Veken LT, van Kessel DA. Prolonged Disease Course of COVID-19 in a Patient with CTLA-4 Haploinsufficiency. Case Reports Immunol 2023; 2023:3977739. [PMID: 37260564 PMCID: PMC10228224 DOI: 10.1155/2023/3977739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 04/23/2023] [Accepted: 05/05/2023] [Indexed: 06/02/2023] Open
Abstract
Patients with primary immunodeficiencies are especially vulnerable to developing severe coronavirus disease 2019 (COVID-19) after infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Cytotoxic T lymphocyte antigen-4 (CTLA-4) is an important regulator of immune responses, and patients who suffer from CTLA4 haploinsufficiency have hyperactivation of effector T cells and infiltration of various organs. Overexpression of CTLA4 has been associated with a more severe disease course in patients with COVID-19, but there have only been a few reports on the disease course of COVID-19 in patients with CTLA4 haploinsufficiency. We report on a 33-year-old female with a history of immune thrombocytopenia, autoimmune haemolytic anaemia, granulomatous-lymphocytic interstitial lung disease, and common variable immunodeficiency who developed COVID-19. She was admitted and discharged from the hospital several times in the months thereafter and remained symptomatic and had a positive SARS-CoV-2 PCR for up to 137 days after the first symptoms. No SARS-CoV-2 antibodies were identified in the patients' serum. The disease was finally controlled after repeated infusions of convalescent plasma and treatment of concurrent bacterial and fungal infections. Genetic analysis revealed a likely pathogenic variant in CTLA4, and CTLA4 expression on regulatory T-cells was low. This case illustrates that patients with primary immunodeficiencies who have a protracted disease course of COVID-19 could benefit from convalescent plasma therapy.
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Affiliation(s)
- T. W. Hoffman
- Department of Pulmonology, St. Antonius Hospital, Koekoekslaan 1, 3435 CM, Nieuwegein, Netherlands
| | - H. L. Leavis
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, Netherlands
| | - B. M. Smits
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, Netherlands
| | - L. T. van der Veken
- Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, Netherlands
| | - D. A. van Kessel
- Department of Pulmonology, St. Antonius Hospital, Koekoekslaan 1, 3435 CM, Nieuwegein, Netherlands
- Department of Pulmonology, Division of Heart and Lungs, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, Netherlands
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17
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George AF, Roan NR. Advances in HIV Research Using Mass Cytometry. Curr HIV/AIDS Rep 2023; 20:76-85. [PMID: 36689119 PMCID: PMC9869313 DOI: 10.1007/s11904-023-00649-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2023] [Indexed: 01/24/2023]
Abstract
PURPOSE OF REVIEW This review describes how advances in CyTOF and high-dimensional analysis methods have furthered our understanding of HIV transmission, pathogenesis, persistence, and immunity. RECENT FINDINGS CyTOF has generated important insight on several aspects of HIV biology: (1) the differences between cells permissive to productive vs. latent HIV infection, and the HIV-induced remodeling of infected cells; (2) factors that contribute to the persistence of the long-term HIV reservoir, in both blood and tissues; and (3) the impact of HIV on the immune system, in the context of both uncontrolled and controlled infection. CyTOF and high-dimensional analysis tools have enabled in-depth assessment of specific host antigens remodeled by HIV, and have revealed insights into the features of HIV-infected cells enabling them to survive and persist, and of the immune cells that can respond to and potentially control HIV replication. CyTOF and other related high-dimensional phenotyping approaches remain powerful tools for translational research, and applied HIV to cohort studies can inform on mechanisms of HIV pathogenesis and persistence, and potentially identify biomarkers for viral eradication or control.
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Affiliation(s)
- Ashley F George
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Urology, University of California at San Francisco, San Francisco, CA, 94143, USA
| | - Nadia R Roan
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, 94158, USA.
- Department of Urology, University of California at San Francisco, San Francisco, CA, 94143, USA.
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18
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Yang G, Wang J, Sun P, Qin J, Yang X, Chen D, Zhang Y, Zhong N, Wang Z. SARS-CoV-2 epitope-specific T cells: Immunity response feature, TCR repertoire characteristics and cross-reactivity. Front Immunol 2023; 14:1146196. [PMID: 36969254 PMCID: PMC10036809 DOI: 10.3389/fimmu.2023.1146196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/01/2023] [Indexed: 03/12/2023] Open
Abstract
The devastating COVID-19 pandemic caused by SARS-CoV-2 and multiple variants or subvariants remains an ongoing global challenge. SARS-CoV-2-specific T cell responses play a critical role in early virus clearance, disease severity control, limiting the viral transmission and underpinning COVID-19 vaccine efficacy. Studies estimated broad and robust T cell responses in each individual recognized at least 30 to 40 SARS-CoV-2 antigen epitopes and associated with COVID-19 clinical outcome. Several key immunodominant viral proteome epitopes, including S protein- and non-S protein-derived epitopes, may primarily induce potent and long-lasting antiviral protective effects. In this review, we summarized the immune response features of immunodominant epitope-specific T cells targeting different SRAS-CoV-2 proteome structures after infection and vaccination, including abundance, magnitude, frequency, phenotypic features and response kinetics. Further, we analyzed the epitopes immunodominance hierarchy in combination with multiple epitope-specific T cell attributes and TCR repertoires characteristics, and discussed the significant implications of cross-reactive T cells toward HCoVs, SRAS-CoV-2 and variants of concern, especially Omicron. This review may be essential for mapping the landscape of T cell responses toward SARS-CoV-2 and optimizing the current vaccine strategy.
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Affiliation(s)
- Gang Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Guangzhou Laboratory, Guangzhou, China
- Department of Pulmonary and Critical Care Medicine, The First People’s Hospital of Yunnan Province, Kunming, China
| | - Junxiang Wang
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Ping Sun
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Jian Qin
- Department of Pulmonary and Critical Care Medicine, The First People’s Hospital of Yunnan Province, Kunming, China
| | - Xiaoyun Yang
- Guangzhou Laboratory, Guangzhou, China
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Daxiang Chen
- Guangzhou Laboratory, Guangzhou, China
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Yunhui Zhang
- Department of Pulmonary and Critical Care Medicine, The First People’s Hospital of Yunnan Province, Kunming, China
- *Correspondence: Zhongfang Wang, ; Nanshan Zhong, ; Yunhui Zhang,
| | - Nanshan Zhong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Guangzhou Laboratory, Guangzhou, China
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Zhongfang Wang, ; Nanshan Zhong, ; Yunhui Zhang,
| | - Zhongfang Wang
- Guangzhou Laboratory, Guangzhou, China
- State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
- *Correspondence: Zhongfang Wang, ; Nanshan Zhong, ; Yunhui Zhang,
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19
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Kapten K, Orczyk K, Smolewska E. Immunity in SARS-CoV-2 Infection: Clarity or Mystery? A Broader Perspective in the Third Year of a Worldwide Pandemic. Arch Immunol Ther Exp (Warsz) 2023; 71:7. [PMID: 36810662 PMCID: PMC9943048 DOI: 10.1007/s00005-023-00673-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/09/2023] [Indexed: 02/23/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and its mechanisms have been thoroughly studied by researchers all over the world with the hope of finding answers that may aid the discovery of new treatment options or effective means of prevention. Still, over 2 years into the pandemic that is an immense burden on health care and economic systems, there seem to be more questions than answers. The character and multitude of immune responses elicited in coronavirus disease 2019 (COVID-19) vary from uncontrollable activation of the inflammatory system, causing extensive tissue damage and consequently leading to severe or even fatal disease, to mild or asymptomatic infections in the majority of patients, resulting in the unpredictability of the current pandemic. The aim of the study was to systematize the available data regarding the immune response to SARS-CoV-2, to provide some clarification among the abundance of the knowledge available. The review contains concise and current information on the most significant immune reactions to COVID-19, including components of both innate and adaptive immunity, with an additional focus on utilizing humoral and cellular responses as effective diagnostic tools. Moreover, the authors discussed the present state of knowledge on SARS-CoV-2 vaccines and their efficacy in cases of immunodeficiency.
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Affiliation(s)
- Katarzyna Kapten
- Department of Pediatric Cardiology and Rheumatology, Central Teaching Hospital of Medical University of Lodz, Lodz, Poland
| | - Krzysztof Orczyk
- Department of Pediatric Cardiology and Rheumatology, Medical University of Lodz, Sporna 36/50, 91-738, Lodz, Poland
| | - Elzbieta Smolewska
- Department of Pediatric Cardiology and Rheumatology, Medical University of Lodz, Sporna 36/50, 91-738, Lodz, Poland.
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20
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Burke B, Rocha SM, Zhan S, Eckley M, Reasoner C, Addetia A, Lewis J, Fagre A, Charley P, Richt JA, Weiss SR, Tjalkens RB, Veesler D, Aboellail T, Schountz T. Regulatory T Cell-like Response to SARS-CoV-2 in Jamaican Fruit Bats ( Artibeus jamaicensis ) Transduced with Human ACE2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.13.528205. [PMID: 36824814 PMCID: PMC9949052 DOI: 10.1101/2023.02.13.528205] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Insectivorous Old World horseshoe bats ( Rhinolophus spp.) are the likely source of the ancestral SARS-CoV-2 prior to its spillover into humans and causing the COVID-19 pandemic. Natural coronavirus infections of bats appear to be principally confined to the intestines, suggesting fecal-oral transmission; however, little is known about the biology of SARS-related coronaviruses in bats. Previous experimental challenges of Egyptian fruit bats ( Rousettus aegyptiacus ) resulted in limited infection restricted to the respiratory tract, whereas insectivorous North American big brown bats ( Eptesicus fuscus ) showed no evidence of infection. In the present study, we challenged Jamaican fruit bats ( Artibeus jamaicensis ) with SARS-CoV-2 to determine their susceptibility. Infection was confined to the intestine for only a few days with prominent viral nucleocapsid antigen in epithelial cells, and mononuclear cells of the lamina propria and Peyer's patches, but with no evidence of infection of other tissues; none of the bats showed visible signs of disease or seroconverted. Expression levels of ACE2 were low in the lungs, which may account for the lack of pulmonary infection. Bats were then intranasally inoculated with a replication-defective adenovirus encoding human ACE2 and 5 days later challenged with SARS-CoV-2. Viral antigen was prominent in lungs for up to 14 days, with loss of pulmonary cellularity during this time; however, the bats did not exhibit weight loss or visible signs of disease. From day 7, bats had low to moderate IgG antibody titers to spike protein by ELISA, and one bat on day 10 had low-titer neutralizing antibodies. CD4 + helper T cells became activated upon ex vivo recall stimulation with SARS-CoV-2 nucleocapsid peptide library and exhibited elevated mRNA expression of the regulatory T cell cytokines interleukin-10 and transforming growth factor-β, which may have limited inflammatory pathology. Collectively, these data show that Jamaican fruit bats are poorly susceptibility to SARS-CoV-2 but that expression of human ACE2 in their lungs leads to robust infection and an adaptive immune response with low-titer antibodies and a regulatory T cell-like response that may explain the lack of prominent inflammation in the lungs. This model will allow for insight of how SARS-CoV-2 infects bats and how bat innate and adaptive immune responses engage the virus without overt clinical disease. Author Summary Bats are reservoir hosts of many viruses that infect humans, yet little is known about how they host these viruses, principally because of a lack of relevant and susceptible bat experimental infection models. Although SARS-CoV-2 originated in bats, no robust infection models of bats have been established. We determined that Jamaican fruit bats are poorly susceptible to SARS-CoV-2; however, their lungs can be transduced with human ACE2, which renders them susceptible to SARS-CoV-2. Despite robust infection of the lungs and diminishment of pulmonary cellularity, the bats showed no overt signs of disease and cleared the infection after two weeks. Despite clearance of infection, only low-titer antibody responses occurred and only a single bat made neutralizing antibody. Assessment of the CD4 + helper T cell response showed that activated cells expressed the regulatory T cell cytokines IL-10 and TGFβ that may have tempered pulmonary inflammation.
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21
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Clancy J, Hoffmann CS, Pickett BE. Transcriptomics secondary analysis of severe human infection with SARS-CoV-2 identifies gene expression changes and predicts three transcriptional biomarkers in leukocytes. Comput Struct Biotechnol J 2023; 21:1403-1413. [PMID: 36785619 PMCID: PMC9908618 DOI: 10.1016/j.csbj.2023.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 02/02/2023] [Accepted: 02/02/2023] [Indexed: 02/11/2023] Open
Abstract
SARS-CoV-2 is the causative agent of COVID-19, which has greatly affected human health since it first emerged. Defining the human factors and biomarkers that differentiate severe SARS-CoV-2 infection from mild infection has become of increasing interest to clinicians. To help address this need, we retrieved 269 public RNA-seq human transcriptome samples from GEO that had qualitative disease severity metadata. We then subjected these samples to a robust RNA-seq data processing workflow to calculate gene expression in PBMCs, whole blood, and leukocytes, as well as to predict transcriptional biomarkers in PBMCs and leukocytes. This process involved using Salmon for read mapping, edgeR to calculate significant differential expression levels, and gene ontology enrichment using Camera. We then performed a random forest machine learning analysis on the read counts data to identify genes that best classified samples based on the COVID-19 severity phenotype. This approach produced a ranked list of leukocyte genes based on their Gini values that includes TGFBI, TTYH2, and CD4, which are associated with both the immune response and inflammation. Our results show that these three genes can potentially classify samples with severe COVID-19 with accuracy of ∼88% and an area under the receiver operating characteristic curve of 92.6--indicating acceptable specificity and sensitivity. We expect that our findings can help contribute to the development of improved diagnostics that may aid in identifying severe COVID-19 cases, guide clinical treatment, and improve mortality rates.
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22
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Park JJ, Lee KAV, Lam SZ, Moon KS, Fang Z, Chen S. Machine learning identifies T cell receptor repertoire signatures associated with COVID-19 severity. Commun Biol 2023; 6:76. [PMID: 36670287 PMCID: PMC9853487 DOI: 10.1038/s42003-023-04447-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/10/2023] [Indexed: 01/21/2023] Open
Abstract
T cell receptor (TCR) repertoires are critical for antiviral immunity. Determining the TCR repertoire composition, diversity, and dynamics and how they change during viral infection can inform the molecular specificity of host responses to viruses such as SARS-CoV-2. To determine signatures associated with COVID-19 disease severity, here we perform a large-scale analysis of over 4.7 billion sequences across 2130 TCR repertoires from COVID-19 patients and healthy donors. TCR repertoire analyses from these data identify and characterize convergent COVID-19-associated CDR3 gene usages, specificity groups, and sequence patterns. Here we show that T cell clonal expansion is associated with the upregulation of T cell effector function, TCR signaling, NF-kB signaling, and interferon-gamma signaling pathways. We also demonstrate that machine learning approaches accurately predict COVID-19 infection based on TCR sequence features, with certain high-power models reaching near-perfect AUROC scores. These analyses provide a systems immunology view of T cell adaptive immune responses to COVID-19.
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Affiliation(s)
- Jonathan J. Park
- grid.47100.320000000419368710Department of Genetics, Yale School of Medicine, New Haven, CT USA ,grid.47100.320000000419368710Systems Biology Institute, Yale University, West Haven, CT USA ,grid.47100.320000000419368710Center for Cancer Systems Biology, Yale University, West Haven, CT USA ,grid.47100.320000000419368710MD-PhD Program, Yale University, New Haven, CT USA ,grid.47100.320000000419368710Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, CT USA
| | - Kyoung A V. Lee
- grid.47100.320000000419368710Department of Genetics, Yale School of Medicine, New Haven, CT USA ,grid.47100.320000000419368710Systems Biology Institute, Yale University, West Haven, CT USA ,grid.47100.320000000419368710Center for Cancer Systems Biology, Yale University, West Haven, CT USA ,grid.47100.320000000419368710Department of Biostatistics, Yale School of Public Health, New Haven, CT USA
| | - Stanley Z. Lam
- grid.47100.320000000419368710Department of Genetics, Yale School of Medicine, New Haven, CT USA ,grid.47100.320000000419368710Systems Biology Institute, Yale University, West Haven, CT USA ,grid.47100.320000000419368710Center for Cancer Systems Biology, Yale University, West Haven, CT USA
| | - Katherine S. Moon
- grid.47100.320000000419368710Department of Genetics, Yale School of Medicine, New Haven, CT USA ,grid.47100.320000000419368710Systems Biology Institute, Yale University, West Haven, CT USA ,grid.47100.320000000419368710Center for Cancer Systems Biology, Yale University, West Haven, CT USA
| | - Zhenhao Fang
- grid.47100.320000000419368710Department of Genetics, Yale School of Medicine, New Haven, CT USA ,grid.47100.320000000419368710Systems Biology Institute, Yale University, West Haven, CT USA ,grid.47100.320000000419368710Center for Cancer Systems Biology, Yale University, West Haven, CT USA
| | - Sidi Chen
- grid.47100.320000000419368710Department of Genetics, Yale School of Medicine, New Haven, CT USA ,grid.47100.320000000419368710Systems Biology Institute, Yale University, West Haven, CT USA ,grid.47100.320000000419368710Center for Cancer Systems Biology, Yale University, West Haven, CT USA ,grid.47100.320000000419368710MD-PhD Program, Yale University, New Haven, CT USA ,grid.47100.320000000419368710Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, CT USA ,grid.47100.320000000419368710Immunobiology Program, Yale University, New Haven, CT USA ,grid.47100.320000000419368710Yale Comprehensive Cancer Center, Yale School of Medicine, New Haven, CT USA ,grid.47100.320000000419368710Yale Stem Cell Center, Yale School of Medicine, New Haven, CT USA ,grid.47100.320000000419368710Yale Center for Biomedical Data Science, Yale School of Medicine, New Haven, CT USA
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23
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Yunis J, Short KR, Yu D. Severe respiratory viral infections: T-cell functions diverging from immunity to inflammation. Trends Microbiol 2023; 31:644-656. [PMID: 36635162 PMCID: PMC9829516 DOI: 10.1016/j.tim.2022.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 01/11/2023]
Abstract
Respiratory viral infections such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A virus (IAV) trigger distinct clinical outcomes defined by immunity-based viral clearance or disease associated with exaggerated and prolonged inflammation. The important role of T cells in shaping both antiviral immunity and inflammation has revived interest in understanding the host-pathogen interactions that lead to the diverse functions of T cells in respiratory viral infections. Inborn deficiencies and acquired insufficiency in immunity can prolong infection and shift the immune response towards exacerbated inflammation, which results from persistent innate immune activation and bystander T-cell activation that is nonspecific to the pathogen but is often driven by cytokines. This review discusses how virus variants, exposure doses, routes of infection, host genetics, and immune history can modulate the activation and function of T cells, thus influencing clinical outcomes. Knowledge of virus-host interaction can inform strategies to prevent immune dysfunction in respiratory viral infection and help in the treatment of associated diseases.
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Affiliation(s)
- Joseph Yunis
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD 4102, Australia,Correspondence:
| | - Kirsty R. Short
- School of Chemistry and Molecular Biosciences, Faculty of Science, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Di Yu
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD 4102, Australia,Ian Frazer Centre for Children’s Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, Australia,Correspondence:
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24
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Rümke LW, Smit WL, Bossink A, Limonard GJM, Muilwijk D, Haas LEM, Reusken C, van der Wal S, Thio BJ, van Os YMG, Gremmels H, Beekman JM, Nijhuis M, Wensing AMJ, Heron M, Thijsen SFT. Impaired SARS-CoV-2 specific T-cell response in patients with severe COVID-19. Front Immunol 2023; 14:1046639. [PMID: 37168853 PMCID: PMC10165493 DOI: 10.3389/fimmu.2023.1046639] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 03/28/2023] [Indexed: 05/13/2023] Open
Abstract
Cellular immune responses are of pivotal importance to understand SARS-CoV-2 pathogenicity. Using an enzyme-linked immunosorbent spot (ELISpot) interferon-γ release assay with wild-type spike, membrane and nucleocapsid peptide pools, we longitudinally characterized functional SARS-CoV-2 specific T-cell responses in a cohort of patients with mild, moderate and severe COVID-19. All patients were included before emergence of the Omicron (B.1.1.529) variant. Our most important finding was an impaired development of early IFN-γ-secreting virus-specific T-cells in severe patients compared to patients with moderate disease, indicating that absence of virus-specific cellular responses in the acute phase may act as a prognostic factor for severe disease. Remarkably, in addition to reactivity against the spike protein, a substantial proportion of the SARS-CoV-2 specific T-cell response was directed against the conserved membrane protein. This may be relevant for diagnostics and vaccine design, especially considering new variants with heavily mutated spike proteins. Our data further strengthen the hypothesis that dysregulated adaptive immunity plays a central role in COVID-19 immunopathogenesis.
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Affiliation(s)
- Lidewij W. Rümke
- Department of Medical Microbiology and Immunology, Diakonessenhuis Utrecht, Utrecht, Netherlands
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Wouter L. Smit
- Department of Medical Microbiology and Immunology, Diakonessenhuis Utrecht, Utrecht, Netherlands
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Ailko Bossink
- Department of Pulmonary Diseases, Diakonessenhuis Utrecht, Utrecht, Netherlands
| | - Gijs J. M. Limonard
- Department of Pulmonary Diseases, Diakonessenhuis Utrecht, Utrecht, Netherlands
| | - Danya Muilwijk
- Department of Pediatric Pulmonology, Wilhelmina Children’s Hospital, University Medical Center, Utrecht University, Utrecht, Netherlands
- Regenerative Medicine Center Utrecht, University Medical Center, Utrecht University, Utrecht, Netherlands
| | - Lenneke E. M. Haas
- Department of Intensive Care, Diakonessenhuis Utrecht, Utrecht, Netherlands
| | - Chantal Reusken
- Centre for Infectious Disease Control, WHO Reference Laboratory for COVID-19, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Sanne van der Wal
- Department of Medical Microbiology and Immunology, Diakonessenhuis Utrecht, Utrecht, Netherlands
| | - Bing J. Thio
- Department of Medical Microbiology and Immunology, Diakonessenhuis Utrecht, Utrecht, Netherlands
| | - Yvonne M. G. van Os
- Occupational Health Office, Department of Human Resources, University Medical Center Utrecht, Utrecht, Netherlands
| | - Hendrik Gremmels
- Department of Medical Microbiology and Immunology, Diakonessenhuis Utrecht, Utrecht, Netherlands
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Jeffrey M. Beekman
- Department of Pediatric Pulmonology, Wilhelmina Children’s Hospital, University Medical Center, Utrecht University, Utrecht, Netherlands
- Regenerative Medicine Center Utrecht, University Medical Center, Utrecht University, Utrecht, Netherlands
| | - Monique Nijhuis
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Annemarie M. J. Wensing
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Michiel Heron
- Department of Medical Microbiology and Immunology, Diakonessenhuis Utrecht, Utrecht, Netherlands
- *Correspondence: Michiel Heron,
| | - Steven F. T. Thijsen
- Department of Medical Microbiology and Immunology, Diakonessenhuis Utrecht, Utrecht, Netherlands
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25
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Fernandes MB, Barata JT. IL-7 and IL-7R in health and disease: An update through COVID times. Adv Biol Regul 2023; 87:100940. [PMID: 36503870 DOI: 10.1016/j.jbior.2022.100940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
The role of IL-7 and IL-7R for normal lymphoid development and an adequately functioning immune system has been recognized for long, with severe immune deficiency and lymphoid leukemia as extreme examples of the consequences of deregulation of the IL-7-IL-7R axis. In this review, we provide an update (focusing on the past couple of years) on IL-7 and IL-7R in health and disease. We highlight the findings on IL-7/IL-7R signaling mechanisms and the, sometimes controversial, impact of IL-7 and its receptor on leukocyte biology, COVID-19, acute lymphoblastic leukemia, and different solid tumors, as well as their relevance as therapeutic tools or targets.
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Affiliation(s)
- Marta B Fernandes
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisbon, Portugal
| | - João T Barata
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisbon, Portugal.
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26
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Arish M, Qian W, Narasimhan H, Sun J. COVID-19 immunopathology: From acute diseases to chronic sequelae. J Med Virol 2023; 95:e28122. [PMID: 36056655 PMCID: PMC9537925 DOI: 10.1002/jmv.28122] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/27/2022] [Accepted: 08/29/2022] [Indexed: 01/17/2023]
Abstract
The clinical manifestation of coronavirus disease 2019 (COVID-19) mainly targets the lung as a primary affected organ, which is also a critical site of immune cell activation by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, recent reports also suggest the involvement of extrapulmonary tissues in COVID-19 pathology. The interplay of both innate and adaptive immune responses is key to COVID-19 management. As a result, a robust innate immune response provides the first line of defense, concomitantly, adaptive immunity neutralizes the infection and builds memory for long-term protection. However, dysregulated immunity, both innate and adaptive, can skew towards immunopathology both in acute and chronic cases. Here we have summarized some of the recent findings that provide critical insight into the immunopathology caused by SARS-CoV-2, in acute and post-acute cases. Finally, we further discuss some of the immunomodulatory drugs in preclinical and clinical trials for dampening the immunopathology caused by COVID-19.
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Affiliation(s)
- Mohd Arish
- Carter Immunology Center, University of Virginia, Charlottesville, VA 22908, USA
| | - Wei Qian
- Carter Immunology Center, University of Virginia, Charlottesville, VA 22908, USA
| | - Harish Narasimhan
- Carter Immunology Center, University of Virginia, Charlottesville, VA 22908, USA.,Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA 22908, USA
| | - Jie Sun
- Carter Immunology Center, University of Virginia, Charlottesville, VA 22908, USA.,Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA 22908, USA.,Division of Infectious Disease and International Health, Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA.,corresponding author.
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27
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Gedda MR, Danaher P, Shao L, Ongkeko M, Chen L, Dinh A, Thioye Sall M, Reddy OL, Bailey C, Wahba A, Dzekunova I, Somerville R, De Giorgi V, Jin P, West K, Panch SR, Stroncek DF. Longitudinal transcriptional analysis of peripheral blood leukocytes in COVID-19 convalescent donors. J Transl Med 2022; 20:587. [PMID: 36510222 PMCID: PMC9742656 DOI: 10.1186/s12967-022-03751-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/03/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND SARS-CoV2 can induce a strong host immune response. Many studies have evaluated antibody response following SARS-CoV2 infections. This study investigated the immune response and T cell receptor diversity in people who had recovered from SARS-CoV2 infection (COVID-19). METHODS Using the nCounter platform, we compared transcriptomic profiles of 162 COVID-19 convalescent donors (CCD) and 40 healthy donors (HD). 69 of the 162 CCDs had two or more time points sampled. RESULTS After eliminating the effects of demographic factors, we found extensive differential gene expression up to 241 days into the convalescent period. The differentially expressed genes were involved in several pathways, including virus-host interaction, interleukin and JAK-STAT signaling, T-cell co-stimulation, and immune exhaustion. A subset of 21 CCD samples was found to be highly "perturbed," characterized by overexpression of PLAU, IL1B, NFKB1, PLEK, LCP2, IRF3, MTOR, IL18BP, RACK1, TGFB1, and others. In addition, one of the clusters, P1 (n = 8) CCD samples, showed enhanced TCR diversity in 7 VJ pairs (TRAV9.1_TCRVA_014.1, TRBV6.8_TCRVB_016.1, TRAV7_TCRVA_008.1, TRGV9_ENST00000444775.1, TRAV18_TCRVA_026.1, TRGV4_ENST00000390345.1, TRAV11_TCRVA_017.1). Multiplexed cytokine analysis revealed anomalies in SCF, SCGF-b, and MCP-1 expression in this subset. CONCLUSIONS Persistent alterations in inflammatory pathways and T-cell activation/exhaustion markers for months after active infection may help shed light on the pathophysiology of a prolonged post-viral syndrome observed following recovery from COVID-19 infection. Future studies may inform the ability to identify druggable targets involving these pathways to mitigate the long-term effects of COVID-19 infection. TRIAL REGISTRATION https://clinicaltrials.gov/ct2/show/NCT04360278 Registered April 24, 2020.
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Affiliation(s)
- Mallikarjuna R. Gedda
- grid.94365.3d0000 0001 2297 5165Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA ,grid.280030.90000 0001 2150 6316Section of Retinal Ganglion Cell Biology, Laboratory of Retinal Cell and Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Patrick Danaher
- grid.510973.90000 0004 5375 2863NanoString Technologies, Seattle, WA 98109 USA
| | - Lipei Shao
- grid.94365.3d0000 0001 2297 5165Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Martin Ongkeko
- grid.94365.3d0000 0001 2297 5165Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Leonard Chen
- grid.94365.3d0000 0001 2297 5165Blood Services Section, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Anh Dinh
- grid.94365.3d0000 0001 2297 5165Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Mame Thioye Sall
- grid.94365.3d0000 0001 2297 5165Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Opal L. Reddy
- grid.94365.3d0000 0001 2297 5165Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Christina Bailey
- grid.510973.90000 0004 5375 2863NanoString Technologies, Seattle, WA 98109 USA
| | - Amy Wahba
- grid.510973.90000 0004 5375 2863NanoString Technologies, Seattle, WA 98109 USA
| | - Inna Dzekunova
- grid.510973.90000 0004 5375 2863NanoString Technologies, Seattle, WA 98109 USA
| | - Robert Somerville
- grid.94365.3d0000 0001 2297 5165Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Valeria De Giorgi
- grid.94365.3d0000 0001 2297 5165Infectious Disease Section, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Ping Jin
- grid.94365.3d0000 0001 2297 5165Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Kamille West
- grid.94365.3d0000 0001 2297 5165Blood Services Section, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
| | - Sandhya R. Panch
- grid.94365.3d0000 0001 2297 5165Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA ,grid.34477.330000000122986657Department of Medicine (Hematology Division), University of Washington/Fred Hutchinson Cancer Center, Seattle, WA 98109 USA
| | - David F. Stroncek
- grid.94365.3d0000 0001 2297 5165Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892 USA
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28
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Upadhyay V, Suryawanshi R, Tasoff P, McCavitt-Malvido M, Kumar GR, Murray VW, Noecker C, Bisanz JE, Hswen Y, Ha C, Sreekumar B, Chen IP, Lynch SV, Ott M, Lee S, Turnbaugh PJ. Mild SARS-CoV-2 infection results in long-lasting microbiota instability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.12.07.519508. [PMID: 36523400 PMCID: PMC9753784 DOI: 10.1101/2022.12.07.519508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Viruses targeting mammalian cells can indirectly alter the gut microbiota, potentially compounding their phenotypic effects. Multiple studies have observed a disrupted gut microbiota in severe cases of SARS-CoV-2 infection that require hospitalization. Yet, despite demographic shifts in disease severity resulting in a large and continuing burden of non-hospitalized infections, we still know very little about the impact of mild SARS-CoV-2 infection on the gut microbiota in the outpatient setting. To address this knowledge gap, we longitudinally sampled 14 SARS-CoV-2 positive subjects who remained outpatient and 4 household controls. SARS-CoV-2 cases exhibited a significantly less stable gut microbiota relative to controls, as long as 154 days after their positive test. These results were confirmed and extended in the K18-hACE2 mouse model, which is susceptible to SARS-CoV-2 infection. All of the tested SARS-CoV-2 variants significantly disrupted the mouse gut microbiota, including USA-WA1/2020 (the original variant detected in the United States), Delta, and Omicron. Surprisingly, despite the fact that the Omicron variant caused the least severe symptoms in mice, it destabilized the gut microbiota and led to a significant depletion in Akkermansia muciniphila . Furthermore, exposure of wild-type C57BL/6J mice to SARS-CoV-2 disrupted the gut microbiota in the absence of severe lung pathology. IMPORTANCE Taken together, our results demonstrate that even mild cases of SARS-CoV-2 can disrupt gut microbial ecology. Our findings in non-hospitalized individuals are consistent with studies of hospitalized patients, in that reproducible shifts in gut microbial taxonomic abundance in response to SARS-CoV-2 have been difficult to identify. Instead, we report a long-lasting instability in the gut microbiota. Surprisingly, our mouse experiments revealed an impact of the Omicron variant, despite producing the least severe symptoms in genetically susceptible mice, suggesting that despite the continued evolution of SARS-CoV-2 it has retained its ability to perturb the intestinal mucosa. These results will hopefully renew efforts to study the mechanisms through which Omicron and future SARS-CoV-2 variants alter gastrointestinal physiology, while also considering the potentially broad consequences of SARS-CoV-2-induced microbiota instability for host health and disease.
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29
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Shafqat A, Omer MH, Ahmad O, Niaz M, Abdulkader HS, Shafqat S, Mushtaq AH, Shaik A, Elshaer AN, Kashir J, Alkattan K, Yaqinuddin A. SARS-CoV-2 epitopes inform future vaccination strategies. Front Immunol 2022; 13:1041185. [PMID: 36505475 PMCID: PMC9732895 DOI: 10.3389/fimmu.2022.1041185] [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] [Received: 09/10/2022] [Accepted: 11/11/2022] [Indexed: 11/27/2022] Open
Abstract
All currently approved COVID-19 vaccines utilize the spike protein as their immunogen. SARS-CoV-2 variants of concern (VOCs) contain mutations in the spike protein, enabling them to escape infection- and vaccination-induced immune responses to cause reinfection. New vaccines are hence being researched intensively. Studying SARS-CoV-2 epitopes is essential for vaccine design, as identifying targets of broadly neutralizing antibody responses and immunodominant T-cell epitopes reveal candidates for inclusion in next-generation COVID-19 vaccines. We summarize the major studies which have reported on SARS-CoV-2 antibody and T-cell epitopes thus far. These results suggest that a future of pan-coronavirus vaccines, which not only protect against SARS-CoV-2 but numerous other coronaviruses, may be possible. The T-cell epitopes of SARS-CoV-2 have gotten less attention than neutralizing antibody epitopes but may provide new strategies to control SARS-CoV-2 infection. T-cells target many SARS-CoV-2 antigens other than spike, recognizing numerous epitopes within these antigens, thereby limiting the chance of immune escape by VOCs that mainly possess spike protein mutations. Therefore, augmenting vaccination-induced T-cell responses against SARS-CoV-2 may provide adequate protection despite broad antibody escape by VOCs.
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Affiliation(s)
- Areez Shafqat
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia,*Correspondence: Areez Shafqat,
| | - Mohamed H. Omer
- School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Omar Ahmad
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Mahnoor Niaz
- Medical College, Aga Khan University, Karachi, Pakistan
| | | | | | | | - Abdullah Shaik
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | | | - Junaid Kashir
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia,Department of Comparative Medicine, King Faisal Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Khaled Alkattan
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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30
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Fiorino S, Carusi A, Hong W, Cernuschi P, Gallo CG, Ferrara E, Maloberti T, Visani M, Lari F, de Biase D, Zippi M. SARS-CoV-2 vaccines: What we know, what we can do to improve them and what we could learn from other well-known viruses. AIMS Microbiol 2022; 8:422-453. [PMID: 36694588 PMCID: PMC9834075 DOI: 10.3934/microbiol.2022029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/24/2022] [Accepted: 11/06/2022] [Indexed: 11/18/2022] Open
Abstract
In recent weeks, the rate of SARS-CoV-2 infections has been progressively increasing all over the globe, even in countries where vaccination programs have been strongly implemented. In these regions in 2021, a reduction in the number of hospitalizations and deaths compared to 2020 was observed. This decrease is certainly associated with the introduction of vaccination measures. The process of the development of effective vaccines represents an important challenge. Overall, the breakthrough infections occurring in vaccinated subjects are in most cases less severe than those observed in unvaccinated individuals. This review examines the factors affecting the immunogenicity of vaccines against SARS-CoV-2 and the possible role of nutrients in modulating the response of distinct immune cells to the vaccination.
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Affiliation(s)
- Sirio Fiorino
- Internal Medicine Unit, Budrio Hospital, Budrio (Bologna), Azienda USL, Bologna, Italy,* Correspondence:
| | - Andrea Carusi
- Internal Medicine Unit, Budrio Hospital, Budrio (Bologna), Azienda USL, Bologna, Italy
| | - Wandong Hong
- Department of Gastroenterology and Hepatology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, Zhejiang, The People's Republic of China
| | - Paolo Cernuschi
- Internal Medicine Unit, Quisana Private Hospital, Ferrara, Italy
| | | | | | - Thais Maloberti
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna-Molecular Diagnostic Unit, Azienda USL di Bologna, Bologna, Italy,Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Michela Visani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna-Molecular Diagnostic Unit, Azienda USL di Bologna, Bologna, Italy
| | - Federico Lari
- Internal Medicine Unit, Budrio Hospital, Budrio (Bologna), Azienda USL, Bologna, Italy
| | - Dario de Biase
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy,Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Maddalena Zippi
- Unit of Gastroenterology and Digestive Endoscopy, Sandro Pertini Hospital, Rome, Italy
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31
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Lee KS, Russ BP, Wong TY, Horspool AM, Winters MT, Barbier M, Bevere JR, Martinez I, Damron FH, Cyphert HA. Obesity and metabolic dysfunction drive sex-associated differential disease profiles in hACE2-mice challenged with SARS-CoV-2. iScience 2022; 25:105038. [PMID: 36068847 PMCID: PMC9436780 DOI: 10.1016/j.isci.2022.105038] [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: 04/26/2022] [Revised: 06/25/2022] [Accepted: 08/25/2022] [Indexed: 12/05/2022] Open
Abstract
Severe outcomes from SARS-CoV-2 infection are highly associated with preexisting comorbid conditions like hypertension, diabetes, and obesity. We utilized the diet-induced obesity (DIO) model of metabolic dysfunction in K18-hACE2 transgenic mice to model obesity as a COVID-19 comorbidity. Female DIO, but not male DIO mice challenged with SARS-CoV-2 were observed to have shortened time to morbidity compared to controls. Increased susceptibility to SARS-CoV-2 in female DIO was associated with increased viral RNA burden and interferon production compared to males. Transcriptomic analysis of the lungs from all mouse cohorts revealed sex- and DIO-associated differential gene expression profiles. Male DIO mice after challenge had decreased expression of antibody-related genes compared to controls, suggesting antibody producing cell localization in the lung. Collectively, this study establishes a preclinical comorbidity model of COVID-19 in mice where we observed sex- and diet-specific responses that begin explaining the effects of obesity and metabolic disease on COVID-19 pathology. Transcriptomic analysis of infected lungs revealed unique sex-dependent differences Obese female mice have high viral RNA burden and interferon production in the lung Male mice have altered antibody and T cell response gene profiles after viral challenge Metabolic dysfunction comorbidity can be studied in the hACE2 mouse model of COVID-19
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Affiliation(s)
- Katherine S. Lee
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, USA
| | - Brynnan P. Russ
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, USA
| | - Ting Y. Wong
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, USA
| | - Alexander M. Horspool
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, USA
| | - Michael T. Winters
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, USA
| | - Mariette Barbier
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, USA
| | - Justin R. Bevere
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, USA
| | - Ivan Martinez
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, USA
- West Virginia University Cancer Institute, School of Medicine, Morgantown, WV, USA
| | - F. Heath Damron
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, USA
- Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV, USA
| | - Holly A. Cyphert
- Department of Biological Sciences, Marshall University, Huntington, WV, USA
- Corresponding author
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Single-Cell Gene Expression Analysis Revealed Immune Cell Signatures of Delta COVID-19. Cells 2022; 11:cells11192950. [PMID: 36230912 PMCID: PMC9563974 DOI: 10.3390/cells11192950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/04/2022] [Accepted: 09/15/2022] [Indexed: 11/17/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) is accompanied by a cytokine storm with the release of many proinflammatory factors and development of respiratory syndrome. Several SARS-CoV-2 lineages have been identified, and the Delta variant (B.1.617), linked with high mortality risk, has become dominant in many countries. Understanding the immune responses associated with COVID-19 lineages may therefore aid the development of therapeutic and diagnostic strategies. Multiple single-cell gene expression studies revealed innate and adaptive immunological factors and pathways correlated with COVID-19 severity. Additional investigations covering host–pathogen response characteristics for infection caused by different lineages are required. Here, we performed single-cell transcriptome profiling of blood mononuclear cells from the individuals with different severity of the COVID-19 and virus lineages to uncover variant specific molecular factors associated with immunity. We identified significant changes in lymphoid and myeloid cells. Our study highlights that an abundant population of monocytes with specific gene expression signatures accompanies Delta lineage of SARS-CoV-2 and contributes to COVID-19 pathogenesis inferring immune components for targeted therapy.
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Kudryavtsev I, Matyushenko V, Stepanova E, Vasilyev K, Rudenko L, Isakova-Sivak I. In Vitro Stimulation with Live SARS-CoV-2 Suggests Th17 Dominance In Virus-Specific CD4+ T Cell Response after COVID-19. Vaccines (Basel) 2022; 10:vaccines10091544. [PMID: 36146622 PMCID: PMC9502469 DOI: 10.3390/vaccines10091544] [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: 07/21/2022] [Revised: 09/14/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
The SARS-CoV-2 and influenza viruses are the main causes of human respiratory tract infections with similar disease manifestation but distinct mechanisms of immunopathology and host response to the infection. In this study, we investigated the SARS-CoV-2-specific CD4+ T cell phenotype in comparison with H1N1 influenza-specific CD4+ T cells. We determined the levels of SARS-CoV-2- and H1N1-specific CD4+ T cell responses in subjects recovered from COVID-19 one to 15 months ago by stimulating PBMCs with live SARS-CoV-2 or H1N1 influenza viruses. We investigated phenotypes and frequencies of main CD4+ T cell subsets specific for SARS-CoV-2 using an activation induced cell marker assay and multicolor flow cytometry, and compared the magnitude of SARS-CoV-2- and H1N1-specific CD4+ T cells. SARS-CoV-2-specific CD4+ T cells were detected 1–15 months post infection and the frequency of SARS-CoV-2-specific central memory CD4+ T cells was increased with the time post-symptom onset. Next, SARS-CoV-2-specific CD4+ T cells predominantly expressed the Th17 phenotype, but the level of Th17 cells in this group was lower than in H1N1-specific CD4+ T cells. Finally, we found that the lower level of total Th17 subset within total SARS-CoV-2-specific CD4+ T cells was linked with the low level of CCR4+CXCR3– ‘classical’ Th17 cells if compared with H1N1-specific Th17 cells. Taken together, our data suggest the involvement of Th17 cells and their separate subsets in the pathogenesis of SARS-CoV-2- and influenza-induced pneumonia; and a better understanding of Th17 mediated antiviral immune responses may lead to the development of new therapeutic strategies.
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Bertoletti A, Le Bert N, Tan AT. Act Early and at the Right Location: SARS-CoV-2 T Cell Kinetics and Tissue Localization. Int J Mol Sci 2022; 23:10679. [PMID: 36142588 PMCID: PMC9505719 DOI: 10.3390/ijms231810679] [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: 06/30/2022] [Revised: 08/24/2022] [Accepted: 09/02/2022] [Indexed: 11/29/2022] Open
Abstract
The emergence of new SARS-CoV-2 lineages able to escape antibodies elicited by infection or vaccination based on the Spike protein of the Wuhan isolates has reduced the ability of Spike-specific antibodies to protect previously infected or vaccinated individuals from infection. Therefore, the role played by T cells in the containment of viral replication and spread after infection has taken a more central stage. In this brief review, we will discuss the role played by T cells in the protection from COVID-19, with a particular emphasis on the kinetics of the T cell response and its localization at the site of primary infection.
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Affiliation(s)
- Antonio Bertoletti
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
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35
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Young A. T cells in SARS-CoV-2 infection and vaccination. Ther Adv Vaccines Immunother 2022; 10:25151355221115011. [PMID: 36051003 PMCID: PMC9425900 DOI: 10.1177/25151355221115011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 07/04/2022] [Indexed: 12/24/2022] Open
Abstract
While antibodies garner the lion’s share of attention in SARS-CoV-2 immunity, cellular immunity (T cells) may be equally, if not more important, in controlling infection. Both CD8+ and CD4+ T cells are elicited earlier and are associated with milder disease, than antibodies, and T-cell activation appears to be necessary for control of infection. Variants of concern (VOCs) such as Omicron have escaped the neutralizing antibody responses after two mRNA vaccine doses, but T-cell immunity is largely intact. The breadth and patient-specific nature of the latter offers a formidable line of defense that can limit the severity of illness, and are likely to be responsible for most of the protection from natural infection or vaccination against VOCs which have evaded the antibody response. Comprehensive searches for T-cell epitopes, T-cell activation from infection and vaccination of specific patient groups, and elicitation of cellular immunity by various alternative vaccine modalities are here reviewed. Development of vaccines that specifically target T cells is called for, to meet the needs of patient groups for whom cellular immunity is weaker, such as the elderly and the immunosuppressed. While VOCs have not yet fully escaped T-cell immunity elicited by natural infection and vaccines, some early reports of partial escape suggest that future VOCs may achieve the dreaded result, dislodging a substantial proportion of cellular immunity, enough to cause a grave public health burden. A proactive, rather than reactive, solution which identifies and targets immutable sequences in SARS-CoV-2, not just those which are conserved, may be the only recourse humankind has to disarm these future VOCs before they disarm us.
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Affiliation(s)
- Arthur Young
- InvVax, 2265 E. Foohill Blvd., Pasadena, CA 91107, USA
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36
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Suster D, Tili E, Nuovo GJ. The differential immune response in mild versus fatal SARS-CoV2 infection. Ann Diagn Pathol 2022; 61:152032. [PMID: 36113259 PMCID: PMC9436872 DOI: 10.1016/j.anndiagpath.2022.152032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 08/28/2022] [Indexed: 12/02/2022]
Abstract
This study compared the immune response in mild versus fatal SARS-CoV2 infection. Forty nasopharyngeal swabs with either productive mild infection (n = 20) or negative for SARS-CoV2 (n = 20) were tested along with ten lung sections from people who died of COVID-19 which contained abundant SARS-CoV2 and ten controls. There was a 25-fold increase in the CD3+T cell numbers in the viral positive nasopharyngeal swabs compared to the controls (p < 0.001) and no change in the CD3+T cell count in the fatal COVID-19 lungs versus the controls. CD11b + and CD206+ macrophage counts were significantly higher in the mild versus fatal disease (p = 0.002). In situ analysis for SARS-CoV2 RNA found ten COVID-19 lung sections that had no/rare detectable virus and also lacked the microangiopathy typical of the viral positive sections. These viral negative lung tissues when compared to the viral positive lung samples showed a highly significant increase in CD3+ and CD8 T cells (p < 0.001), equivalent numbers of CD163+ cells, and significantly less PDL1, CD11b and CD206+ cells (p = 0.002). It is concluded that mild SARS-CoV2 infection is marked by a much stronger CD3/CD8 T cell, CD11b, and CD206 macrophage response than the fatal lung disease where viral RNA is abundant.
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Affiliation(s)
- David Suster
- Rutgers University Hospital Department of Pathology, Newark, NJ, USA
| | - Esmerina Tili
- The Ohio State University Wexner Medical Center, Department of Anesthesiology, College of Medicine, Columbus, OH, USA
| | - Gerard J Nuovo
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA; GnomeDX, Powell, OH, USA.
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Olea B, Albert E, Giménez E, Torres I, Amat P, Remigia MJ, Alberola J, Carbonell N, Ferreres J, Blasco ML, Navarro D. SARS-CoV-2-reactive IFN-γ-producing CD4 + and CD8 + T cells in blood do not correlate with clinical severity in unvaccinated critically ill COVID-19 patients. Sci Rep 2022; 12:14271. [PMID: 35995830 PMCID: PMC9395536 DOI: 10.1038/s41598-022-18659-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 08/17/2022] [Indexed: 11/18/2022] Open
Abstract
We examined the relationship between peripheral blood levels of SARS-CoV-2 S (Spike protein)1/M (Membrane protein)-reactive IFN-γ-producing CD4+ and CD8+ T cells, serum levels of biomarkers of clinical severity, and mortality in critically ill COVID-19 patients. The potential association between SARS-CoV-2-S-Receptor Binding Domain (RBD)-specific IgG levels in sera and mortality was also investigated. SARS-CoV-2 T cells and anti-RBD IgG levels were monitored in 71 non-consecutive patients (49 male and 22 female; median age, 65 years) by whole-blood flow cytometry and Enzyme-linked immunosorbent assay (ELISA), respectively (326 specimens). SARS-CoV-2 RNA loads in paired tracheal aspirates [TA] (n = 147) were available from 54 patients. Serum levels of interleukin-6, ferritin, D-Dimer, lactose dehydrogenase and C-reactive protein in paired sera were known. SARS-CoV-2 T cells (either CD4+, CD8+ or both) were detectable in 70 patients. SARS-CoV-2 IFN-γ CD4+ T-cell responses were documented more frequently than their CD8+ counterparts (62 vs. 56 patients) and were of greater magnitude overall. Detectable SARS-CoV-2 S1/M-reactive CD8+ and CD4+ T-cell responses were associated with higher SARS-CoV-2 RNA loads in TA. SARS-CoV-2 RNA load in TA decreased over time, irrespective of the dynamics of SARS-CoV-2-reactive CD8+ and CD4+ T cells. No correlation was found between SARS-CoV-2 IFN-γ T-cell counts, anti-RBD IgG concentrations and biomarker serum levels (Rho ≤ 0.3). The kinetics of both T cell subsets was comparable between those who died or survived, whereas anti-RBD IgG levels were higher across different time points in deceased patients than in survivors. Enumeration of peripheral blood levels of SARS-CoV-2-S1/M-reactive IFN-γ CD4+ and CD8+ T cells does not predict viral clearance from the lower respiratory tract or poor clinical outcomes in critically ill COVID-19 patients. In contrast, anti-RBD IgG levels were directly associated with increased mortality.
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Affiliation(s)
- Beatriz Olea
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - Eliseo Albert
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - Estela Giménez
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - Ignacio Torres
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - Paula Amat
- Hematology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - María José Remigia
- Hematology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - Juan Alberola
- Department of Microbiology, School of Medicine, University of Valencia, Av. Blasco Ibáñez 17, 46010, Valencia, Spain
| | - Nieves Carbonell
- Medical Intensive Care Unit, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - José Ferreres
- Medical Intensive Care Unit, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - María Luisa Blasco
- Medical Intensive Care Unit, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - David Navarro
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain. .,Department of Microbiology, School of Medicine, University of Valencia, Av. Blasco Ibáñez 17, 46010, Valencia, Spain.
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RBD-VLP Vaccines Adjuvanted with Alum or SWE Protect K18-hACE2 Mice against SARS-CoV-2 VOC Challenge. mSphere 2022; 7:e0024322. [PMID: 35968964 PMCID: PMC9429941 DOI: 10.1128/msphere.00243-22] [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] [Indexed: 11/20/2022] Open
Abstract
The ongoing COVID-19 pandemic has contributed largely to the global vaccine disparity. Development of protein subunit vaccines can help alleviate shortages of COVID-19 vaccines delivered to low-income countries. Here, we evaluated the efficacy of a three-dose virus-like particle (VLP) vaccine composed of hepatitis B surface antigen (HBsAg) decorated with the receptor binding domain (RBD) from the Wuhan or Beta SARS-CoV-2 strain adjuvanted with either aluminum hydroxide (alum) or squalene in water emulsion (SWE). RBD HBsAg vaccines were compared to the standard two doses of Pfizer mRNA vaccine. Alum-adjuvanted vaccines were composed of either HBsAg conjugated with Beta RBD alone (β RBD HBsAg+Al) or a combination of both Beta RBD HBsAg and Wuhan RBD HBsAg (β/Wu RBD HBsAg+Al). RBD vaccines adjuvanted with SWE were formulated with Beta RBD HBsAg (β RBD HBsAg+SWE) or without HBsAg (β RBD+SWE). Both alum-adjuvanted RBD HBsAg vaccines generated functional RBD IgG against multiple SARS-CoV-2 variants of concern (VOC), decreased viral RNA burden, and lowered inflammation in the lung against Alpha or Beta challenge in K18-hACE2 mice. However, only β/Wu RBD HBsAg+Al was able to afford 100% survival to mice challenged with Alpha or Beta VOC. Furthermore, mice immunized with β RBD HBsAg+SWE induced cross-reactive neutralizing antibodies against major VOC of SARS-CoV-2, lowered viral RNA burden in the lung and brain, and protected mice from Alpha or Beta challenge similarly to mice immunized with Pfizer mRNA. However, RBD+SWE immunization failed to protect mice from VOC challenge. Our findings demonstrate that RBD HBsAg VLP vaccines provided similar protection profiles to the approved Pfizer mRNA vaccines used worldwide and may offer protection against SARS-CoV-2 VOC. IMPORTANCE Global COVID-19 vaccine distribution to low-income countries has been a major challenge of the pandemic. To address supply chain issues, RBD virus-like particle (VLP) vaccines that are cost-effective and capable of large-scale production were developed and evaluated for efficacy in preclinical mouse studies. We demonstrated that RBD-VLP vaccines protected K18-hACE2 mice against Alpha or Beta challenge similarly to Pfizer mRNA vaccination. Our findings showed that the VLP platform can be utilized to formulate immunogenic and efficacious COVID-19 vaccines.
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39
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Nelson RW, Chen Y, Venezia OL, Majerus RM, Shin DS, Carrington MN, Yu XG, Wesemann DR, Moon JJ, Luster AD. SARS-CoV-2 epitope-specific CD4 + memory T cell responses across COVID-19 disease severity and antibody durability. Sci Immunol 2022; 7:eabl9464. [PMID: 35857584 PMCID: PMC9097883 DOI: 10.1126/sciimmunol.abl9464] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 04/15/2022] [Indexed: 01/14/2023]
Abstract
CD4+ T cells are central to long-term immunity against viruses through the functions of T helper 1 (TH1) and T follicular helper (TFH) cell subsets. To better understand the role of these subsets in coronavirus disease 2019 (COVID-19) immunity, we conducted a longitudinal study of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific CD4+ T cell and antibody responses in convalescent individuals who seroconverted during the first wave of the pandemic in Boston, MA, USA, across a range of COVID-19 disease severities. Analyses of spike (S) and nucleocapsid (N) epitope-specific CD4+ T cells using peptide and major histocompatibility complex class II (pMHCII) tetramers demonstrated expanded populations of T cells recognizing the different SARS-CoV-2 epitopes in most individuals compared with prepandemic controls. Individuals who experienced a milder disease course not requiring hospitalization had a greater percentage of circulating TFH (cTFH) and TH1 cells among SARS-CoV-2-specific cells. Analysis of SARS-CoV-2-specific CD4+ T cells responses in a subset of individuals with sustained anti-S antibody responses after viral clearance also revealed an increased proportion of memory cTFH cells. Our findings indicate that efficient early disease control also predicts favorable long-term adaptive immunity.
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Affiliation(s)
- Ryan W. Nelson
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School; Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Yuezhou Chen
- Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School; Boston, MA, USA
| | - Olivia L. Venezia
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Harvard Medical School; Boston, MA, USA
| | | | - Daniel S. Shin
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School; Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - MGH COVID-19 Collection & Processing Team†
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School; Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
- Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School; Boston, MA, USA
- Queens University of Charlotte, Charlotte, NC, USA
- Ragon Institute of MGH, MIT and Harvard; Cambridge, MA, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute; Bethesda, MD, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Harvard Medical School; Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Mary N. Carrington
- Ragon Institute of MGH, MIT and Harvard; Cambridge, MA, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute; Bethesda, MD, USA
| | - Xu G. Yu
- Ragon Institute of MGH, MIT and Harvard; Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Harvard Medical School; Boston, MA, USA
| | - Duane R. Wesemann
- Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School; Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard; Cambridge, MA, USA
| | - James J. Moon
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Andrew D. Luster
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
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Rovito R, Augello M, Ben-Haim A, Bono V, d'Arminio Monforte A, Marchetti G. Hallmarks of Severe COVID-19 Pathogenesis: A Pas de Deux Between Viral and Host Factors. Front Immunol 2022; 13:912336. [PMID: 35757770 PMCID: PMC9231592 DOI: 10.3389/fimmu.2022.912336] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/02/2022] [Indexed: 12/15/2022] Open
Abstract
Two years into Coronavirus Disease 2019 (COVID-19) pandemic, a comprehensive characterization of the pathogenesis of severe and critical forms of COVID-19 is still missing. While a deep dysregulation of both the magnitude and functionality of innate and adaptive immune responses have been described in severe COVID-19, the mechanisms underlying such dysregulations are still a matter of scientific debate, in turn hampering the identification of new therapies and of subgroups of patients that would most benefit from individual clinical interventions. Here we review the current understanding of viral and host factors that contribute to immune dysregulation associated with COVID-19 severity in the attempt to unfold and broaden the comprehension of COVID-19 pathogenesis and to define correlates of protection to further inform strategies of targeted therapeutic interventions.
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Affiliation(s)
- Roberta Rovito
- Clinic of Infectious Diseases and Tropical Medicine, Azienda Socio Sanitaria Territoriale (ASST) Santi Paolo e Carlo, Department of Health Sciences, University of Milan, Milan, Italy
| | - Matteo Augello
- Clinic of Infectious Diseases and Tropical Medicine, Azienda Socio Sanitaria Territoriale (ASST) Santi Paolo e Carlo, Department of Health Sciences, University of Milan, Milan, Italy
| | - Assaf Ben-Haim
- Clinic of Infectious Diseases and Tropical Medicine, Azienda Socio Sanitaria Territoriale (ASST) Santi Paolo e Carlo, Department of Health Sciences, University of Milan, Milan, Italy
| | - Valeria Bono
- Clinic of Infectious Diseases and Tropical Medicine, Azienda Socio Sanitaria Territoriale (ASST) Santi Paolo e Carlo, Department of Health Sciences, University of Milan, Milan, Italy
| | - Antonella d'Arminio Monforte
- Clinic of Infectious Diseases and Tropical Medicine, Azienda Socio Sanitaria Territoriale (ASST) Santi Paolo e Carlo, Department of Health Sciences, University of Milan, Milan, Italy
| | - Giulia Marchetti
- Clinic of Infectious Diseases and Tropical Medicine, Azienda Socio Sanitaria Territoriale (ASST) Santi Paolo e Carlo, Department of Health Sciences, University of Milan, Milan, Italy
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Seyran M. Artificial intelligence and clinical data suggest the T cell-mediated SARS-CoV-2 nonstructural protein intranasal vaccines for global COVID-19 immunity. Vaccine 2022; 40:4296-4300. [PMID: 35778279 PMCID: PMC9226295 DOI: 10.1016/j.vaccine.2022.06.052] [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: 06/14/2021] [Revised: 06/13/2022] [Accepted: 06/20/2022] [Indexed: 11/11/2022]
Abstract
Advanced computational methodologies suggested SARS-CoV-2, nonstructural proteins ORF1AB, ORF3a, as the source of immunodominant peptides for T cell presentation. T cell immunity is long-lasting and compatible with COVID-19 pathology. Based on the supporting clinical data, nonstructural SARS-CoV-2 protein vaccines could provide global immunity against COVID-19.
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Affiliation(s)
- Murat Seyran
- The University of Vienna, Doctoral Studies in Natural and Technical Sciences (SPL 44), Währinger Straße, A-1090 Vienna, Austria.
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42
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La Manna MP, Shekarkar Azgomi M, Tamburini B, Badami GD, Mohammadnezhad L, Dieli F, Caccamo N. Phenotypic and Immunometabolic Aspects on Stem Cell Memory and Resident Memory CD8+ T Cells. Front Immunol 2022; 13:884148. [PMID: 35784300 PMCID: PMC9247337 DOI: 10.3389/fimmu.2022.884148] [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: 02/25/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
The immune system, smartly and surprisingly, saves the exposure of a particular pathogen in its memory and reacts to the pathogen very rapidly, preventing serious diseases.Immunologists have long been fascinated by understanding the ability to recall and respond faster and more vigorously to a pathogen, known as “memory”.T-cell populations can be better described by using more sophisticated techniques to define phenotype, transcriptional and epigenetic signatures and metabolic pathways (single-cell resolution), which uncovered the heterogeneity of the memory T-compartment. Phenotype, effector functions, maintenance, and metabolic pathways help identify these different subsets. Here, we examine recent developments in the characterization of the heterogeneity of the memory T cell compartment. In particular, we focus on the emerging role of CD8+ TRM and TSCM cells, providing evidence on how their immunometabolism or modulation can play a vital role in their generation and maintenance in chronic conditions such as infections or autoimmune diseases.
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Affiliation(s)
- Marco Pio La Manna
- Central Laboratory of Advanced Diagnosis and Biomedical Research (CLADIBIOR) Azienda Ospedaliera Universitaria Policlinico (A.O.U.P.) Paolo Giaccone, University of Palermo, Palermo, Italy
- Department of Biomedicine, Neurosciences and Advanced Diagnostic (Bi.N.D.), University of Palermo, Palermo, Italy
| | - Mojtaba Shekarkar Azgomi
- Central Laboratory of Advanced Diagnosis and Biomedical Research (CLADIBIOR) Azienda Ospedaliera Universitaria Policlinico (A.O.U.P.) Paolo Giaccone, University of Palermo, Palermo, Italy
- Department of Biomedicine, Neurosciences and Advanced Diagnostic (Bi.N.D.), University of Palermo, Palermo, Italy
| | - Bartolo Tamburini
- Central Laboratory of Advanced Diagnosis and Biomedical Research (CLADIBIOR) Azienda Ospedaliera Universitaria Policlinico (A.O.U.P.) Paolo Giaccone, University of Palermo, Palermo, Italy
- Department of Biomedicine, Neurosciences and Advanced Diagnostic (Bi.N.D.), University of Palermo, Palermo, Italy
| | - Giusto Davide Badami
- Central Laboratory of Advanced Diagnosis and Biomedical Research (CLADIBIOR) Azienda Ospedaliera Universitaria Policlinico (A.O.U.P.) Paolo Giaccone, University of Palermo, Palermo, Italy
- Department of Biomedicine, Neurosciences and Advanced Diagnostic (Bi.N.D.), University of Palermo, Palermo, Italy
| | - Leila Mohammadnezhad
- Central Laboratory of Advanced Diagnosis and Biomedical Research (CLADIBIOR) Azienda Ospedaliera Universitaria Policlinico (A.O.U.P.) Paolo Giaccone, University of Palermo, Palermo, Italy
- Department of Biomedicine, Neurosciences and Advanced Diagnostic (Bi.N.D.), University of Palermo, Palermo, Italy
| | - Francesco Dieli
- Central Laboratory of Advanced Diagnosis and Biomedical Research (CLADIBIOR) Azienda Ospedaliera Universitaria Policlinico (A.O.U.P.) Paolo Giaccone, University of Palermo, Palermo, Italy
- Department of Biomedicine, Neurosciences and Advanced Diagnostic (Bi.N.D.), University of Palermo, Palermo, Italy
| | - Nadia Caccamo
- Central Laboratory of Advanced Diagnosis and Biomedical Research (CLADIBIOR) Azienda Ospedaliera Universitaria Policlinico (A.O.U.P.) Paolo Giaccone, University of Palermo, Palermo, Italy
- Department of Biomedicine, Neurosciences and Advanced Diagnostic (Bi.N.D.), University of Palermo, Palermo, Italy
- *Correspondence: Nadia Caccamo,
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Cords L, Knapp M, Woost R, Schulte S, Kummer S, Ackermann C, Beisel C, Peine S, Johansson AM, Kwok WWH, Günther T, Fischer N, Wittner M, Addo MM, Huber S, Schulze zur Wiesch J. High and Sustained Ex Vivo Frequency but Altered Phenotype of SARS-CoV-2-Specific CD4 + T-Cells in an Anti-CD20-Treated Patient with Prolonged COVID-19. Viruses 2022; 14:v14061265. [PMID: 35746736 PMCID: PMC9228841 DOI: 10.3390/v14061265] [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: 05/01/2022] [Revised: 05/31/2022] [Accepted: 06/08/2022] [Indexed: 02/06/2023] Open
Abstract
Here, we longitudinally assessed the ex vivo frequency and phenotype of SARS-CoV-2 membrane protein (aa145-164) epitope-specific CD4+ T-cells of an anti-CD20-treated patient with prolonged viral positivity in direct comparison to an immunocompetent patient through an MHC class II DRB1*11:01 Tetramer analysis. We detected a high and stable SARS-CoV-2 membrane-specific CD4+ T-cell response in both patients, with higher frequencies of virus-specific CD4+ T-cells in the B-cell-depleted patient. However, we found an altered virus-specific CD4+ T-cell memory phenotype in the B-cell-depleted patient that was skewed towards late differentiated memory T-cells, as well as reduced frequencies of SARS-CoV-2-specific CD4+ T-cells with CD45RA- CXCR5+ PD-1+ circulating T follicular helper cell (cTFH) phenotype. Furthermore, we observed a delayed contraction of CD127- virus-specific effector cells. The expression of the co-inhibitory receptors TIGIT and LAG-3 fluctuated on the virus-specific CD4+ T-cells of the patient, but were associated with the inflammation markers IL-6 and CRP. Our findings indicate that, despite B-cell depletion and a lack of B-cell-T-cell interaction, a robust virus-specific CD4+ T-cell response can be primed that helps to control the viral replication, but which is not sufficient to fully abrogate the infection.
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Affiliation(s)
- Leon Cords
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (L.C.); (M.K.); (R.W.); (S.S.); (S.K.); (C.A.); (C.B.); (M.W.); (M.M.A.); (S.H.)
| | - Maximilian Knapp
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (L.C.); (M.K.); (R.W.); (S.S.); (S.K.); (C.A.); (C.B.); (M.W.); (M.M.A.); (S.H.)
| | - Robin Woost
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (L.C.); (M.K.); (R.W.); (S.S.); (S.K.); (C.A.); (C.B.); (M.W.); (M.M.A.); (S.H.)
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 20246 Hamburg, Germany;
| | - Sophia Schulte
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (L.C.); (M.K.); (R.W.); (S.S.); (S.K.); (C.A.); (C.B.); (M.W.); (M.M.A.); (S.H.)
| | - Silke Kummer
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (L.C.); (M.K.); (R.W.); (S.S.); (S.K.); (C.A.); (C.B.); (M.W.); (M.M.A.); (S.H.)
| | - Christin Ackermann
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (L.C.); (M.K.); (R.W.); (S.S.); (S.K.); (C.A.); (C.B.); (M.W.); (M.M.A.); (S.H.)
| | - Claudia Beisel
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (L.C.); (M.K.); (R.W.); (S.S.); (S.K.); (C.A.); (C.B.); (M.W.); (M.M.A.); (S.H.)
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 20246 Hamburg, Germany;
| | - Sven Peine
- Institute of Transfusion Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany;
| | | | - William Wai-Hung Kwok
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA; (A.M.J.); (W.W.-H.K.)
| | - Thomas Günther
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany;
| | - Nicole Fischer
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 20246 Hamburg, Germany;
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany;
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Melanie Wittner
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (L.C.); (M.K.); (R.W.); (S.S.); (S.K.); (C.A.); (C.B.); (M.W.); (M.M.A.); (S.H.)
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 20246 Hamburg, Germany;
| | - Marylyn Martina Addo
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (L.C.); (M.K.); (R.W.); (S.S.); (S.K.); (C.A.); (C.B.); (M.W.); (M.M.A.); (S.H.)
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 20246 Hamburg, Germany;
| | - Samuel Huber
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (L.C.); (M.K.); (R.W.); (S.S.); (S.K.); (C.A.); (C.B.); (M.W.); (M.M.A.); (S.H.)
| | - Julian Schulze zur Wiesch
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (L.C.); (M.K.); (R.W.); (S.S.); (S.K.); (C.A.); (C.B.); (M.W.); (M.M.A.); (S.H.)
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 20246 Hamburg, Germany;
- Correspondence:
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Aswad M, Hamza H, Pechkovsky A, Zikrach A, Popov T, Zohar Y, Shahar E, Louria-Hayon I. High-CBD Extract (CBD-X) Downregulates Cytokine Storm Systemically and Locally in Inflamed Lungs. Front Immunol 2022; 13:875546. [PMID: 35651623 PMCID: PMC9149302 DOI: 10.3389/fimmu.2022.875546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 04/19/2022] [Indexed: 12/21/2022] Open
Abstract
Cytokine storm refers to the dysregulated production of inflammatory mediators leading to hyperinflammation. They are often detrimental, and worsen the severity of COVID-19 and other infectious or inflammatory diseases. Cannabinoids are known to have anti-inflammatory effects but their possible therapeutic value on cytokine storms has not been fully elucidated. In vivo and ex vivo studies were carried out to investigate the effects of high-THC and high-CBD extracts on cytokine production in immune cells. Significant differences between the extracts were observed. Subsequent experiments focusing on a specific high CBD extract (CBD-X) showed significant reductions in pro-inflammatory cytokines in human-derived PBMCs, neutrophils and T cells. In vivo mouse studies, using a systemically inflamed mouse model, showed reductions in pro-inflammatory cytokines TNFα and IL-1β and a concurrent increase in the anti-inflammatory cytokine IL-10 in response to CBD-X extract treatment. Lung inflammation, as in severe COVID-19 disease, is characterized by increased T-cell homing to the lungs. Our investigation revealed that CBD-X extract impaired T-cell migration induced by the chemoattractant SDF1. In addition, the phosphorylation levels of T cell receptor (TCR) signaling proteins Lck and Zap70 were significantly reduced, demonstrating an inhibitory effect on the early events downstream to TCR activation. In a lung inflamed mouse model, we observed a reduction in leukocytes including neutrophil migration to the lungs and decreased levels of IL-1β, MCP-1, IL-6 and TNFα, in response to the administration of the high-CBD extract. The results presented in this work offer that certain high-CBD extract has a high potential in the management of pathological conditions, in which the secretion of cytokines is dysregulated, as it is in severe COVID-19 disease or other infectious or inflammatory diseases.
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Affiliation(s)
- Miran Aswad
- Medical Cannabis Research and Innovation Center, Rambam Health Care Campus, Haifa, Israel
| | - Haya Hamza
- Medical Cannabis Research and Innovation Center, Rambam Health Care Campus, Haifa, Israel
| | - Antonina Pechkovsky
- Medical Cannabis Research and Innovation Center, Rambam Health Care Campus, Haifa, Israel
| | - Anastasiia Zikrach
- Medical Cannabis Research and Innovation Center, Rambam Health Care Campus, Haifa, Israel
| | - Tania Popov
- Medical Cannabis Research and Innovation Center, Rambam Health Care Campus, Haifa, Israel
| | - Yaniv Zohar
- Pathology Department, Rambam Health Care Campus, Haifa, Israel
| | - Eduardo Shahar
- Clinical Immunology Unit, Rambam Health Care Campus, Haifa, Israel
| | - Igal Louria-Hayon
- Medical Cannabis Research and Innovation Center, Rambam Health Care Campus, Haifa, Israel.,Clinical Research Institute at Rambam (CRIR), Rambam Health Care Campus, Haifa, Israel
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45
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The Role of Exposomes in the Pathophysiology of Autoimmune Diseases II: Pathogens. PATHOPHYSIOLOGY 2022; 29:243-280. [PMID: 35736648 PMCID: PMC9231084 DOI: 10.3390/pathophysiology29020020] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/28/2022] [Accepted: 05/29/2022] [Indexed: 11/21/2022] Open
Abstract
In our continuing examination of the role of exposomes in autoimmune disease, we use this review to focus on pathogens. Infections are major contributors to the pathophysiology of autoimmune diseases through various mechanisms, foremost being molecular mimicry, when the structural similarity between the pathogen and a human tissue antigen leads to autoimmune reactivity and even autoimmune disease. The three best examples of this are oral pathogens, SARS-CoV-2, and the herpesviruses. Oral pathogens reach the gut, disturb the microbiota, increase gut permeability, cause local inflammation, and generate autoantigens, leading to systemic inflammation, multiple autoimmune reactivities, and systemic autoimmunity. The COVID-19 pandemic put the spotlight on SARS-CoV-2, which has been called “the autoimmune virus.” We explore in detail the evidence supporting this. We also describe how viruses, in particular herpesviruses, have a role in the induction of many different autoimmune diseases, detailing the various mechanisms involved. Lastly, we discuss the microbiome and the beneficial microbiota that populate it. We look at the role of the gut microbiome in autoimmune disorders, because of its role in regulating the immune system. Dysbiosis of the microbiota in the gut microbiome can lead to multiple autoimmune disorders. We conclude that understanding the precise roles and relationships shared by all these factors that comprise the exposome and identifying early events and root causes of these disorders can help us to develop more targeted therapeutic protocols for the management of this worldwide epidemic of autoimmunity.
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46
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Khalifehzadeh-Esfahani Z, Fattahi S, Heidari Haratemeh Z, Jafarinia M. The Role of Immune Regulatory Molecules in COVID-19. Viral Immunol 2022; 35:359-364. [PMID: 35443826 DOI: 10.1089/vim.2021.0211] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
As the fifth pandemic in the 21st century, coronavirus 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become the most prominent global concern in the last 2 years. Variable manifestations characterize SARS-CoV-2 infection. Despite the design and production of effective vaccines and their considerable effect on reducing the COVID-19 prevalence and mortality rate, no definitive cure for the disease has yet been found. Mutations may also affect the effectiveness of vaccines. The host immune response to the pathogen has a critical role in the course of the disease. Positive and negative signals often balance the immune system. Immune regulatory molecules, also known as immune checkpoint receptors, balance the immune responses. These molecules mainly have inhibitory functions and prevent hyperactivation of immune cells or trigger adverse signaling pathways. For a decade, the immune checkpoint blockade, as a therapeutic target for cancer immunotherapy, has been utilized. Some of the inhibitory receptors are recognized as exhaustion markers on T cells. The signaling pathway of these markers restricts the function of T cells against viral infection. Dysregulation of T cells was observed in SARS-CoV-2 infection and can modify proliferation, differentiation, cytokine production, and type of response. The pivotal role of immune inhibitory receptors in the function of acquired, cell-mediated, immune defense T cells makes them a fascinating subject to study. This review article summarized recent findings on immune regulatory molecules and their role in SARS-CoV-2 infection, hoping to find a way to design novel treatments.
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Affiliation(s)
| | - Soheila Fattahi
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | | | - Morteza Jafarinia
- Shiraz Neuroscience Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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47
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Sedegah M, Porter C, Hollingdale MR, Ganeshan H, Huang J, Goforth CW, Belmonte M, Belmonte A, Weir DL, Lizewski RA, Lizewski SE, Sealfon SC, Jani V, Cheng Y, Inoue S, Velasco R, Villasante E, Sun P, Letizia AG. CHARM: COVID-19 Health Action Response for Marines-Association of antigen-specific interferon-gamma and IL2 responses with asymptomatic and symptomatic infections after a positive qPCR SARS-CoV-2 test. PLoS One 2022; 17:e0266691. [PMID: 35390102 PMCID: PMC8989306 DOI: 10.1371/journal.pone.0266691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/24/2022] [Indexed: 11/30/2022] Open
Abstract
SARS-CoV-2 T cell responses are associated with COVID-19 recovery, and Class I- and Class II-restricted epitopes have been identified in the spike (S), nucleocapsid (N) and membrane (M) proteins and others. This prospective COVID-19 Health Action Response for Marines (CHARM) study enabled assessment of T cell responses against S, N and M proteins in symptomatic and asymptomatic SARS-CoV-2 infected participants. At enrollment all participants were negative by qPCR; follow-up occurred biweekly and bimonthly for the next 6 weeks. Study participants who tested positive by qPCR SARS-CoV-2 test were enrolled in an immune response sub-study. FluoroSpot interferon-gamma (IFN-γ) and IL2 responses following qPCR-confirmed infection at enrollment (day 0), day 7 and 14 and more than 28 days later were measured using pools of 17mer peptides covering S, N, and M proteins, or CD4+CD8 peptide pools containing predicted epitopes from multiple SARS-CoV-2 antigens. Among 124 asymptomatic and 105 symptomatic participants, SARS-CoV-2 infection generated IFN-γ responses to the S, N and M proteins that persisted longer in asymptomatic cases. IFN-γ responses were significantly (p = 0.001) more frequent to the N pool (51.4%) than the M pool (18.9%) among asymptomatic but not symptomatic subjects. Asymptomatic IFN-γ responders to the CD4+CD8 pool responded more frequently to the S pool (55.6%) and N pool (57.1%), than the M pool (7.1%), but not symptomatic participants. The frequencies of IFN-γ responses to the S and N+M pools peaked 7 days after the positive qPCR test among asymptomatic (S pool: 22.2%; N+M pool: 28.7%) and symptomatic (S pool: 15.3%; N+M pool 21.9%) participants and dropped by >28 days. Magnitudes of post-infection IFN-γ and IL2 responses to the N+M pool were significantly correlated with IFN-γ and IL2 responses to the N and M pools. These data further support the central role of Th1-biased cell mediated immunity IFN-γ and IL2 responses, particularly to the N protein, in controlling COVID-19 symptoms, and justify T cell-based COVID-19 vaccines that include the N and S proteins.
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Affiliation(s)
- Martha Sedegah
- Agile Vaccines and Therapeutics Department, Naval Medical Research Center, Silver Spring, MD, United States of America
| | - Chad Porter
- Virology Department, Naval Medical Research Center, Silver Spring, MD, United States of America
| | - Michael R. Hollingdale
- Agile Vaccines and Therapeutics Department, Naval Medical Research Center, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation, Bethesda, MD, United States of America
| | - Harini Ganeshan
- Agile Vaccines and Therapeutics Department, Naval Medical Research Center, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation, Bethesda, MD, United States of America
| | - Jun Huang
- Agile Vaccines and Therapeutics Department, Naval Medical Research Center, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation, Bethesda, MD, United States of America
| | - Carl W. Goforth
- Virology Department, Naval Medical Research Center, Silver Spring, MD, United States of America
| | - Maria Belmonte
- Agile Vaccines and Therapeutics Department, Naval Medical Research Center, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation, Bethesda, MD, United States of America
| | - Arnel Belmonte
- Agile Vaccines and Therapeutics Department, Naval Medical Research Center, Silver Spring, MD, United States of America
- GDIT, MD, United States of America
| | - Dawn L. Weir
- Virology Department, Naval Medical Research Center, Silver Spring, MD, United States of America
| | | | | | - Stuart C. Sealfon
- Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Vihasi Jani
- Virology Department, Naval Medical Research Center, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation, Bethesda, MD, United States of America
| | - Ying Cheng
- Virology Department, Naval Medical Research Center, Silver Spring, MD, United States of America
- Leidos, Reston, VA, United States of America
| | - Sandra Inoue
- Agile Vaccines and Therapeutics Department, Naval Medical Research Center, Silver Spring, MD, United States of America
- GDIT, MD, United States of America
| | - Rachael Velasco
- Agile Vaccines and Therapeutics Department, Naval Medical Research Center, Silver Spring, MD, United States of America
| | - Eileen Villasante
- Agile Vaccines and Therapeutics Department, Naval Medical Research Center, Silver Spring, MD, United States of America
| | - Peifang Sun
- Virology Department, Naval Medical Research Center, Silver Spring, MD, United States of America
| | - Andrew G. Letizia
- Virology Department, Naval Medical Research Center, Silver Spring, MD, United States of America
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48
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Brownlie D, Rødahl I, Varnaite R, Asgeirsson H, Glans H, Falck-Jones S, Vangeti S, Buggert M, Ljunggren HG, Michaëlsson J, Gredmark-Russ S, Smed-Sörensen A, Marquardt N. Comparison of Lung-Homing Receptor Expression and Activation Profiles on NK Cell and T Cell Subsets in COVID-19 and Influenza. Front Immunol 2022; 13:834862. [PMID: 35371005 PMCID: PMC8966396 DOI: 10.3389/fimmu.2022.834862] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/24/2022] [Indexed: 12/11/2022] Open
Abstract
Respiratory viral infections with SARS-CoV-2 and influenza viruses commonly induce a strong infiltration of immune cells into the human lung, with potential detrimental effects on the integrity of the lung tissue. Despite comprising the largest fractions of circulating lymphocytes in the lung, rather little is known about how peripheral blood natural killer (NK) cell and T cell subsets are equipped for lung-homing in COVID-19 and influenza. Here, we provide a detailed comparative analysis of NK cells and T cells in patients infected with SARS-CoV-2 or influenza virus, focusing on the protein and gene expression of chemokine receptors known to be involved in recruitment to the lung. For this, we used 28-colour flow cytometry as well as re-analysis of a publicly available single-cell RNA-seq dataset from bronchoalveolar lavage (BAL) fluid. Frequencies of NK cells and T cells expressing CXCR3, CXCR6, and CCR5 were altered in peripheral blood of COVID-19 and influenza patients, in line with increased transcript expression of CXCR3, CXCR6, and CCR5 and their respective ligands in BAL fluid. NK cells and T cells expressing lung-homing receptors displayed stronger phenotypic signs of activation compared to cells lacking lung-homing receptors, and activation was overall stronger in influenza compared to COVID-19. Together, our results indicate a role for CXCR3+, CXCR6+, and/or CCR5+ NK cells and T cells that potentially migrate to the lungs in moderate COVID-19 and influenza patients, identifying common targets for future therapeutic interventions in respiratory viral infections.
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Affiliation(s)
- Demi Brownlie
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Inga Rødahl
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Renata Varnaite
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Hilmir Asgeirsson
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Hedvig Glans
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Sara Falck-Jones
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Sindhu Vangeti
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Marcus Buggert
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Hans-Gustaf Ljunggren
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Jakob Michaëlsson
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Sara Gredmark-Russ
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Smed-Sörensen
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Nicole Marquardt
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
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49
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Nelson CE, Namasivayam S, Foreman TW, Kauffman KD, Sakai S, Dorosky DE, Lora NE, Brooks K, Potter EL, Garza NL, Lafont BAP, Johnson RF, Roederer M, Sher A, Weiskopf D, Sette A, de Wit E, Hickman HD, Brenchley JM, Via LE, Barber DL. Mild SARS-CoV-2 infection in rhesus macaques is associated with viral control prior to antigen-specific T cell responses in tissues. Sci Immunol 2022; 7:eabo0535. [PMID: 35271298 PMCID: PMC8995035 DOI: 10.1126/sciimmunol.abo0535] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/04/2022] [Indexed: 12/24/2022]
Abstract
SARS-CoV-2 primarily replicates in mucosal sites, and more information is needed about immune responses in infected tissues. Here, we used rhesus macaques to model protective primary immune responses in tissues during mild COVID-19. Viral RNA levels were highest on days 1-2 post-infection and fell precipitously thereafter. 18F-fluorodeoxyglucose (FDG)-avid lung abnormalities and interferon (IFN)-activated monocytes and macrophages in the bronchoalveolar lavage (BAL) were found on days 3-4 post-infection. Virus-specific effector CD8+ and CD4+ T cells became detectable in the BAL and lung tissue on days 7-10, after viral RNA, radiologic evidence of lung inflammation, and IFN-activated myeloid cells had substantially declined. Notably, SARS-CoV-2-specific T cells were not detectable in the nasal turbinates, salivary glands, and tonsils on day 10 post-infection. Thus, SARS-CoV-2 replication wanes in the lungs of rhesus macaques prior to T cell responses, and in the nasal and oral mucosa despite the apparent lack of antigen-specific T cells, suggesting that innate immunity efficiently restricts viral replication during mild COVID-19.
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Affiliation(s)
- Christine E. Nelson
- T lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Sivaranjani Namasivayam
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Taylor W. Foreman
- T lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Keith D. Kauffman
- T lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Shunsuke Sakai
- T lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Danielle E. Dorosky
- T lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Nickiana E. Lora
- T lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - NIAID/DIR Tuberculosis Imaging Program3†
- T lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
- Division of Intramural Research, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
- ImmunoTechnology Section, Vaccine Research Center, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- SARS-CoV-2 Virology Core, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
- Laboratory of Virology, Division of Intramural Research, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Hamilton, MT, USA
- Viral Immunity and Pathogenesis Unit, Laboratory of Clinical Immunology and Microbiology, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
- Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
- Institute of Infectious Disease & Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Kelsie Brooks
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - E. Lake Potter
- ImmunoTechnology Section, Vaccine Research Center, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Nicole L. Garza
- SARS-CoV-2 Virology Core, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Bernard A. P. Lafont
- SARS-CoV-2 Virology Core, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Reed F. Johnson
- SARS-CoV-2 Virology Core, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Mario Roederer
- ImmunoTechnology Section, Vaccine Research Center, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Alan Sher
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Emmie de Wit
- Laboratory of Virology, Division of Intramural Research, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Hamilton, MT, USA
| | - Heather D. Hickman
- Viral Immunity and Pathogenesis Unit, Laboratory of Clinical Immunology and Microbiology, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Jason M. Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Laura E. Via
- Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
- Institute of Infectious Disease & Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Daniel L. Barber
- T lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
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50
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T cell responses to SARS-CoV-2 in humans and animals. J Microbiol 2022; 60:276-289. [PMID: 35157219 PMCID: PMC8852923 DOI: 10.1007/s12275-022-1624-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/28/2021] [Accepted: 12/28/2021] [Indexed: 02/08/2023]
Abstract
SARS-CoV-2, the causative agent of COVID-19, first emerged in 2019. Antibody responses against SARS-CoV-2 have been given a lot of attention. However, the armamentarium of humoral and T cells may have differing roles in different viral infections. Though the exact role of T cells in COVID-19 remains to be elucidated, prior experience with human coronavirus has revealed an essential role of T cells in the outcomes of viral infections. Moreover, an increasing body of evidence suggests that T cells might be effective against SARS-CoV-2. This review summarizes the role of T cells in mouse CoV, human pathogenic respiratory CoV in general and SARS-CoV-2 in specific.
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