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Coulon PG, Prakash S, Dhanushkodi NR, Srivastava R, Zayou L, Tifrea DF, Edwards RA, Figueroa CJ, Schubl SD, Hsieh L, Nesburn AB, Kuppermann BD, Bahraoui E, Vahed H, Gil D, Jones TM, Ulmer JB, BenMohamed L. High frequencies of alpha common cold coronavirus/SARS-CoV-2 cross-reactive functional CD4 + and CD8 + memory T cells are associated with protection from symptomatic and fatal SARS-CoV-2 infections in unvaccinated COVID-19 patients. Front Immunol 2024; 15:1343716. [PMID: 38605956 PMCID: PMC11007208 DOI: 10.3389/fimmu.2024.1343716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 03/08/2024] [Indexed: 04/13/2024] Open
Abstract
Background Cross-reactive SARS-CoV-2-specific memory CD4+ and CD8+ T cells are present in up to 50% of unexposed, pre-pandemic, healthy individuals (UPPHIs). However, the characteristics of cross-reactive memory CD4+ and CD8+ T cells associated with subsequent protection of asymptomatic coronavirus disease 2019 (COVID-19) patients (i.e., unvaccinated individuals who never develop any COVID-19 symptoms despite being infected with SARS-CoV-2) remains to be fully elucidated. Methods This study compares the antigen specificity, frequency, phenotype, and function of cross-reactive memory CD4+ and CD8+ T cells between common cold coronaviruses (CCCs) and SARS-CoV-2. T-cell responses against genome-wide conserved epitopes were studied early in the disease course in a cohort of 147 unvaccinated COVID-19 patients who were divided into six groups based on the severity of their symptoms. Results Compared to severely ill COVID-19 patients and patients with fatal COVID-19 outcomes, the asymptomatic COVID-19 patients displayed significantly: (i) higher rates of co-infection with the 229E alpha species of CCCs (α-CCC-229E); (ii) higher frequencies of cross-reactive functional CD134+CD137+CD4+ and CD134+CD137+CD8+ T cells that cross-recognized conserved epitopes from α-CCCs and SARS-CoV-2 structural, non-structural, and accessory proteins; and (iii) lower frequencies of CCCs/SARS-CoV-2 cross-reactive exhausted PD-1+TIM3+TIGIT+CTLA4+CD4+ and PD-1+TIM3+TIGIT+CTLA4+CD8+ T cells, detected both ex vivo and in vitro. Conclusions These findings (i) support a crucial role of functional, poly-antigenic α-CCCs/SARS-CoV-2 cross-reactive memory CD4+ and CD8+ T cells, induced following previous CCCs seasonal exposures, in protection against subsequent severe COVID-19 disease and (ii) provide critical insights into developing broadly protective, multi-antigen, CD4+, and CD8+ T-cell-based, universal pan-Coronavirus vaccines capable of conferring cross-species protection.
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Affiliation(s)
- Pierre-Gregoire Coulon
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Swayam Prakash
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Nisha R. Dhanushkodi
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Ruchi Srivastava
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Latifa Zayou
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Delia F. Tifrea
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California Irvine, Irvine, CA, United States
| | - Robert A. Edwards
- Department of Pathology and Laboratory Medicine, School of Medicine, University of California Irvine, Irvine, CA, United States
| | - Cesar J. Figueroa
- Department of Surgery, Divisions of Trauma, Burns and Critical Care, School of Medicine, University of California Irvine, Irvine, CA, United States
| | - Sebastian D. Schubl
- Department of Surgery, Divisions of Trauma, Burns and Critical Care, School of Medicine, University of California Irvine, Irvine, CA, United States
| | - Lanny Hsieh
- Department of Medicine, Division of Infectious Diseases and Hospitalist Program, School of Medicine, University of California Irvine, Irvine, CA, United States
| | - Anthony B. Nesburn
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Baruch D. Kuppermann
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | | | - Hawa Vahed
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA, United States
| | - Daniel Gil
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA, United States
| | - Trevor M. Jones
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA, United States
| | - Jeffrey B. Ulmer
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA, United States
| | - Lbachir BenMohamed
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
- Université Paul Sabatier, Infinity, Inserm, Toulouse, France
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA, United States
- Institute for Immunology, The University of California Irvine, School of Medicine, Irvine, CA, United States
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2
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Williams GP, Yu ED, Shapiro K, Wang E, Freuchet A, Frazier A, Lindestam Arlehamn CS, Sette A, da Silva Antunes R. Investigating viral and autoimmune T cell responses associated with post-acute sequelae of COVID-19. Hum Immunol 2024:110770. [PMID: 38433036 DOI: 10.1016/j.humimm.2024.110770] [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: 09/24/2023] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 03/05/2024]
Abstract
Post-acute sequelae of COVID-19 (PASC), or Long COVID, is a chronic condition following acute SARS-CoV-2 infection. Symptoms include exertion fatigue, respiratory issues, myalgia, and neurological manifestations such as 'brain fog,' posing concern for their debilitating nature and potential role in other neurological disorders. However, the underlying potential pathogenic mechanisms of the neurological complications of PASC is largely unknown. Herein, we investigated differences in antigen-specific T cell responses from the peripheral blood towards SARS-CoV-2, latent viruses, or neuronal antigens in 14 PASC individuals with neurological manifestations (PASC-N) versus 22 individuals fully recovered from COVID-19. We employed Activation Induced Marker (AIM), ICS and FluoroSpot assays to determine the specificity and magnitude of CD4+ and CD8+ T cell responses towards SARS-CoV-2 (Spike and rest of proteome), latent viruses (CMV, EBV), and several neuronal antigens. Overall, we observed similar antigen-specific T cell frequencies and cytokine effector T cell responses between PASC donors compared to recovered controls for all antigens tested (viral or autoantigen) in both CD4+ and CD8+ T cell compartments. Our findings suggest that PASC-N does not appear to be associated with changes in antigen-specific T cell responses towards a subset of disease-relevant targets, but more studies in a larger cohort are needed to confirm these unaltered responses.
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Affiliation(s)
- Gregory P Williams
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, San Diego, CA, USA
| | - Esther Dawen Yu
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, San Diego, CA, USA
| | - Kendra Shapiro
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, San Diego, CA, USA
| | - Eric Wang
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, San Diego, CA, USA
| | - Antoine Freuchet
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, San Diego, CA, USA
| | - April Frazier
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, San Diego, CA, USA
| | | | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, San Diego, CA, USA; University of California San Diego School of Medicine, La Jolla, San Diego, CA, USA
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3
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Prakash S, Dhanushkodi NR, Zayou L, Ibraim IC, Quadiri A, Coulon PG, Tifrea DF, Suzer B, Shaik AM, Chilukuri A, Edwards RA, Singer M, Vahed H, Nesburn AB, Kuppermann BD, Ulmer JB, Gil D, Jones TM, BenMohamed L. Cross-protection induced by highly conserved human B, CD4 +, and CD8 + T-cell epitopes-based vaccine against severe infection, disease, and death caused by multiple SARS-CoV-2 variants of concern. Front Immunol 2024; 15:1328905. [PMID: 38318166 PMCID: PMC10839970 DOI: 10.3389/fimmu.2024.1328905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/02/2024] [Indexed: 02/07/2024] Open
Abstract
Background The coronavirus disease 2019 (COVID-19) pandemic has created one of the largest global health crises in almost a century. Although the current rate of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections has decreased significantly, the long-term outlook of COVID-19 remains a serious cause of morbidity and mortality worldwide, with the mortality rate still substantially surpassing even that recorded for influenza viruses. The continued emergence of SARS-CoV-2 variants of concern (VOCs), including multiple heavily mutated Omicron sub-variants, has prolonged the COVID-19 pandemic and underscores the urgent need for a next-generation vaccine that will protect from multiple SARS-CoV-2 VOCs. Methods We designed a multi-epitope-based coronavirus vaccine that incorporated B, CD4+, and CD8+ T- cell epitopes conserved among all known SARS-CoV-2 VOCs and selectively recognized by CD8+ and CD4+ T-cells from asymptomatic COVID-19 patients irrespective of VOC infection. The safety, immunogenicity, and cross-protective immunity of this pan-variant SARS-CoV-2 vaccine were studied against six VOCs using an innovative triple transgenic h-ACE-2-HLA-A2/DR mouse model. Results The pan-variant SARS-CoV-2 vaccine (i) is safe , (ii) induces high frequencies of lung-resident functional CD8+ and CD4+ TEM and TRM cells , and (iii) provides robust protection against morbidity and virus replication. COVID-19-related lung pathology and death were caused by six SARS-CoV-2 VOCs: Alpha (B.1.1.7), Beta (B.1.351), Gamma or P1 (B.1.1.28.1), Delta (lineage B.1.617.2), and Omicron (B.1.1.529). Conclusion A multi-epitope pan-variant SARS-CoV-2 vaccine bearing conserved human B- and T- cell epitopes from structural and non-structural SARS-CoV-2 antigens induced cross-protective immunity that facilitated virus clearance, and reduced morbidity, COVID-19-related lung pathology, and death caused by multiple SARS-CoV-2 VOCs.
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Affiliation(s)
- Swayam Prakash
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Nisha R Dhanushkodi
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Latifa Zayou
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Izabela Coimbra Ibraim
- High Containment Facility, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Afshana Quadiri
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Pierre Gregoire Coulon
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Delia F Tifrea
- Department of Pathology and Laboratory Medicine, School of Medicine, the University of California Irvine, Irvine, CA, United States
| | - Berfin Suzer
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Amin Mohammed Shaik
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Amruth Chilukuri
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Robert A Edwards
- Department of Pathology and Laboratory Medicine, School of Medicine, the University of California Irvine, Irvine, CA, United States
| | - Mahmoud Singer
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Hawa Vahed
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA, United States
| | - Anthony B Nesburn
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Baruch D Kuppermann
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
| | - Jeffrey B Ulmer
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA, United States
| | - Daniel Gil
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA, United States
| | - Trevor M Jones
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA, United States
| | - Lbachir BenMohamed
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA, United States
- Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA, United States
- Division of Infectious Diseases and Hospitalist Program, Department of Medicine, School of Medicine, the University of California Irvine, Irvine, CA, United States
- Institute for Immunology; University of California Irvine, School of Medicine, Irvine, CA, United States
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4
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Benede N, Tincho MB, Walters A, Subbiah V, Ngomti A, Baguma R, Butters C, Hahnle L, Mennen M, Skelem S, Adriaanse M, Facey-Thomas H, Scott C, Day J, Spracklen TF, van Graan S, Balla SR, Moyo-Gwete T, Moore PL, MacGinty R, Botha M, Workman L, Johnson M, Goldblatt D, Zar HJ, Ntusi NA, Zühlke L, Webb K, Riou C, Burgers WA, Keeton RS. Distinct T cell polyfunctional profile in SARS-CoV-2 seronegative children associated with endemic human coronavirus cross-reactivity. iScience 2024; 27:108728. [PMID: 38235336 PMCID: PMC10792240 DOI: 10.1016/j.isci.2023.108728] [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: 07/10/2023] [Revised: 10/19/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024] Open
Abstract
SARS-CoV-2 infection in children typically results in asymptomatic or mild disease. There is a paucity of studies on SARS-CoV-2 antiviral immunity in African children. We investigated SARS-CoV-2-specific T cell responses in 71 unvaccinated asymptomatic South African children who were seropositive or seronegative for SARS-CoV-2. SARS-CoV-2-specific CD4+ T cell responses were detectable in 83% of seropositive and 60% of seronegative children. Although the magnitude of the CD4+ T cell response did not differ significantly between the two groups, their functional profiles were distinct, with SARS-CoV-2 seropositive children exhibiting a higher proportion of polyfunctional T cells compared to their seronegative counterparts. The frequency of SARS-CoV-2-specific CD4+ T cells in seronegative children was associated with the endemic human coronavirus (HCoV) HKU1 IgG response. Overall, the presence of SARS-CoV-2-responding T cells in seronegative children may result from cross-reactivity to endemic coronaviruses and could contribute to the relative protection from disease observed in SARS-CoV-2-infected children.
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Affiliation(s)
- Ntombi Benede
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Marius B. Tincho
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Avril Walters
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Vennesa Subbiah
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Amkele Ngomti
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Richard Baguma
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Claire Butters
- Division of Paediatric Rheumatology, Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, University of Cape Town, Observatory, South Africa
| | - Lina Hahnle
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory, South Africa
| | - Mathilda Mennen
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory, South Africa
| | - Sango Skelem
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory, South Africa
| | - Marguerite Adriaanse
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory, South Africa
| | - Heidi Facey-Thomas
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
| | - Christiaan Scott
- Division of Paediatric Rheumatology, Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, University of Cape Town, Observatory, South Africa
| | - Jonathan Day
- Division of Paediatric Rheumatology, Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, University of Cape Town, Observatory, South Africa
| | - Timothy F. Spracklen
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
- Cape Heart Institute, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
- South African Medical Research Council, Francie Van Zijl Drive, Parow Cape Town, South Africa
| | - Strauss van Graan
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- SA MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Sashkia R. Balla
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- SA MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Thandeka Moyo-Gwete
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- SA MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Penny L. Moore
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- SA MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Rae MacGinty
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
- Medical Research Council (MRC) Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Maresa Botha
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
- Medical Research Council (MRC) Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Lesley Workman
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
- Medical Research Council (MRC) Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Marina Johnson
- Great Ormond Street Institute of Child Health Biomedical Research Centre, University College London, London, UK
| | - David Goldblatt
- Great Ormond Street Institute of Child Health Biomedical Research Centre, University College London, London, UK
| | - Heather J. Zar
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
- Medical Research Council (MRC) Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | - Ntobeko A.B. Ntusi
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory, South Africa
- Cape Heart Institute, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | - Liesl Zühlke
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
- Cape Heart Institute, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
- South African Medical Research Council, Francie Van Zijl Drive, Parow Cape Town, South Africa
| | - Kate Webb
- Division of Paediatric Rheumatology, Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital, University of Cape Town, Observatory, South Africa
- Crick African Network, The Francis Crick Institute, London, UK
| | - Catherine Riou
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | - Wendy A. Burgers
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | - Roanne S. Keeton
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
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5
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Bellocchio L, Dipalma G, Inchingolo AM, Inchingolo AD, Ferrante L, Del Vecchio G, Malcangi G, Palermo A, Qendro A, Inchingolo F. COVID-19 on Oral Health: A New Bilateral Connection for the Pandemic. Biomedicines 2023; 12:60. [PMID: 38255167 PMCID: PMC10813615 DOI: 10.3390/biomedicines12010060] [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: 11/27/2023] [Revised: 12/14/2023] [Accepted: 12/23/2023] [Indexed: 01/24/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and transmission are generally known to be produced by respiratory droplets and aerosols from the oral cavity (O.C.) of infected subjects, as stated by the World Health Organization. Saliva also retains the viral particles and aids in the spread of COVID-19. Angiotensin-converting enzyme Type 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2) are two of the numerous factors that promote SARS-CoV-2 infection, expressed by O.C. structures, various mucosa types, and the epithelia of salivary glands. A systemic SARS-CoV-2 infection might result from viral replication in O.C. cells. On the other hand, cellular damage of different subtypes in the O.C. might be associated with various clinical signs and symptoms. Factors interfering with SARS-CoV-2 infection potential might represent fertile ground for possible local pharmacotherapeutic interventions, which may confine SARS-CoV-2 virus entry and transmission in the O.C., finally representing a way to reduce COVID-19 incidence and severity.
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Affiliation(s)
- Luigi Bellocchio
- INSERM, U1215 NeuroCentre Magendie, Endocannabinoids and Neuroadaptation, University of Bordeaux, 33063 Bordeaux, France;
| | - Gianna Dipalma
- Department of Interdisciplinary Medicine, University of Study “Aldo Moro”, 70124 Bari, Italy; (A.M.I.); (A.D.I.); (L.F.); (G.D.V.); (F.I.)
| | - Angelo Michele Inchingolo
- Department of Interdisciplinary Medicine, University of Study “Aldo Moro”, 70124 Bari, Italy; (A.M.I.); (A.D.I.); (L.F.); (G.D.V.); (F.I.)
| | - Alessio Danilo Inchingolo
- Department of Interdisciplinary Medicine, University of Study “Aldo Moro”, 70124 Bari, Italy; (A.M.I.); (A.D.I.); (L.F.); (G.D.V.); (F.I.)
| | - Laura Ferrante
- Department of Interdisciplinary Medicine, University of Study “Aldo Moro”, 70124 Bari, Italy; (A.M.I.); (A.D.I.); (L.F.); (G.D.V.); (F.I.)
| | - Gaetano Del Vecchio
- Department of Interdisciplinary Medicine, University of Study “Aldo Moro”, 70124 Bari, Italy; (A.M.I.); (A.D.I.); (L.F.); (G.D.V.); (F.I.)
| | - Giuseppina Malcangi
- Department of Interdisciplinary Medicine, University of Study “Aldo Moro”, 70124 Bari, Italy; (A.M.I.); (A.D.I.); (L.F.); (G.D.V.); (F.I.)
| | - Andrea Palermo
- College of Medicine and Dentistry, Birmingham B4 6BN, UK;
| | - Andis Qendro
- Faculty of Dental Medicine, University of Medicine, 1005 Tirana, Albania;
| | - Francesco Inchingolo
- Department of Interdisciplinary Medicine, University of Study “Aldo Moro”, 70124 Bari, Italy; (A.M.I.); (A.D.I.); (L.F.); (G.D.V.); (F.I.)
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6
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Shamabadi NS, Bagasra AB, Pawar S, Bagasra O. Potential use of endemic human coronaviruses to stimulate immunity against pathogenic SARS-CoV-2 and its variants. Libyan J Med 2023; 18:2209949. [PMID: 37186902 DOI: 10.1080/19932820.2023.2209949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
While severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes significant morbidity and mortality in humans, there is a wide range of disease outcomes following virus exposures. Some individuals are asymptomatic while others develop complications within a few days after infection that can lead to fatalities in a smaller portion of the population. In the present study, we have analyzed the factors that may influence the outcome of post-SARS-CoV-2 infection. One factor that may influence virus control is pre-existing immunity conferred by an individual's past exposures to endemic coronaviruses (eCOVIDs) which cause the common cold in humans and generally, most children are exposed to one of the four eCOVIDs before 2 years of age. Here, we have carried out protein sequence analyses to show the amino acid homologies between the four eCOVIDs (i.e. OC43, HKU1, 229E, and NL63) as well as examining the cross-reactive immune responses between SARS-CoV-2 and eCOVIDs by epidemiologic analyses. Our results show that the nations where continuous exposures to eCOVIDs are very high due to religious and traditional causes showed significantly lower cases and low mortality rates per 100,000. We hypothesize that in the areas of the globe where Muslims are in majority and due to religious practices are regularly exposed to eCOVIDs they show a significantly lower infection, as well as mortality rate, and that is due to pre-existing cross-immunity against SARS-CoV-2. This is due to cross-reactive antibodies and T-cells that recognize SARS-CoV-2 antigens. We also have reviewed the current literature that has also proposed that human infections with eCOVIDs impart protection against disease caused by subsequent exposure to SARS-CoV-2. We propose that a nasal spray vaccine consisting of selected genes of eCOVIDs would be beneficial against SARS-CoV-2 and other pathogenic coronaviruses.
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Affiliation(s)
| | - Anisah B Bagasra
- Department of Psychology, Kennesaw State University, Kennesaw, GA, USA
| | - Shrikant Pawar
- Department of Computer Science and Biology, Claflin University, SC, USA
| | - Omar Bagasra
- South Carolina Center for Biotechnology, Claflin University, Orangeburg, SC, USA
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7
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Wang L, Nicols A, Turtle L, Richter A, Duncan CJA, Dunachie SJ, Klenerman P, Payne RP. T cell immune memory after covid-19 and vaccination. BMJ MEDICINE 2023; 2:e000468. [PMID: 38027416 PMCID: PMC10668147 DOI: 10.1136/bmjmed-2022-000468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023]
Abstract
The T cell memory response is a crucial component of adaptive immunity responsible for limiting or preventing viral reinfection. T cell memory after infection with the SARS-CoV-2 virus or vaccination is broad, and spans multiple viral proteins and epitopes, about 20 in each individual. So far the T cell memory response is long lasting and provides a high level of cross reactivity and hence resistance to viral escape by variants of the SARS-CoV-2 virus, such as the omicron variant. All current vaccine regimens tested produce robust T cell memory responses, and heterologous regimens will probably enhance protective responses through increased breadth. T cell memory could have a major role in protecting against severe covid-19 disease through rapid viral clearance and early presentation of epitopes, and the presence of cross reactive T cells might enhance this protection. T cell memory is likely to provide ongoing protection against admission to hospital and death, and the development of a pan-coronovirus vaccine might future proof against new pandemic strains.
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Affiliation(s)
- Lulu Wang
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
| | - Alex Nicols
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
| | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Alex Richter
- Institute of Immunology and Immunotherapy, College of Medical and Dental Science, University of Birmingham, Birmingham, UK
| | - Christopher JA Duncan
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
- Department of Infection and Tropical Medicine, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Susanna J Dunachie
- NDM Centre For Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University Faculty of Science, Bangkok, Thailand
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, Oxfordshire, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Rebecca P Payne
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Newcastle University, Newcastle upon Tyne, UK
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da Silva Antunes R, Weiskopf D, Sidney J, Rubiro P, Peters B, Arlehamn CSL, Grifoni A, Sette A. The MegaPool Approach to Characterize Adaptive CD4+ and CD8+ T Cell Responses. Curr Protoc 2023; 3:e934. [PMID: 37966108 PMCID: PMC10662678 DOI: 10.1002/cpz1.934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Epitopes recognized by T cells are a collection of short peptide fragments derived from specific antigens or proteins. Immunological research to study T cell responses is hindered by the extreme degree of heterogeneity of epitope targets, which are usually derived from multiple antigens; within a given antigen, hundreds of different T cell epitopes can be recognized, differing from one individual to the next because T cell epitope recognition is restricted by the epitopes' ability to bind to MHC molecules, which are extremely polymorphic in different individuals. Testing large pools encompassing hundreds of peptides is technically challenging because of logistical considerations regarding solvent-induced toxicity. To address this issue, we developed the MegaPool (MP) approach based on sequential lyophilization of large numbers of peptides that can be used in a variety of assays to measure T cell responses, including ELISPOT, intracellular cytokine staining, and activation-induced marker assays, and that has been validated in the study of infectious diseases, allergies, and autoimmunity. Here, we describe the procedures for generating and testing MPs, starting with peptide synthesis and lyophilization, as well as a step-by-step guide and recommendations for their handling and experimental usage. Overall, the MP approach is a powerful strategy for studying T cell responses and understanding the immune system's role in health and disease. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Generation of peptide pools ("MegaPools") Basic Protocol 2: MegaPool testing and quantitation of antigen-specific T cell responses.
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Affiliation(s)
- Ricardo da Silva Antunes
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - John Sidney
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Paul Rubiro
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| | | | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
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9
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da Silva Antunes R, Garrigan E, Quiambao LG, Dhanda SK, Marrama D, Westernberg L, Wang E, Abawi A, Sutherland A, Armstrong SK, Brickman TJ, Sidney J, Frazier A, Merkel TJ, Peters B, Sette A. T cell reactivity to Bordetella pertussis is highly diverse regardless of childhood vaccination. Cell Host Microbe 2023; 31:1404-1416.e4. [PMID: 37490913 PMCID: PMC10528758 DOI: 10.1016/j.chom.2023.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/17/2023] [Accepted: 06/27/2023] [Indexed: 07/27/2023]
Abstract
The incidence of whooping cough due to Bordetella pertussis (BP) infections has increased recently. It is believed that the shift from whole-cell pertussis (wP) vaccines to acellular pertussis (aP) vaccines may be contributing to this rise. While T cells are key in controlling and preventing disease, nearly all knowledge relates to antigens in aP vaccines. A whole-genome mapping of human BP-specific CD4+ T cell responses was performed in healthy vaccinated adults and revealed unexpected broad reactivity to hundreds of antigens. The overall pattern and magnitude of T cell responses to aP and non-aP vaccine antigens are similar regardless of childhood vaccination, suggesting that asymptomatic infections drive the pattern of T cell reactivity in adults. Lastly, lack of Th1/Th2 polarization to non-aP vaccine antigens suggests these antigens have the potential to counteract aP vaccination Th2 bias. These findings enhance our insights into human T cell responses to BP and identify potential targets for next-generation pertussis vaccines.
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Affiliation(s)
- Ricardo da Silva Antunes
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA.
| | - Emily Garrigan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Lorenzo G Quiambao
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Sandeep Kumar Dhanda
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Daniel Marrama
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Luise Westernberg
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Eric Wang
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Adam Abawi
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Aaron Sutherland
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Sandra K Armstrong
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Timothy J Brickman
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - John Sidney
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - April Frazier
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Tod J Merkel
- Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), 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
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), 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
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10
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da Silva Antunes R, Grifoni A, Frazier A, Weiskopf D, Sette A. An update on studies characterizing adaptive immune responses in SARS-CoV-2 infection and COVID-19 vaccination. Int Immunol 2023; 35:353-359. [PMID: 37148294 PMCID: PMC10406159 DOI: 10.1093/intimm/dxad014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/03/2023] [Indexed: 05/08/2023] Open
Abstract
In this brief opinion piece, we highlight our studies characterizing adaptive SARS-CoV-2 immune responses in infection and vaccination, and the ability of SARS-CoV-2-specific T cells to recognize emerging variants of concern, and the role of pre-existing cross-reactive T cells. In the context of the debate on correlates of protection, the pandemic's progression in the past 3 years underlined the need to consider how different adaptive immune responses might differentially contribute to protection from SARS-CoV-2 infection versus COVID-19 disease. Lastly, we discuss how cross-reactive T cell responses may be useful in generating a broad adaptive immunity, recognizing different variants and viral families. Considering vaccines with broadly conserved antigens could improve preparedness for future infectious disease outbreaks.
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Affiliation(s)
- Ricardo da Silva Antunes
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA 92037, USA
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA 92037, USA
| | - April Frazier
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA 92037, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA 92037, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); 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, USA
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11
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Tarke A, Zhang Y, Methot N, Narowski TM, Phillips E, Mallal S, Frazier A, Filaci G, Weiskopf D, Dan JM, Premkumar L, Scheuermann RH, Sette A, Grifoni A. Targets and cross-reactivity of human T cell recognition of common cold coronaviruses. Cell Rep Med 2023; 4:101088. [PMID: 37295422 PMCID: PMC10242702 DOI: 10.1016/j.xcrm.2023.101088] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/17/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023]
Abstract
The coronavirus (CoV) family includes several viruses infecting humans, highlighting the importance of exploring pan-CoV vaccine strategies to provide broad adaptive immune protection. We analyze T cell reactivity against representative Alpha (NL63) and Beta (OC43) common cold CoVs (CCCs) in pre-pandemic samples. S, N, M, and nsp3 antigens are immunodominant, as shown for severe acute respiratory syndrome 2 (SARS2), while nsp2 and nsp12 are Alpha or Beta specific. We further identify 78 OC43- and 87 NL63-specific epitopes, and, for a subset of those, we assess the T cell capability to cross-recognize sequences from representative viruses belonging to AlphaCoV, sarbecoCoV, and Beta-non-sarbecoCoV groups. We find T cell cross-reactivity within the Alpha and Beta groups, in 89% of the instances associated with sequence conservation >67%. However, despite conservation, limited cross-reactivity is observed for sarbecoCoV, indicating that previous CoV exposure is a contributing factor in determining cross-reactivity. Overall, these results provide critical insights in developing future pan-CoV vaccines.
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Affiliation(s)
- Alison Tarke
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Experimental Medicine and Center of Excellence for Biomedical Research (CEBR), University of Genoa, 16132 Genoa, Italy
| | - Yun Zhang
- J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Nils Methot
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Tara M Narowski
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599-7290, USA
| | - Elizabeth Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA 6150, Australia
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA 6150, Australia
| | - April Frazier
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Gilberto Filaci
- Center of Excellence for Biomedical Research, Department of Internal Medicine, University of Genoa, 16132 Genoa, Italy; Biotherapy Unit, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Jennifer M Dan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), 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
| | - Lakshmanane Premkumar
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599-7290, USA
| | - Richard H Scheuermann
- J. Craig Venter Institute, La Jolla, CA 92037, USA; Department of Pathology, University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), 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.
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA.
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12
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Benede NSB, Tincho MB, Walters A, Subbiah V, Ngomti A, Baguma R, Butters C, Mennen M, Skelem S, Adriaanse M, van Graan S, Balla SR, Moyo-Gwete T, Moore PL, Botha M, Workman L, Zar HJ, Ntusi NAB, Zühlke L, Webb K, Riou C, Burgers WA, Keeton RS. Distinct T cell functional profiles in SARS-CoV-2 seropositive and seronegative children associated with endemic human coronavirus cross-reactivity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.16.23290059. [PMID: 37292954 PMCID: PMC10246143 DOI: 10.1101/2023.05.16.23290059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
SARS-CoV-2 infection in children typically results in asymptomatic or mild disease. There is a paucity of studies on antiviral immunity in African children. We investigated SARS-CoV-2-specific T cell responses in 71 unvaccinated asymptomatic South African children who were seropositive or seronegative for SARS-CoV-2. SARS-CoV-2-specific CD4+ T cell responses were detectable in 83% of seropositive and 60% of seronegative children. Although the magnitude of the CD4+ T cell response did not differ significantly between the two groups, their functional profiles were distinct, with SARS-CoV-2 seropositive children exhibiting a higher proportion of polyfunctional T cells compared to their seronegative counterparts. The frequency of SARS-CoV-2-specific CD4+ T cells in seronegative children was associated with the endemic human coronavirus (HCoV) HKU1 IgG response. Overall, the presence of SARS-CoV-2-responding T cells in seronegative children may result from cross-reactivity to endemic coronaviruses and could contribute to the relative protection from disease observed in SARS-CoV-2-infected children.
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Affiliation(s)
- Ntombi S. B. Benede
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Marius B. Tincho
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Avril Walters
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Vennesa Subbiah
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Amkele Ngomti
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Richard Baguma
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Claire Butters
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
| | - Mathilda Mennen
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory, South Africa
| | - Sango Skelem
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory, South Africa
| | - Marguerite Adriaanse
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory, South Africa
| | - Strauss van Graan
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Sashkia R. Balla
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Thandeka Moyo-Gwete
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Penny L. Moore
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Maresa Botha
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
- Medical Research Council (MRC) Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Lesley Workman
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
- Medical Research Council (MRC) Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Heather J. Zar
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
- Medical Research Council (MRC) Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | - Ntobeko A. B. Ntusi
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
- Cape Heart Institute, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
| | - Liesl Zühlke
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
- Cape Heart Institute, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
- South African Medical Research Council, Francie Van Zijl Drive, Parow Cape Town, South Africa
| | - Kate Webb
- South African Medical Research Council, Francie Van Zijl Drive, Parow Cape Town, South Africa
- Crick African Network, The Francis Crick Institute, London, United Kingdom
| | - Catherine Riou
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | - Wendy A. Burgers
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | - Roanne S. Keeton
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
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13
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Westphal T, Mader M, Karsten H, Cords L, Knapp M, Schulte S, Hermanussen L, Peine S, Ditt V, Grifoni A, Addo MM, Huber S, Sette A, Lütgehetmann M, Pischke S, Kwok WW, Sidney J, Schulze zur Wiesch J. Evidence for broad cross-reactivity of the SARS-CoV-2 NSP12-directed CD4 + T-cell response with pre-primed responses directed against common cold coronaviruses. Front Immunol 2023; 14:1182504. [PMID: 37215095 PMCID: PMC10196118 DOI: 10.3389/fimmu.2023.1182504] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/06/2023] [Indexed: 05/24/2023] Open
Abstract
Introduction The nonstructural protein 12 (NSP12) of the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) has a high sequence identity with common cold coronaviruses (CCC). Methods Here, we comprehensively assessed the breadth and specificity of the NSP12-specific T-cell response after in vitro T-cell expansion with 185 overlapping 15-mer peptides covering the entire SARS-CoV-2 NSP12 at single-peptide resolution in a cohort of 27 coronavirus disease 2019 (COVID-19) patients. Samples of nine uninfected seronegative individuals, as well as five pre-pandemic controls, were also examined to assess potential cross-reactivity with CCCs. Results Surprisingly, there was a comparable breadth of individual NSP12 peptide-specific CD4+ T-cell responses between COVID-19 patients (mean: 12.82 responses; range: 0-25) and seronegative controls including pre-pandemic samples (mean: 12.71 responses; range: 0-21). However, the NSP12-specific T-cell responses detected in acute COVID-19 patients were on average of a higher magnitude. The most frequently detected CD4+ T-cell peptide specificities in COVID-19 patients were aa236-250 (37%) and aa246-260 (44%), whereas the peptide specificities aa686-700 (50%) and aa741-755 (36%), were the most frequently detected in seronegative controls. In CCC-specific peptide-expanded T-cell cultures of seronegative individuals, the corresponding SARS-CoV-2 NSP12 peptide specificities also elicited responses in vitro. However, the NSP12 peptide-specific CD4+ T-cell response repertoire only partially overlapped in patients analyzed longitudinally before and after a SARS-CoV-2 infection. Discussion The results of the current study indicate the presence of pre-primed, cross-reactive CCC-specific T-cell responses targeting conserved regions of SARS-CoV-2, but they also underline the complexity of the analysis and the limited understanding of the role of the SARS-CoV-2 specific T-cell response and cross-reactivity with the CCCs.
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Affiliation(s)
- Tim Westphal
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Maria Mader
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hendrik Karsten
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Leon Cords
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maximilian Knapp
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sophia Schulte
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lennart Hermanussen
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sven Peine
- Institute of Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Vanessa Ditt
- Institute of Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, United States
| | - Marylyn Martina Addo
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Department for Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Institute of Infection Research and Vaccine Development, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Samuel Huber
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, United States
| | - Marc Lütgehetmann
- German Center for Infection Research Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sven Pischke
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - William W. Kwok
- Benaroya Research Institute at Virginia Mason, Seattle, WA, United States
| | - John Sidney
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, United States
| | - Julian Schulze zur Wiesch
- Infectious Diseases Unit I, Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
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14
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da Silva Antunes R, Garrigan E, Quiambao LG, Dhanda SK, Marrama D, Westernberg L, Wang E, Sutherland A, Armstrong SK, Brickman TJ, Sidney J, Frazier A, Merkel T, Peters B, Sette A. Genome-wide characterization of T cell responses to Bordetella pertussis reveals broad reactivity and similar polarization irrespective of childhood vaccination profiles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.24.534182. [PMID: 36993748 PMCID: PMC10055406 DOI: 10.1101/2023.03.24.534182] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The incidence of whooping cough (pertussis), the respiratory disease caused by Bordetella pertussis (BP) has increased in recent years, and it is suspected that the switch from whole-cell pertussis (wP) to acellular pertussis (aP) vaccines may be a contributing factor to the rise in morbidity. While a growing body of evidence indicates that T cells play a role in the control and prevention of symptomatic disease, nearly all data on human BP-specific T cells is related to the four antigens contained in the aP vaccines, and data detailing T cell responses to additional non-aP antigens, are lacking. Here, we derived a full-genome map of human BP-specific CD4+ T cell responses using a high-throughput ex vivo Activation Induced Marker (AIM) assay, to screen a peptide library spanning over 3000 different BP ORFs. First, our data show that BP specific-CD4+ T cells are associated with a large and previously unrecognized breadth of responses, including hundreds of targets. Notably, fifteen distinct non-aP vaccine antigens were associated with reactivity comparable to that of the aP vaccine antigens. Second, the overall pattern and magnitude of CD4+ T cell reactivity to aP and non-aP vaccine antigens was similar regardless of aP vs wP childhood vaccination history, suggesting that the profile of T cell reactivity in adults is not driven by vaccination, but rather is likely driven by subsequent asymptomatic or sub-clinical infections. Finally, while aP vaccine responses were Th1/Th2 polarized as a function of childhood vaccination, CD4+ T cell responses to non-aP BP antigens vaccine responses were not, suggesting that these antigens could be used to avoid the Th2 bias associated with aP vaccination. Overall, these findings enhance our understanding of human T cell responses against BP and suggest potential targets for designing next-generation pertussis vaccines.
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Affiliation(s)
- Ricardo da Silva Antunes
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, San Diego, California, USA
| | - Emily Garrigan
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, San Diego, California, USA
| | - Lorenzo G Quiambao
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, San Diego, California, USA
| | - Sandeep Kumar Dhanda
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, San Diego, California, USA
| | - Daniel Marrama
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, San Diego, California, USA
| | - Luise Westernberg
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, San Diego, California, USA
| | - Eric Wang
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, San Diego, California, USA
| | - Aaron Sutherland
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, San Diego, California, USA
| | - Sandra K Armstrong
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Timothy J Brickman
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, San Diego, California, USA
| | - April Frazier
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, San Diego, California, USA
| | - Tod Merkel
- Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, San Diego, California, USA
- University of California San Diego School of Medicine, La Jolla, San Diego, California, USA
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, San Diego, California, USA
- University of California San Diego School of Medicine, La Jolla, San Diego, California, USA
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15
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Denis J, Garnier A, Cheutin L, Ferrier A, Timera H, Jarjaval F, Hejl C, Billon-Denis E, Ricard D, Tournier JN, Trignol A, Mura M. Long-term systemic and mucosal SARS-CoV-2 IgA response and its association with persistent smell and taste disorders. Front Immunol 2023; 14:1140714. [PMID: 36969158 PMCID: PMC10031022 DOI: 10.3389/fimmu.2023.1140714] [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: 01/09/2023] [Accepted: 02/21/2023] [Indexed: 03/29/2023] Open
Abstract
Introduction Current approved COVID-19 vaccines, notably mRNA and adenoviral vectored technologies, still fail to fully protect against infection and transmission of various SARS-CoV-2 variants. The mucosal immunity at the upper respiratory tract represents the first line of defense against respiratory viruses such as SARS-CoV-2 and is thus critical to develop vaccine blocking human-to-human transmission. Methods We measured systemic and mucosal Immunoglobulin A (IgA) response in serum and saliva from 133 healthcare workers from Percy teaching military hospital following a mild infection (SARS-CoV-2 Wuhan strain, n=58) or not infected (n=75), and after SARS-CoV-2 vaccination (Vaxzevria®/Astrazeneca and/or Comirnaty®/Pfizer). Results While serum anti-SARS-CoV-2 Spike IgA response lasted up to 16 months post-infection, IgA response in saliva had mostly fallen to baseline level at 6 months post-infection. Vaccination could reactivate the mucosal response generated by prior infection, but failed to induce a significant mucosal IgA response by itself. Early post-COVID-19 serum anti-Spike-NTD IgA titer correlated with seroneutralization titers. Interestingly, its saliva counterpart positively correlated with persistent smell and taste disorders more than one year after mild COVID-19. Discussion As breakthrough infections have been correlated with IgA levels, other vaccine platforms inducing a better mucosal immunity are needed to control COVID-19 infection in the future. Our results encourage further studies to explore the prognosis potential of anti-Spike-NTD IgA in saliva at predicting persistent smell and taste disorders.
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Affiliation(s)
- Jessica Denis
- Microbiology and Infectious Diseases Department, Institut de Recherche Biomédicale de Armées, Brétigny-sur-Orge, France
| | - Annabelle Garnier
- Microbiology and Infectious Diseases Department, Institut de Recherche Biomédicale de Armées, Brétigny-sur-Orge, France
| | - Laurence Cheutin
- Microbiology and Infectious Diseases Department, Institut de Recherche Biomédicale de Armées, Brétigny-sur-Orge, France
| | - Audrey Ferrier
- Microbiology and Infectious Diseases Department, Institut de Recherche Biomédicale de Armées, Brétigny-sur-Orge, France
| | - Hawa Timera
- Microbiology and Infectious Diseases Department, Institut de Recherche Biomédicale de Armées, Brétigny-sur-Orge, France
| | - Fanny Jarjaval
- Microbiology and Infectious Diseases Department, Institut de Recherche Biomédicale de Armées, Brétigny-sur-Orge, France
| | - Carine Hejl
- Hôpital d’Instruction des Armées Percy, Clamart, France
- Ecole du Val-de-Grâce, Paris, France
| | - Emmanuelle Billon-Denis
- Microbiology and Infectious Diseases Department, Institut de Recherche Biomédicale de Armées, Brétigny-sur-Orge, France
| | | | - Damien Ricard
- Hôpital d’Instruction des Armées Percy, Clamart, France
- Ecole du Val-de-Grâce, Paris, France
- Centre Borelli Unité Mixte de Recherche (UMR) 9010/Université Paris-Saclay, ENS Paris-Saclay, Centre National de la Recherche Scientifique (CNRS), Service de Santé des Armées (SSA), Université de Paris Cité, Institut National de la Santé et de la Recherche Médicale (INSERM) 4, Gif-sur-Yvette, France
| | - Jean-Nicolas Tournier
- Microbiology and Infectious Diseases Department, Institut de Recherche Biomédicale de Armées, Brétigny-sur-Orge, France
- Ecole du Val-de-Grâce, Paris, France
| | - Aurélie Trignol
- Microbiology and Infectious Diseases Department, Institut de Recherche Biomédicale de Armées, Brétigny-sur-Orge, France
- Université Paris Cité, VIFASOM (UPR 7330 Vigilance Fatigue, Sommeil et Santé Publique), Paris, France
| | - Marie Mura
- Microbiology and Infectious Diseases Department, Institut de Recherche Biomédicale de Armées, Brétigny-sur-Orge, France
- Innovation Lab: Vaccines, Institut Pasteur, Paris, France
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16
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Yang KWK, Paris CF, Gorman KT, Rattsev I, Yoo RH, Chen Y, Desman JM, Wei TY, Greenstein JL, Taylor CO, Ray SC. Factors associated with resistance to SARS-CoV-2 infection discovered using large-scale medical record data and machine learning. PLoS One 2023; 18:e0278466. [PMID: 36812214 PMCID: PMC9946212 DOI: 10.1371/journal.pone.0278466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/06/2022] [Indexed: 02/24/2023] Open
Abstract
There have been over 621 million cases of COVID-19 worldwide with over 6.5 million deaths. Despite the high secondary attack rate of COVID-19 in shared households, some exposed individuals do not contract the virus. In addition, little is known about whether the occurrence of COVID-19 resistance differs among people by health characteristics as stored in the electronic health records (EHR). In this retrospective analysis, we develop a statistical model to predict COVID-19 resistance in 8,536 individuals with prior COVID-19 exposure using demographics, diagnostic codes, outpatient medication orders, and count of Elixhauser comorbidities in EHR data from the COVID-19 Precision Medicine Platform Registry. Cluster analyses identified 5 patterns of diagnostic codes that distinguished resistant from non-resistant patients in our study population. In addition, our models showed modest performance in predicting COVID-19 resistance (best performing model AUROC = 0.61). Monte Carlo simulations conducted indicated that the AUROC results are statistically significant (p < 0.001) for the testing set. We hope to validate the features found to be associated with resistance/non-resistance through more advanced association studies.
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Affiliation(s)
- Kai-Wen K. Yang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States of America
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, United States of America
| | - Chloé F. Paris
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States of America
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, United States of America
| | - Kevin T. Gorman
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States of America
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, United States of America
| | - Ilia Rattsev
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States of America
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, United States of America
| | - Rebecca H. Yoo
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States of America
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, United States of America
| | - Yijia Chen
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States of America
| | - Jacob M. Desman
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States of America
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, United States of America
| | - Tony Y. Wei
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States of America
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, United States of America
| | - Joseph L. Greenstein
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States of America
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, United States of America
| | - Casey Overby Taylor
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States of America
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, United States of America
- Department of Medicine, Division of General Internal Medicine, Johns Hopkins School of Medicine, Baltimore, MD, United States of America
| | - Stuart C. Ray
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, United States of America
- * E-mail:
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17
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Perico L, Todeschini M, Casiraghi F, Mister M, Pezzotta A, Peracchi T, Tomasoni S, Trionfini P, Benigni A, Remuzzi G. Long-term adaptive response in COVID-19 vaccine recipients and the effect of a booster dose. Front Immunol 2023; 14:1123158. [PMID: 36926327 PMCID: PMC10011096 DOI: 10.3389/fimmu.2023.1123158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/16/2023] [Indexed: 03/08/2023] Open
Abstract
We examined the immune response in subjects previously infected with SARS-CoV2 and infection-naïve 9 months after primary 2-dose COVID-19 mRNA vaccination and 3 months after the booster dose in a longitudinal cohort of healthcare workers. Nine months after primary vaccination, previously infected subjects exhibited higher residual antibody levels, with significant neutralizing activity against distinct variants compared to infection-naïve subjects. The higher humoral response was associated with higher levels of receptor binding domain (RBD)-specific IgG+ and IgA+ memory B cells. The booster dose increased neither neutralizing activity, nor the B and T cell frequencies. Conversely, infection-naïve subjects needed the booster to achieve comparable levels of neutralizing antibodies as those found in previously infected subjects after primary vaccination. The neutralizing titer correlated with anti-RBD IFNγ producing T cells, in the face of sustained B cell response. Notably, pre-pandemic samples showed high Omicron cross-reactivity. These data show the importance of the booster dose in reinforcing immunological memory and increasing circulating antibodies in infection-naïve subjects.
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Affiliation(s)
- Luca Perico
- Department of Molecular Medicine, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Marta Todeschini
- Department of Molecular Medicine, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Federica Casiraghi
- Department of Molecular Medicine, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Marilena Mister
- Department of Molecular Medicine, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Anna Pezzotta
- Department of Molecular Medicine, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Tobia Peracchi
- Department of Molecular Medicine, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Susanna Tomasoni
- Department of Molecular Medicine, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Piera Trionfini
- Department of Molecular Medicine, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Ariela Benigni
- Department of Molecular Medicine, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Giuseppe Remuzzi
- Department of Molecular Medicine, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
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18
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Li Y, Merbah M, Wollen-Roberts S, Beckman B, Mdluli T, Swafford I, Mayer SV, King J, Corbitt C, Currier JR, Liu H, Esber A, Pinyakorn S, Parikh A, Francisco LV, Phanuphak N, Maswai J, Owuoth J, Kibuuka H, Iroezindu M, Bahemana E, Vasan S, Ake JA, Modjarrad K, Gromowski G, Paquin-Proulx D, Rolland M. Coronavirus Antibody Responses before COVID-19 Pandemic, Africa and Thailand. Emerg Infect Dis 2022; 28:2214-2225. [PMID: 36220131 PMCID: PMC9622245 DOI: 10.3201/eid2811.221041] [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] [Indexed: 11/19/2022] Open
Abstract
Prior immune responses to coronaviruses might affect human SARS-CoV-2 response. We screened 2,565 serum and plasma samples collected from 2013 through early 2020, before the COVID-19 pandemic began, from 2,250 persons in 4 countries in Africa (Kenya, Nigeria, Tanzania, and Uganda) and in Thailand, including persons living with HIV-1. We detected IgG responses to SARS-CoV-2 spike (S) subunit 2 protein in 1.8% of participants. Profiling against 23 coronavirus antigens revealed that responses to S, subunit 2, or subunit 1 proteins were significantly more frequent than responses to the receptor-binding domain, S-Trimer, or nucleocapsid proteins (p<0.0001). We observed similar responses in persons with or without HIV-1. Among all coronavirus antigens tested, SARS-CoV-2, SARS-CoV-1, and Middle East respiratory syndrome coronavirus antibody responses were much higher in participants from Africa than in participants from Thailand (p<0.01). We noted less pronounced differences for endemic coronaviruses. Serosurveys could affect vaccine and monoclonal antibody distribution across global populations.
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