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Marchal A, Cirulli ET, Neveux I, Bellos E, Thwaites RS, Schiabor Barrett KM, Zhang Y, Nemes-Bokun I, Kalinova M, Catchpole A, Tangye SG, Spaan AN, Lack JB, Ghosn J, Burdet C, Gorochov G, Tubach F, Hausfater P, Dalgard CL, Zhang SY, Zhang Q, Chiu C, Fellay J, Grzymski JJ, Sancho-Shimizu V, Abel L, Casanova JL, Cobat A, Bolze A. Lack of association between classical HLA genes and asymptomatic SARS-CoV-2 infection. HGG ADVANCES 2024; 5:100300. [PMID: 38678364 DOI: 10.1016/j.xhgg.2024.100300] [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: 12/04/2023] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 04/29/2024] Open
Abstract
Human genetic studies of critical COVID-19 pneumonia have revealed the essential role of type I interferon-dependent innate immunity to SARS-CoV-2 infection. Conversely, an association between the HLA-B∗15:01 allele and asymptomatic SARS-CoV-2 infection in unvaccinated individuals was recently reported, suggesting a contribution of pre-existing T cell-dependent adaptive immunity. We report a lack of association of classical HLA alleles, including HLA-B∗15:01, with pre-omicron asymptomatic SARS-CoV-2 infection in unvaccinated participants in a prospective population-based study in the United States (191 asymptomatic vs. 945 symptomatic COVID-19 cases). Moreover, we found no such association in the international COVID Human Genetic Effort cohort (206 asymptomatic vs. 574 mild or moderate COVID-19 cases and 1,625 severe or critical COVID-19 cases). Finally, in the Human Challenge Characterisation study, the three HLA-B∗15:01 individuals infected with SARS-CoV-2 developed symptoms. As with other acute primary infections studied, no classical HLA alleles favoring an asymptomatic course of SARS-CoV-2 infection were identified.
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Affiliation(s)
- Astrid Marchal
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; University Paris Cité, Imagine Institute, Paris, France
| | | | - Iva Neveux
- Department of Internal Medicine, University of Nevada School of Medicine, Reno, NV, USA
| | - Evangelos Bellos
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ryan S Thwaites
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, Bethesda, MD, USA
| | - Ivana Nemes-Bokun
- Department of Infectious Disease, Imperial College London, London, UK
| | | | | | - Stuart G Tangye
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia; School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, New South Wales, Australia
| | - András N Spaan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA; Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Justin B Lack
- NIAID Collaborative Bioinformatics Resource, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD, USA
| | - Jade Ghosn
- Infection, Antimicrobials, Modelling, Evolution (IAME), INSERM, UMR1137, University Paris Cité, Paris, France; AP-HP, Bichat-Claude Bernard Hospital, Infectious and Tropical Diseases Department, Paris, France
| | - Charles Burdet
- Infection, Antimicrobials, Modelling, Evolution (IAME), INSERM, UMR1137, University Paris Cité, Paris, France; AP-HP, Hôpital Bichat, Centre d'Investigation Clinique, INSERM CIC 1425, Paris, France; Département Epidémiologie, Biostatistiques et Recherche Clinique, Hôpital Bichat, Assistance Publique-Hôpitaux de Paris, 75018 Paris, France
| | - Guy Gorochov
- Sorbonne Université, INSERM Centre d'Immunologie et des Maladies Infectieuses, CIMI-Paris, Département d'immunologie Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Florence Tubach
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpital Pitié-Salpêtrière, Département de Santé Publique, Unitéde Recherche Clinique PSL-CFX, CIC-1901, Paris, France
| | - Pierre Hausfater
- Emergency Department, Hôpital Pitié-Salpêtrière, APHP-Sorbonne Université, Paris, France; GRC-14 BIOSFAST Sorbonne Université, UMR INSERM 1135, CIMI, Sorbonne Université, Paris, France
| | - Clifton L Dalgard
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; University Paris Cité, Imagine Institute, Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Qian Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; University Paris Cité, Imagine Institute, Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Christopher Chiu
- Department of Infectious Disease, Imperial College London, London, UK
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland; Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Joseph J Grzymski
- Department of Internal Medicine, University of Nevada School of Medicine, Reno, NV, USA; Renown Health, Reno, NV, USA
| | - Vanessa Sancho-Shimizu
- Department of Infectious Disease, Imperial College London, London, UK; Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London, UK
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; University Paris Cité, Imagine Institute, Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; University Paris Cité, Imagine Institute, Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA; Department of Pediatrics, Necker Hospital for Sick Children, Paris, France; Howard Hughes Medical Institute, New York, NY, USA
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; University Paris Cité, Imagine Institute, Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.
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3
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Bastard P, Gervais A, Taniguchi M, Saare L, Särekannu K, Le Voyer T, Philippot Q, Rosain J, Bizien L, Asano T, Garcia-Prat M, Parra-Martínez A, Migaud M, Tsumura M, Conti F, Belot A, Rivière JG, Morio T, Tanaka J, Javouhey E, Haerynck F, Duvlis S, Ozcelik T, Keles S, Tandjaoui-Lambiotte Y, Escoda S, Husain M, Pan-Hammarström Q, Hammarström L, Ahlijah G, Abi Haidar A, Soudee C, Arseguel V, Abolhassani H, Sahanic S, Tancevski I, Nukui Y, Hayakawa S, Chrousos GP, Michos A, Tatsi EB, Filippatos F, Rodriguez-Palmero A, Troya J, Tipu I, Meyts I, Roussel L, Ostrowski SR, Schidlowski L, Prando C, Condino-Neto A, Cheikh N, Bousfiha AA, El Bakkouri J, Peterson P, Pujol A, Lévy R, Quartier P, Vinh DC, Boisson B, Béziat V, Zhang SY, Borghesi A, Pession A, Andreakos E, Marr N, Mentis AFA, Mogensen TH, Rodríguez-Gallego C, Soler-Palacin P, Colobran R, Tillmann V, Neven B, Trouillet-Assant S, Brodin P, Abel L, Jouanguy E, Zhang Q, Martinón-Torres F, Salas A, Gómez-Carballa A, Gonzalez-Granado LI, Kisand K, Okada S, Puel A, Cobat A, Casanova JL. Higher COVID-19 pneumonia risk associated with anti-IFN-α than with anti-IFN-ω auto-Abs in children. J Exp Med 2024; 221:e20231353. [PMID: 38175961 PMCID: PMC10771097 DOI: 10.1084/jem.20231353] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/22/2023] [Accepted: 11/15/2023] [Indexed: 01/06/2024] Open
Abstract
We found that 19 (10.4%) of 183 unvaccinated children hospitalized for COVID-19 pneumonia had autoantibodies (auto-Abs) neutralizing type I IFNs (IFN-α2 in 10 patients: IFN-α2 only in three, IFN-α2 plus IFN-ω in five, and IFN-α2, IFN-ω plus IFN-β in two; IFN-ω only in nine patients). Seven children (3.8%) had Abs neutralizing at least 10 ng/ml of one IFN, whereas the other 12 (6.6%) had Abs neutralizing only 100 pg/ml. The auto-Abs neutralized both unglycosylated and glycosylated IFNs. We also detected auto-Abs neutralizing 100 pg/ml IFN-α2 in 4 of 2,267 uninfected children (0.2%) and auto-Abs neutralizing IFN-ω in 45 children (2%). The odds ratios (ORs) for life-threatening COVID-19 pneumonia were, therefore, higher for auto-Abs neutralizing IFN-α2 only (OR [95% CI] = 67.6 [5.7-9,196.6]) than for auto-Abs neutralizing IFN-ω only (OR [95% CI] = 2.6 [1.2-5.3]). ORs were also higher for auto-Abs neutralizing high concentrations (OR [95% CI] = 12.9 [4.6-35.9]) than for those neutralizing low concentrations (OR [95% CI] = 5.5 [3.1-9.6]) of IFN-ω and/or IFN-α2.
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Affiliation(s)
- Paul Bastard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Pediatric Hematology-Immunology and Rheumatology Unit, Necker Hospital for Sick Children, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Adrian Gervais
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Maki Taniguchi
- Dept. of Pediatrics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Liisa Saare
- Dept. of Pediatrics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Karita Särekannu
- Molecular Pathology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Tom Le Voyer
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Quentin Philippot
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Jérémie Rosain
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Lucy Bizien
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Takaki Asano
- Dept. of Pediatrics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Marina Garcia-Prat
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d’Hebron, Vall d’Hebron Research Institute, Vall d’Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Alba Parra-Martínez
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d’Hebron, Vall d’Hebron Research Institute, Vall d’Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Mélanie Migaud
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Miyuki Tsumura
- Dept. of Pediatrics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Francesca Conti
- Pediatric Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- Dept. of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Alexandre Belot
- National Reference Center for Rheumatic, and Autoimmune and Systemic Diseases in Children, Lyon, France
- Immunopathology Federation LIFE, Hospices Civils de Lyon, Lyon, France
- Hospices Civils de Lyon, Lyon, France
- International Center of Research in Infectiology, Lyon University, International Center of Research in Infectiology, Lyon University, INSERM U1111, CNRS UMR 5308, ENS, UCBL, Lyon, France
| | - Jacques G. Rivière
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d’Hebron, Vall d’Hebron Research Institute, Vall d’Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Tomohiro Morio
- Dept. of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Junko Tanaka
- Dept. of Epidemiology, Infectious Disease Control and Prevention, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Etienne Javouhey
- Pediatric Intensive Care Unit, Hospices Civils de Lyon, Hopital Femme Mère Enfant, Lyon, France
| | - Filomeen Haerynck
- Dept. of Paediatric Immunology and Pulmonology, Center for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium
| | - Sotirija Duvlis
- Faculty of Medical Sciences, University “Goce Delchev”, Stip, Republic of Northern Macedonia
- Institute of Public Health of the Republic of North Macedonia, Skopje, North Macedonia
| | - Tayfun Ozcelik
- Dept. of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Sevgi Keles
- Meram Medical Faculty, Necmettin Erbakan University, Konya, Turkey
| | - Yacine Tandjaoui-Lambiotte
- Pulmonology and Infectious Disease Department, Saint Denis Hospital, Saint Denis, France
- INSERM UMR 1137 IAME, Paris, France
- INSERM UMR 1272 Hypoxia and Lung, Bobigny, France
| | - Simon Escoda
- Pediatric Dept., Saint-Denis Hospital, Saint-Denis, France
| | - Maya Husain
- Pediatric Dept., Saint-Denis Hospital, Saint-Denis, France
| | - Qiang Pan-Hammarström
- Division of Immunology, Dept. of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Lennart Hammarström
- Division of Immunology, Dept. of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Gloria Ahlijah
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
| | - Anthony Abi Haidar
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
| | - Camille Soudee
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
| | - Vincent Arseguel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
| | - Hassan Abolhassani
- Division of Immunology, Dept. of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children’s Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Sabina Sahanic
- Dept. of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Ivan Tancevski
- Dept. of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Yoko Nukui
- Dept. of Infection Control and Prevention, Medical Hospital, TMDU, Tokyo, Japan
| | - Seiichi Hayakawa
- Dept. of Pediatrics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - George P. Chrousos
- University Research Institute of Maternal and Child Health and Precision Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Athanasios Michos
- University Research Institute of Maternal and Child Health and Precision Medicine, National and Kapodistrian University of Athens, Athens, Greece
- First Dept. of Pediatics, National and Kapodistrian University of Athens, Athens, Greece
| | - Elizabeth-Barbara Tatsi
- University Research Institute of Maternal and Child Health and Precision Medicine, National and Kapodistrian University of Athens, Athens, Greece
- First Dept. of Pediatics, National and Kapodistrian University of Athens, Athens, Greece
| | - Filippos Filippatos
- University Research Institute of Maternal and Child Health and Precision Medicine, National and Kapodistrian University of Athens, Athens, Greece
- First Dept. of Pediatics, National and Kapodistrian University of Athens, Athens, Greece
| | - Agusti Rodriguez-Palmero
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Spain
- Dept. of Pediatrics, Germans Trias i Pujol University Hospital, UAB, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Jesus Troya
- Dept. of Internal Medicine, Infanta Leonor University Hospital, Madrid, Spain
| | - Imran Tipu
- University of Management and Technology, Lahore, Pakistan
| | - Isabelle Meyts
- Dept. of Immunology, Laboratory of Inborn Errors of Immunity, Microbiology and Transplantation, KU Leuven, Leuven, Belgium
- Dept. of Pediatrics, Jeffrey Modell Diagnostic and Research Network Center, University Hospitals Leuven, Leuven, Belgium
| | - Lucie Roussel
- Dept. of Medicine, Division of Infectious Diseases, McGill University Health Centre, Montréal, Canada
- Infectious Disease Susceptibility Program, Research Institute–McGill University Health Centre, Montréal, Canada
| | - Sisse Rye Ostrowski
- Dept. of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Laire Schidlowski
- Faculdades Pequeno Príncipe, Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Brazil
| | - Carolina Prando
- Faculdades Pequeno Príncipe, Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Brazil
| | - Antonio Condino-Neto
- Dept. of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Nathalie Cheikh
- Pediatric Hematology Unit, University Hospital of Besançon, Besançon, France
| | - Ahmed A. Bousfiha
- Dept. of Pediatric Infectious Disease and Clinical Immunology, CHU Ibn Rushd and LICIA, Laboratoire d’Immunologie Clinique, Inflammation et Allergie, Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, Morocco
| | - Jalila El Bakkouri
- Laboratory of Immunology, CHU Ibn Rushd and LICIA, Laboratoire d’Immunologie Clinique, Inflammation et Allergie, Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, Morocco
| | - Pärt Peterson
- Molecular Pathology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Aurora Pujol
- Neurometabolic Diseases Laboratory, IDIBELL-Hospital Duran i Reynals, CIBERER U759, and Catalan Institution of Research and Advanced Studies, Barcelona, Spain
| | - Romain Lévy
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- Pediatric Hematology-Immunology and Rheumatology Unit, Necker Hospital for Sick Children, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Pierre Quartier
- University Paris Cité, Imagine Institute, Paris, France
- Pediatric Hematology-Immunology and Rheumatology Unit, Necker Hospital for Sick Children, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Donald C. Vinh
- Dept. of Medicine, Division of Infectious Diseases, McGill University Health Centre, Montréal, Canada
- Infectious Disease Susceptibility Program, Research Institute–McGill University Health Centre, Montréal, Canada
| | - Bertrand Boisson
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Vivien Béziat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Alessandro Borghesi
- Neonatal Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Andrea Pession
- Pediatric Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Evangelos Andreakos
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Nico Marr
- Research Branch, Sidra Medicine, Doha, Qatar
| | - Alexios-Fotios A. Mentis
- University Research Institute of Maternal and Child Health and Precision Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Trine H. Mogensen
- Dept. of Infectious Diseases, Aarhus University Hospital, Skejby, Denmark
- Dept. of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Carlos Rodríguez-Gallego
- Hospital Universitario de Gran Canaria Dr Negrín, Canarian Health System, Las Palmas, Spain
- Dept. of Clinical Sciences, University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
- Dept. of Medical and Surgical Sciences, School of Medicine, University of Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Pere Soler-Palacin
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d’Hebron, Vall d’Hebron Research Institute, Vall d’Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Roger Colobran
- Immunology Division, Genetics Dept., Hospital Universitari Vall d’Hebron, Vall d’Hebron Research Institute, Vall d’Hebron Barcelona Hospital Campus, UAB, Barcelona, Spain
| | - Vallo Tillmann
- Dept. of Pediatrics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Bénédicte Neven
- University Paris Cité, Imagine Institute, Paris, France
- Pediatric Hematology-Immunology and Rheumatology Unit, Necker Hospital for Sick Children, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Sophie Trouillet-Assant
- Hospices Civils de Lyon, Lyon, France
- International Center of Research in Infectiology, Lyon University, International Center of Research in Infectiology, Lyon University, INSERM U1111, CNRS UMR 5308, ENS, UCBL, Lyon, France
- Joint Research Unit, Hospices Civils de Lyon-bio Mérieux, Hospices Civils de Lyon, Lyon Sud Hospital, Pierre-Bénite, France
- International Center of Research in Infectiology, Lyon University, INSERM U1111, CNRS UMR 5308, ENS, UCBL, Lyon, France
| | - Petter Brodin
- Unit for Clinical Pediatrics, Dept. of Women’s and Children’s Health, Karolinska Institutet, Solna, Sweden
- Department of Immunology and Inflammation, Imperial College London, London, UK
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Emmanuelle Jouanguy
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Qian Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Federico Martinón-Torres
- Translational Pediatrics and Infectious Diseases, Pediatrics Dept., Hospital Clínico Universitario de Santiago, Servizo Galego de Saude (SERGAS), Santiago de Compostela, Spain
- GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago (IDIS), Universidad de Santiago de Compostela, Galicia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Antonio Salas
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Facultade de Medicina, Unidade de Xenética, Instituto de Ciencias Forenses, Universidade de Santiago de Compostela, and GenPoB Research Group, IDIS, SERGAS, Galicia, Spain
| | - Alberto Gómez-Carballa
- GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago (IDIS), Universidad de Santiago de Compostela, Galicia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Facultade de Medicina, Unidade de Xenética, Instituto de Ciencias Forenses, Universidade de Santiago de Compostela, and GenPoB Research Group, IDIS, SERGAS, Galicia, Spain
| | - Luis I. Gonzalez-Granado
- Immunodeficiencies Unit, Hospital 12 de octubre, Research Institute Hospital 12 octubre, Madrid, Spain
| | - Kai Kisand
- Molecular Pathology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Satoshi Okada
- Dept. of Pediatrics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
- Dept. of Pediatrics, Necker Hospital for Sick Children, AP-HP, Paris, France
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Fam BSDO, Feira MF, Cadore NA, Sbruzzi R, Hünemeier T, Abel L, Zhang Q, Casanova JL, Vianna FSL. Human genetic determinants of COVID-19 in Brazil: challenges and future plans. Genet Mol Biol 2024; 46:e20230128. [PMID: 38226654 DOI: 10.1590/1678-4685-gmb-2023-0128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 11/14/2023] [Indexed: 01/17/2024] Open
Abstract
COVID-19 pandemic represented a worldwide major challenge in different areas, and efforts undertaken by the scientific community led to the understanding of some of the genetic determinants that influence the different COVID-19 outcomes. In this paper, we review the studies about the role of human genetics in COVID-19 severity and how Brazilian studies also contributed to those findings. Rare variants in genes related to Inborn Errors of Immunity (IEI) in the type I interferons pathway, and its phenocopies, have been described as being causative of severe outcomes. IEI and its phenocopies are present in Brazil, not only in COVID-19 patients, but also in autoimmune conditions and severe reactions to yellow fever vaccine. In addition, studies focusing on common variants and GWAS studies encompassing worldwide patients have found several loci associated with COVID-19 severity. A GWAS study including only Brazilian COVID-19 patients identified a new locus 1q32.1 associated with COVID-19 severity. Thus, more comprehensive studies considering the Brazilian genomic diversity should be performed, since they can help to reveal not only what are the genetic determinants that contribute to the different outcomes for COVID-19 in the Brazilian population, but in the understanding of human genetics in different health conditions.
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Affiliation(s)
- Bibiana S de Oliveira Fam
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Laboratório de Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Instituto Nacional de Genética Médica Populacional (INaGeMP), Porto Alegre, RS, Brazil
| | - Marilea Furtado Feira
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Laboratório de Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Instituto Nacional de Genética Médica Populacional (INaGeMP), Porto Alegre, RS, Brazil
| | - Nathan Araujo Cadore
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Laboratório de Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Instituto Nacional de Genética Médica Populacional (INaGeMP), Porto Alegre, RS, Brazil
| | - Renan Sbruzzi
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Laboratório de Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Instituto Nacional de Genética Médica Populacional (INaGeMP), Porto Alegre, RS, Brazil
| | - Tábita Hünemeier
- Universidade de São Paulo, Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, São Paulo, SP, Brazil
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas/Universitat Pompeu Fabra), Barcelona, Spain
| | - Laurent Abel
- The Rockefeller University, Rockefeller Branch, St. Giles Laboratory of Human Genetics of Infectious Diseases, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Imagine Institute, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
| | - Qian Zhang
- The Rockefeller University, Rockefeller Branch, St. Giles Laboratory of Human Genetics of Infectious Diseases, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
| | - Jean-Laurent Casanova
- The Rockefeller University, Rockefeller Branch, St. Giles Laboratory of Human Genetics of Infectious Diseases, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Imagine Institute, Paris, France
- University Paris Cité, Imagine Institute, Paris, France
- Necker Hospital for Sick Children, Department of Pediatrics, Paris, France
| | - Fernanda Sales Luiz Vianna
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Laboratório de Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Instituto Nacional de Genética Médica Populacional (INaGeMP), Porto Alegre, RS, Brazil
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6
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Marchal A, Cirulli ET, Neveux I, Bellos E, Thwaites RS, Schiabor Barrett KM, Zhang Y, Nemes-Bokun I, Kalinova M, Catchpole A, Tangye SG, Spaan AN, Lack JB, Ghosn J, Burdet C, Gorochov G, Tubach F, Hausfater P, Dalgard CL, Zhang SY, Zhang Q, Chiu C, Fellay J, Grzymski JJ, Sancho-Shimizu V, Abel L, Casanova JL, Cobat A, Bolze A. Lack of association between HLA and asymptomatic SARS-CoV-2 infection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.06.23299623. [PMID: 38168184 PMCID: PMC10760282 DOI: 10.1101/2023.12.06.23299623] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Human genetic studies of critical COVID-19 pneumonia have revealed the essential role of type I interferon-dependent innate immunity to SARS-CoV-2 infection. Conversely, an association between the HLA-B*15:01 allele and asymptomatic SARS-CoV-2 infection in unvaccinated individuals was recently reported, suggesting a contribution of pre-existing T cell-dependent adaptive immunity. We report a lack of association of classical HLA alleles, including HLA-B*15:01, with pre-omicron asymptomatic SARS-CoV-2 infection in unvaccinated participants in a prospective population-based study in the US (191 asymptomatic vs. 945 symptomatic COVID-19 cases). Moreover, we found no such association in the international COVID Human Genetic Effort cohort (206 asymptomatic vs. 574 mild or moderate COVID-19 cases and 1,625 severe or critical COVID-19 cases). Finally, in the Human Challenge Characterisation study, the three HLA-B*15:01 individuals infected with SARS-CoV-2 developed symptoms. As with other acute primary infections, no classical HLA alleles favoring an asymptomatic course of SARS-CoV-2 infection were identified. These findings suggest that memory T-cell immunity to seasonal coronaviruses does not strongly influence the outcome of SARS-CoV-2 infection in unvaccinated individuals.
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Affiliation(s)
- Astrid Marchal
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France, EU
- University Paris Cité, Imagine Institute, Paris, France, EU
| | | | - Iva Neveux
- Department of Internal Medicine, University of Nevada School of Medicine, Reno, NV, USA
| | - Evangelos Bellos
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
| | - Ryan S. Thwaites
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | | | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, Bethesda, MD, USA
| | - Ivana Nemes-Bokun
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
| | | | | | - Stuart G. Tangye
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, NSW, Australia
| | - András N. Spaan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands, EU
| | - Justin B. Lack
- NIAID Collaborative Bioinformatics Resource, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD, USA
| | - Jade Ghosn
- Infection, Antimicrobials, Modelling, Evolution (IAME), INSERM, UMR1137, University of Paris, Paris, France, EU
- AP-HP, Bichat Claude Bernard Hospital, Infectious and Tropical Diseases Department, Paris, France, EU
| | - Charles Burdet
- Infection, Antimicrobials, Modelling, Evolution (IAME), INSERM, UMR1137, University of Paris, Paris, France, EU
- Epidémiologie clinique du Centre d’Investigation Clinique (CIC-EP), INSERM CIC 1425, Hôpital Bichat, 75018 Paris, France, EU
- Département Epidémiologie, Biostatistiques et Recherche Clinique, Hôpital Bichat, Assistance Publique-Hôpitaux de Paris, 75018 Paris, France, EU
| | - Guy Gorochov
- Sorbonne Université, INSERM Centre d’Immunologie et des Maladies Infectieuses, CIMI-Paris, Département d’immunologie Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France, EU
| | - Florence Tubach
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, AP-HP, Hôpital Pitié Salpêtrière, Département de Santé Publique, Unité de Recherche Clinique PSL-CFX, CIC-1901, Paris, France, EU
| | - Pierre Hausfater
- Emergency Department, Hôpital Pitié-Salpêtrière, APHP-Sorbonne Université, Paris, France, EU
- GRC-14 BIOFAST Sorbonne Université, UMR INSERM 1135, CIMI, Sorbonne Université, Paris, France, EU
| | | | | | | | | | | | | | | | | | | | - Clifton L. Dalgard
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France, EU
- University Paris Cité, Imagine Institute, Paris, France, EU
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Qian Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France, EU
- University Paris Cité, Imagine Institute, Paris, France, EU
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Christopher Chiu
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Joseph J. Grzymski
- Department of Internal Medicine, University of Nevada School of Medicine, Reno, NV, USA
- Renown Health, Reno, NV, USA
| | - Vanessa Sancho-Shimizu
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
- Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London, UK
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France, EU
- University Paris Cité, Imagine Institute, Paris, France, EU
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France, EU
- University Paris Cité, Imagine Institute, Paris, France, EU
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France, EU
- University Paris Cité, Imagine Institute, Paris, France, EU
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
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