Inborn errors of type I IFN immunity in patients with life-threatening COVID-19

Author:

Zhang Qian1ORCID,Bastard Paul23ORCID,Liu Zhiyong1,Le Pen Jérémie4ORCID,Moncada-Velez Marcela1ORCID,Chen Jie1,Ogishi Masato1ORCID,Sabli Ira K. D.5ORCID,Hodeib Stephanie5ORCID,Korol Cecilia2ORCID,Rosain Jérémie23,Bilguvar Kaya6ORCID,Ye Junqiang7,Bolze Alexandre8ORCID,Bigio Benedetta1ORCID,Yang Rui1ORCID,Arias Andrés Augusto1910ORCID,Zhou Qinhua1ORCID,Zhang Yu1112,Onodi Fanny13,Korniotis Sarantis13,Karpf Léa13,Philippot Quentin23,Chbihi Marwa23ORCID,Bonnet-Madin Lucie14ORCID,Dorgham Karim15ORCID,Smith Nikaïa16ORCID,Schneider William M.4ORCID,Razooky Brandon S.4ORCID,Hoffmann Hans-Heinrich4ORCID,Michailidis Eleftherios4ORCID,Moens Leen17,Han Ji Eun1ORCID,Lorenzo Lazaro23ORCID,Bizien Lucy23ORCID,Meade Philip18ORCID,Neehus Anna-Lena23ORCID,Ugurbil Aileen Camille1ORCID,Corneau Aurélien19,Kerner Gaspard23ORCID,Zhang Peng1ORCID,Rapaport Franck1ORCID,Seeleuthner Yoann23,Manry Jeremy23ORCID,Masson Cecile20ORCID,Schmitt Yohann20,Schlüter Agatha21ORCID,Le Voyer Tom23ORCID,Khan Taushif22ORCID,Li Juan1,Fellay Jacques232425ORCID,Roussel Lucie26ORCID,Shahrooei Mohammad2728,Alosaimi Mohammed F.29ORCID,Mansouri Davood303132,Al-Saud Haya33,Al-Mulla Fahd34ORCID,Almourfi Feras33ORCID,Al-Muhsen Saleh Zaid35,Alsohime Fahad29ORCID,Al Turki Saeed3637ORCID,Hasanato Rana29ORCID,van de Beek Diederik38ORCID,Biondi Andrea39,Bettini Laura Rachele39ORCID,D’Angio’ Mariella39,Bonfanti Paolo40ORCID,Imberti Luisa41,Sottini Alessandra41,Paghera Simone41,Quiros-Roldan Eugenia42,Rossi Camillo43,Oler Andrew J.44ORCID,Tompkins Miranda F.45ORCID,Alba Camille45ORCID,Vandernoot Isabelle46,Goffard Jean-Christophe47,Smits Guillaume46ORCID,Migeotte Isabelle48,Haerynck Filomeen49,Soler-Palacin Pere50ORCID,Martin-Nalda Andrea50ORCID,Colobran Roger51ORCID,Morange Pierre-Emmanuel52,Keles Sevgi53,Çölkesen Fatma54ORCID,Ozcelik Tayfun55,Yasar Kadriye Kart56ORCID,Senoglu Sevtap56ORCID,Karabela Şemsi Nur56ORCID,Rodríguez-Gallego Carlos5758ORCID,Novelli Giuseppe59ORCID,Hraiech Sami60,Tandjaoui-Lambiotte Yacine6162ORCID,Duval Xavier6364,Laouénan Cédric636465ORCID,Snow Andrew L.66ORCID,Dalgard Clifton L.4567ORCID,Milner Joshua D.68,Vinh Donald C.26ORCID,Mogensen Trine H.6970ORCID,Marr Nico2271ORCID,Spaan András N.172ORCID,Boisson Bertrand123ORCID,Boisson-Dupuis Stéphanie123ORCID,Bustamante Jacinta12373ORCID,Puel Anne123ORCID,Ciancanelli Michael J.174ORCID,Meyts Isabelle1775ORCID,Maniatis Tom776ORCID,Soumelis Vassili1377,Amara Ali14,Nussenzweig Michel7879ORCID,García-Sastre Adolfo18808182ORCID,Krammer Florian18ORCID,Pujol Aurora21ORCID,Duffy Darragh16ORCID,Lifton Richard P.838485,Zhang Shen-Ying123,Gorochov Guy15,Béziat Vivien123ORCID,Jouanguy Emmanuelle123ORCID,Sancho-Shimizu Vanessa5ORCID,Rice Charles M.4,Abel Laurent123ORCID,Notarangelo Luigi D.1112ORCID,Cobat Aurélie123ORCID,Su Helen C.1112ORCID,Casanova Jean-Laurent1237986ORCID,Foti Giuseppe,Bellani Giacomo,Citerio Giuseppe,Contro Ernesto,Pesci Alberto,Valsecchi Maria Grazia,Cazzaniga Marina,Abad Jorge,Aguilera-Albesa Sergio,Akcan Ozge Metin,Darazam Ilad Alavi,Aldave Juan C.,Ramos Miquel Alfonso,Nadji Seyed Alireza,Alkan Gulsum,Allardet-Servent Jerome,Allende Luis M.,Alsina Laia,Alyanakian Marie-Alexandra,Amador-Borrero Blanca,Amoura Zahir,Antolí Arnau,Arslan Sevket,Assant Sophie,Auguet Terese,Azot Axelle,Bajolle Fanny,Baldolli Aurélie,Ballester Maite,Feldman Hagit Baris,Barrou Benoit,Beurton Alexandra,Bilbao Agurtzane,Blanchard-Rohner Geraldine,Blanco Ignacio,Blandinières Adeline,Blazquez-Gamero Daniel,Bloomfield Marketa,Bolivar-Prados Mireia,Borie Raphael,Bosteels Cédric,Bousfiha Ahmed A.,Bouvattier Claire,Boyarchuk Oksana,Bueno Maria Rita P.,Bustamante Jacinta,Cáceres Agra Juan José,Calimli Semra,Capra Ruggero,Carrabba Maria,Casasnovas Carlos,Caseris Marion,Castelle Martin,Castelli Francesco,de Vera Martín Castillo,Castro Mateus V.,Catherinot Emilie,Chalumeau Martin,Charbit Bruno,Cheng Matthew P.,Clavé Père,Clotet Bonaventura,Codina Anna,Colkesen Fatih,Çölkesen Fatma,Colobran Roger,Comarmond Cloé,Dalmau David,Darley David Ross,Dauby Nicolas,Dauger Stéphane,de Pontual Loic,Dehban Amin,Delplancq Geoffroy,Demoule Alexandre,Diehl 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B.,Matthews Gail V.,Mayaux Julien,Mège Jean-Louis,Melki Isabelle,Meritet Jean-François,Metin Ozge,Meyts Isabelle,Mezidi Mehdi,Migeotte Isabelle,Millereux Maude,Mirault Tristan,Mircher Clotilde,Mirsaeidi Mehdi,Melián Abián Montesdeoca,Martinez Antonio Morales,Morange Pierre,Mordacq Clémence,Morelle Guillaume,Mouly Stéphane,Muñoz-Barrera Adrián,Naesens Leslie,Nafati Cyril,Neves João Farela,Ng Lisa F. P.,Medina Yeray Novoa,Cuadros Esmeralda Nuñez,Ocejo-Vinyals J. 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A.,Behillil Sylvie,Bielicki Julia,Bruijning Patricia,Burdet Charles,Caumes Eric,Charpentier Charlotte,Coignard Bruno,Costa Yolande,Couffin-Cadiergues Sandrine,Damond Florence,Dechanet Aline,Delmas Christelle,Descamps Diane,Duval Xavier,Ecobichon Jean-Luc,Enouf Vincent,Espérou Hélène,Frezouls Wahiba,Houhou Nadhira,Ilic-Habensus Emila,Kafif Ouifiya,Kikoine John,Le Hingrat Quentin,Lebeaux David,Leclercq Anne,Lehacaut Jonathan,Letrou Sophie,Lina Bruno,Lucet Jean-Christophe,Malvy Denis,Manchon Pauline,Mandic Milica,Meghadecha Mohamed,Motiejunaite Justina,Nouroudine Mariama,Piquard Valentine,Postolache Andreea,Quintin Caroline,Rexach Jade,Roufai Layidé,Terzian Zaven,Thy Michael,Tubiana Sarah,van der Werf Sylvie,Vignali Valérie,Visseaux Benoit,Yazdanpanah Yazdan,van Agtmael Michiel,Algera Anna Geke,van Baarle Frank,Bax Diane,Beudel Martijn,Bogaard Harm Jan,Bomers Marije,Bos Lieuwe,Botta Michela,de Brabander Justin,de Bree Godelieve,Brouwer Matthijs C.,de Bruin Sanne,Bugiani Marianna,Bulle Esther,Chouchane O.,Cloherty Alex,Elbers Paul,Fleuren Lucas,Geerlings Suzanne,Geerts Bart,Geijtenbeek Theo,Girbes Armand,Goorhuis Bram,Grobusch Martin P.,Hafkamp Florianne,Hagens Laura,Hamann Jorg,Harris Vanessa,Hemke Robert,Hermans Sabine M.,Heunks Leo,Hollmann Markus W.,Horn Janneke,Hovius Joppe W.,de Jong Menno D.,Koning Rutger,van Mourik Niels,Nellen Jeaninne,Paulus Frederique,Peters Edgar,van der Poll Tom,Preckel Benedikt,Prins Jan M.,Raasveld Jorinde,Reijnders Tom,Schinkel Michiel,Schultz Marcus J.,Schuurman Alex,Sigaloff Kim,Smit Marry,Stijnis Cornelis S.,Stilma Willemke,Teunissen Charlotte,Thoral Patrick,Tsonas Anissa,van der Valk Marc,Veelo Denise,Vlaar Alexander P.J.,de Vries Heder,van Vugt Michèle,Wiersinga W. Joost,Wouters Dorien,Zwinderman A. H. (Koos),van de Beek Diederik,Abel Laurent,Aiuti Alessandro,Al Muhsen Saleh,Al-Mulla Fahd,Anderson Mark S.,Arias Andrés Augusto,Feldman Hagit Baris,Bogunovic Dusan,Bolze Alexandre,Bondarenko Anastasiia,Bousfiha Ahmed A.,Brodin Petter,Bryceson Yenan,Bustamante Carlos D.,Butte Manish,Casari Giorgio,Chakravorty Samya,Christodoulou John,Cirulli Elizabeth,Condino-Neto Antonio,Cooper Megan A.,Dalgard Clifton L.,David Alessia,DeRisi Joseph L.,Desai Murkesh,Drolet Beth A.,Espinosa Sara,Fellay Jacques,Flores Carlos,Franco Jose Luis,Gregersen Peter K.,Haerynck Filomeen,Hagin David,Halwani Rabih,Heath Jim,Henrickson Sarah E.,Hsieh Elena,Imai Kohsuke,Itan Yuval,Karamitros Timokratis,Kisand Kai,Ku Cheng-Lung,Lau Yu-Lung,Ling Yun,Lucas Carrie L.,Maniatis Tom,Mansouri Davoud,Marodi Laszlo,Meyts Isabelle,Milner Joshua,Mironska Kristina,Mogensen Trine,Morio Tomohiro,Ng Lisa F. P.,Notarangelo Luigi D.,Novelli Antonio,Novelli Giuseppe,O’Farrelly Cliona,Okada Satoshi,Ozcelik Tayfun,de Diego Rebeca Perez,Planas Anna M.,Prando Carolina,Pujol Aurora,Quintana-Murci Lluis,Renia Laurent,Renieri Alessandra,Rodríguez-Gallego Carlos,Sancho-Shimizu Vanessa,Sankaran Vijay,Barrett Kelly Schiabor,Shahrooei Mohammed,Snow Andrew,Soler-Palacín Pere,Spaan András N.,Tangye Stuart,Turvey Stuart,Uddin Furkan,Uddin Mohammed J.,van de Beek Diederik,Vazquez Sara E.,Vinh Donald C.,von Bernuth Horst,Washington Nicole,Zawadzki Pawel,Su Helen C.,Casanova Jean-Laurent,Jing Huie,Tung Wesley,Luthers Christopher R.,Bauman Bradly M.,Shafer Samantha,Zheng Lixin,Zhang Zinan,Kubo Satoshi,Chauvin Samuel D.,Meguro Kazuyuki,Shaw Elana,Lenardo Michael,Lack Justin,Karlins Eric,Hupalo Daniel M.,Rosenberger John,Sukumar Gauthaman,Wilkerson Matthew D.,Zhang Xijun, , , , , , , ,

Affiliation:

1. St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.

2. Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France.

3. University of Paris, Imagine Institute, Paris, France.

4. Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA.

5. Department of Paediatric Infectious Diseases & Virology, Imperial College London, London, UK.

6. Yale Center for Genome Analysis and Department of Genetics, Yale School of Medicine, New Haven, CT, USA.

7. Zukerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA.

8. Helix, San Mateo, CA, USA.

9. Primary Immunodeficiencies Group, University of Antioquia UdeA, Medellin, Colombia.

10. School of Microbiology, University of Antioquia UdeA, Medellin, Colombia.

11. Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA.

12. NIAID Clinical Genomics Program, NIH, Bethesda, MD, USA.

13. Université de Paris, Institut de Recherche Saint-Louis, INSERM U976, Hôpital Saint-Louis, Paris, France.

14. Laboratory of Genomes & Cell Biology of Disease, INSERM U944, CNRS UMR 7212, Université de Paris, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, Paris, France.

15. Sorbonne Université, Inserm, Centre d’Immunologie et des Maladies Infectieuses–Paris (CIMI PARIS), Assistance Publique-Hôpitaux de Paris (AP-HP) Hôpital Pitié-Salpêtrière, Paris, France.

16. Translational Immunology Lab, Institut Pasteur, Paris, France.

17. Laboratory for Inborn Errors of Immunity, Department of Microbiology, Immunology and Transplantation, Department of Pediatrics, University Hospitals Leuven, KU Leuven, Leuven, Belgium.

18. Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

19. Sorbonne Université, UMS037, PASS, Plateforme de Cytométrie de la Pitié-Salpêtrière CyPS, Paris, France.

20. Bioinformatics Platform, Structure Fédérative de Recherche Necker, INSERM UMR1163, Université de Paris, Imagine Institute, Paris, France.

21. Neurometabolic Diseases Laboratory, IDIBELL-Hospital Duran i Reynals, CIBERER U759, and Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain.

22. Department of Immunology, Research Branch, Sidra Medicine, Doha, Qatar.

23. School of Life sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.

24. Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.

25. Swiss Institue of Bioinformatics, Lausanne, Switzerland.

26. Infectious Disease Susceptibility Program, Research Institute, McGill University Health Centre, Montréal, Québec, Canada.

27. Specialized Immunology Laboratory of Dr. Shahrooei, Sina Medical Complex, Ahvaz, Iran.

28. Department of Microbiology and Immunology, Clinical and Diagnostic Immunology, KU Leuven, Leuven, Belgium.

29. Department of Pathology and Laboratory Medicine, College of Medicine, King Saud University, Riyadh, Saudi Arabia.

30. Department of Clinical Immunology and Infectious Diseases, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.

31. The Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of, Tuberculosis and Lung Diseases (NRITLD), Masih Daneshvari Hospital, Shahid Beheshti, University of Medical Sciences, Tehran, Iran.

32. Pediatric Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti, Iran.

33. National Center of Genomics Technology, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.

34. Dasman Diabetes Institute, Department of Genetics and Bioinformatics, Kuwait.

35. Immunology Research Laboratory, Department of Pediatrics, College of Medicine and King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia.

36. Translational Pathology, Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Misery of National Guard Health Affairs, Riyadh, Saudi Arabia.

37. Cancer & Blood Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia.

38. Amsterdam UMC, Department of Neurology, Amsterdam Neuroscience, Amsterdam, Netherlands.

39. Pediatric Departement and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale, San Gerardo, Monza, Italy.

40. Department of Infectious Diseases, San Gerardo Hospital–University of Milano-Bicocca, Monza, Italy.

41. CREA Laboratory, Diagnostic Laboratory, ASST Spedali Civili di Brescia, Brescia, Italy.

42. Department of Infectious and Tropical Diseases, University of Brescia and ASST Spedali di Brescia, Brescia, Italy.

43. Chief Medical Officer, ASST Spedali Civili di Brescia, Brescia, Italy.

44. Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID, NIH, Bethesda, MD, USA.

45. PRIMER, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.

46. Center of Human Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium.

47. Department of Internal Medicine, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium.

48. Fonds de la Recherche Scientifique (FNRS) and Center of Human Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium.

49. Department of Paediatric Immunology and Pulmonology, Centre for Primary Immunodeficiency Ghent (CPIG), PID Research Lab, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium.

50. 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, Catalonia, Spain.

51. Immunology Division, Genetics Department, Hospital Universitari Vall d’Hebron, Vall d’Hebron Research Institute, Vall d’Hebron Barcelona Hospital Campus, UAB, Barcelona, Catalonia, Spain.

52. Aix Marseille Univ, INSERM, INRAE, C2VN, CHU Timone, Marseille, France.

53. Necmettin Erbakan University, Meram Medical Faculty, Division of Pediatric Allergy and Immunology, Konya, Turkey.

54. Department of Infectious Diseases and Clinical Microbiology, Konya Training and Research Hospital, Konya, Turkey.

55. Department of Molecular Biology and Genetics, Bilkent University, Bilkent-Ankara, Turkey.

56. Departments of Infectious Diseases and Clinical Microbiology, Bakirkoy Dr. Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey.

57. Department of Immunology, Hospital Universitario de G.C. Dr. Negrín, Canarian Health System, Las Palmas de Gran Canaria, Spain.

58. University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain.

59. Department of Biomedicine and Prevention, University of Rome “Tor Vergata,” Rome, Italy.

60. Intensive Care Unit, AP-HM, Marseille, France.

61. Avicenne Hospital Intensive Care Unit, APHP, Bobigny, INSERM U1272 Hypoxia & Lung, Paris, France.

62. PH Réanimation CHU Avicenne, Bobigny, INSERM U1272 Hypoxie & Poumon, Paris, France.

63. Université de Paris, IAME UMR-S 1137, INSERM, Paris, France.

64. Inserm CIC 1425, Paris, France.

65. AP-HP, Département Epidémiologie Biostatistiques et Recherche Clinique, Hôpital Bichat, Paris, France.

66. Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.

67. Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.

68. Division of Pediatric Allergy, Immunology and Rheumatology, Columbia University, New York, USA.

69. Department of Infectious Diseases, Aarhus University Hospital, Skejby, Denmark.

70. Department of Biomedicine, Aarhus University, Aarhus, Denmark.

71. College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.

72. Department of Medical Microbiology, Utrecht UMC, Utrecht, Netherlands.

73. Study Center for Primary Immunodeficiencies, Necker Hospital for Sick Children, Paris, France.

74. Turnstone Biologics, New York, NY, USA.

75. Department of Pediatrics, University Hospitals Leuven, KU Leuven, Leuven, Belgium.

76. New York Genome Center, New York, NY, USA.

77. AP-HP, Hôpital Saint-Louis, Laboratoire d’Immunologie, Paris, France.

78. Laboratory of Molecular Immunology, Rockefeller University, New York, NY, USA.

79. Howard Hughes Medical Institute, New York, NY, USA.

80. Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

81. Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

82. The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

83. Laboratory of Genetics and Genomics, The Rockefeller University, New York, NY, USA.

84. Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.

85. Yale Center for Genome Analysis, Yale School of Medicine, New Haven, CT, USA.

86. Pediatric Hematology and Immunology Unit, Necker Hospital for Sick Children, AP-HP, Paris, France.

Abstract

The genetics underlying severe COVID-19 The immune system is complex and involves many genes, including those that encode cytokines known as interferons (IFNs). Individuals that lack specific IFNs can be more susceptible to infectious diseases. Furthermore, the autoantibody system dampens IFN response to prevent damage from pathogen-induced inflammation. Two studies now examine the likelihood that genetics affects the risk of severe coronavirus disease 2019 (COVID-19) through components of this system (see the Perspective by Beck and Aksentijevich). Q. Zhang et al. used a candidate gene approach and identified patients with severe COVID-19 who have mutations in genes involved in the regulation of type I and III IFN immunity. They found enrichment of these genes in patients and conclude that genetics may determine the clinical course of the infection. Bastard et al. identified individuals with high titers of neutralizing autoantibodies against type I IFN-α2 and IFN-ω in about 10% of patients with severe COVID-19 pneumonia. These autoantibodies were not found either in infected people who were asymptomatic or had milder phenotype or in healthy individuals. Together, these studies identify a means by which individuals at highest risk of life-threatening COVID-19 can be identified. Science , this issue p. eabd4570 , p. eabd4585 ; see also p. 404

Funder

National Institutes of Health

Howard Hughes Medical Institute

ST. GILES FOUNDATION

National Center for Advancing Translational Sciences

Rockefeller University

French National Research Agency

the Integrative Biology of Emerging Infectious Diseases Laboratory of Excellence

National Human Genome Research Institute

the French Foundation for Medical Research

NIH Clinical and Translational Science Award

Emergent Ventures

Publisher

American Association for the Advancement of Science (AAAS)

Subject

Multidisciplinary

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