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

Abstract

Clinical outcome upon infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ranges from silent infection to lethal coronavirus disease 2019 (COVID-19). We have found an enrichment in rare variants predicted to be loss-of-function (LOF) at the 13 human loci known to govern Toll-like receptor 3 (TLR3)- and interferon regulatory factor 7 (IRF7)-dependent type I interferon (IFN) immunity to influenza virus in 659 patients with life-threatening COVID-19 pneumonia relative to 534 subjects with asymptomatic or benign infection. By testing these and other rare variants at these 13 loci, we experimentally defined LOF variants underlying autosomal-recessive or autosomal-dominant deficiencies in 23 patients (3.5%) 17 to 77 years of age. We show that human fibroblasts with mutations affecting this circuit are vulnerable to SARS-CoV-2. Inborn errors of TLR3- and IRF7-dependent type I IFN immunity can underlie life-threatening COVID-19 pneumonia in patients with no prior severe infection.

• Authors: Qian Zhang, Paul Bastard, Zhiyong Liu, Jérémie Le Pen, Marcela Moncada-Velez, Jie Chen, Masato Ogishi, Ira K D Sabli, Stephanie Hodeib, Cecilia Korol, Jérémie Rosain, Kaya Bilguvar, Junqiang Ye, Alexandre Bolze, Benedetta Bigio, Rui Yang, Andrés Augusto Arias, Qinhua Zhou, Yu Zhang, Fanny Onodi, Sarantis Korniotis, Léa Karpf, Quentin Philippot, Marwa Chbihi, Lucie Bonnet-Madin, Karim Dorgham, Nikaïa Smith, William M Schneider, Brandon S Razooky, Hans-Heinrich Hoffmann, Eleftherios Michailidis, Leen Moens, Ji Eun Han, Lazaro Lorenzo, Lucy Bizien, Philip Meade, Anna-Lena Neehus, Aileen Camille Ugurbil, Aurélien Corneau, Gaspard Kerner, Peng Zhang, Franck Rapaport, Yoann Seeleuthner, Jeremy Manry, Cecile Masson, Yohann Schmitt, Agatha Schlüter, Tom Le Voyer, Taushif Khan, Juan Li, Jacques Fellay, Lucie Roussel, Mohammad Shahrooei, Mohammed F Alosaimi, Davood Mansouri, Haya Al-Saud, Fahd Al-Mulla, Feras Almourfi, Saleh Zaid Al-Muhsen, Fahad Alsohime, Saeed Al Turki, Rana Hasanato, Diederik van de Beek, Andrea Biondi, Laura Rachele Bettini, Mariella D'Angio', Paolo Bonfanti, Luisa Imberti, Alessandra Sottini, Simone Paghera, Eugenia Quiros-Roldan, Camillo Rossi, Andrew J Oler, Miranda F Tompkins, Camille Alba, Isabelle Vandernoot, Jean-Christophe Goffard, Guillaume Smits, Isabelle Migeotte, Filomeen Haerynck, Pere Soler-Palacin, Andrea Martin-Nalda, Roger Colobran, Pierre-Emmanuel Morange, Sevgi Keles, Fatma Çölkesen, Tayfun Ozcelik, Kadriye Kart Yasar, Sevtap Senoglu, Şemsi Nur Karabela, Carlos Rodríguez-Gallego, Giuseppe Novelli, Sami Hraiech, Yacine Tandjaoui-Lambiotte, Xavier Duval, Cédric Laouénan, COVID-STORM Clinicians, COVID Clinicians, Imagine COVID Group, French COVID Cohort Study Group, CoV-Contact Cohort, Amsterdam UMC Covid-19 Biobank, COVID Human Genetic Effort, NIAID-USUHS/TAGC COVID Immunity Group, Andrew L Snow, Clifton L Dalgard, Joshua D Milner, Donald C Vinh, Trine H Mogensen, Nico Marr, András N Spaan, Bertrand Boisson, Stéphanie Boisson-Dupuis, Jacinta Bustamante, Anne Puel, Michael J Ciancanelli, Isabelle Meyts, Tom Maniatis, Vassili Soumelis, Ali Amara, Michel Nussenzweig, Adolfo García-Sastre, Florian Krammer, Aurora Pujol, Darragh Duffy, Richard P Lifton, Shen-Ying Zhang, Guy Gorochov, Vivien Béziat, Emmanuelle Jouanguy, Vanessa Sancho-Shimizu, Charles M Rice, Laurent Abel, Luigi D Notarangelo, Aurélie Cobat, Helen C Su, Jean-Laurent Casanova
• Journal: Science (New York, N.Y.) (Science) Vol. 370 Issue 6515 (10 23 2020) ISSN: 1095-9203 [Electronic] United States
• PMID: 32972995 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)
• Copyright: Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Chemical References

• IFNAR1 protein, human
• IRF7 protein, human
• Interferon Regulatory Factor-7
• Interferon Type I
• TLR3 protein, human
• Toll-Like Receptor 3
• Receptor, Interferon alpha-beta

Topics

• Adolescent
• Adult
• Aged
• Aged, 80 and over
• Alleles
• Asymptomatic Infections
• Betacoronavirus
• COVID-19
• Child
• Child, Preschool
• Coronavirus Infections (genetics, immunology)
• Female
• Genetic Loci
• Genetic Predisposition to Disease
• Humans
• Infant
• Interferon Regulatory Factor-7 (deficiency, genetics)
• Interferon Type I (immunology)
• Loss of Function Mutation
• Male
• Middle Aged
• Pandemics
• Pneumonia, Viral (genetics, immunology)
• Receptor, Interferon alpha-beta (deficiency, genetics)
• SARS-CoV-2
• Toll-Like Receptor 3 (deficiency, genetics)
• Young Adult