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Uslu K, Ozcelik F, Zararsiz G, Eldem V, Cephe A, Sahin IO, Yuksel RC, Sipahioglu H, Ozer Simsek Z, Baspinar O, Akalin H, Simsek Y, Gundogan K, Tutar N, Karayol Akin A, Ozkul Y, Yildiz O, Dundar M. Deciphering the host genetic factors conferring susceptibility to severe COVID-19 using exome sequencing. Genes Immun 2024; 25:14-42. [PMID: 38123822 DOI: 10.1038/s41435-023-00232-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 12/23/2023]
Abstract
The COVID-19 pandemic remains a significant public health concern despite the new vaccines and therapeutics. The clinical course of acute SARS-CoV-2 infection is highly variable and influenced by several factors related to the virus and the host. Numerous genetic studies, including candidate gene, exome, and genome sequencing studies, genome-wide association studies, and other omics efforts, have proposed various Mendelian and non-Mendelian associations with COVID-19 course. In this study, we conducted whole-exome sequencing on 90 unvaccinated patients from Turkey with no known comorbidities associated with severe COVID-19. Of these patients, 30 had severe, 30 had moderate, and 30 had mild/asymptomatic disease. We identified rare variants in genes associated with SARS-CoV-2 susceptibility and pathogenesis, with an emphasis on genes related to the regulation of inflammation, and discussed these in the context of the clinical course of the patients. In addition, we compared the frequencies of common variants between each group. Even though no variant remained statistically significant after correction for multiple testing, we observed that certain previously associated genes and variants showed significant associations before correction. Our study contributes to the existing literature regarding the genetic susceptibility to SARS-CoV-2. Future studies would be beneficial characterizing the host genetic properties in different populations.
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Affiliation(s)
- Kubra Uslu
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Firat Ozcelik
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Gokmen Zararsiz
- Department of Biostatistics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
- Drug Application and Research Center (ERFARMA), Erciyes University, Kayseri, Turkey
| | - Vahap Eldem
- Department of Biology, Faculty of Science, Istanbul University, Istanbul, Turkey
| | - Ahu Cephe
- Institutional Data Management and Analytics Units, Erciyes University Rectorate, Kayseri, Turkey
| | - Izem Olcay Sahin
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Recep Civan Yuksel
- Division of Intensive Care Medicine, Department of Internal Medicine, Kayseri City Education and Research Hospital, Kayseri, Turkey
| | - Hilal Sipahioglu
- Division of Intensive Care Medicine, Department of Internal Medicine, Kayseri City Education and Research Hospital, Kayseri, Turkey
| | - Zuhal Ozer Simsek
- Division of Intensive Care Medicine, Department of Internal Medicine, Kayseri City Education and Research Hospital, Kayseri, Turkey
| | - Osman Baspinar
- Department of Internal Medicine, Kayseri City Education and Research Hospital, Kayseri, Turkey
| | - Hilal Akalin
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Yasin Simsek
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Kayseri City Education and Research Hospital, Kayseri, Turkey
| | - Kursat Gundogan
- Division of Intensive Care Medicine, Department of Internal Medicine, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Nuri Tutar
- Department of Chest Diseases, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Aynur Karayol Akin
- Department of Anesthesiology and Reanimation, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Yusuf Ozkul
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Orhan Yildiz
- Department of Infectious Diseases, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Munis Dundar
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, Turkey.
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2
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Covill LE, Sendel A, Campbell TM, Piiroinen I, Enoksson SL, Borgström EW, Hansen S, Ma K, Marits P, Norlin AC, Smith CIE, Kåhlin J, Eriksson LI, Bergman P, Bryceson YT. Evaluation of Genetic or Cellular Impairments in Type I IFN Immunity in a Cohort of Young Adults with Critical COVID-19. J Clin Immunol 2024; 44:50. [PMID: 38231281 PMCID: PMC10794435 DOI: 10.1007/s10875-023-01641-1] [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: 11/23/2023] [Accepted: 12/13/2023] [Indexed: 01/18/2024]
Abstract
Several genetic and immunological risk factors for severe COVID-19 have been identified, with monogenic conditions relating to 13 genes of type I interferon (IFN) immunity proposed to explain 4.8% of critical cases. However, previous cohorts have been clinically heterogeneous and were not subjected to thorough genetic and immunological analyses. We therefore aimed to systematically investigate the prevalence of rare genetic variants causing inborn errors of immunity (IEI) and functionally interrogate the type I IFN pathway in young adults that suffered from critical COVID-19 yet lacked comorbidities. We selected and clinically characterized a cohort of 38 previously healthy individuals under 50 years of age who were treated in intensive care units due to critical COVID-19. Blood samples were collected after convalescence. Two patients had IFN-α autoantibodies. Genome sequencing revealed very rare variants in the type I IFN pathway in 31.6% of the patients, which was similar to controls. Analyses of cryopreserved leukocytes did not indicate any defect in plasmacytoid dendritic cell sensing of TLR7 and TLR9 agonists in patients carrying variants in these pathways. However, lymphocyte STAT phosphorylation and protein upregulation upon IFN-α stimulation revealed three possible cases of impaired type I IFN signaling in carriers of rare variants. Together, our results suggest a strategy of functional screening followed by genome analyses and biochemical validation to uncover undiagnosed causes of critical COVID-19.
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Affiliation(s)
- L E Covill
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - A Sendel
- Division of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - T M Campbell
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - I Piiroinen
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - S Lind Enoksson
- Division of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - E Wahren Borgström
- Division of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - S Hansen
- Division of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - K Ma
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - P Marits
- Division of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - A C Norlin
- Division of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - C I E Smith
- Division of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - J Kåhlin
- Division of Perioperative Medicine and Intensive Care, Karolinska University Hospital, Stockholm, Sweden
| | - L I Eriksson
- Division of Perioperative Medicine and Intensive Care, Karolinska University Hospital, Stockholm, Sweden
| | - P Bergman
- Division of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
- Division of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Y T Bryceson
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institute, Stockholm, Sweden.
- Division of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden.
- Broegelmann Laboratory, Department of Clinical Sciences, University of Bergen, Bergen, Norway.
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3
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Bastard P, Vazquez SE, Liu J, Laurie MT, Wang CY, Gervais A, Le Voyer T, Bizien L, Zamecnik C, Philippot Q, Rosain J, Catherinot E, Willmore A, Mitchell AM, Bair R, Garçon P, Kenney H, Fekkar A, Salagianni M, Poulakou G, Siouti E, Sahanic S, Tancevski I, Weiss G, Nagl L, Manry J, Duvlis S, Arroyo-Sánchez D, Paz Artal E, Rubio L, Perani C, Bezzi M, Sottini A, Quaresima V, Roussel L, Vinh DC, Reyes LF, Garzaro M, Hatipoglu N, Boutboul D, Tandjaoui-Lambiotte Y, Borghesi A, Aliberti A, Cassaniti I, Venet F, Monneret G, Halwani R, Sharif-Askari NS, Danielson J, Burrel S, Morbieu C, Stepanovskyy Y, Bondarenko A, Volokha A, Boyarchuk O, Gagro A, Neuville M, Neven B, Keles S, Hernu R, Bal A, Novelli A, Novelli G, Saker K, Ailioaie O, Antolí A, Jeziorski E, Rocamora-Blanch G, Teixeira C, Delaunay C, Lhuillier M, Le Turnier P, Zhang Y, Mahevas M, Pan-Hammarström Q, Abolhassani H, Bompoil T, Dorgham K, Gorochov G, Laouenan C, Rodríguez-Gallego C, Ng LFP, Renia L, Pujol A, Belot A, Raffi F, Allende LM, Martinez-Picado J, Ozcelik T, Imberti L, Notarangelo LD, Troya J, Solanich X, Zhang SY, Puel A, Wilson MR, Trouillet-Assant S, Abel L, Jouanguy E, Ye CJ, Cobat A, Thompson LM, Andreakos E, Zhang Q, Anderson MS, Casanova JL, DeRisi JL. Vaccine breakthrough hypoxemic COVID-19 pneumonia in patients with auto-Abs neutralizing type I IFNs. Sci Immunol 2023; 8:eabp8966. [PMID: 35857576 PMCID: PMC9210448 DOI: 10.1126/sciimmunol.abp8966] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/26/2022] [Indexed: 12/15/2022]
Abstract
Life-threatening "breakthrough" cases of critical COVID-19 are attributed to poor or waning antibody (Ab) response to SARS-CoV-2 vaccines in individuals already at risk. Preexisting auto-Abs neutralizing type I IFNs underlie at least 15% of critical COVID-19 pneumonia cases in unvaccinated individuals; their contribution to hypoxemic breakthrough cases in vaccinated people is unknown. We studied a cohort of 48 individuals (aged 20 to 86 years) who received two doses of a messenger RNA (mRNA) vaccine and developed a breakthrough infection with hypoxemic COVID-19 pneumonia 2 weeks to 4 months later. Ab levels to the vaccine, neutralization of the virus, and auto-Abs to type I IFNs were measured in the plasma. Forty-two individuals had no known deficiency of B cell immunity and a normal Ab response to the vaccine. Among them, 10 (24%) had auto-Abs neutralizing type I IFNs (aged 43 to 86 years). Eight of these 10 patients had auto-Abs neutralizing both IFN-α2 and IFN-ω, whereas two neutralized IFN-ω only. No patient neutralized IFN-β. Seven neutralized type I IFNs at 10 ng/ml and three at 100 pg/ml only. Seven patients neutralized SARS-CoV-2 D614G and Delta efficiently, whereas one patient neutralized Delta slightly less efficiently. Two of the three patients neutralizing only type I IFNs at 100 pg/ml neutralized both D614G and Delta less efficiently. Despite two mRNA vaccine inoculations and the presence of circulating Abs capable of neutralizing SARS-CoV-2, auto-Abs neutralizing type I IFNs may underlie a notable proportion of hypoxemic COVID-19 pneumonia cases, highlighting the importance of this particularly vulnerable population.
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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
- Imagine Institute, University of Paris Cité, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
- Department of Pediatrics, Necker Hospital for Sick Children, AP-HP, Paris, France
| | - Sara E Vazquez
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jamin Liu
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA, USA
| | - Matthew T Laurie
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Chung Yu Wang
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Adrian Gervais
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University of Paris Cité, Paris, France
| | - Tom Le Voyer
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University of Paris Cité, Paris, France
| | - Lucy Bizien
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University of Paris Cité, Paris, France
| | - Colin Zamecnik
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Quentin Philippot
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University of Paris Cité, Paris, France
| | - Jérémie Rosain
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University of Paris Cité, Paris, France
| | | | | | | | - Rebecca Bair
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Pierre Garçon
- Intensive Care Unit, Grand Hôpital de l'Est Francilien Site de Marne-la-Vallée, Jossigny, France
| | - Heather Kenney
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
| | - Arnaud Fekkar
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University of Paris Cité, Paris, France
- Service de Parasitologie-Mycologie, Groupe Hospitalier Pitié Salpêtrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Maria Salagianni
- Laboratory of Immunobiology, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Garyphallia Poulakou
- 3rd Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, "Sotiria" General Hospital of Chest Diseases, Athens, Greece
| | - Eleni Siouti
- Laboratory of Immunobiology, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Sabina Sahanic
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Ivan Tancevski
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Günter Weiss
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Laurenz Nagl
- Department of Internal Medicine V, Medical University of Innsbruck, Innsbruck, Austria
| | - Jérémy Manry
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University of Paris Cité, Paris, France
| | - Sotirija Duvlis
- Faculty of Medical Sciences, University "Goce Delchev", Stip, Republic of North Macedonia
- Institute of Public Health, Skopje, Republic of North Macedonia
| | - Daniel Arroyo-Sánchez
- Department of Immunology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12) and Department of Immunology, Ophthalmology and ENT, Complutense University School of Medicine, CIBERINFEC, Madrid, Spain
| | - Estela Paz Artal
- Department of Immunology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12) and Department of Immunology, Ophthalmology and ENT, Complutense University School of Medicine, CIBERINFEC, Madrid, Spain
| | - Luis Rubio
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | | | | | - Alessandra Sottini
- CREA Laboratory, Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Virginia Quaresima
- CREA Laboratory, Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Lucie Roussel
- Department of Medicine, Division of Infectious Diseases, McGill University Health Centre, Montréal, Québec, Canada
- Infectious Disease Susceptibility Program, Research Institute-McGill University Health Centre, Montréal, Québec, Canada
| | - Donald C Vinh
- Department of Medicine, Division of Infectious Diseases, McGill University Health Centre, Montréal, Québec, Canada
- Infectious Disease Susceptibility Program, Research Institute-McGill University Health Centre, Montréal, Québec, Canada
| | - Luis Felipe Reyes
- Department of Microbiology, Universidad de La Sabana, Chía, Colombia
- Department of Critical Care Medicine, Clínica Universidad de La Sabana, Chía, Colombia
| | - Margaux Garzaro
- Department of Infectious Diseases, Necker Hospital for Sick Children, AP-HP, Paris, France
| | - Nevin Hatipoglu
- Pediatric Infectious Diseases Unit, Bakirkoy Dr. Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - David Boutboul
- Department of Immunology, Saint-Louis Hospital, AP-HP, Paris, France
| | - Yacine Tandjaoui-Lambiotte
- INSERM UMR 1137 IAME, Paris, France
- INSERM UMR 1272 Hypoxie and Poumon, Bobigny, France
- Pneumology and Infectiology Department, CH Saint Denis, Saint-Denis, France
| | - Alessandro Borghesi
- Neonatal Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Anna Aliberti
- Anesthesia and Intensive Care, Rianimazione I, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Irene Cassaniti
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Fabienne Venet
- Laboratoire d'Immunologie, Hospices Civils de Lyon, Hôpital Edouard Herriot, Lyon, France
- EA 7426, Pathophysiology of Injury-Induced Immunosuppression, Université Claude Bernard Lyon 1, Hospices Civils de Lyon, Hôpital Edouard Herriot-BioMérieux, Lyon, France
- CIRI, INSERM U1111, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Guillaume Monneret
- Laboratoire d'Immunologie, Hospices Civils de Lyon, Hôpital Edouard Herriot, Lyon, France
- EA 7426, Pathophysiology of Injury-Induced Immunosuppression, Université Claude Bernard Lyon 1, Hospices Civils de Lyon, Hôpital Edouard Herriot-BioMérieux, Lyon, France
| | - Rabih Halwani
- Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Immunology Research Laboratory, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Narjes Saheb Sharif-Askari
- Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Jeffrey Danielson
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
| | - Sonia Burrel
- Sorbonne Université, INSERM U1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié Salpêtrière, Service de Virologie, Paris, France
| | - Caroline Morbieu
- Internal Medicine Department, Louis Mourier Hospital, AP-HP, Paris, France
| | | | | | - Alla Volokha
- Shupyk National Healthcare University of Ukraine, Kyiv, Ukraine
| | - Oksana Boyarchuk
- Department of Children's Diseases and Pediatric Surgery, I. Horbachevsky Ternopil National Medical University, Ternopil, Ukraine
| | - Alenka Gagro
- Department of Pediatrics, Children's Hospital Zagreb, University of Zagreb School of Medicine, Zagreb, Josip Juraj Strossmayer University of Osijek, Medical Faculty Osijek, Osijek, Croatia
| | | | - Bénédicte Neven
- Department of Pediatrics Hematology Immunology and Rheumatology, Necker Hospital for Sick Children, AP-HP, Paris, France
| | - Sevgi Keles
- Meram Medical Faculty, Necmettin Erbakan University, Konya, Turkey
| | - Romain Hernu
- Service des Urgences, Groupement Hospitalier Nord, Hospices Civils de Lyon, Lyon, France
| | - Antonin Bal
- Laboratoire de virologie, Institut Agent Infectieux, Groupement Hospitalier Nord, Hospices Civils de Lyon, Lyon, France
| | - Antonio Novelli
- Laboratory of Medical Genetics, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, Rome, Italy
| | - Kahina Saker
- Joint Research Unit, Hospices Civils de Lyon-bio Mérieux, Hospices Civils de Lyon, Lyon Sud Hospital, Pierre-Bénite, France; and International Center of Research in Infectiology, Lyon University, INSERM U1111, CNRS UMR 5308, ENS, UCBL, Lyon, France
| | - Oana Ailioaie
- Service de Génétique, Hôpital Raymond Poincaré, AP-HP, Garches, France
| | - Arnau Antolí
- Department of Internal Medicine, Hospital Universitari de Bellvitge, IDIBELL, Barcelona, Spain
| | - Eric Jeziorski
- General Pediatric Department, PCCEI, CeRéMAIA, University of Montpellier, CHU Montpellier, Montpellier, France
| | - Gemma Rocamora-Blanch
- Department of Internal Medicine, Hospital Universitari de Bellvitge, IDIBELL, Barcelona, Spain
| | - Carla Teixeira
- Unidade de Infeciologia e Imunodeficiências, Centro Materno-infantil do Norte, Centro Hospitalar Universitário do Porto, Porto, Portugal
| | - Clarisse Delaunay
- Department of Infectious Diseases, CHU Nantes, and INSERM UIC 1413, CHU, Nantes, France
| | - Marine Lhuillier
- Geriatric Department, CHU Nantes, Hopital Bellier, Nantes, France
| | - Paul Le Turnier
- Department of Infectious Diseases, CHU Nantes, and INSERM UIC 1413, CHU, Nantes, France
| | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
- NIAID Clinical Genomics Program, NIH, Bethesda, MD, USA
| | - Matthieu Mahevas
- Necker Enfants Malades Institute (INEM), INSERM U1151/CNRS UMR 8253, University of Paris Cité, Paris, France
- Departement of Internal Medicine, Henri Mondor University Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris-Est Créteil University (UPEC), Créteil, France
- INSERM U955, Team 2, Mondor Biomedical Research Institute (IMRB), Paris-Est Créteil University (UPEC), Créteil, France
| | - Qiang Pan-Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet, SE14183 Huddinge, Sweden
| | - Hassan Abolhassani
- Department of Biosciences and Nutrition, Karolinska Institutet, SE14183 Huddinge, Sweden
| | - Thierry Bompoil
- Biologie/Pathologie, CHU-Nantes-Hôtel Dieu, Institut de Biologie, Nantes, France
| | - Karim Dorgham
- Sorbonne Université, Inserm, Centre d'Immunologie et des Maladies Infectieuses, (CIMI-Paris), Paris, France
| | - Guy Gorochov
- Sorbonne Université, Inserm, Centre d'Immunologie et des Maladies Infectieuses, (CIMI-Paris), Paris, France
- Département d'Immunologie, Assistance Publique Hôpitaux de Paris (AP-HP), Hôpital Pitié-Salpétrière, Paris, France
| | - Cédric Laouenan
- INSERM UMR 1137 IAME, Paris, France
- Université de Paris, IAME UMR-S 1137, INSERM, Paris, France
- Département Epidémiologie Biostatistiques et Recherche Clinique, Hôpital Bichat, AP-HP, Paris, France
| | - Carlos Rodríguez-Gallego
- Department of Clinical Sciences, University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Canary Islands, Spain
- Department of Immunology, University Hospital of Gran Canaria Dr. Negrín, Canarian Health System, Las Palmas de Gran Canaria, Spain
| | - Lisa F P Ng
- A*STAR Infectious Disease Labs, Agency for Science, Technology and Research, Singapore, Singapore
| | - Laurent Renia
- A*STAR Infectious Disease Labs, Agency for Science, Technology and Research, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technology University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technology University, Singapore, Singapore
| | - Aurora Pujol
- Neurometabolic Diseases Laboratory, IDIBELL-Hospital Duran i Reynals, CIBERER U759, and Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Alexandre Belot
- Joint Research Unit, Hospices Civils de Lyon-bio Mérieux, Hospices Civils de Lyon, Lyon Sud Hospital, Pierre-Bénite, France; and International Center of Research in Infectiology, Lyon University, INSERM U1111, CNRS UMR 5308, ENS, UCBL, Lyon, France
- CNRS UMR 5308, ENS, UCBL, Lyon, France; National Referee Centre for Rheumatic, and Autoimmune and Systemic Diseases in Children (RAISE), Lyon, France; and Immunopathology Federation LIFE, Hospices Civils de Lyon, Lyon, France
| | - François Raffi
- Department of Infectious Diseases, CHU Nantes, and INSERM UIC 1413, CHU, Nantes, France
| | - Luis M Allende
- Department of Immunology, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12) and Department of Immunology, Ophthalmology and ENT, Complutense University School of Medicine, CIBERINFEC, Madrid, Spain
| | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute and Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
- Infectious Diseases and Immunity, Center for Health and Social Care Research (CESS), Faculty of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Tayfun Ozcelik
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Luisa Imberti
- CREA Laboratory, Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
| | - Jesus Troya
- Department of Internal Medicine, Infanta Leonor University Hospital, Madrid, Spain
| | - Xavier Solanich
- Department of Internal Medicine, Hospital Universitari de Bellvitge, IDIBELL, Barcelona, Spain
| | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University of Paris Cité, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University of Paris Cité, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
| | - Michael R Wilson
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Sophie Trouillet-Assant
- Hospices Civils de Lyon, Lyon, France; and International Center of Research in Infectiology, Lyon University, INSERM U1111, CNRS UMR 5308, ENS, UCBL, Lyon, France
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University of Paris Cité, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, 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
- Imagine Institute, University of Paris Cité, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
| | - Chun Jimmie Ye
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- ImmunoX Initiative, University of California, San Francisco, San Francisco, CA 94143, USA
- Departments of Epidemiology and Biostatistics and Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University of Paris Cité, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
| | - Leslie M Thompson
- Departments of Psychiatry and Human Behavior and Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA
| | - Evangelos Andreakos
- Laboratory of Immunobiology, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Qian Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University of Paris Cité, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
| | - Mark S Anderson
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University of Paris Cité, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
- Department of Pediatrics, Necker Hospital for Sick Children, AP-HP, Paris, France
- Howard Hughes Medical Institute, New York, NY, USA
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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4
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Pan-Hammarström Q, Casanova JL. Human genetic and immunological determinants of SARS-CoV-2 and Epstein-Barr virus diseases in childhood: Insightful contrasts. J Intern Med 2023; 294:127-144. [PMID: 36906905 DOI: 10.1111/joim.13628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
Abstract
There is growing evidence to suggest that severe disease in children infected with common viruses that are typically benign in other children can result from inborn errors of immunity or their phenocopies. Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a cytolytic respiratory RNA virus, can lead to acute hypoxemic COVID-19 pneumonia in children with inborn errors of type I interferon (IFN) immunity or autoantibodies against IFNs. These patients do not appear to be prone to severe disease during infection with Epstein-Barr virus (EBV), a leukocyte-tropic DNA virus that can establish latency. By contrast, various forms of severe EBV disease, ranging from acute hemophagocytosis to chronic or long-term illnesses, such as agammaglobulinemia and lymphoma, can manifest in children with inborn errors disrupting specific molecular bridges involved in the control of EBV-infected B cells by cytotoxic T cells. The patients with these disorders do not seem to be prone to severe COVID-19 pneumonia. These experiments of nature reveal surprising levels of redundancy of two different arms of immunity, with type I IFN being essential for host defense against SARS-CoV-2 in respiratory epithelial cells, and certain surface molecules on cytotoxic T cells essential for host defense against EBV in B lymphocytes.
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Affiliation(s)
| | - Jean-Laurent Casanova
- St Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, New York, USA
- Howard Hughes Medical Institute, New York, New York, USA
- Laboratory of Human Genetics of Infectious Diseases, Inserm, Paris, France
- Imagine Institute, Paris Cité University, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
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5
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Işık YE, Aydın Z. Comparative analysis of machine learning approaches for predicting respiratory virus infection and symptom severity. PeerJ 2023; 11:e15552. [PMID: 37404475 PMCID: PMC10317018 DOI: 10.7717/peerj.15552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 05/23/2023] [Indexed: 07/06/2023] Open
Abstract
Respiratory diseases are among the major health problems causing a burden on hospitals. Diagnosis of infection and rapid prediction of severity without time-consuming clinical tests could be beneficial in preventing the spread and progression of the disease, especially in countries where health systems remain incapable. Personalized medicine studies involving statistics and computer technologies could help to address this need. In addition to individual studies, competitions are also held such as Dialogue for Reverse Engineering Assessment and Methods (DREAM) challenge which is a community-driven organization with a mission to research biology, bioinformatics, and biomedicine. One of these competitions was the Respiratory Viral DREAM Challenge, which aimed to develop early predictive biomarkers for respiratory virus infections. These efforts are promising, however, the prediction performance of the computational methods developed for detecting respiratory diseases still has room for improvement. In this study, we focused on improving the performance of predicting the infection and symptom severity of individuals infected with various respiratory viruses using gene expression data collected before and after exposure. The publicly available gene expression dataset in the Gene Expression Omnibus, named GSE73072, containing samples exposed to four respiratory viruses (H1N1, H3N2, human rhinovirus (HRV), and respiratory syncytial virus (RSV)) was used as input data. Various preprocessing methods and machine learning algorithms were implemented and compared to achieve the best prediction performance. The experimental results showed that the proposed approaches obtained a prediction performance of 0.9746 area under the precision-recall curve (AUPRC) for infection (i.e., shedding) prediction (SC-1), 0.9182 AUPRC for symptom class prediction (SC-2), and 0.6733 Pearson correlation for symptom score prediction (SC-3) by outperforming the best leaderboard scores of Respiratory Viral DREAM Challenge (a 4.48% improvement for SC-1, a 13.68% improvement for SC-2, and a 13.98% improvement for SC-3). Additionally, over-representation analysis (ORA), which is a statistical method for objectively determining whether certain genes are more prevalent in pre-defined sets such as pathways, was applied using the most significant genes selected by feature selection methods. The results show that pathways associated with the 'adaptive immune system' and 'immune disease' are strongly linked to pre-infection and symptom development. These findings contribute to our knowledge about predicting respiratory infections and are expected to facilitate the development of future studies that concentrate on predicting not only infections but also the associated symptoms.
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Affiliation(s)
- Yunus Emre Işık
- Department of Management Information Systems, Sivas Cumhuriyet University, Sivas, Turkey
| | - Zafer Aydın
- Department of Computer Engineering, Abdullah Gül University, Kayseri, Turkey
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6
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Ahuja SK, Manoharan MS, Lee GC, McKinnon LR, Meunier JA, Steri M, Harper N, Fiorillo E, Smith AM, Restrepo MI, Branum AP, Bottomley MJ, Orrù V, Jimenez F, Carrillo A, Pandranki L, Winter CA, Winter LA, Gaitan AA, Moreira AG, Walter EA, Silvestri G, King CL, Zheng YT, Zheng HY, Kimani J, Blake Ball T, Plummer FA, Fowke KR, Harden PN, Wood KJ, Ferris MT, Lund JM, Heise MT, Garrett N, Canady KR, Abdool Karim SS, Little SJ, Gianella S, Smith DM, Letendre S, Richman DD, Cucca F, Trinh H, Sanchez-Reilly S, Hecht JM, Cadena Zuluaga JA, Anzueto A, Pugh JA, Agan BK, Root-Bernstein R, Clark RA, Okulicz JF, He W. Immune resilience despite inflammatory stress promotes longevity and favorable health outcomes including resistance to infection. Nat Commun 2023; 14:3286. [PMID: 37311745 PMCID: PMC10264401 DOI: 10.1038/s41467-023-38238-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 04/17/2023] [Indexed: 06/15/2023] Open
Abstract
Some people remain healthier throughout life than others but the underlying reasons are poorly understood. Here we hypothesize this advantage is attributable in part to optimal immune resilience (IR), defined as the capacity to preserve and/or rapidly restore immune functions that promote disease resistance (immunocompetence) and control inflammation in infectious diseases as well as other causes of inflammatory stress. We gauge IR levels with two distinct peripheral blood metrics that quantify the balance between (i) CD8+ and CD4+ T-cell levels and (ii) gene expression signatures tracking longevity-associated immunocompetence and mortality-associated inflammation. Profiles of IR metrics in ~48,500 individuals collectively indicate that some persons resist degradation of IR both during aging and when challenged with varied inflammatory stressors. With this resistance, preservation of optimal IR tracked (i) a lower risk of HIV acquisition, AIDS development, symptomatic influenza infection, and recurrent skin cancer; (ii) survival during COVID-19 and sepsis; and (iii) longevity. IR degradation is potentially reversible by decreasing inflammatory stress. Overall, we show that optimal IR is a trait observed across the age spectrum, more common in females, and aligned with a specific immunocompetence-inflammation balance linked to favorable immunity-dependent health outcomes. IR metrics and mechanisms have utility both as biomarkers for measuring immune health and for improving health outcomes.
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Affiliation(s)
- Sunil K Ahuja
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA.
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA.
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
| | - Muthu Saravanan Manoharan
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Grace C Lee
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Pharmacotherapy Education and Research Center, School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- College of Pharmacy, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Lyle R McKinnon
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, 4001, South Africa
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Justin A Meunier
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
| | - Maristella Steri
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, 09042, Italy
| | - Nathan Harper
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
| | - Edoardo Fiorillo
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, 09042, Italy
| | - Alisha M Smith
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
| | - Marcos I Restrepo
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Anne P Branum
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
| | - Matthew J Bottomley
- Transplantation Research Immunology Group, Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX1 2JD, UK
- Oxford Kidney Unit, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK
| | - Valeria Orrù
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, 09042, Italy
| | - Fabio Jimenez
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
| | - Andrew Carrillo
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
| | - Lavanya Pandranki
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Caitlyn A Winter
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
- Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Lauryn A Winter
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
- Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Alvaro A Gaitan
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
| | - Alvaro G Moreira
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Elizabeth A Walter
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Guido Silvestri
- Department of Pathology, Emory University School of Medicine & Emory National Primate Research Center, Atlanta, GA, 30322, USA
| | - Christopher L King
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- National Resource Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650107, China
| | - Hong-Yi Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- National Resource Center for Non-Human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650107, China
| | - Joshua Kimani
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - T Blake Ball
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Francis A Plummer
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Keith R Fowke
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Paul N Harden
- Oxford Kidney Unit, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK
| | - Kathryn J Wood
- Transplantation Research Immunology Group, Nuffield Department of Surgical Sciences, University of Oxford, Oxford, OX1 2JD, UK
| | - Martin T Ferris
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jennifer M Lund
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Global Health, University of Washington, Seattle, WA, 98195, USA
| | - Mark T Heise
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Kristen R Canady
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, 4001, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | - Susan J Little
- Department of Medicine, University of California, La Jolla, CA, 92093, USA
- San Diego Center for AIDS Research, University of California San Diego, La Jolla, CA, 92093, USA
| | - Sara Gianella
- Department of Medicine, University of California, La Jolla, CA, 92093, USA
- San Diego Center for AIDS Research, University of California San Diego, La Jolla, CA, 92093, USA
| | - Davey M Smith
- Department of Medicine, University of California, La Jolla, CA, 92093, USA
- San Diego Center for AIDS Research, University of California San Diego, La Jolla, CA, 92093, USA
- Veterans Affairs San Diego Healthcare System, San Diego, CA, 92161, USA
| | - Scott Letendre
- Department of Medicine, University of California, La Jolla, CA, 92093, USA
| | - Douglas D Richman
- San Diego Center for AIDS Research, University of California San Diego, La Jolla, CA, 92093, USA
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Monserrato, 09042, Italy
- Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, 07100, Italy
| | - Hanh Trinh
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
| | - Sandra Sanchez-Reilly
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Joan M Hecht
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
| | - Jose A Cadena Zuluaga
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Antonio Anzueto
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Jacqueline A Pugh
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Brian K Agan
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | | | - Robert A Clark
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
| | - Jason F Okulicz
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Department of Medicine, Infectious Diseases Service, Brooke Army Medical Center, San Antonio, TX, 78234, USA
| | - Weijing He
- VA Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX, 78229, USA
- The Foundation for Advancing Veterans' Health Research, San Antonio, TX, 78229, USA
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7
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Lee D, Le Pen J, Yatim A, Dong B, Aquino Y, Ogishi M, Pescarmona R, Talouarn E, Rinchai D, Zhang P, Perret M, Liu Z, Jordan I, Elmas Bozdemir S, Bayhan GI, Beaufils C, Bizien L, Bisiaux A, Lei W, Hasan M, Chen J, Gaughan C, Asthana A, Libri V, Luna JM, Jaffré F, Hoffmann HH, Michailidis E, Moreews M, Seeleuthner Y, Bilguvar K, Mane S, Flores C, Zhang Y, Arias AA, Bailey R, Schlüter A, Milisavljevic B, Bigio B, Le Voyer T, Materna M, Gervais A, Moncada-Velez M, Pala F, Lazarov T, Levy R, Neehus AL, Rosain J, Peel J, Chan YH, Morin MP, Pino-Ramirez RM, Belkaya S, Lorenzo L, Anton J, Delafontaine S, Toubiana J, Bajolle F, Fumadó V, DeDiego ML, Fidouh N, Rozenberg F, Pérez-Tur J, Chen S, Evans T, Geissmann F, Lebon P, Weiss SR, Bonnet D, Duval X, Pan-Hammarström Q, Planas AM, Meyts I, Haerynck F, Pujol A, Sancho-Shimizu V, Dalgard CL, Bustamante J, Puel A, Boisson-Dupuis S, Boisson B, Maniatis T, Zhang Q, Bastard P, Notarangelo L, Béziat V, Perez de Diego R, Rodriguez-Gallego C, Su HC, Lifton RP, Jouanguy E, Cobat A, Alsina L, Keles S, Haddad E, Abel L, Belot A, Quintana-Murci L, Rice CM, Silverman RH, Zhang SY, Casanova JL. Inborn errors of OAS-RNase L in SARS-CoV-2-related multisystem inflammatory syndrome in children. Science 2023; 379:eabo3627. [PMID: 36538032 PMCID: PMC10451000 DOI: 10.1126/science.abo3627] [Citation(s) in RCA: 51] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 08/16/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
Multisystem inflammatory syndrome in children (MIS-C) is a rare and severe condition that follows benign COVID-19. We report autosomal recessive deficiencies of OAS1, OAS2, or RNASEL in five unrelated children with MIS-C. The cytosolic double-stranded RNA (dsRNA)-sensing OAS1 and OAS2 generate 2'-5'-linked oligoadenylates (2-5A) that activate the single-stranded RNA-degrading ribonuclease L (RNase L). Monocytic cell lines and primary myeloid cells with OAS1, OAS2, or RNase L deficiencies produce excessive amounts of inflammatory cytokines upon dsRNA or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) stimulation. Exogenous 2-5A suppresses cytokine production in OAS1-deficient but not RNase L-deficient cells. Cytokine production in RNase L-deficient cells is impaired by MDA5 or RIG-I deficiency and abolished by mitochondrial antiviral-signaling protein (MAVS) deficiency. Recessive OAS-RNase L deficiencies in these patients unleash the production of SARS-CoV-2-triggered, MAVS-mediated inflammatory cytokines by mononuclear phagocytes, thereby underlying MIS-C.
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Affiliation(s)
- Danyel Lee
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Jérémie Le Pen
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Ahmad Yatim
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Beihua Dong
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Yann Aquino
- Human Evolutionary Genetics Unit, Institut Pasteur, Paris City University, CNRS UMR 2000, Paris, France
- Doctoral College, Sorbonne University, Paris, France
| | - Masato Ogishi
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | | | - Estelle Talouarn
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Darawan Rinchai
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Magali Perret
- Laboratory of Immunology, Lyon Sud Hospital, Lyon, France
| | - Zhiyong Liu
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Iolanda Jordan
- Pediatric Intensive Care Department, Hospital Sant Joan de Déu, Barcelona, Spain
- Kids Corona Platform, Barcelona, Spain
- Center for Biomedical Network Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- Department of Surgery and Surgical Specializations, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
- Respiratory and Immunological Dysfunction in Pediatric Critically Ill Patients, Institute of Recerca Sant Joan de Déu, Barcelona, Spain
| | | | | | - Camille Beaufils
- Immunology and Rheumatology Division, Department of Pediatrics, University of Montreal, CHU Sainte-Justine, Montreal, QC, Canada
| | - Lucy Bizien
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Aurelie Bisiaux
- Human Evolutionary Genetics Unit, Institut Pasteur, Paris City University, CNRS UMR 2000, Paris, France
| | - Weite Lei
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Milena Hasan
- Center for Translational Research, Institut Pasteur, Paris City University, Paris, France
| | - Jie Chen
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Christina Gaughan
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Abhishek Asthana
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Valentina Libri
- Center for Translational Research, Institut Pasteur, Paris City University, Paris, France
| | - Joseph M. Luna
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
- Department of Biochemistry and Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH, USA
| | - Fabrice Jaffré
- Department of Surgery, Weill Cornell Medical College, New York, NY, USA
| | - H.-Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Eleftherios Michailidis
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Marion Moreews
- International Center of Infectiology Research (CIRI), University of Lyon, INSERM U1111, Claude Bernard University, Lyon 1, CNRS, UMR5308, ENS of Lyon, Lyon, France
| | - Yoann Seeleuthner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Kaya Bilguvar
- Departments of Neurosurgery and Genetics and Yale Center for Genome Analysis, Yale School of Medicine, New Haven, CT, USA
- Department of Medical Genetics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Shrikant Mane
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Carlos Flores
- Research Unit, Nuestra Señora de la Candelaria University Hospital, Santa Cruz de Tenerife, Spain
- Genomics Division, Institute of Technology and Renewable Energies (ITER), Granadilla de Abona, Spain
- CIBERES, ISCIII, Madrid, Spain
| | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
- NIAID Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
| | - Andrés A. Arias
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Primary Immunodeficiencies Group, University of Antioquia (UdeA), Medellin, Colombia
- School of Microbiology, University of Antioquia (UdeA), Medellin, Colombia
| | - Rasheed Bailey
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Agatha Schlüter
- Neurometabolic Diseases Laboratory, IDIBELL–Hospital Duran I Reynals, CIBERER U759, ISIiii, Madrid, Spain
| | - Baptiste Milisavljevic
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Benedetta Bigio
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Tom Le Voyer
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Marie Materna
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Adrian Gervais
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Marcela Moncada-Velez
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Francesca Pala
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
| | - Tomi Lazarov
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Romain Levy
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Anna-Lena Neehus
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Jérémie Rosain
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Jessica Peel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Yi-Hao Chan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Marie-Paule Morin
- Immunology and Rheumatology Division, Department of Pediatrics, University of Montreal, CHU Sainte-Justine, Montreal, QC, Canada
| | | | - Serkan Belkaya
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Lazaro Lorenzo
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jordi Anton
- Department of Surgery and Surgical Specializations, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
- Pediatric Rheumatology Division, Hospital Sant Joan de Déu, Barcelona, Spain
- Study Group for Immune Dysfunction Diseases in Children (GEMDIP), Institute of Recerca Sant Joan de Déu, Barcelona, Spain
| | | | - Julie Toubiana
- Department of General Pediatrics and Pediatric Infectious Diseases, Necker Hospital for Sick Children, Assistance Publique–Hôpitaux de Paris (AP-HP), Paris City University, Paris, France
- Biodiversity and Epidemiology of Bacterial Pathogens, Pasteur Institute, Paris, France
| | - Fanny Bajolle
- Department of Pediatric Cardiology, Necker Hospital for Sick Children, AP-HP, Paris City University, Paris, France
| | - Victoria Fumadó
- Kids Corona Platform, Barcelona, Spain
- Department of Surgery and Surgical Specializations, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
- Pediatrics Infectious Diseases Division, Hospital Sant Joan de Déu, Barcelona, Spain
- Infectious Diseases and Microbiome, Institute of Recerca Sant Joan de Déu, Barcelona, Spain
| | - Marta L. DeDiego
- Department of Molecular and Cellular Biology, National Center for Biotechnology (CNB-CSIC), Madrid, Spain
| | - Nadhira Fidouh
- Laboratory of Virology, Bichat–Claude Bernard Hospital, Paris, France
| | - Flore Rozenberg
- Laboratory of Virology, AP-HP, Cochin Hospital, Paris, France
| | - Jordi Pérez-Tur
- Molecular Genetics Unit, Institute of Biomedicine of Valencia (IBV-CSIC), Valencia, Spain
- CIBERNED, ISCIII, Madrid, Spain
- Joint Research Unit in Neurology and Molecular Genetics, Institut of Investigation Sanitaria La Fe, Valencia, Spain
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medical College, New York, NY, USA
| | - Todd Evans
- Department of Surgery, Weill Cornell Medical College, New York, NY, USA
| | - Frédéric Geissmann
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pierre Lebon
- Medical School, Paris City University, Paris, France
| | - Susan R. Weiss
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Damien Bonnet
- Department of Pediatric Cardiology, Necker Hospital for Sick Children, AP-HP, Paris City University, Paris, France
| | - Xavier Duval
- Bichat–Claude Bernard Hospital, Paris, France
- University Paris Diderot, Paris 7, UFR of Médecine-Bichat, Paris, France
- IAME, INSERM, UMRS1137, Paris City University, Paris, France
- Infectious and Tropical Diseases Department, AP-HP, Bichat–Claude Bernard Hospital, Paris, France
| | - CoV-Contact Cohort§
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Human Evolutionary Genetics Unit, Institut Pasteur, Paris City University, CNRS UMR 2000, Paris, France
- Doctoral College, Sorbonne University, Paris, France
- Laboratory of Immunology, Lyon Sud Hospital, Lyon, France
- Pediatric Intensive Care Department, Hospital Sant Joan de Déu, Barcelona, Spain
- Kids Corona Platform, Barcelona, Spain
- Center for Biomedical Network Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- Department of Surgery and Surgical Specializations, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
- Respiratory and Immunological Dysfunction in Pediatric Critically Ill Patients, Institute of Recerca Sant Joan de Déu, Barcelona, Spain
- Bursa City Hospital, Bursa, Turkey
- Ankara City Hospital, Yildirim Beyazit University, Ankara, Turkey
- Immunology and Rheumatology Division, Department of Pediatrics, University of Montreal, CHU Sainte-Justine, Montreal, QC, Canada
- Center for Translational Research, Institut Pasteur, Paris City University, Paris, France
- Department of Biochemistry and Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH, USA
- Department of Surgery, Weill Cornell Medical College, New York, NY, USA
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
- International Center of Infectiology Research (CIRI), University of Lyon, INSERM U1111, Claude Bernard University, Lyon 1, CNRS, UMR5308, ENS of Lyon, Lyon, France
- Departments of Neurosurgery and Genetics and Yale Center for Genome Analysis, Yale School of Medicine, New Haven, CT, USA
- Department of Medical Genetics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Research Unit, Nuestra Señora de la Candelaria University Hospital, Santa Cruz de Tenerife, Spain
- Genomics Division, Institute of Technology and Renewable Energies (ITER), Granadilla de Abona, Spain
- CIBERES, ISCIII, Madrid, Spain
- Department of Clinical Sciences, University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
- NIAID Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
- Primary Immunodeficiencies Group, University of Antioquia (UdeA), Medellin, Colombia
- School of Microbiology, University of Antioquia (UdeA), Medellin, Colombia
- Neurometabolic Diseases Laboratory, IDIBELL–Hospital Duran I Reynals, CIBERER U759, ISIiii, Madrid, Spain
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Pediatrics Department, Hospital Sant Joan de Déu, Barcelona, Spain
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
- Pediatric Rheumatology Division, Hospital Sant Joan de Déu, Barcelona, Spain
- Study Group for Immune Dysfunction Diseases in Children (GEMDIP), Institute of Recerca Sant Joan de Déu, Barcelona, Spain
- Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium
- Department of General Pediatrics and Pediatric Infectious Diseases, Necker Hospital for Sick Children, Assistance Publique–Hôpitaux de Paris (AP-HP), Paris City University, Paris, France
- Biodiversity and Epidemiology of Bacterial Pathogens, Pasteur Institute, Paris, France
- Department of Pediatric Cardiology, Necker Hospital for Sick Children, AP-HP, Paris City University, Paris, France
- Pediatrics Infectious Diseases Division, Hospital Sant Joan de Déu, Barcelona, Spain
- Infectious Diseases and Microbiome, Institute of Recerca Sant Joan de Déu, Barcelona, Spain
- Department of Molecular and Cellular Biology, National Center for Biotechnology (CNB-CSIC), Madrid, Spain
- Laboratory of Virology, Bichat–Claude Bernard Hospital, Paris, France
- Laboratory of Virology, AP-HP, Cochin Hospital, Paris, France
- Molecular Genetics Unit, Institute of Biomedicine of Valencia (IBV-CSIC), Valencia, Spain
- CIBERNED, ISCIII, Madrid, Spain
- Joint Research Unit in Neurology and Molecular Genetics, Institut of Investigation Sanitaria La Fe, Valencia, Spain
- Medical School, Paris City University, Paris, France
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Bichat–Claude Bernard Hospital, Paris, France
- University Paris Diderot, Paris 7, UFR of Médecine-Bichat, Paris, France
- IAME, INSERM, UMRS1137, Paris City University, Paris, France
- Infectious and Tropical Diseases Department, AP-HP, Bichat–Claude Bernard Hospital, Paris, France
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Department of Neuroscience and Experimental Therapeutics, Institute for Biomedical Research of Barcelona (IIBB), Spanish National Research Council (CSIC), Barcelona, Spain
- Institute for Biomedical Investigations August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Department of Pediatrics, University Hospitals Leuven and Laboratory for Inborn Errors of Immunity, KU Leuven, Leuven, Belgium
- Primary Immunodeficiency Research Laboratory, Center for Primary Immunodeficiency Ghent, Ghent University Hospital, Ghent, Belgium
- Neurometabolic Diseases Laboratory, IDIBELL–Hospital Duran I Reynals; and Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
- CIBERER U759, ISCiii, Madrid, Spain
- Department of Paediatric Infectious Diseases and Virology, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London, UK
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Department of Anatomy, Physiology, and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Study Center for Primary Immunodeficiencies, Necker Hospital for Sick Children, AP-HP, Paris, France
- New York Genome Center, New York, NY, USA
- Pediatric Hematology-Immunology and Rheumatology Unit, Necker Hospital for Sick Children, AP-HP, Paris, France
- Laboratory of Immunogenetics of Human Diseases, Innate Immunity Group, IdiPAZ Institute for Health Research, La Paz Hospital, Madrid, Spain
- Interdepartmental Group of Immunodeficiencies, Madrid, Spain
- Department of Immunology, University Hospital of Gran Canaria Dr. Negrín, Canarian Health System, Las Palmas de Gran Canaria, Spain
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
- Clinical Immunology and Primary Immunodeficiencies Unit, Pediatric Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu, Barcelona, Spain
- Necmettin Erbakan University, Konya, Turkey
- Department of Pediatrics, Department of Microbiology, Immunology and Infectious Diseases, University of Montreal and Immunology and Rheumatology Division, CHU Sainte-Justine, Montreal, QC, Canada
- National Reference Center for Rheumatic, Autoimmune and Systemic Diseases in Children (RAISE), Pediatric Nephrology, Rheumatology, Dermatology Unit, Hospital of Mother and Child, Hospices Civils of Lyon, Lyon, France
- Human Genomics and Evolution, Collège de France, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - COVID Human Genetic Effort¶
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Human Evolutionary Genetics Unit, Institut Pasteur, Paris City University, CNRS UMR 2000, Paris, France
- Doctoral College, Sorbonne University, Paris, France
- Laboratory of Immunology, Lyon Sud Hospital, Lyon, France
- Pediatric Intensive Care Department, Hospital Sant Joan de Déu, Barcelona, Spain
- Kids Corona Platform, Barcelona, Spain
- Center for Biomedical Network Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- Department of Surgery and Surgical Specializations, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
- Respiratory and Immunological Dysfunction in Pediatric Critically Ill Patients, Institute of Recerca Sant Joan de Déu, Barcelona, Spain
- Bursa City Hospital, Bursa, Turkey
- Ankara City Hospital, Yildirim Beyazit University, Ankara, Turkey
- Immunology and Rheumatology Division, Department of Pediatrics, University of Montreal, CHU Sainte-Justine, Montreal, QC, Canada
- Center for Translational Research, Institut Pasteur, Paris City University, Paris, France
- Department of Biochemistry and Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH, USA
- Department of Surgery, Weill Cornell Medical College, New York, NY, USA
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
- International Center of Infectiology Research (CIRI), University of Lyon, INSERM U1111, Claude Bernard University, Lyon 1, CNRS, UMR5308, ENS of Lyon, Lyon, France
- Departments of Neurosurgery and Genetics and Yale Center for Genome Analysis, Yale School of Medicine, New Haven, CT, USA
- Department of Medical Genetics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Research Unit, Nuestra Señora de la Candelaria University Hospital, Santa Cruz de Tenerife, Spain
- Genomics Division, Institute of Technology and Renewable Energies (ITER), Granadilla de Abona, Spain
- CIBERES, ISCIII, Madrid, Spain
- Department of Clinical Sciences, University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
- NIAID Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
- Primary Immunodeficiencies Group, University of Antioquia (UdeA), Medellin, Colombia
- School of Microbiology, University of Antioquia (UdeA), Medellin, Colombia
- Neurometabolic Diseases Laboratory, IDIBELL–Hospital Duran I Reynals, CIBERER U759, ISIiii, Madrid, Spain
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Pediatrics Department, Hospital Sant Joan de Déu, Barcelona, Spain
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
- Pediatric Rheumatology Division, Hospital Sant Joan de Déu, Barcelona, Spain
- Study Group for Immune Dysfunction Diseases in Children (GEMDIP), Institute of Recerca Sant Joan de Déu, Barcelona, Spain
- Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium
- Department of General Pediatrics and Pediatric Infectious Diseases, Necker Hospital for Sick Children, Assistance Publique–Hôpitaux de Paris (AP-HP), Paris City University, Paris, France
- Biodiversity and Epidemiology of Bacterial Pathogens, Pasteur Institute, Paris, France
- Department of Pediatric Cardiology, Necker Hospital for Sick Children, AP-HP, Paris City University, Paris, France
- Pediatrics Infectious Diseases Division, Hospital Sant Joan de Déu, Barcelona, Spain
- Infectious Diseases and Microbiome, Institute of Recerca Sant Joan de Déu, Barcelona, Spain
- Department of Molecular and Cellular Biology, National Center for Biotechnology (CNB-CSIC), Madrid, Spain
- Laboratory of Virology, Bichat–Claude Bernard Hospital, Paris, France
- Laboratory of Virology, AP-HP, Cochin Hospital, Paris, France
- Molecular Genetics Unit, Institute of Biomedicine of Valencia (IBV-CSIC), Valencia, Spain
- CIBERNED, ISCIII, Madrid, Spain
- Joint Research Unit in Neurology and Molecular Genetics, Institut of Investigation Sanitaria La Fe, Valencia, Spain
- Medical School, Paris City University, Paris, France
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Bichat–Claude Bernard Hospital, Paris, France
- University Paris Diderot, Paris 7, UFR of Médecine-Bichat, Paris, France
- IAME, INSERM, UMRS1137, Paris City University, Paris, France
- Infectious and Tropical Diseases Department, AP-HP, Bichat–Claude Bernard Hospital, Paris, France
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Department of Neuroscience and Experimental Therapeutics, Institute for Biomedical Research of Barcelona (IIBB), Spanish National Research Council (CSIC), Barcelona, Spain
- Institute for Biomedical Investigations August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Department of Pediatrics, University Hospitals Leuven and Laboratory for Inborn Errors of Immunity, KU Leuven, Leuven, Belgium
- Primary Immunodeficiency Research Laboratory, Center for Primary Immunodeficiency Ghent, Ghent University Hospital, Ghent, Belgium
- Neurometabolic Diseases Laboratory, IDIBELL–Hospital Duran I Reynals; and Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
- CIBERER U759, ISCiii, Madrid, Spain
- Department of Paediatric Infectious Diseases and Virology, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London, UK
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Department of Anatomy, Physiology, and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Study Center for Primary Immunodeficiencies, Necker Hospital for Sick Children, AP-HP, Paris, France
- New York Genome Center, New York, NY, USA
- Pediatric Hematology-Immunology and Rheumatology Unit, Necker Hospital for Sick Children, AP-HP, Paris, France
- Laboratory of Immunogenetics of Human Diseases, Innate Immunity Group, IdiPAZ Institute for Health Research, La Paz Hospital, Madrid, Spain
- Interdepartmental Group of Immunodeficiencies, Madrid, Spain
- Department of Immunology, University Hospital of Gran Canaria Dr. Negrín, Canarian Health System, Las Palmas de Gran Canaria, Spain
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
- Clinical Immunology and Primary Immunodeficiencies Unit, Pediatric Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu, Barcelona, Spain
- Necmettin Erbakan University, Konya, Turkey
- Department of Pediatrics, Department of Microbiology, Immunology and Infectious Diseases, University of Montreal and Immunology and Rheumatology Division, CHU Sainte-Justine, Montreal, QC, Canada
- National Reference Center for Rheumatic, Autoimmune and Systemic Diseases in Children (RAISE), Pediatric Nephrology, Rheumatology, Dermatology Unit, Hospital of Mother and Child, Hospices Civils of Lyon, Lyon, France
- Human Genomics and Evolution, Collège de France, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | | | - Anna M. Planas
- Department of Neuroscience and Experimental Therapeutics, Institute for Biomedical Research of Barcelona (IIBB), Spanish National Research Council (CSIC), Barcelona, Spain
- Institute for Biomedical Investigations August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Isabelle Meyts
- Department of Pediatrics, University Hospitals Leuven and Laboratory for Inborn Errors of Immunity, KU Leuven, Leuven, Belgium
| | - Filomeen Haerynck
- Primary Immunodeficiency Research Laboratory, Center for Primary Immunodeficiency Ghent, Ghent University Hospital, Ghent, Belgium
| | - Aurora Pujol
- Neurometabolic Diseases Laboratory, IDIBELL–Hospital Duran I Reynals; and Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
- CIBERER U759, ISCiii, Madrid, Spain
| | - Vanessa Sancho-Shimizu
- Department of Paediatric Infectious Diseases and Virology, Imperial College London, London, UK
- Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London, UK
| | - Clifford L. Dalgard
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Department of Anatomy, Physiology, and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jacinta Bustamante
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
- Study Center for Primary Immunodeficiencies, Necker Hospital for Sick Children, AP-HP, Paris, France
| | - Anne Puel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Stéphanie Boisson-Dupuis
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | | | - Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Paul Bastard
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
- Pediatric Hematology-Immunology and Rheumatology Unit, Necker Hospital for Sick Children, AP-HP, Paris, France
| | - Luigi Notarangelo
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
| | - Vivien Béziat
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Rebeca Perez de Diego
- Laboratory of Immunogenetics of Human Diseases, Innate Immunity Group, IdiPAZ Institute for Health Research, La Paz Hospital, Madrid, Spain
- Interdepartmental Group of Immunodeficiencies, Madrid, Spain
| | - Carlos Rodriguez-Gallego
- Department of Clinical Sciences, University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
- Department of Immunology, University Hospital of Gran Canaria Dr. Negrín, Canarian Health System, Las Palmas de Gran Canaria, Spain
| | - Helen C. Su
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
- NIAID Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA
| | - Richard P. Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Emmanuelle Jouanguy
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Aurélie Cobat
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Laia Alsina
- Kids Corona Platform, Barcelona, Spain
- Department of Surgery and Surgical Specializations, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
- Study Group for Immune Dysfunction Diseases in Children (GEMDIP), Institute of Recerca Sant Joan de Déu, Barcelona, Spain
- Clinical Immunology and Primary Immunodeficiencies Unit, Pediatric Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu, Barcelona, Spain
| | | | - Elie Haddad
- Department of Pediatrics, Department of Microbiology, Immunology and Infectious Diseases, University of Montreal and Immunology and Rheumatology Division, CHU Sainte-Justine, Montreal, QC, Canada
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Alexandre Belot
- International Center of Infectiology Research (CIRI), University of Lyon, INSERM U1111, Claude Bernard University, Lyon 1, CNRS, UMR5308, ENS of Lyon, Lyon, France
- National Reference Center for Rheumatic, Autoimmune and Systemic Diseases in Children (RAISE), Pediatric Nephrology, Rheumatology, Dermatology Unit, Hospital of Mother and Child, Hospices Civils of Lyon, Lyon, France
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Institut Pasteur, Paris City University, CNRS UMR 2000, Paris, France
- Human Genomics and Evolution, Collège de France, Paris, France
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Robert H. Silverman
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Shen-Ying Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Paris City University, Imagine Institute, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
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8
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Vavougios GD, de Erausquin GA, Snyder HM. Type I interferon signaling in SARS-CoV-2 associated neurocognitive disorder (SAND): Mapping host-virus interactions to an etiopathogenesis. Front Neurol 2022; 13:1063298. [PMID: 36570454 PMCID: PMC9771386 DOI: 10.3389/fneur.2022.1063298] [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: 10/06/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022] Open
Abstract
Epidemiological, clinical, and radiological studies have provided insights into the phenomenology and biological basis of cognitive impairment in COVID-19 survivors. Furthermore, its association with biomarkers associated with neuroinflammation and neurodegeneration supports the notion that it is a distinct aspect of LongCOVID syndrome with specific underlying biology. Accounting for the latter, translational studies on SARS-CoV-2's interactions with its hosts have provided evidence on type I interferon dysregulation, which is seen in neuroinflammatory and neurodegenerative diseases. To date, studies attempting to describe this overlap have only described common mechanisms. In this manuscript, we attempt to propose a mechanistic model based on the host-virus interaction hypothesis. We discuss the molecular basis for a SARS-CoV-2-associated neurocognitive disorder (SAND) focusing on specific genes and pathways with potential mechanistic implications, several of which have been predicted by Vavougios and their research group. Furthermore, our hypothesis links translational evidence on interferon-responsive gene perturbations introduced by SARS-CoV-2 and known dysregulated pathways in dementia. Discussion emphasizes the crosstalk between central and peripheral immunity via danger-associated molecular patterns in inducing SAND's emergence in the absence of neuroinfection. Finally, we outline approaches to identifying targets that are both testable and druggable, and could serve in the design of future clinical and translational studies.
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Affiliation(s)
- George D. Vavougios
- Department of Neurology, University of Cyprus, Lefkosia, Cyprus,Department of Respiratory Medicine, University of Thessaly, Larisa, Greece,*Correspondence: George D. Vavougios ;
| | - Gabriel A. de Erausquin
- The Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, UTHSA, San Antonio, TX, United States
| | - Heather M. Snyder
- Division of Medical and Scientific Relations, Alzheimer's Association, Chicago, IL, United States
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9
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van der Made CI, Netea MG, van der Veerdonk FL, Hoischen A. Clinical implications of host genetic variation and susceptibility to severe or critical COVID-19. Genome Med 2022; 14:96. [PMID: 35986347 PMCID: PMC9390103 DOI: 10.1186/s13073-022-01100-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 08/03/2022] [Indexed: 01/08/2023] Open
Abstract
Since the start of the coronavirus disease 2019 (COVID-19) pandemic, important insights have been gained into virus biology and the host factors that modulate the human immune response against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 displays a highly variable clinical picture that ranges from asymptomatic disease to lethal pneumonia. Apart from well-established general risk factors such as advanced age, male sex and chronic comorbidities, differences in host genetics have been shown to influence the individual predisposition to develop severe manifestations of COVID-19. These differences range from common susceptibility loci to rare genetic variants with strongly predisposing effects, or proven pathogenic variants that lead to known or novel inborn errors of immunity (IEI), which constitute a growing group of heterogeneous Mendelian disorders with increased susceptibility to infectious disease, auto-inflammation, auto-immunity, allergy or malignancies. The current genetic findings point towards a convergence of common and rare genetic variants that impact the interferon signalling pathways in patients with severe or critical COVID-19. Monogenic risk factors that impact IFN-I signalling have an expected prevalence between 1 and 5% in young, previously healthy individuals (<60 years of age) with critical COVID-19. The identification of these IEI such as X-linked TLR7 deficiency indicates a possibility for targeted genetic screening and personalized clinical management. This review aims to provide an overview of our current understanding of the host genetic factors that predispose to severe manifestations of COVID-19 and focuses on rare variants in IFN-I signalling genes and their potential clinical implications.
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10
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M M, F C, M G, S F, A B. How to: diagnose inborn errors of intrinsic and innate immunity to viral, bacterial, mycobacterial and fungal infections. Clin Microbiol Infect 2022; 28:1441-1448. [DOI: 10.1016/j.cmi.2022.07.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 07/04/2022] [Accepted: 07/23/2022] [Indexed: 11/03/2022]
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11
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Virus Infection and Systemic Inflammation: Lessons Learnt from COVID-19 and Beyond. Cells 2022; 11:cells11142198. [PMID: 35883640 PMCID: PMC9316821 DOI: 10.3390/cells11142198] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/28/2022] [Accepted: 07/09/2022] [Indexed: 02/06/2023] Open
Abstract
Respiratory infections with newly emerging zoonotic viruses such as SARS-CoV-2, the etiological agent of COVID-19, often lead to the perturbation of the human innate and adaptive immune responses causing severe disease with high mortality. The responsible mechanisms are commonly virus-specific and often include either over-activated or delayed local interferon responses, which facilitate efficient viral replication in the primary target organ, systemic viral spread, and rapid onset of organ-specific and harmful inflammatory responses. Despite the distinct replication strategies, human infections with SARS-CoV-2 and highly pathogenic avian influenza viruses demonstrate remarkable similarities and differences regarding the mechanisms of immune induction, disease dynamics, as well as the long-term sequelae, which will be discussed in this review. In addition, we will highlight some important lessons about the effectiveness of antiviral and immunomodulatory therapeutic strategies that this pandemic has taught us.
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12
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Redin C, Thorball CW, Fellay J. Host genomics of SARS-CoV-2 infection. Eur J Hum Genet 2022; 30:908-914. [PMID: 35768520 PMCID: PMC9244159 DOI: 10.1038/s41431-022-01136-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/02/2022] [Accepted: 06/13/2022] [Indexed: 01/08/2023] Open
Abstract
SARS-CoV-2 infected a large fraction of humans in the past 2 years. The clinical presentation of acute infection varies greatly between individuals, ranging from asymptomatic or mild to life-threatening COVID-19 pneumonia with multi-organ complications. Demographic and comorbid factors explain part of this variability, yet it became clear early in the pandemic that human genetic variation also plays a role in the stark differences observed amongst SARS-CoV-2 infected individuals. Using tools and approaches successfully developed for human genomic studies in the previous decade, large international collaborations embarked in the exploration of the genetic determinants of multiple outcomes of SARS-CoV-2 infection, with a special emphasis on disease severity. Genome-wide association studies identified multiple common genetic variants associated with COVID-19 pneumonia, most of which in regions encoding genes with known or suspected immune function. However, the downstream, functional work required to understand the precise causal variants at each locus has only begun. The interrogation of rare genetic variants using targeted, exome, or genome sequencing approaches has shown that defects in genes involved in type I interferon response explain some of the most severe cases. By highlighting genes and pathways involved in SARS-CoV-2 pathogenesis and host-virus interactions, human genomic studies not only revealed novel preventive and therapeutic targets, but also paved the way for more individualized disease management.
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Affiliation(s)
- Claire Redin
- Precision Medicine Unit, Biomedical Data Science Center, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Christian W Thorball
- Precision Medicine Unit, Biomedical Data Science Center, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Jacques Fellay
- Precision Medicine Unit, Biomedical Data Science Center, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland. .,School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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13
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Guerrero‐Preston R, Rivera‐Amill V, Caraballo K, Rodríguez‐Torres S, Purcell‐Wiltz A, García AA, Torres RS, Zamuner FT, Zanettini C, MacKay MJ, Baits R, Salgado D, Khullar G, Metti J, Baker T, Dudley J, Vale K, Pérez G, De Jesús L, Miranda Y, Ortiz D, García‐Negrón A, Viera L, Ortiz A, Canabal JA, Romaguera J, Jiménez‐Velázquez I, Marchionni L, Rodríguez‐Orengo JF, Baez A, Mason CE, Sidransky D. Precision health diagnostic and surveillance network uses
S
gene target failure (SGTF) combined with sequencing technologies to track emerging SARS‐CoV‐2 variants. Immun Inflamm Dis 2022; 10:e634. [PMID: 35634961 PMCID: PMC9092005 DOI: 10.1002/iid3.634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 11/23/2022] Open
Abstract
Introduction The severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) pandemic revealed a worldwide lack of effective molecular surveillance networks at local, state, and national levels, which are essential to identify, monitor, and limit viral community spread. SARS‐CoV‐2 variants of concern (VOCs) such as Alpha and Omicron, which show increased transmissibility and immune evasion, rapidly became dominant VOCs worldwide. Our objective was to develop an evidenced‐based genomic surveillance algorithm, combining reverse transcription polymerase chain reaction (RT‐PCR) and sequencing technologies to quickly identify highly contagious VOCs, before cases accumulate exponentially. Methods Deidentified data were obtained from 508,969 patients tested for coronavirus disease 2019 (COVID‐19) with the TaqPath COVID‐19 RT‐PCR Combo Kit (ThermoFisher) in four CLIA‐certified clinical laboratories in Puerto Rico (n = 86,639) and in three CLIA‐certified clinical laboratories in the United States (n = 422,330). Results TaqPath data revealed a frequency of S Gene Target Failure (SGTF) > 47% for the last week of March 2021 in both, Puerto Rico and US laboratories. The monthly frequency of SGTF in Puerto Rico steadily increased exponentially from 4% in November 2020 to 47% in March 2021. The weekly SGTF rate in US samples was high (>8%) from late December to early January and then also increased exponentially through April (48%). The exponential increase in SGFT prevalence in Puerto Rico was concurrent with a sharp increase in VOCs among all SARS‐CoV‐2 sequences from Puerto Rico uploaded to Global Influenza Surveillance and Response System (GISAID) (n = 461). Alpha variant frequency increased from <1% in the last week of January 2021 to 51.5% of viral sequences from Puerto Rico collected in the last week of March 2021. Conclusions According to the proposed evidence‐based algorithm, approximately 50% of all SGTF patients should be managed with VOCs self‐quarantine and contact tracing protocols, while WGS confirms their lineage in genomic surveillance laboratories. Our results suggest this workflow is useful for tracking VOCs with SGTF.
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Affiliation(s)
| | - Vanessa Rivera‐Amill
- Center for Research Resources Ponce Health Sciences University‐Ponce Research Institute Ponce Puerto Rico
| | | | | | - Ana Purcell‐Wiltz
- LifeGene‐Biomarks, Inc San Juan Puerto Rico
- Biology Department University of Puerto Rico Río Piedras Puerto Rico
| | - Andrea A. García
- Center for Research Resources Ponce Health Sciences University‐Ponce Research Institute Ponce Puerto Rico
| | - Raphael S. Torres
- Center for Research Resources Ponce Health Sciences University‐Ponce Research Institute Ponce Puerto Rico
| | - Fernando T. Zamuner
- Department of Otolaryngology‐Head and Neck Surgery Johns Hopkins University School of Medicine Baltimore Maryland USA
| | - Claudio Zanettini
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine Cornell University New York New York USA
| | | | | | | | | | | | | | | | | | - Gabriela Pérez
- Neurology Medicine Department Palmetto General Hospital Miami Florida USA
| | | | | | | | | | - Liliana Viera
- Department of Surgery University of Puerto Rico School of Medicine San Juan Puerto Rico
| | - Alberto Ortiz
- Internal Medicine Department University of Puerto Rico School of Medicine San Juan Puerto Rico
| | - Jorge A. Canabal
- Internal Medicine Department University of Puerto Rico School of Medicine San Juan Puerto Rico
| | - Josefina Romaguera
- Obstetrics and Gynecology Department University of Puerto Rico School of Medicine San Juan Puerto Rico
| | | | - Luigi Marchionni
- Department of Otolaryngology‐Head and Neck Surgery Johns Hopkins University School of Medicine Baltimore Maryland USA
| | | | - Adriana Baez
- Otolaryngology Department University of Puerto Rico School of Medicine San Juan Puerto Rico
| | | | - David Sidransky
- Department of Otolaryngology‐Head and Neck Surgery Johns Hopkins University School of Medicine Baltimore Maryland USA
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14
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Liu P, Fang M, Luo Y, Zheng F, Jin Y, Cheng F, Zhu H, Jin X. Rare Variants in Inborn Errors of Immunity Genes Associated With Covid-19 Severity. Front Cell Infect Microbiol 2022; 12:888582. [PMID: 35694544 PMCID: PMC9184678 DOI: 10.3389/fcimb.2022.888582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/21/2022] [Indexed: 01/08/2023] Open
Abstract
Host genetic factors have been shown to play an important role in SARS-CoV-2 infection and the course of Covid-19 disease. The genetic contributions of common variants influencing Covid-19 susceptibility and severity have been extensively studied in diverse populations. However, the studies of rare genetic defects arising from inborn errors of immunity (IEI) are relatively few, especially in the Chinese population. To fill this gap, we used a deeply sequenced dataset of nearly 500 patients, all of Chinese descent, to investigate putative functional rare variants. Specifically, we annotated rare variants in our call set and selected likely deleterious missense (LDM) and high-confidence predicted loss-of-function (HC-pLoF) variants. Further, we analyzed LDM and HC-pLoF variants between non-severe and severe Covid-19 patients by (a) performing gene- and pathway-level association analyses, (b) testing the number of mutations in previously reported genes mapped from LDM and HC-pLoF variants, and (c) uncovering candidate genes via protein-protein interaction (PPI) network analysis of Covid-19-related genes and genes defined from LDM and HC-pLoF variants. From our analyses, we found that (a) pathways Tuberculosis (hsa:05152), Primary Immunodeficiency (hsa:05340), and Influenza A (hsa:05164) showed significant enrichment in severe patients compared to the non-severe ones, (b) HC-pLoF mutations were enriched in Covid-19-related genes in severe patients, and (c) several candidate genes, such as IL12RB1, TBK1, TLR3, and IFNGR2, are uncovered by PPI network analysis and worth further investigation. These regions generally play an essential role in regulating antiviral innate immunity responses to foreign pathogens and in responding to many inflammatory diseases. We believe that our identified candidate genes/pathways can be potentially used as Covid-19 diagnostic markers and help distinguish patients at higher risk.
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Affiliation(s)
- Panhong Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Beijing Genomeics Institute At Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Mingyan Fang
- Beijing Genomeics Institute At Shenzhen, BGI-Shenzhen, Shenzhen, China
- Beijing Genomeics Institute In Singapore, BGI-Singapore, Singapore, Singapore
| | - Yuxue Luo
- Beijing Genomeics Institute At Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Fang Zheng
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yan Jin
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fanjun Cheng
- Department of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huanhuan Zhu
- Beijing Genomeics Institute At Shenzhen, BGI-Shenzhen, Shenzhen, China
- *Correspondence: Xin Jin, ; Huanhuan Zhu,
| | - Xin Jin
- Beijing Genomeics Institute At Shenzhen, BGI-Shenzhen, Shenzhen, China
- Beijing Genomeics Institute In Singapore, BGI-Singapore, Singapore, Singapore
- School of Medicine, South China University of Technology, Guangzhou, China
- *Correspondence: Xin Jin, ; Huanhuan Zhu,
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15
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Youssry I, Abd Elaziz D, Ayad N, Eyada I. The Cause–Effect Dilemma of Hematologic Changes in COVID-19: One Year after the Start of the Pandemic. Hematol Rep 2022; 14:95-102. [PMID: 35466178 PMCID: PMC9036247 DOI: 10.3390/hematolrep14020014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/19/2022] [Accepted: 03/24/2022] [Indexed: 01/08/2023] Open
Abstract
COVID-19 is a systemic infection that leads to multisystem affection, including hematological changes. On the other hand, the patients who have certain hematological diseases are more susceptible to COVID-19 infection. The aim of this review is to examine the wide spectrum of hematological changes that are reported to occur due to COVID-19 infection. Most of the studies over the past year mainly show that most of these changes are mainly non-specific, but are of prognostic value. On the other hand, the susceptibility of hematological patients to COVID-19 infection and complications remains questionable. Patients with certain hematological diseases (including malignancy) and those who are treated by aggressive immunosuppressive therapy have shown higher rates of COVID-19 infection and complications. On the other hand, for most of the patients suffering from other chronic hematological conditions, no evidence has shown a greater risk of infection, compared to the general population.
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Affiliation(s)
- Ilham Youssry
- Pediatric Hematology and BMT Unit, Cairo University, Giza 12613, Egypt;
| | - Dalia Abd Elaziz
- Pediatric Department, Faculty of Medicine, Cairo University, Giza 12211, Egypt; (D.A.E.); (I.E.)
| | - Nardeen Ayad
- Pediatric Hematology and BMT Unit, Cairo University, Giza 12613, Egypt;
- Correspondence:
| | - Iman Eyada
- Pediatric Department, Faculty of Medicine, Cairo University, Giza 12211, Egypt; (D.A.E.); (I.E.)
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16
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Novel prognostic determinants of COVID-19-related mortality: A pilot study on severely-ill patients in Russia. PLoS One 2022; 17:e0264072. [PMID: 35213582 PMCID: PMC8880431 DOI: 10.1371/journal.pone.0264072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 02/02/2022] [Indexed: 12/12/2022] Open
Abstract
COVID-19 pandemic has posed a severe healthcare challenge calling for an integrated approach in determining the clues for early non-invasive diagnostics of the potentially severe cases and efficient patient stratification. Here we analyze the clinical, laboratory and CT scan characteristics associated with high risk of COVID-19-related death outcome in the cohort of severely-ill patients in Russia. The data obtained reveal that elevated dead lymphocyte counts, decreased early apoptotic lymphocytes, decreased CD14+/HLA-Dr+ monocytes, increased expression of JNK in PBMCs, elevated IL-17 and decreased PAI-1 serum levels are associated with a high risk of COVID-19-related mortality thus suggesting them to be new prognostic factors. This set of determinants could be used as early predictors of potentially severe course of COVID-19 for trials of prevention or timely treatment.
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17
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Bastard P, Zhang Q, Zhang SY, Jouanguy E, Casanova JL. Type I interferons and SARS-CoV-2: from cells to organisms. Curr Opin Immunol 2022; 74:172-182. [PMID: 35149239 PMCID: PMC8786610 DOI: 10.1016/j.coi.2022.01.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 01/12/2022] [Accepted: 01/15/2022] [Indexed: 02/06/2023]
Abstract
Type I interferons (IFNs) have broad and potent antiviral activity. We review the interplay between type I IFNs and SARS-CoV-2. Human cells infected with SARS-CoV-2 in vitro produce low levels of type I IFNs, and SARS-CoV-2 proteins can inhibit various steps in type I IFN production and response. Exogenous type I IFNs inhibit viral growth in vitro. In various animal species infected in vivo, type I IFN deficiencies underlie higher viral loads and more severe disease than in control animals. The early administration of exogenous type I IFNs improves infection control. In humans, inborn errors of, and auto-antibodies against type I IFNs underlie life-threatening COVID-19 pneumonia. Overall, type I IFNs are essential for host defense against SARS-CoV-2 in individual cells and whole organisms.
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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 of Paris, 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, AP-HP, Paris, France.
| | - Qian Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; University of Paris, 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 of Paris, 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 of Paris, 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 of Paris, 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, AP-HP, Paris, France; Howard Hughes Medical Institute, New York, NY, USA.
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18
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Human genetic and immunological determinants of critical COVID-19 pneumonia. Nature 2022; 603:587-598. [PMID: 35090163 DOI: 10.1038/s41586-022-04447-0] [Citation(s) in RCA: 193] [Impact Index Per Article: 96.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/19/2022] [Indexed: 11/08/2022]
Abstract
SARS-CoV-2 infection is benign in most individuals but, in ˜10% of cases, it triggers hypoxemic COVID-19 pneumonia, which becomes critical in ˜3% of cases. The ensuing risk of death (˜1%) doubles every five years from childhood onward and is ˜1.5 times greater in men than in women. What are the molecular and cellular determinants of critical COVID-19 pneumonia? Inborn errors of type I IFNs, including autosomal TLR3 and X-linked TLR7 deficiencies, are found in ˜1-5% of patients with critical pneumonia under 60 years old, and a lower proportion in older patients. Pre-existing autoantibodies neutralizing IFN-α, -β, and/or -ω, which are more common in men than in women, are found in ˜15-20% of patients with critical pneumonia over 70 years old, and a lower proportion in younger patients. Thus, at least 15% of cases of critical COVID-19 pneumonia can apparently be explained. The TLR3- and TLR7-dependent production of type I IFNs by respiratory epithelial cells and plasmacytoid dendritic cells, respectively, is essential for host defense against SARS-CoV-2. In ways that can depend on age and sex, insufficient type I IFN immunity in the respiratory tract during the first few days of infection may account for the spread of the virus, leading to pulmonary and systemic inflammation.
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19
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Murray MF. Enabling Diagnostic Resulting as a New Category of Secondary Genomic Findings. J Pers Med 2022; 12:jpm12020158. [PMID: 35207647 PMCID: PMC8878546 DOI: 10.3390/jpm12020158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/19/2021] [Accepted: 12/30/2021] [Indexed: 02/01/2023] Open
Abstract
Over the past decade, the secondary analysis of existing DNA datasets for clinical resulting has become an established practice. However, this established practice is typically limited to only one category of secondary genomic findings, the identification of “disease risk”. Diagnostic resulting has been left out of secondary genomic findings. In medical practice, diagnostic resulting is triggered when a test is ordered for a patient based on a recognizable clinical indication for evaluation; most genetic and genomic testing is carried out in support of diagnostic evaluations. The secondary analysis of existing DNA data has the potential to cost less and have more rapid turnaround times for diagnostic results compared to current DNA diagnostic approaches that typically generate a new dataset with every test ordered. Worldwide, innovative health systems could position themselves to deliver valid secondary genomic finding results in both the established category of disease risk results, as well as a new category of diagnostic results. To support the ongoing delivery of both categories of secondary findings, health systems will need comprehensive genomic datasets for patients and secure workflows that allow for repeated access to that data for on-demand secondary analysis.
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Affiliation(s)
- Michael F Murray
- Yale Center for Genomic Health, Yale School of Medicine, New Haven, CT 06510, USA
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20
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High rate of clinically unrecognized SARS-CoV-2 infections in pediatric palliative care patients. Eur J Pediatr 2022; 181:847-851. [PMID: 34467455 PMCID: PMC8408038 DOI: 10.1007/s00431-021-04242-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 10/29/2022]
Abstract
Little is known about the frequency and clinical course of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in pediatric patients with severe comorbidities. In this prospective cross-sectional trial, the seroprevalence of SARS-CoV-2-IgG in patients with life-limiting conditions being treated by a large specialized pediatric palliative home-care team was determined. In order to gain insight into the infection chain, close contacts of seropositive patients were also included in the study. We analyzed the sera of 39 patients and found a 25.6% seroprevalence for SARS-CoV-2. No SARS-CoV-2 infections were known prior to the study. No significant difference was found in the symptom load between seropositive and seronegative patients during the risk period for SARS-CoV-2 infections. Of the 20 close contacts tested, only one was seropositive for SARS-CoV-2.Conclusions: Our results indicate a substantially high prevalence of silent SARS-CoV-2 infections in pediatric palliative care patients. Surprisingly, no severe outcomes were seen in this fragile patient collective with severe comorbidities. The chain of infection and thus the reason for the high frequency of SARS-CoV-2 infections in pediatric palliative care patients remain unclear. What is Known: •Even though severe disease courses of COVID-19 have been reported in children, there are yet no established risk factors for SARS-CoV-2 in pediatric patients. What is New: •In this cross-sectional seroprevalence study of palliative pediatric patients with severe life-limiting conditions, a high rate of seropositive patients (25.6%) was found. •Surprisingly, all seropositive patients were previously unrecognized, despite the severe comorbidities of our collective.
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21
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Potential long-term effects of SARS-CoV-2 infection on the pulmonary vasculature: a global perspective. Nat Rev Cardiol 2021; 19:314-331. [PMID: 34873286 PMCID: PMC8647069 DOI: 10.1038/s41569-021-00640-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/25/2021] [Indexed: 12/13/2022]
Abstract
The lungs are the primary target of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, with severe hypoxia being the cause of death in the most critical cases. Coronavirus disease 2019 (COVID-19) is extremely heterogeneous in terms of severity, clinical phenotype and, importantly, global distribution. Although the majority of affected patients recover from the acute infection, many continue to suffer from late sequelae affecting various organs, including the lungs. The role of the pulmonary vascular system during the acute and chronic stages of COVID-19 has not been adequately studied. A thorough understanding of the origins and dynamic behaviour of the SARS-CoV-2 virus and the potential causes of heterogeneity in COVID-19 is essential for anticipating and treating the disease, in both the acute and the chronic stages, including the development of chronic pulmonary hypertension. Both COVID-19 and chronic pulmonary hypertension have assumed global dimensions, with potential complex interactions. In this Review, we present an update on the origins and behaviour of the SARS-CoV-2 virus and discuss the potential causes of the heterogeneity of COVID-19. In addition, we summarize the pathobiology of COVID-19, with an emphasis on the role of the pulmonary vasculature, both in the acute stage and in terms of the potential for developing chronic pulmonary hypertension. We hope that the information presented in this Review will help in the development of strategies for the prevention and treatment of the continuing COVID-19 pandemic. In this Review, the authors discuss the potential causes of the heterogeneity of COVID-19 and summarize the pathobiology of the disease, with an emphasis on the role of the pulmonary vasculature in the acute stage and the potential for developing chronic pulmonary hypertension. A thorough understanding of the dynamic behaviour of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential to understanding its heterogeneous effects on the pulmonary vasculature in patients with coronavirus disease 2019 (COVID-19). The severity and clinical phenotype of COVID-19 are influenced by host factors, including socioeconomic factors and genetics. Silent hypoxia is a major and independent cause of lung damage in COVID-19; the use of modern imaging techniques is proving to be very valuable in identifying silent hypoxia. The pulmonary vascular system has a major role in the pathobiology of COVID-19. Both COVID-19 and chronic pulmonary hypertension are global diseases with a complex interaction.
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22
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Abstract
PURPOSE OF REVIEW This review is meant to describe the genetic associations with pediatric severe COVID-19 pneumonia and the postinfectious complication of the multisystem inflammatory syndrome in children (MIS-C). Multiple genetic approaches have been carried out, primarily in adults with extrapolation to children, including genome-wide association studies (GWAS), whole exome and whole genome sequencing (WES/WGS), and target gene analyses. RECENT FINDINGS Data from adults with severe COVID-19 have identified genomic regions (human leukocyte antigen locus and 3p21.31) as potential risk factors. Genes related to viral entry into cells (ABO blood group locus, ACE2, TMPRS22) have been linked to severe COVID-19 patients by GWAS and target gene approaches. Type I interferon (e.g. IFNAR2) and antiviral gene (e.g. TLR7) associations have been identified by several genetic approaches in severe COVID-19. WES has noted associations with several immune regulatory genes (e.g. SOCS1). Target gene approaches have identified mutations in perforin-mediated cytolytic pathway genes in children and adults with severe COVID-19 and children with MIS-C. SUMMARY Several genetic associations have been identified in individuals with severe COVID-19 and MIS-C via various genetic approaches. Broadly speaking, COVID-19 genetic associations include genes involved with antiviral functions, viral cell entry, immune regulation, chemotaxis of white blood cells, and lymphocyte cytolytic function.
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Affiliation(s)
- Grant S. Schulert
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Sydney A. Blum
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center
| | - Randy Q. Cron
- Division of Rheumatology, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
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23
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Douillard V, Castelli EC, Mack SJ, Hollenbach JA, Gourraud PA, Vince N, Limou S. Current HLA Investigations on SARS-CoV-2 and Perspectives. Front Genet 2021; 12:774922. [PMID: 34912378 PMCID: PMC8667766 DOI: 10.3389/fgene.2021.774922] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/08/2021] [Indexed: 01/11/2023] Open
Abstract
The rapid, global spread of the SARS-CoV-2 virus during the current pandemic has triggered numerous efforts in clinical and research settings to better understand the host genetics' interactions and the severity of COVID-19. Due to the established major role played by MHC/HLA polymorphism in infectious disease course and susceptibility, immunologists and geneticists have teamed up to investigate its contribution to the SARS-CoV-2 infection and COVID-19 progression. A major goal of the Covid-19|HLA & Immunogenetics Consortium is to support and unify these efforts. Here, we present a review of HLA immunogenomics studies in the SARS-CoV-2 pandemic and reflect on the role of various HLA data, their limitation and future perspectives.
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Affiliation(s)
- Venceslas Douillard
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
| | | | - Steven J. Mack
- Division of Allergy, Immunology and Bone Marrow Transplantation, Department of Pediatrics, School of Medicine, University of California, San Francisco, CA, United States
| | - Jill A. Hollenbach
- Department of Neurology, University of California, San Francisco and Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, United States
| | - Pierre-Antoine Gourraud
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
| | - Nicolas Vince
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
| | - Sophie Limou
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
- Ecole Centrale de Nantes, Department of Computer Sciences and Mathematics in Biology, Nantes, France
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24
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Espejo-Paeres C, Espliguero RA, Uribarri A, Antón-Huguet B, Romero R, Fernández-Rozas I, Becerra-Muñoz VM, Alfonso-Rodríguez E, Huang J, Ortega-Armas ME, Pepe M, González A, Bertolazzi M, Cerrato E, Quezada A, Raposeiras-Roubin S, Vedia O, Feltes-Guzmán G, Akin I, Carrero-Fernández A, Macaya C, Estrada V, Núñez-Gil IJ. Predictors of poor prognosis in healthy, young, individuals with SARS-CoV-2 infections. Clin Microbiol Infect 2021; 28:273-278. [PMID: 34600119 PMCID: PMC8481119 DOI: 10.1016/j.cmi.2021.09.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 09/16/2021] [Accepted: 09/19/2021] [Indexed: 01/08/2023]
Abstract
Objectives To identify predictors of poor prognosis in previously healthy young individuals admitted to hospital with coronavirus disease 2019 (COVID-19). Methods We studied a cohort of patients hospitalized with COVID-19. All patients without co-morbidities, without usual treatments and ≤65 years old were selected from an international registry (HOPE-COVID-19, NCT04334291). We focused on baseline variables—symptoms and signs at admission—to analyse risk factors for poor prognosis. The primary end point was a composite of major adverse clinical events during hospitalization including mortality, mechanical ventilation, high-flow nasal oxygen therapy, prone, sepsis, systemic inflammatory response syndrome and embolic events. Results Overall, 773 healthy young patients were included. The primary composite end point was observed in 29% (225/773) and the overall mortality rate was 3.6% (28/773). In the combined event group, 75% (168/225) of patients were men and the mean age was 49 (±11) years, whereas in the non-combined event group, the prevalence of male gender was 43% (238/548) and the mean age was 42 (±13) years (p < 0.001 for both). On admission, respiratory insufficiency and cough were described in 51.4% (114/222) and 76% (170/223) of patients, respectively, in the combined event group, versus 7.9% (42/533) and 56% (302/543) of patients in the other group (p < 0.001 for both). The strongest independent predictor for the combined end point was desaturation (Spo2 <92%) (OR 5.40; 95% CI 3.34–8.75; p < 0.001), followed by tachypnoea (OR 3.17; 95% CI 1.93–5.21; p < 0.001), male gender (OR 3.01; 95% CI 1.96–4.61; p < 0.001) and pulmonary infiltrates on chest X-ray at admission (OR 2.21; 95% CI 1.18–4.16; p 0.014). Conclusions Major adverse clinical events were unexpectedly high considering the baseline characteristics of the cohort. Signs of respiratory compromise at admission and male gender, were predictive for poor prognosis among young healthy patients hospitalized with COVID-19.
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Affiliation(s)
| | | | - Aitor Uribarri
- Hospital Clínico Universitario de Valladolid, Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Valladolid, Spain
| | | | - Rodolfo Romero
- Hospital Universitario Getafe, Universidad Europea Madrid, Spain
| | | | - Víctor Manuel Becerra-Muñoz
- Hospital Universitario Virgen de la Victoria, Universidad de Málaga (UMA), Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Málaga, Spain
| | | | - Jia Huang
- The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | | | - Martino Pepe
- Azienda Ospedaliero-universitaria Consorziale Policlinico di Bari, Italy
| | - Adelina González
- Hospital Universitario Infanta Sofia, San Sebastián de los Reyes, Madrid, Spain
| | | | - Enrico Cerrato
- San Luigi Gonzaga University Hospital, Rivoli, Turin, Italy
| | - Antonio Quezada
- Hospital Clínico Universitario, Incliva, Universidad de Valencia, Valencia, Spain
| | | | - Oscar Vedia
- Hospital Clínico San Carlos. Universidad Complutense de Madrid, Instituto de Investigación, Sanitaria del Hospital Clínico San Carlos (IdISSC). Madrid, Spain
| | | | - Ibrahim Akin
- First Department of Medicine, Medical Faculty Mannheim, University Heidelberg, Mannheim, Germany, DZHK (German Centre for Cardiovascular Research), Partner Site, Heidelberg-Mannheim, Mannheim, 68167, Germany
| | | | - Carlos Macaya
- Hospital Clínico San Carlos. Universidad Complutense de Madrid, Instituto de Investigación, Sanitaria del Hospital Clínico San Carlos (IdISSC). Madrid, Spain
| | - Vicente Estrada
- Hospital Clínico San Carlos. Universidad Complutense de Madrid, Instituto de Investigación, Sanitaria del Hospital Clínico San Carlos (IdISSC). Madrid, Spain
| | - Iván J Núñez-Gil
- Hospital Clínico San Carlos. Universidad Complutense de Madrid, Instituto de Investigación, Sanitaria del Hospital Clínico San Carlos (IdISSC). Madrid, Spain
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25
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Ku C, Chen I, Lai M. Infection-induced inflammation from specific inborn errors of immunity to COVID-19. FEBS J 2021; 288:5021-5041. [PMID: 33971084 PMCID: PMC8236961 DOI: 10.1111/febs.15961] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/10/2021] [Accepted: 05/07/2021] [Indexed: 01/07/2023]
Abstract
Inborn errors of immunity (IEIs) are a group of genetically defined disorders leading to defective immunity. Some IEIs have been linked to mutations of immune receptors or signaling molecules, resulting in defective signaling of respective cascades essential for combating specific pathogens. However, it remains incompletely understood why in selected IEIs, such as X-linked lymphoproliferative syndrome type 2 (XLP-2), hypo-immune response to specific pathogens results in persistent inflammation. Moreover, mechanisms underlying the generation of anticytokine autoantibodies are mostly unknown. Recently, IEIs have been associated with coronavirus disease 2019 (COVID-19), with a small proportion of patients that contract severe COVID-19 displaying loss-of-function mutations in genes associated with type I interferons (IFNs). Moreover, approximately 10% of patients with severe COVID-19 possess anti-type I IFN-neutralizing autoantibodies. Apart from IEIs that impair immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), SARS-CoV-2 encodes several proteins that suppress early type I IFN production. One primary consequence of the lack of type I IFNs during early SARS-CoV-2 infection is the increased inflammation associated with COVID-19. In XLP-2, resolution of inflammation rescued experimental subjects from infection-induced mortality. Recent studies also indicate that targeting inflammation could alleviate COVID-19. In this review, we discuss infection-induced inflammation in IEIs, using XLP-2 and COVID-19 as examples. We suggest that resolving inflammation may represent an effective therapeutic approach to these diseases.
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Affiliation(s)
- Cheng‐Lung Ku
- Laboratory of Human Immunology and Infectious DiseasesGraduate Institute of Clinical Medical SciencesChang Gung UniversityTaoyuanTaiwan,Department of NephrologyLinkou Chang Gung Memorial HospitalTaoyuanTaiwan
| | - I‐Ting Chen
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
| | - Ming‐Zong Lai
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
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26
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Chu CF, Sabath F, Fibi-Smetana S, Sun S, Öllinger R, Noeßner E, Chao YY, Rinke L, Winheim E, Rad R, Krug AB, Taher L, Zielinski CE. Convalescent COVID-19 Patients Without Comorbidities Display Similar Immunophenotypes Over Time Despite Divergent Disease Severities. Front Immunol 2021; 12:601080. [PMID: 34867933 PMCID: PMC8634761 DOI: 10.3389/fimmu.2021.601080] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 07/23/2021] [Indexed: 01/12/2023] Open
Abstract
COVID-19, the disease caused by SARS-CoV-2 infection, can assume a highly variable disease course, ranging from asymptomatic infection, which constitutes the majority of cases, to severe respiratory failure. This implies a diverse host immune response to SARS-CoV-2. However, the immunological underpinnings underlying these divergent disease courses remain elusive. We therefore set out to longitudinally characterize immune signatures of convalescent COVID-19 patients stratified according to their disease severity. Our unique convalescent COVID-19 cohort consists of 74 patients not confounded by comorbidities. This is the first study of which we are aware that excludes immune abrogations associated with non-SARS-CoV-2 related risk factors of disease severity. Patients were followed up and analyzed longitudinally (2, 4 and 6 weeks after infection) by high-dimensional flow cytometric profiling of peripheral blood mononuclear cells (PBMCs), in-depth serum analytics, and transcriptomics. Immune phenotypes were correlated to disease severity. Convalescence was overall associated with uniform immune signatures, but distinct immune signatures for mildly versus severely affected patients were detectable within a 2-week time window after infection.
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Affiliation(s)
- Chang-Feng Chu
- Institute of Virology, Technical University of Munich, Munich, Germany
- Central Institute for Translational Cancer Research (TranslaTUM), Technical University of Munich, Munich, Germany
- Infection Immunology, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Friedrich Schiller University, Jena, Germany
| | - Florian Sabath
- Central Institute for Translational Cancer Research (TranslaTUM), Technical University of Munich, Munich, Germany
| | - Silvia Fibi-Smetana
- Institute of Biomedical Informatics, Graz University of Technology, Graz, Austria
| | - Shan Sun
- Institute of Virology, Technical University of Munich, Munich, Germany
- Central Institute for Translational Cancer Research (TranslaTUM), Technical University of Munich, Munich, Germany
| | - Rupert Öllinger
- Central Institute for Translational Cancer Research (TranslaTUM), Technical University of Munich, Munich, Germany
| | - Elfriede Noeßner
- Immunoanalytics-Tissue Control of Immunocytes, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Ying-Yin Chao
- Institute of Virology, Technical University of Munich, Munich, Germany
- Central Institute for Translational Cancer Research (TranslaTUM), Technical University of Munich, Munich, Germany
| | - Linus Rinke
- Institute for Immunology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Elena Winheim
- Institute for Immunology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Roland Rad
- Central Institute for Translational Cancer Research (TranslaTUM), Technical University of Munich, Munich, Germany
| | - Anne B. Krug
- Institute for Immunology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Leila Taher
- Institute of Biomedical Informatics, Graz University of Technology, Graz, Austria
| | - Christina E. Zielinski
- Institute of Virology, Technical University of Munich, Munich, Germany
- Central Institute for Translational Cancer Research (TranslaTUM), Technical University of Munich, Munich, Germany
- Infection Immunology, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Friedrich Schiller University, Jena, Germany
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27
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Apostolidou S, Harbauer T, Lasch P, Biermann D, Hempel M, Lütgehetmann M, Pfefferle S, Herrmann J, Rüffer A, Reinshagen K, Kozlik-Feldmann R, Gieras A, Kniep I, Oh J, Singer D, Ebenebe CU, Kobbe R. Fatal COVID-19 in a Child with Persistence of SARS-CoV-2 Despite Extensive Multidisciplinary Treatment: A Case Report. CHILDREN-BASEL 2021; 8:children8070564. [PMID: 34208887 PMCID: PMC8304245 DOI: 10.3390/children8070564] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 05/27/2021] [Accepted: 06/28/2021] [Indexed: 02/07/2023]
Abstract
Critical Coronavirus disease 2019 (COVID-19) developed in a 7-year-old girl with a history of dystrophy, microcephaly, and central hypothyroidism. Starting with gastrointestinal symptoms, the patient developed severe myocarditis followed by progressive multiple organ failure complicated by Pseudomonas aeruginosa bloodstream infection. Intensive care treatment consisting of invasive ventilation, drainage of pleural effusion, and high catecholamine therapy could not prevent the progression of heart failure, leading to the implantation of venoarterial extracorporeal life support (VA-ECLS) and additional left ventricle support catheter (Impella® pump). Continuous venovenous hemofiltration (CVVH) and extracorporeal hemadsorption therapy (CytoSorb®) were initiated. Whole exome sequencing revealed a mutation of unknown significance in DExH-BOX helicase 30 (DHX30), a gene encoding a RNA helicase. COVID-19 specific antiviral and immunomodulatory treatment did not lead to viral clearance or control of hyperinflammation resulting in the patient’s death on extracorporeal life support-(ECLS)-day 20. This fatal case illustrates the potential severity of pediatric COVID-19 and suggests further evaluation of antiviral treatment strategies and vaccination programs for children.
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Affiliation(s)
- Sofia Apostolidou
- Division of Neonatology and Pediatric Critical Care Medicine, University Children’s Hospital, University Medical Center Eppendorf, 20246 Hamburg, Germany; (S.A.); (T.H.); (D.S.); (C.U.E.)
| | - Theresa Harbauer
- Division of Neonatology and Pediatric Critical Care Medicine, University Children’s Hospital, University Medical Center Eppendorf, 20246 Hamburg, Germany; (S.A.); (T.H.); (D.S.); (C.U.E.)
| | - Peter Lasch
- Pediatric Intensive Care Medicine, Department of Pediatrics, Clinic Bremen-Mitte, Bremen Hospital Group, 28205 Bremen, Germany;
| | - Daniel Biermann
- Departments of Pediatric Cardiology and Pediatric Cardiac Surgery, Clinic for Children’s Heart Medicine, University Heart and Vascular Center Hamburg, 20246 Hamburg, Germany; (D.B.); (A.R.); (R.K.-F.)
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany;
| | - Marc Lütgehetmann
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (S.P.)
| | - Susanne Pfefferle
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.L.); (S.P.)
| | - Jochen Herrmann
- Section of Pediatric Radiology, Department of Diagnostic and Interventional Radiology and Nuclear Medicine, University Children’s Hospital, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany;
| | - André Rüffer
- Departments of Pediatric Cardiology and Pediatric Cardiac Surgery, Clinic for Children’s Heart Medicine, University Heart and Vascular Center Hamburg, 20246 Hamburg, Germany; (D.B.); (A.R.); (R.K.-F.)
| | - Konrad Reinshagen
- Department of Pediatric Surgery, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany;
| | - Rainer Kozlik-Feldmann
- Departments of Pediatric Cardiology and Pediatric Cardiac Surgery, Clinic for Children’s Heart Medicine, University Heart and Vascular Center Hamburg, 20246 Hamburg, Germany; (D.B.); (A.R.); (R.K.-F.)
| | - Anna Gieras
- Department of Immunology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany;
| | - Inga Kniep
- Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, 22529 Hamburg, Germany;
| | - Jun Oh
- Department of Pediatric Nephrology, University Children’s Hospital, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany;
| | - Dominique Singer
- Division of Neonatology and Pediatric Critical Care Medicine, University Children’s Hospital, University Medical Center Eppendorf, 20246 Hamburg, Germany; (S.A.); (T.H.); (D.S.); (C.U.E.)
| | - Chinedu Ulrich Ebenebe
- Division of Neonatology and Pediatric Critical Care Medicine, University Children’s Hospital, University Medical Center Eppendorf, 20246 Hamburg, Germany; (S.A.); (T.H.); (D.S.); (C.U.E.)
| | - Robin Kobbe
- First Department of Medicine, Division of Infectious Diseases, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- Correspondence: ; Tel.: +49-1-522-281-5646
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28
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Bastard P, Zhang Q, Cobat A, Jouanguy E, Zhang SY, Abel L, Casanova JL. Insufficient type I IFN immunity underlies life-threatening COVID-19 pneumonia. C R Biol 2021; 344:19-25. [PMID: 34213846 DOI: 10.5802/crbiol.36] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We established the COVID Human Genetic Effort (www.covidhge.com) to discover the human genetic and immunological bases of the vast interindividual clinical variability between humans infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We found that about 3% of patients with life-threatening coronavirus disease 2019 (COVID-19) pneumonia were ill because of inborn errors of genes controlling type I interferon (IFN)-dependent immunity (which controls influenza virus), and at least 10% of patients with life-threatening COVID-19 pneumonia had neutralizing auto-Abs against some of the 17 individual type I IFNs. These findings indicate that impaired type I IFN immunity underlies life-threatening COVID-19 pneumonia in at least 13% of patients. These discoveries pave the way for further research into unexplained severe cases, and provide a rationale for preventing and treating the disease in individuals at risk, with recombinant type I IFNs.
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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.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.,University of Paris, Imagine Institute, Paris, France
| | - Qian Zhang
- 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 of Paris, Imagine Institute, Paris, France
| | - Emmanuelle Jouanguy
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Inserm U1163, Necker Hospital for Sick Children, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.,University of Paris, Imagine Institute, Paris, France
| | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Inserm U1163, Necker Hospital for Sick Children, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.,University of Paris, Imagine Institute, Paris, France
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Inserm U1163, Necker Hospital for Sick Children, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.,University of Paris, Imagine Institute, Paris, France
| | - Jean-Laurent Casanova
- Howard Hughes Medical Institute, New York, NY, USA.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Inserm U1163, Necker Hospital for Sick Children, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.,University of Paris, Imagine Institute, Paris, France
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29
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Spinelli FR, Meylan F, O'Shea JJ, Gadina M. JAK inhibitors: Ten years after. Eur J Immunol 2021; 51:1615-1627. [PMID: 33930196 DOI: 10.1002/eji.202048922] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/27/2021] [Indexed: 12/15/2022]
Abstract
The European Journal of Immunology was launched 50 years ago, coinciding with the discovery of many cytokines and growth factors and the emergence of an entirely new field of research. Ultimately, our knowledge about the biological activity of these factors allowed us to better understand how the immune system functions in the context of inflammatory and autoimmune diseases leading to the development of targeted biologic therapies. The study of cytokine signal transduction led to the discovery of Janus kinases (JAK), and the consideration of therapeutically targeting JAKs to treat immune and inflammatory diseases. This year also marks the tenth anniversary of the approval of the first JAK inhibitor (jakinib) and now there are a total of nine approved jakinibs for treatment of rheumatologic, dermatologic, gastrointestinal, and neoplastic indications and most recently COVID-19. Here, we summarized the discoveries that led to development of first-generation jakinibs, discussed some of the newer, possibly more selective jakinibs, as well as jakinibs that also target other kinases. We also illustrated the rationale behind the application of these drugs in the treatment of COVID-19 cytokine storm. In this review, we will discuss the clinical success of jakinibs, the gaps in our understanding of their biological activities as well as challenges in regard to their clinical application.
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Affiliation(s)
- Francesca Romana Spinelli
- Dipartimento di Scienze Cliniche Internistiche, Anestesiologiche e Cardiovascolari-Reumatologia, Sapienza Università di Roma, Rome, Italy
| | - Françoise Meylan
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Translational Immunology Section, Bethesda, MD, USA
| | - John J O'Shea
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Massimo Gadina
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Translational Immunology Section, Bethesda, MD, USA
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Monticelli M, Mele BH, Andreotti G, Cubellis MV, Riccio G. Why does SARS-CoV-2 hit in different ways? Host genetic factors can influence the acquisition or the course of COVID-19. Eur J Med Genet 2021; 64:104227. [PMID: 33872774 PMCID: PMC8051015 DOI: 10.1016/j.ejmg.2021.104227] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 03/14/2021] [Accepted: 04/12/2021] [Indexed: 02/08/2023]
Abstract
The identification of high-risk factors for the infection by SARS-CoV-2 and the negative outcome of COVID-19 is crucial. The genetic background of the host might account for individual responses to SARS-CoV-2 infection besides age and comorbidities. A list of candidate polymorphisms is needed to drive targeted screens, given the existence of frequent polymorphisms in the general population. We carried out text mining in the scientific literature to draw up a list of genes referable to the term "SARS-CoV*". We looked for frequent mutations that are likely to affect protein function in these genes. Ten genes, mostly involved in innate immunity, and thirteen common variants were identified, for some of these the involvement in COVID-19 is supported by publicly available epidemiological data. We looked for available data on the population distribution of these variants and we demonstrated that the prevalence of five of them, Arg52Cys (rs5030737), Gly54Asp (rs1800450) and Gly57Glu (rs1800451) in MBL2, Ala59Thr (rs25680) in CD27, and Val197Met (rs12329760) in TMPRSS2, correlates with the number of cases and/or deaths of COVID-19 observed in different countries. The association of the TMPRSS2 variant provides epidemiological evidence of the usefulness of transmembrane protease serine 2 inhibitors for the cure of COVID-19. The identified genetic variants represent a basis for the design of a cost-effective assay for population screening of genetic risk factors in the COVID-19 pandemic.
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Affiliation(s)
- Maria Monticelli
- Department of Biology, Università Federico II, 80126, Napoli, Italy.
| | - Bruno Hay Mele
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy.
| | | | - Maria Vittoria Cubellis
- Department of Biology, Università Federico II, 80126, Napoli, Italy; Istituto di Chimica Biomolecolare -CNR, 80078, Pozzuoli, Italy.
| | - Guglielmo Riccio
- Scuola di Specializzazione in Pediatria, Università degli Studi di Trieste, 34127, Trieste, Italy.
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Hetzel M, Ackermann M, Lachmann N. Beyond "Big Eaters": The Versatile Role of Alveolar Macrophages in Health and Disease. Int J Mol Sci 2021; 22:3308. [PMID: 33804918 PMCID: PMC8036607 DOI: 10.3390/ijms22073308] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/19/2021] [Accepted: 03/20/2021] [Indexed: 02/07/2023] Open
Abstract
Macrophages act as immune scavengers and are important cell types in the homeostasis of various tissues. Given the multiple roles of macrophages, these cells can also be found as tissue resident macrophages tightly integrated into a variety of tissues in which they fulfill crucial and organ-specific functions. The lung harbors at least two macrophage populations: interstitial and alveolar macrophages, which occupy different niches and functions. In this review, we provide the latest insights into the multiple roles of alveolar macrophages while unraveling the distinct factors which can influence the ontogeny and function of these cells. Furthermore, we will highlight pulmonary diseases, which are associated with dysfunctional macrophages, concentrating on congenital diseases as well as pulmonary infections and impairment of immunological pathways. Moreover, we will provide an overview about different treatment approaches targeting macrophage dysfunction. Improved knowledge of the role of macrophages in the onset of pulmonary diseases may provide the basis for new pharmacological and/or cell-based immunotherapies and will extend our understanding to other macrophage-related disorders.
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Affiliation(s)
- Miriam Hetzel
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (M.H.); (M.A.)
- REBIRTH Research Center for Translational and Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Mania Ackermann
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (M.H.); (M.A.)
- REBIRTH Research Center for Translational and Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, 30625 Hannover, Germany
| | - Nico Lachmann
- REBIRTH Research Center for Translational and Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, 30625 Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625 Hannover, Germany
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32
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Betti M, Bertolotti M, Ferrante D, Roveta A, Pelazza C, Giacchero F, Penpa S, Massarino C, Bolgeo T, Cassinari A, Mussa M, Chichino G, Maconi A. Baseline clinical characteristics and prognostic factors in hospitalized COVID-19 patients aged ≤ 65 years: A retrospective observational study. PLoS One 2021; 16:e0248829. [PMID: 33760885 PMCID: PMC7990225 DOI: 10.1371/journal.pone.0248829] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 03/07/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Individual differences in susceptibility to SARS-CoV-2 infection, symptomatology and clinical manifestation of COVID-19 have thus far been observed but little is known about the prognostic factors of young patients. METHODS A retrospective observational study was conducted on 171 patients aged ≤ 65 years hospitalized in Alessandria's Hospital from 1st March to 30th April 2020 with laboratory confirmed COVID-19. Epidemiological data, symptoms at onset, clinical manifestations, Charlson Comorbidity Index, laboratory parameters, radiological findings and complications were considered. Patients were divided into two groups on the basis of COVID-19 severity. Multivariable logistic regression analysis was used to establish factors associated with the development of a moderate or severe disease. FINDINGS A total of 171 patients (89 with mild/moderate disease, 82 with severe/critical disease), of which 61% males and a mean age (± SD) of 53.6 (± 9.7) were included. The multivariable logistic model identified age (50-65 vs 18-49; OR = 3.23 CI95% 1.42-7.37), platelet count (per 100 units of increase OR = 0.61 CI95% 0.42-0.89), c-reactive protein (CPR) (per unit of increase OR = 1.12 CI95% 1.06-1.20) as risk factors for severe or critical disease. The multivariable logistic model showed a good discriminating capacity with a C-index value of 0.76. INTERPRETATION Patients aged ≥ 50 years with low platelet count and high CRP are more likely to develop severe or critical illness. These findings might contribute to improved clinical management.
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Affiliation(s)
- Marta Betti
- Infrastruttura Ricerca Formazione Innovazione, Dipartimento Attività Integrate Ricerca Innovazione, Azienda Ospedaliera “SS Antonio e Biagio e Cesare Arrigo”, Alessandria, Italy
- * E-mail:
| | - Marinella Bertolotti
- Infrastruttura Ricerca Formazione Innovazione, Dipartimento Attività Integrate Ricerca Innovazione, Azienda Ospedaliera “SS Antonio e Biagio e Cesare Arrigo”, Alessandria, Italy
| | - Daniela Ferrante
- Unit of Medical Statistics, Department of Translational Medicine, University of “Piemonte Orientale” and Cancer Epidemiology, CPO Piemonte, Novara, Italy
| | - Annalisa Roveta
- Infrastruttura Ricerca Formazione Innovazione, Dipartimento Attività Integrate Ricerca Innovazione, Azienda Ospedaliera “SS Antonio e Biagio e Cesare Arrigo”, Alessandria, Italy
| | - Carolina Pelazza
- Infrastruttura Ricerca Formazione Innovazione, Dipartimento Attività Integrate Ricerca Innovazione, Azienda Ospedaliera “SS Antonio e Biagio e Cesare Arrigo”, Alessandria, Italy
| | - Fabio Giacchero
- Infrastruttura Ricerca Formazione Innovazione, Dipartimento Attività Integrate Ricerca Innovazione, Azienda Ospedaliera “SS Antonio e Biagio e Cesare Arrigo”, Alessandria, Italy
| | - Serena Penpa
- Infrastruttura Ricerca Formazione Innovazione, Dipartimento Attività Integrate Ricerca Innovazione, Azienda Ospedaliera “SS Antonio e Biagio e Cesare Arrigo”, Alessandria, Italy
| | - Costanza Massarino
- Infrastruttura Ricerca Formazione Innovazione, Dipartimento Attività Integrate Ricerca Innovazione, Azienda Ospedaliera “SS Antonio e Biagio e Cesare Arrigo”, Alessandria, Italy
| | - Tatiana Bolgeo
- Infrastruttura Ricerca Formazione Innovazione, Dipartimento Attività Integrate Ricerca Innovazione, Azienda Ospedaliera “SS Antonio e Biagio e Cesare Arrigo”, Alessandria, Italy
| | - Antonella Cassinari
- Infrastruttura Ricerca Formazione Innovazione, Dipartimento Attività Integrate Ricerca Innovazione, Azienda Ospedaliera “SS Antonio e Biagio e Cesare Arrigo”, Alessandria, Italy
| | - Marco Mussa
- Infectious Diseases Unit, Azienda Ospedaliera “SS Antonio e Biagio e Cesare Arrigo”, Alessandria, Italy
| | - Guido Chichino
- Infectious Diseases Unit, Azienda Ospedaliera “SS Antonio e Biagio e Cesare Arrigo”, Alessandria, Italy
| | - Antonio Maconi
- Infrastruttura Ricerca Formazione Innovazione, Dipartimento Attività Integrate Ricerca Innovazione, Azienda Ospedaliera “SS Antonio e Biagio e Cesare Arrigo”, Alessandria, Italy
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Naslavsky MS, Vidigal M, Matos LDRB, Cória VR, Batista PB, Razuk Á, Saldiva PHN, Dolhnikoff M, Schidlowski L, Prando C, Cunha-Neto E, Condino-Neto A, Passos-Bueno MR, Zatz M. Extreme phenotypes approach to investigate host genetics and COVID-19 outcomes. Genet Mol Biol 2021; 44:e20200302. [PMID: 33651876 PMCID: PMC7924362 DOI: 10.1590/1678-4685-gmb-2020-0302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 01/18/2021] [Indexed: 12/12/2022] Open
Abstract
COVID-19 comprises clinical outcomes of SARS-CoV-2 infection and is highly heterogeneous, ranging from asymptomatic individuals to deceased young adults without comorbidities. There is growing evidence that host genetics play an important role in COVID-19 severity, including inborn errors of immunity, age-related inflammation and immunosenescence. Here we present a brief review on the known order of events from infection to severe system-wide disturbance due to COVID-19 and summarize potential candidate genes and pathways. Finally, we propose a strategy of subject's ascertainment based on phenotypic extremes to take part in genomic studies and elucidate intrinsic risk factors involved in COVID-19 severe outcomes.
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Affiliation(s)
- Michel Satya Naslavsky
- Universidade de São Paulo, Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, Centro de Pesquisa sobre o Genoma Humano e Células-Tronco, São Paulo, SP, Brazil
| | - Mateus Vidigal
- Universidade de São Paulo, Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, Centro de Pesquisa sobre o Genoma Humano e Células-Tronco, São Paulo, SP, Brazil
| | - Larissa do Rêgo Barros Matos
- Universidade de São Paulo, Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, Centro de Pesquisa sobre o Genoma Humano e Células-Tronco, São Paulo, SP, Brazil
| | - Vivian Romanholi Cória
- Universidade de São Paulo, Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, Centro de Pesquisa sobre o Genoma Humano e Células-Tronco, São Paulo, SP, Brazil
| | | | | | | | - Marisa Dolhnikoff
- Faculdade de Medicina da Universidade de São Paulo (FMUSP), Departamento de Patologia, São Paulo, SP, Brazil
| | - Laire Schidlowski
- Instituto de Pesquisa Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Hospital Pequeno Príncipe, Curitiba, PR, Brazil
| | - Carolina Prando
- Instituto de Pesquisa Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Hospital Pequeno Príncipe, Curitiba, PR, Brazil
| | - Edécio Cunha-Neto
- Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Instituto do Coração, São Paulo, SP, Brazil
| | - Antonio Condino-Neto
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Laboratório de Imunologia Humana, São Paulo, Brazil
| | - Maria Rita Passos-Bueno
- Universidade de São Paulo, Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, Centro de Pesquisa sobre o Genoma Humano e Células-Tronco, São Paulo, SP, Brazil
| | - Mayana Zatz
- Universidade de São Paulo, Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, Centro de Pesquisa sobre o Genoma Humano e Células-Tronco, São Paulo, SP, Brazil
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34
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Kosmicki JA, Horowitz JE, Banerjee N, Lanche R, Marcketta A, Maxwell E, Bai X, Sun D, Backman JD, Sharma D, Kang HM, O'Dushlaine C, Yadav A, Mansfield AJ, Li AH, Watanabe K, Gurski L, McCarthy SE, Locke AE, Khalid S, O'Keeffe S, Mbatchou J, Chazara O, Huang Y, Kvikstad E, O'Neill A, Nioi P, Parker MM, Petrovski S, Runz H, Szustakowski JD, Wang Q, Wong E, Cordova-Palomera A, Smith EN, Szalma S, Zheng X, Esmaeeli S, Davis JW, Lai YP, Chen X, Justice AE, Leader JB, Mirshahi T, Carey DJ, Verma A, Sirugo G, Ritchie MD, Rader DJ, Povysil G, Goldstein DB, Kiryluk K, Pairo-Castineira E, Rawlik K, Pasko D, Walker S, Meynert A, Kousathanas A, Moutsianas L, Tenesa A, Caulfield M, Scott R, Wilson JF, Baillie JK, Butler-Laporte G, Nakanishi T, Lathrop M, Richards JB, Jones M, Balasubramanian S, Salerno W, Shuldiner AR, Marchini J, Overton JD, Habegger L, Cantor MN, Reid JG, Baras A, Abecasis GR, Ferreira MA. A catalog of associations between rare coding variants and COVID-19 outcomes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2020.10.28.20221804. [PMID: 33655273 PMCID: PMC7924298 DOI: 10.1101/2020.10.28.20221804] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes coronavirus disease-19 (COVID-19), a respiratory illness that can result in hospitalization or death. We investigated associations between rare genetic variants and seven COVID-19 outcomes in 543,213 individuals, including 8,248 with COVID-19. After accounting for multiple testing, we did not identify any clear associations with rare variants either exome-wide or when specifically focusing on (i) 14 interferon pathway genes in which rare deleterious variants have been reported in severe COVID-19 patients; (ii) 167 genes located in COVID-19 GWAS risk loci; or (iii) 32 additional genes of immunologic relevance and/or therapeutic potential. Our analyses indicate there are no significant associations with rare protein-coding variants with detectable effect sizes at our current sample sizes. Analyses will be updated as additional data become available, with results publicly browsable at https://rgc-covid19.regeneron.com.
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Affiliation(s)
- J A Kosmicki
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - J E Horowitz
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - N Banerjee
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - R Lanche
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A Marcketta
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - E Maxwell
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - X Bai
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - D Sun
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - J D Backman
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - D Sharma
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - H M Kang
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - C O'Dushlaine
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A Yadav
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A J Mansfield
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A H Li
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - K Watanabe
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - L Gurski
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - S E McCarthy
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A E Locke
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - S Khalid
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - S O'Keeffe
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - J Mbatchou
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - O Chazara
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Y Huang
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - E Kvikstad
- Bristol Myers Squibb, Route 206 and Province Line Road, Princeton, NJ 08543, USA
| | - A O'Neill
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - P Nioi
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - M M Parker
- Alnylam Pharmaceuticals, 675 West Kendall St, Cambridge, MA 02142, USA
| | - S Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - H Runz
- Biogen, 300 Binney St, Cambridge, MA 02142, USA
| | - J D Szustakowski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - Q Wang
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, UK
| | - E Wong
- Biogen, 300 Binney St, Cambridge, MA 02142, USA
| | | | - E N Smith
- Takeda California Inc., 9625 Towne Centre Dr, San Diego, CA 92121, USA
| | - S Szalma
- Takeda California Inc., 9625 Towne Centre Dr, San Diego, CA 92121, USA
| | - X Zheng
- AbbVie, Inc., 1 N. Waukegan Rd, North Chicago, IL 60064, USA
| | - S Esmaeeli
- AbbVie, Inc., 1 N. Waukegan Rd, North Chicago, IL 60064, USA
| | - J W Davis
- AbbVie, Inc., 1 N. Waukegan Rd, North Chicago, IL 60064, USA
| | - Y-P Lai
- Pfizer, Inc., 1 Portland Street, Cambridge MA 02139, USA
| | - X Chen
- Pfizer, Inc., 1 Portland Street, Cambridge MA 02139, USA
| | | | | | | | | | - A Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - G Sirugo
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - M D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - D J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - G Povysil
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - D B Goldstein
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Genetics & Development, Columbia University, New York, NY 10032, USA
| | - K Kiryluk
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA
| | - E Pairo-Castineira
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - K Rawlik
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
| | - D Pasko
- Genomics England, London EC1M 6BQ, UK
| | - S Walker
- Genomics England, London EC1M 6BQ, UK
| | - A Meynert
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | | | | | - A Tenesa
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Teviot Place, Edinburgh EH8 9AG, UK
| | - M Caulfield
- Genomics England, London EC1M 6BQ, UK
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - R Scott
- Genomics England, London EC1M 6BQ, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - J F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Teviot Place, Edinburgh EH8 9AG, UK
| | - J K Baillie
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh, EH16 5SA, UK
| | - G Butler-Laporte
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec H3T 1E2, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec H3A 0G4, Canada
| | - T Nakanishi
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montréal, Québec H3A 0G4, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
- Research Fellow, Japan Society for the Promotion of Science
| | - M Lathrop
- Department of Human Genetics, McGill University, Montréal, Québec H3A 0G4, Canada
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec H3A 0G4, Canada
| | - J B Richards
- Lady Davis Institute, Jewish General Hospital, Montréal, Québec H3T 1E2, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec H3A 0G4, Canada
- Department of Human Genetics, McGill University, Montréal, Québec H3A 0G4, Canada
- Department of Twins Research, King's College London, London WC2R 2LS, UK
| | - M Jones
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - S Balasubramanian
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - W Salerno
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A R Shuldiner
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - J Marchini
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - J D Overton
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - L Habegger
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - M N Cantor
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - J G Reid
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - A Baras
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - G R Abecasis
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
| | - M A Ferreira
- Regeneron Genetics Center, 777 Old Saw Mill River Rd., Tarrytown, NY 10591, USA
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35
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Fragala MS, Goldberg ZN, Goldberg SE. Return to Work: Managing Employee Population Health During the COVID-19 Pandemic. Popul Health Manag 2021; 24:S3-S15. [PMID: 33347795 PMCID: PMC7875125 DOI: 10.1089/pop.2020.0261] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Coronavirus disease-2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has abruptly transformed the outlook of employer health benefits plans for 2020 and 2021. Containing the spread of the virus and facilitating care of those infected have quickly emerged as immediate priorities. Employers have adjusted health benefits coverage to make COVID-19 testing and treatment accessible and remove barriers to care in order to facilitate the containment of the disease. Employers also are introducing strategies focused on testing, surveillance, workplace modifications, and hygiene to keep workforces healthy and workplaces safe. This paper is intended to provide evidence-based perspectives for self-insured employers for managing population health during the COVID-19 pandemic. Such considerations include (1) return to work practices focused on mitigating the spread of COVID-19 through safety practices, testing and surveillance; and (2) anticipating the impact of COVID-19 on health benefits and costs (including adaptations in delivery of care, social and behavioral health needs, and managing interrupted care for chronic conditions).
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36
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Marcus N, Frizinsky S, Hagin D, Ovadia A, Hanna S, Farkash M, Maoz-Segal R, Agmon-Levin N, Broides A, Nahum A, Rosenberg E, Kuperman AA, Dinur-Schejter Y, Berkun Y, Toker O, Goldberg S, Confino-Cohen R, Scheuerman O, Badarneh B, Epstein-Rigbi N, Etzioni A, Dalal I, Somech R. Minor Clinical Impact of COVID-19 Pandemic on Patients With Primary Immunodeficiency in Israel. Front Immunol 2021; 11:614086. [PMID: 33519822 PMCID: PMC7840610 DOI: 10.3389/fimmu.2020.614086] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/01/2020] [Indexed: 12/13/2022] Open
Abstract
In the last few months the world has witnessed a global pandemic due to severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection causing coronavirus disease 2019 (COVID-19). Obviously, this pandemic affected individuals differently, with a significant impact on populations considered to be at high-risk. One such population, was assumed to be patients with primary genetic defect involving components or pathways of the immune system. While human immunity against COVID-19 is not fully understood, it is, so far, well documented, that both adaptive and innate cells have a critical role in protection against SARS-CoV-2. Here, we aimed to summarize the clinical and laboratory data on primary immunodeficiency (PID) patients in Israel, who were tested positive for SARS-CoV-2, in order to estimate the impact of COVID-19 on such patients. Data was collected from mid-February to end-September. During this time Israel experienced two “waves” of COVID-19 diseases; the first, from mid-February to mid-May and the second from mid-June and still ongoing at the end of data collection. A total of 20 PID patients, aged 4 months to 60 years, were tested positive for SARS-CoV-2, all but one, were detected during the second wave. Fourteen of the patients were on routine monthly IVIG replacement therapy at the time of virus detection. None of the patients displayed severe illness and none required hospitalization; moreover, 7/20 patients were completely asymptomatic. Possible explanations for the minimal clinical impact of COVID-19 pandemic observed in our PID patients include high level of awareness, extra-precautions, and even self-isolation. It is also possible that only specific immune pathways (e.g. type I interferon signaling), may increase the risk for a more severe course of disease and these are not affected in many of the PID patients. In some cases, lack of an immune response actually may be a protective measure against the development of COVID-19 sequelae.
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Affiliation(s)
- Nufar Marcus
- Allergy and Immunology Unit, Schneider Children's Medical Center of Israel, Felsenstein Medical Research Center, Kipper Institute of Immunology, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Jeffrey Modell Foundation Israeli Network for Primary Immunodeficiency, New York, NY, United States
| | - Shirly Frizinsky
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Jeffrey Modell Foundation Israeli Network for Primary Immunodeficiency, New York, NY, United States.,Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, "Edmond and Lily Safra" Children's Hospital, Sheba Medical Center, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel.,Clinical Immunology, Angioedema and Allergy Unit, Center for Autoimmune Diseases, Sheba Medical Center, Tel Hashomer, Israel.,Sackler School of Medicine, Tel Aviv University, Ramat-Aviv, Israel
| | - David Hagin
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Jeffrey Modell Foundation Israeli Network for Primary Immunodeficiency, New York, NY, United States.,Department of Medicine, Allergy and Clinical Immunology Unit, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Adi Ovadia
- The Jeffrey Modell Foundation Israeli Network for Primary Immunodeficiency, New York, NY, United States.,Pediatric Allergy Unit, E. Wolfson Medical Center, Holon, Israel.,Pediatric Department, E. Wolfson Medical Center, Holon, Israel
| | - Suhair Hanna
- The Jeffrey Modell Foundation Israeli Network for Primary Immunodeficiency, New York, NY, United States.,Ruth Children Hospital, Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Michael Farkash
- Allergy and Immunology Unit, Schneider Children's Medical Center of Israel, Felsenstein Medical Research Center, Kipper Institute of Immunology, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Jeffrey Modell Foundation Israeli Network for Primary Immunodeficiency, New York, NY, United States
| | - Ramit Maoz-Segal
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Clinical Immunology, Angioedema and Allergy Unit, Center for Autoimmune Diseases, Sheba Medical Center, Tel Hashomer, Israel.,Sackler School of Medicine, Tel Aviv University, Ramat-Aviv, Israel
| | - Nancy Agmon-Levin
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Clinical Immunology, Angioedema and Allergy Unit, Center for Autoimmune Diseases, Sheba Medical Center, Tel Hashomer, Israel.,Sackler School of Medicine, Tel Aviv University, Ramat-Aviv, Israel
| | - Arnon Broides
- The Jeffrey Modell Foundation Israeli Network for Primary Immunodeficiency, New York, NY, United States.,Immunology Clinic, Soroka University Medical Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Amit Nahum
- The Jeffrey Modell Foundation Israeli Network for Primary Immunodeficiency, New York, NY, United States.,Immunology Clinic, Soroka University Medical Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Elli Rosenberg
- The Jeffrey Modell Foundation Israeli Network for Primary Immunodeficiency, New York, NY, United States.,Immunology Clinic, Soroka University Medical Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Amir Asher Kuperman
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.,Blood Coagulation Service and Pediatric Hematology Clinic, Galilee Medical Center, Nahariya, Israel
| | - Yael Dinur-Schejter
- The Jeffrey Modell Foundation Israeli Network for Primary Immunodeficiency, New York, NY, United States.,Bone Marrow Transplantation Department, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Yackov Berkun
- The Jeffrey Modell Foundation Israeli Network for Primary Immunodeficiency, New York, NY, United States.,Department of Pediatrics, Mount Scopus Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Ori Toker
- The Jeffrey Modell Foundation Israeli Network for Primary Immunodeficiency, New York, NY, United States.,Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.,The Allergy and Immunology Unit, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Shmuel Goldberg
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.,Pediatric Pulmonary Unit, Pediatric Division, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Ronit Confino-Cohen
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Allergy and Clinical Immunology Unit, Meir Medical Center, Kfar-Saba, Israel
| | - Oded Scheuerman
- Pediatrics B, Schneider Children Medical Center Israel, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Basel Badarneh
- Allergy and Immunology Unit, Schneider Children's Medical Center of Israel, Felsenstein Medical Research Center, Kipper Institute of Immunology, Petach Tikva, Israel.,Pediatric Department, Allergy and Immunology Clinic, Carmel Medical Center, Technion Faculty of Medicine, Haifa, Israel
| | - Na'ama Epstein-Rigbi
- Institute of Allergy, Immunology and Pediatric Pulmonology, Shamir (Former Assaf Harofeh) Medical Center, Zerifin, Israel
| | - Amos Etzioni
- The Jeffrey Modell Foundation Israeli Network for Primary Immunodeficiency, New York, NY, United States.,Ruth Children Hospital, Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Ilan Dalal
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Jeffrey Modell Foundation Israeli Network for Primary Immunodeficiency, New York, NY, United States.,Pediatric Allergy Unit, E. Wolfson Medical Center, Holon, Israel.,Pediatric Department, E. Wolfson Medical Center, Holon, Israel
| | - Raz Somech
- The Jeffrey Modell Foundation Israeli Network for Primary Immunodeficiency, New York, NY, United States.,Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, "Edmond and Lily Safra" Children's Hospital, Sheba Medical Center, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
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Piroth L, Cottenet J, Mariet AS, Bonniaud P, Blot M, Tubert-Bitter P, Quantin C. Comparison of the characteristics, morbidity, and mortality of COVID-19 and seasonal influenza: a nationwide, population-based retrospective cohort study. THE LANCET RESPIRATORY MEDICINE 2020; 9:251-259. [PMID: 33341155 PMCID: PMC7832247 DOI: 10.1016/s2213-2600(20)30527-0] [Citation(s) in RCA: 352] [Impact Index Per Article: 88.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 11/02/2020] [Accepted: 11/05/2020] [Indexed: 12/12/2022]
Abstract
Background To date, influenza epidemics have been considered suitable for use as a model for the COVID-19 epidemic, given that they are respiratory diseases with similar modes of transmission. However, data directly comparing the two diseases are scarce. Methods We did a nationwide retrospective cohort study using the French national administrative database (PMSI), which includes discharge summaries for all hospital admissions in France. All patients hospitalised for COVID-19 from March 1 to April 30, 2020, and all patients hospitalised for influenza between Dec 1, 2018, and Feb 28, 2019, were included. The diagnosis of COVID-19 (International Classification of Diseases [10th edition] codes U07.10, U07.11, U07.12, U07.14, or U07.15) or influenza (J09, J10, or J11) comprised primary, related, or associated diagnosis. Comparisons of risk factors, clinical characteristics, and outcomes between patients hospitalised for COVID-19 and influenza were done, with data also stratified by age group. Findings 89 530 patients with COVID-19 and 45 819 patients with influenza were hospitalised in France during the respective study periods. The median age of patients was 68 years (IQR 52–82) for COVID-19 and 71 years (34–84) for influenza. Patients with COVID-19 were more frequently obese or overweight, and more frequently had diabetes, hypertension, and dyslipidaemia than patients with influenza, whereas those with influenza more frequently had heart failure, chronic respiratory disease, cirrhosis, and deficiency anaemia. Patients admitted to hospital with COVID-19 more frequently developed acute respiratory failure, pulmonary embolism, septic shock, or haemorrhagic stroke than patients with influenza, but less frequently developed myocardial infarction or atrial fibrillation. In-hospital mortality was higher in patients with COVID-19 than in patients with influenza (15 104 [16·9%] of 89 530 vs 2640 [5·8%] of 45 819), with a relative risk of death of 2·9 (95% CI 2·8–3·0) and an age-standardised mortality ratio of 2·82. Of the patients hospitalised, the proportion of paediatric patients (<18 years) was smaller for COVID-19 than for influenza (1227 [1·4%] vs 8942 [19·5%]), but a larger proportion of patients younger than 5 years needed intensive care support for COVID-19 than for influenza (14 [2·3%] of 613 vs 65 [0·9%] of 6973). In adolescents (11–17 years), the in-hospital mortality was ten-times higher for COVID-19 than for influenza (five [1·1% of 458 vs one [0·1%] of 804), and patients with COVID-19 were more frequently obese or overweight. Interpretation The presentation of patients with COVID-19 and seasonal influenza requiring hospitalisation differs considerably. Severe acute respiratory syndrome coronavirus 2 is likely to have a higher potential for respiratory pathogenicity, leading to more respiratory complications and to higher mortality. In children, although the rate of hospitalisation for COVID-19 appears to be lower than for influenza, in-hospital mortality is higher; however, low patient numbers limit this finding. These findings highlight the importance of appropriate preventive measures for COVID-19, as well as the need for a specific vaccine and treatment. Funding French National Research Agency.
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Affiliation(s)
- Lionel Piroth
- Inserm CIC 1432, Clinical Epidemiology/Clinical Trials Unit, Clinical Investigation Centre, Dijon University Hospital, Dijon, France; Infectious Diseases Department, Dijon University Hospital, Dijon, France; Faculty of Medicine, University of Bourgogne-Franche-Comté, Dijon, France
| | - Jonathan Cottenet
- Biostatistics and Bioinformatics (DIM), Dijon University Hospital, Dijon, France; Faculty of Medicine, University of Bourgogne-Franche-Comté, Dijon, France
| | - Anne-Sophie Mariet
- Inserm CIC 1432, Clinical Epidemiology/Clinical Trials Unit, Clinical Investigation Centre, Dijon University Hospital, Dijon, France; Biostatistics and Bioinformatics (DIM), Dijon University Hospital, Dijon, France; Faculty of Medicine, University of Bourgogne-Franche-Comté, Dijon, France
| | - Philippe Bonniaud
- Reference Centre for Rare Pulmonary Diseases, Pulmonary Medicine and Intensive Care Unit Department, Dijon University Hospital, Dijon, France; Faculty of Medicine, University of Bourgogne-Franche-Comté, Dijon, France; Inserm LNC UMR1231, LipSTIC LabEx Team, Dijon, France
| | - Mathieu Blot
- Infectious Diseases Department, Dijon University Hospital, Dijon, France
| | - Pascale Tubert-Bitter
- Université Paris-Saclay, UVSQ, Université Paris-Sud, Inserm, High-Dimensional Biostatistics for Drug Safety and Genomics, CESP, Villejuif, France
| | - Catherine Quantin
- Inserm CIC 1432, Clinical Epidemiology/Clinical Trials Unit, Clinical Investigation Centre, Dijon University Hospital, Dijon, France; Biostatistics and Bioinformatics (DIM), Dijon University Hospital, Dijon, France; Faculty of Medicine, University of Bourgogne-Franche-Comté, Dijon, France; Université Paris-Saclay, UVSQ, Université Paris-Sud, Inserm, High-Dimensional Biostatistics for Drug Safety and Genomics, CESP, Villejuif, France.
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Brandão‐de‐Resende C, Diniz‐Filho A, Almeida Brito F, Vasconcelos‐Santos DV. SARS‐CoV‐2 and COVID‐19 for the ophthalmologist. Clin Exp Ophthalmol 2020; 49:70-80. [DOI: 10.1111/ceo.13877] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 10/26/2020] [Accepted: 10/28/2020] [Indexed: 02/07/2023]
Affiliation(s)
- Camilo Brandão‐de‐Resende
- Hospital São Geraldo Hospital das Clínicas da Universidade Federal de Minas Gerais Belo Horizonte Brazil
- Departamento de Oftalmologia e Otorrinolaringologia Faculdade de Medicina da Universidade Federal de Minas Gerais Belo Horizonte Brazil
- Programa de Pós‐Graduação em Ciências da Saúde, Infectologia e Medicina Tropical Universidade Federal de Minas Gerais Belo Horizonte Brazil
| | - Alberto Diniz‐Filho
- Hospital São Geraldo Hospital das Clínicas da Universidade Federal de Minas Gerais Belo Horizonte Brazil
- Departamento de Oftalmologia e Otorrinolaringologia Faculdade de Medicina da Universidade Federal de Minas Gerais Belo Horizonte Brazil
| | - Fabiano Almeida Brito
- Departamento de Propedêutica Complementar Faculdade de Medicina da Universidade Federal de Minas Gerais Belo Horizonte Brazil
- Assessoria Científica Instituto Hermes Pardini Belo Horizonte Brazil
| | - Daniel Vitor Vasconcelos‐Santos
- Hospital São Geraldo Hospital das Clínicas da Universidade Federal de Minas Gerais Belo Horizonte Brazil
- Departamento de Oftalmologia e Otorrinolaringologia Faculdade de Medicina da Universidade Federal de Minas Gerais Belo Horizonte Brazil
- Programa de Pós‐Graduação em Ciências da Saúde, Infectologia e Medicina Tropical Universidade Federal de Minas Gerais Belo Horizonte Brazil
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39
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Borocco C, Pouletty M, Galeotti C, Meinzer U, Faye A, Koné-Paut I, Ouldali N, Melki I. Response to 'Correspondence on 'Paediatric multisystem inflammatory syndrome temporally associated with SARS-CoV-2 mimicking Kawasaki disease (Kawa-COVID19): a multicentre cohort'' by Mastrolia et al. Ann Rheum Dis 2020; 81:e219. [PMID: 33023959 DOI: 10.1136/annrheumdis-2020-218814] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 09/26/2020] [Indexed: 12/30/2022]
Affiliation(s)
- Charlotte Borocco
- Department of Paediatric Rheumatology, Reference Centre for Autoinflammatory Diseases and Amyloidosis (CEREMAIA), Bicêtre University Hospital, AP-HP, Le Kremlin-Bicetre, France.,University of Paris Sud Saclay, Paris, France
| | - Marie Pouletty
- General Pediatrics, Infectious Disease and Internal Medicine Department, Reference center for Rheumatic, AutoImmune and Systemic diseases in children (RAISE), Hôpital Robert Debre, AP-HP, Paris, 75019, France
| | - Caroline Galeotti
- Department of Paediatric Rheumatology, Reference Centre for Autoinflammatory Diseases and Amyloidosis (CEREMAIA), Bicêtre University Hospital, AP-HP, Le Kremlin-Bicetre, France
| | - Ulrich Meinzer
- General Pediatrics, Infectious Disease and Internal Medicine Department, Reference center for Rheumatic, AutoImmune and Systemic diseases in children (RAISE), Hôpital Robert Debre, AP-HP, Paris, 75019, France.,Center for Research on Inflammation, UMR1149, INSERM, Paris, France
| | - Albert Faye
- General Pediatrics, Infectious Disease and Internal Medicine Department, Reference center for Rheumatic, AutoImmune and Systemic diseases in children (RAISE), Hôpital Robert Debre, AP-HP, Paris, 75019, France.,UMR 1123, ECEVE, INSERM, Paris, France
| | - Isabelle Koné-Paut
- Department of Paediatric Rheumatology, Reference Centre for Autoinflammatory Diseases and Amyloidosis (CEREMAIA), Bicêtre University Hospital, AP-HP, Le Kremlin-Bicetre, France.,University of Paris Sud Saclay, Paris, France
| | - Naim Ouldali
- General Pediatrics, Infectious Disease and Internal Medicine Department, Reference center for Rheumatic, AutoImmune and Systemic diseases in children (RAISE), Hôpital Robert Debre, AP-HP, Paris, 75019, France.,UMR 1123, ECEVE, INSERM, Paris, France
| | - Isabelle Melki
- General Pediatrics, Infectious Disease and Internal Medicine Department, Reference center for Rheumatic, AutoImmune and Systemic diseases in children (RAISE), Hôpital Robert Debre, AP-HP, Paris, 75019, France .,Laboratory of Neurogenetics and Neuroinflammation, Institute Imagine Institute of Genetic Diseases, Paris, France.,Pediatric Hematology-Immunology and Rheumatology Department, Reference center for Rheumatic, AutoImmune and Systemic diseases in children (RAISE), Hôpital Necker-Enfants Malades, AP-HP, Paris, France
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40
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Mulinari Turin de Oliveira N, Fernandes da Silva Figueiredo I, Cristine Malaquias da Silva L, Sauruk da Silva K, Regis Bueno L, Barbosa da Luz B, Rita Corso C, Paula Werner MF, Soares Fernandes E, Maria-Ferreira D. Tissue Proteases and Immune Responses: Influencing Factors of COVID-19 Severity and Mortality. Pathogens 2020; 9:E817. [PMID: 33036180 PMCID: PMC7600261 DOI: 10.3390/pathogens9100817] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/02/2020] [Accepted: 10/04/2020] [Indexed: 12/18/2022] Open
Abstract
The coronavirus disease 19 (COVID-19) is caused by the highly transmissible severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has affected the global population despite socioeconomic status and amazed surveillance agencies for its incidence, mortality, and recovery rates. COVID-19 affects all age groups; however, it is suggested to progress into severe disease and cause mortality in over 10% of the confirmed cases, depending on the individual characteristics of the affected population. One of the biggest unanswered questions it is why only some individuals develop into the severe stages of the disease. Current data indicate that most of the critically ill are the elderly or those with comorbidities such as hypertension, diabetes, and asthma. However, it has been noted that, in some populations, severe disease is mostly observed in much younger individuals (<60-years old) with no reported underlying medical conditions. Certainly, many factors may contribute to disease severity including intrinsic host factors such as genetic variants, the expression levels of tissue proteins, among others. Considering all these aspects, this review aims to discuss how the expression levels of tissue proteases and the different profiles of immune responses influence the susceptibility to COVID-19 as well as disease severity and outcome.
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Affiliation(s)
- Natália Mulinari Turin de Oliveira
- Faculdades Pequeno Príncipe, Av. Iguaçu No 333, Curitiba, PR 80250-200, Brazil; (N.M.T.d.O.); (I.F.d.S.F.); (L.C.M.d.S.); (K.S.d.S.); (L.R.B.); (C.R.C.); (E.S.F.)
- Instituto de Pesquisa Pelé Pequeno Príncipe, Av. Silva Jardim No 1532, Curitiba, PR 80250-200, Brazil
| | - Isabella Fernandes da Silva Figueiredo
- Faculdades Pequeno Príncipe, Av. Iguaçu No 333, Curitiba, PR 80250-200, Brazil; (N.M.T.d.O.); (I.F.d.S.F.); (L.C.M.d.S.); (K.S.d.S.); (L.R.B.); (C.R.C.); (E.S.F.)
- Instituto de Pesquisa Pelé Pequeno Príncipe, Av. Silva Jardim No 1532, Curitiba, PR 80250-200, Brazil
| | - Liziane Cristine Malaquias da Silva
- Faculdades Pequeno Príncipe, Av. Iguaçu No 333, Curitiba, PR 80250-200, Brazil; (N.M.T.d.O.); (I.F.d.S.F.); (L.C.M.d.S.); (K.S.d.S.); (L.R.B.); (C.R.C.); (E.S.F.)
- Instituto de Pesquisa Pelé Pequeno Príncipe, Av. Silva Jardim No 1532, Curitiba, PR 80250-200, Brazil
| | - Karien Sauruk da Silva
- Faculdades Pequeno Príncipe, Av. Iguaçu No 333, Curitiba, PR 80250-200, Brazil; (N.M.T.d.O.); (I.F.d.S.F.); (L.C.M.d.S.); (K.S.d.S.); (L.R.B.); (C.R.C.); (E.S.F.)
- Instituto de Pesquisa Pelé Pequeno Príncipe, Av. Silva Jardim No 1532, Curitiba, PR 80250-200, Brazil
| | - Laryssa Regis Bueno
- Faculdades Pequeno Príncipe, Av. Iguaçu No 333, Curitiba, PR 80250-200, Brazil; (N.M.T.d.O.); (I.F.d.S.F.); (L.C.M.d.S.); (K.S.d.S.); (L.R.B.); (C.R.C.); (E.S.F.)
- Instituto de Pesquisa Pelé Pequeno Príncipe, Av. Silva Jardim No 1532, Curitiba, PR 80250-200, Brazil
| | - Bruna Barbosa da Luz
- Departamento de Farmacologia, Universidade Federal do Paraná, Curitiba, PR 81531-980, Brazil; (B.B.d.L.); (M.F.P.W.)
| | - Cláudia Rita Corso
- Faculdades Pequeno Príncipe, Av. Iguaçu No 333, Curitiba, PR 80250-200, Brazil; (N.M.T.d.O.); (I.F.d.S.F.); (L.C.M.d.S.); (K.S.d.S.); (L.R.B.); (C.R.C.); (E.S.F.)
- Instituto de Pesquisa Pelé Pequeno Príncipe, Av. Silva Jardim No 1532, Curitiba, PR 80250-200, Brazil
| | - Maria Fernanda Paula Werner
- Departamento de Farmacologia, Universidade Federal do Paraná, Curitiba, PR 81531-980, Brazil; (B.B.d.L.); (M.F.P.W.)
| | - Elizabeth Soares Fernandes
- Faculdades Pequeno Príncipe, Av. Iguaçu No 333, Curitiba, PR 80250-200, Brazil; (N.M.T.d.O.); (I.F.d.S.F.); (L.C.M.d.S.); (K.S.d.S.); (L.R.B.); (C.R.C.); (E.S.F.)
- Instituto de Pesquisa Pelé Pequeno Príncipe, Av. Silva Jardim No 1532, Curitiba, PR 80250-200, Brazil
| | - Daniele Maria-Ferreira
- Faculdades Pequeno Príncipe, Av. Iguaçu No 333, Curitiba, PR 80250-200, Brazil; (N.M.T.d.O.); (I.F.d.S.F.); (L.C.M.d.S.); (K.S.d.S.); (L.R.B.); (C.R.C.); (E.S.F.)
- Instituto de Pesquisa Pelé Pequeno Príncipe, Av. Silva Jardim No 1532, Curitiba, PR 80250-200, Brazil
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