{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,24]],"date-time":"2026-10-24T00:02:29Z","timestamp":1792800149396,"version":"4.5.0"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2020,6,9]],"date-time":"2020-06-09T00:00:00Z","timestamp":1591660800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Laboratoire d\u2019Excellence","award":["ANR-10-LABX-62-IBEID"],"award-info":[{"award-number":["ANR-10-LABX-62-IBEID"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,5,18]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>Human encephalitis represents a medical challenge from a diagnostic and therapeutic point of view. We investigated the cause of 2 fatal cases of encephalitis of unknown origin in immunocompromised patients.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>Untargeted metatranscriptomics was applied on the brain tissue of 2 patients to search for pathogens (viruses, bacteria, fungi, or protozoans) without a prior hypothesis.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Umbre arbovirus, an orthobunyavirus never previously identified in humans, was found in 2 patients. In situ hybridization and reverse transcriptase\u2013quantitative polymerase chain reaction (RT-qPCR) showed that Umbre virus infected neurons and replicated at high titers. The virus was not detected in cerebrospinal fluid by RT-qPCR. Viral sequences related to Koongol virus, another orthobunyavirus close to Umbre virus, were found in Culex pipiens mosquitoes captured in the south of France where the patients had spent some time before the onset of symptoms, demonstrating the presence of the same clade of arboviruses in Europe and their potential public health impact. A serological survey conducted in the same area did not identify individuals positive for Umbre virus. The absence of seropositivity in the population may not reflect the actual risk of disease transmission in immunocompromised individuals.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>Umbre arbovirus can cause encephalitis in immunocompromised humans and is present in Europe.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/cid\/ciaa308","type":"journal-article","created":{"date-parts":[[2020,3,18]],"date-time":"2020-03-18T20:10:58Z","timestamp":1584562258000},"page":"1701-1708","source":"Crossref","is-referenced-by-count":32,"title":["Identification of Umbre Orthobunyavirus as a Novel Zoonotic Virus Responsible for Lethal Encephalitis in 2 French Patients with Hypogammaglobulinemia"],"prefix":"10.1093","volume":"72","author":[{"given":"Philippe","family":"P\u00e9rot","sequence":"first","affiliation":[{"name":"Pathogen Discovery Laboratory, Institut Pasteur, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Franck","family":"Bielle","sequence":"additional","affiliation":[{"name":"D\u00e9partement de Neuropathologie Raymond Escourolle, Assistance Publique \u2013 H\u00f4pitaux de Paris (AP-HP)-Sorbonne, Groupe Hospitalier Piti\u00e9-Salp\u00eatri\u00e8re, Paris, France"},{"name":"Sorbonne Universit\u00e9, Brain Institute (Institut du Cerveau et de la Moelle \u00e9pini\u00e8re; Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale [INSERM], Unit\u00e9 Mixte de Recherche Sant\u00e9 1127; Centre National de la Recherche Scientifique [CNRS], Unit\u00e9 Mixte de Recherche [UMR] 7225), Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8504-4675","authenticated-orcid":false,"given":"Thomas","family":"Bigot","sequence":"additional","affiliation":[{"name":"Hub de Bioinformatique et Biostatistique \u2013 D\u00e9partement Biologie Computationnelle, Institut Pasteur, Unit\u00e9 de Service et de Recherche 3756 CNRS, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vincent","family":"Foulongne","sequence":"additional","affiliation":[{"name":"Pathogenesis and Control of Chronic Infections, INSERM, University of Montpellier, Etablissement Fran\u00e7ais du Sang, Centre Hospitalier Universitaire (CHU) Montpellier, Montpellier, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karine","family":"Bollor\u00e9","sequence":"additional","affiliation":[{"name":"Pathogenesis and Control of Chronic Infections, INSERM, University of Montpellier, Etablissement Fran\u00e7ais du Sang, Centre Hospitalier Universitaire (CHU) Montpellier, Montpellier, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Delphine","family":"Chr\u00e9tien","sequence":"additional","affiliation":[{"name":"Pathogen Discovery Laboratory, Institut Pasteur, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patricia","family":"Gil","sequence":"additional","affiliation":[{"name":"Centre de Coop\u00e9ration Internationale en Recherche Agronomique Pour le D\u00e9veloppement (CIRAD), UMR ASTRE, Montpellier, France"},{"name":"ASTRE, CIRAD, Institut National de la Recherche Agronomique, University of Montpellier, Montpellier, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seraf\u00edn","family":"Guti\u00e9rrez","sequence":"additional","affiliation":[{"name":"Centre de Coop\u00e9ration Internationale en Recherche Agronomique Pour le D\u00e9veloppement (CIRAD), UMR ASTRE, Montpellier, France"},{"name":"ASTRE, CIRAD, Institut National de la Recherche Agronomique, University of Montpellier, Montpellier, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gr\u00e9gory","family":"L\u2019Ambert","sequence":"additional","affiliation":[{"name":"Entente Interd\u00e9partementale Pour la D\u00e9moustication M\u00e9diterran\u00e9e, Montpellier, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karima","family":"Mokhtari","sequence":"additional","affiliation":[{"name":"D\u00e9partement de Neuropathologie Raymond Escourolle, Assistance Publique \u2013 H\u00f4pitaux de Paris (AP-HP)-Sorbonne, Groupe Hospitalier Piti\u00e9-Salp\u00eatri\u00e8re, Paris, France"},{"name":"Sorbonne Universit\u00e9, Brain Institute (Institut du Cerveau et de la Moelle \u00e9pini\u00e8re; Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale [INSERM], Unit\u00e9 Mixte de Recherche Sant\u00e9 1127; Centre National de la Recherche Scientifique [CNRS], Unit\u00e9 Mixte de Recherche [UMR] 7225), Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan","family":"Hellert","sequence":"additional","affiliation":[{"name":"Structural Virology Unit, Institut Pasteur, CNRS UMR 3569, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marie","family":"Flamand","sequence":"additional","affiliation":[{"name":"Structural Virology Unit, Institut Pasteur, CNRS UMR 3569, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carole","family":"Tamietti","sequence":"additional","affiliation":[{"name":"Structural Virology Unit, Institut Pasteur, CNRS UMR 3569, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muriel","family":"Coulpier","sequence":"additional","affiliation":[{"name":"UMR Virologie, Agence Nationale de S\u00e9curit\u00e9 Sanitaire de l\u2019Alimentation, de l\u2019Environnement et du Travail, \u00c9cole Nationale V\u00e9t\u00e9rinaire d\u2019Alfort, Institut National de Recherche Pour l\u2019Agriculture, l\u2019Alimentation et l\u2019Environnement, Universit\u00e9 Paris Est, Ecole Nationale V\u00e9t\u00e9rinaire d\u2019Alfort, Maisons-Alfort, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anne","family":"Huard de Verneuil","sequence":"additional","affiliation":[{"name":"UMR Virologie, Agence Nationale de S\u00e9curit\u00e9 Sanitaire de l\u2019Alimentation, de l\u2019Environnement et du Travail, \u00c9cole Nationale V\u00e9t\u00e9rinaire d\u2019Alfort, Institut National de Recherche Pour l\u2019Agriculture, l\u2019Alimentation et l\u2019Environnement, Universit\u00e9 Paris Est, Ecole Nationale V\u00e9t\u00e9rinaire d\u2019Alfort, Maisons-Alfort, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah","family":"Temmam","sequence":"additional","affiliation":[{"name":"Pathogen Discovery Laboratory, Institut Pasteur, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Th\u00e9r\u00e8se","family":"Couderc","sequence":"additional","affiliation":[{"name":"Biology of Infection Unit, Institut Pasteur, INSERM U1117, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edouard","family":"De Sousa Cunha","sequence":"additional","affiliation":[{"name":"D\u00e9partement de Neuropathologie Raymond Escourolle, Assistance Publique \u2013 H\u00f4pitaux de Paris (AP-HP)-Sorbonne, Groupe Hospitalier Piti\u00e9-Salp\u00eatri\u00e8re, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susana","family":"Boluda","sequence":"additional","affiliation":[{"name":"D\u00e9partement de Neuropathologie Raymond Escourolle, Assistance Publique \u2013 H\u00f4pitaux de Paris (AP-HP)-Sorbonne, Groupe Hospitalier Piti\u00e9-Salp\u00eatri\u00e8re, Paris, France"},{"name":"Sorbonne Universit\u00e9, Brain Institute (Institut du Cerveau et de la Moelle \u00e9pini\u00e8re; Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale [INSERM], Unit\u00e9 Mixte de Recherche Sant\u00e9 1127; Centre National de la Recherche Scientifique [CNRS], Unit\u00e9 Mixte de Recherche [UMR] 7225), Paris, France"},{"name":"Centre National de R\u00e9f\u00e9rence des Agents Transmissibles Non Conventionnels (Reference Center for Nonconventional Transmissible Agents), Laboratory and Neuropathology Network for the Surveillance of Creutzfeldt-Jakob Disease, Sant\u00e9 Publique France, AP-HP, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isabelle","family":"Plu","sequence":"additional","affiliation":[{"name":"D\u00e9partement de Neuropathologie Raymond Escourolle, Assistance Publique \u2013 H\u00f4pitaux de Paris (AP-HP)-Sorbonne, Groupe Hospitalier Piti\u00e9-Salp\u00eatri\u00e8re, Paris, France"},{"name":"Sorbonne Universit\u00e9, Brain Institute (Institut du Cerveau et de la Moelle \u00e9pini\u00e8re; Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale [INSERM], Unit\u00e9 Mixte de Recherche Sant\u00e9 1127; Centre National de la Recherche Scientifique [CNRS], Unit\u00e9 Mixte de Recherche [UMR] 7225), Paris, France"},{"name":"Centre National de R\u00e9f\u00e9rence des Agents Transmissibles Non Conventionnels (Reference Center for Nonconventional Transmissible Agents), Laboratory and Neuropathology Network for the Surveillance of Creutzfeldt-Jakob Disease, Sant\u00e9 Publique France, AP-HP, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marie Bernadette","family":"Delisle","sequence":"additional","affiliation":[{"name":"Laboratoire de Neuropathologie, Laboratoire Universitaire d\u2019Anatomie et Cytologie Pathologiques, CHU de Toulouse, Universit\u00e9 Toulouse III\u2014Paul Sabatier, Toulouse, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fabrice","family":"Bonneville","sequence":"additional","affiliation":[{"name":"Department of Neuroradiology, CHU de Toulouse and UMR 1214 Toulouse NeuroImaging Center, Universit\u00e9 de Toulouse, INSERM, Toulouse, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Brassat","sequence":"additional","affiliation":[{"name":"Centre de Ressources et de Comp\u00e9tences Scl\u00e9rose en Plaques, Pole des Neurosciences CHU Toulouse and UMR 1043, Universit\u00e9 de Toulouse III, Toulouse, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claire","family":"Fieschi","sequence":"additional","affiliation":[{"name":"Service d\u2019Immunologie Clinique, H\u00f4pital Saint-Louis, Assistance Publique\u2013H\u00f4pitaux de Paris, Universit\u00e9 de Paris, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marion","family":"Malphettes","sequence":"additional","affiliation":[{"name":"Service d\u2019Immunologie Clinique, H\u00f4pital Saint-Louis, Assistance Publique\u2013H\u00f4pitaux de Paris, Universit\u00e9 de Paris, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charles","family":"Duyckaerts","sequence":"additional","affiliation":[{"name":"D\u00e9partement de Neuropathologie Raymond Escourolle, Assistance Publique \u2013 H\u00f4pitaux de Paris (AP-HP)-Sorbonne, Groupe Hospitalier Piti\u00e9-Salp\u00eatri\u00e8re, Paris, France"},{"name":"Sorbonne Universit\u00e9, Brain Institute (Institut du Cerveau et de la Moelle \u00e9pini\u00e8re; Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale [INSERM], Unit\u00e9 Mixte de Recherche Sant\u00e9 1127; Centre National de la Recherche Scientifique [CNRS], Unit\u00e9 Mixte de Recherche [UMR] 7225), Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9182-5846","authenticated-orcid":false,"given":"Bertrand","family":"Mathon","sequence":"additional","affiliation":[{"name":"Sorbonne Universit\u00e9, Brain Institute (Institut du Cerveau et de la Moelle \u00e9pini\u00e8re; Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale [INSERM], Unit\u00e9 Mixte de Recherche Sant\u00e9 1127; Centre National de la Recherche Scientifique [CNRS], Unit\u00e9 Mixte de Recherche [UMR] 7225), Paris, France"},{"name":"AP-HP, H\u00f4pitaux Universitaires Piti\u00e9-Salp\u00eatri\u00e8re Charles-Foix, Department of Neurosurgery, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sophie","family":"Demeret","sequence":"additional","affiliation":[{"name":"Department of Neurology, Neuro ICU, Groupe Hospitalier Piti\u00e9-Salp\u00eatri\u00e8re, AP-HP, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Danielle","family":"Seilhean","sequence":"additional","affiliation":[{"name":"D\u00e9partement de Neuropathologie Raymond Escourolle, Assistance Publique \u2013 H\u00f4pitaux de Paris (AP-HP)-Sorbonne, Groupe Hospitalier Piti\u00e9-Salp\u00eatri\u00e8re, Paris, France"},{"name":"Sorbonne Universit\u00e9, Brain Institute (Institut du Cerveau et de la Moelle \u00e9pini\u00e8re; Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale [INSERM], Unit\u00e9 Mixte de Recherche Sant\u00e9 1127; Centre National de la Recherche Scientifique [CNRS], Unit\u00e9 Mixte de Recherche [UMR] 7225), Paris, France"},{"name":"Centre National de R\u00e9f\u00e9rence des Agents Transmissibles Non Conventionnels (Reference Center for Nonconventional Transmissible Agents), Laboratory and Neuropathology Network for the Surveillance of Creutzfeldt-Jakob Disease, Sant\u00e9 Publique France, AP-HP, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marc","family":"Eloit","sequence":"additional","affiliation":[{"name":"Pathogen Discovery Laboratory, Institut Pasteur, Paris, France"},{"name":"Ecole Nationale V\u00e9t\u00e9rinaire d\u2019Alfort, Maisons-Alfort, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,6,9]]},"reference":[{"key":"2021051810405828400_CIT0001","doi-asserted-by":"crossref","first-page":"1565","DOI":"10.1086\/509330","article-title":"Beyond viruses: clinical profiles and etiologies associated with encephalitis","volume":"43","author":"Glaser","year":"2006","journal-title":"Clin Infect Dis"},{"key":"2021051810405828400_CIT0002","doi-asserted-by":"crossref","first-page":"1114","DOI":"10.1093\/cid\/cit458","article-title":"Case definitions, diagnostic algorithms, and priorities in encephalitis: consensus statement of the international encephalitis consortium","volume":"57","author":"Venkatesan","year":"2013","journal-title":"Clin Infect Dis"},{"key":"2021051810405828400_CIT0003","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1016\/j.cmi.2017.05.002","article-title":"Update and new insights in encephalitis","volume":"23","author":"Mailles","year":"2017","journal-title":"Clin Microbiol Infect"},{"key":"2021051810405828400_CIT0004","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1146\/annurev-virology-110615-035630","article-title":"Climate change and the arboviruses: lessons from the evolution of the dengue and yellow fever viruses","volume":"3","author":"Tabachnick","year":"2016","journal-title":"Annu Rev Virol"},{"key":"2021051810405828400_CIT0005","doi-asserted-by":"crossref","first-page":"219","DOI":"10.3390\/v7010219","article-title":"Usutu virus: an emerging flavivirus in Europe","volume":"7","author":"Ashraf","year":"2015","journal-title":"Viruses"},{"key":"2021051810405828400_CIT0006"},{"key":"2021051810405828400_CIT0007","first-page":"1420","article-title":"Virus isolations from mosquitoes collected in North Arcot district, Madras state, and Chittoor district, Andhra Pradesh between November 1955 and October 1957","volume":"57","author":"Dandawate","year":"1969","journal-title":"Indian J Med Res"},{"key":"2021051810405828400_CIT0008","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1007\/s13311-016-0443-5","article-title":"Encephalitic arboviruses: emergence, clinical presentation, and neuropathogenesis","volume":"13","author":"Salimi","year":"2016","journal-title":"Neurotherapeutics"},{"key":"2021051810405828400_CIT0009","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1038\/icb.1979.52","article-title":"Isolation of virus strains from mosquitoes collected in Queensland, 1972\u20131976","volume":"57","author":"Doherty","year":"1979","journal-title":"Aust J Exp Biol Med Sci"},{"key":"2021051810405828400_CIT0010","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1038\/icb.1963.2","article-title":"Studies of arthropod-borne virus infections in Queensland. 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