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A new SARS-CoV-2 variant with high lethality poorly detected by RT-PCR on nasopharyngeal samples: an observational study.
Fillâtre, Pierre; Dufour, Marie-José; Behillil, Sylvie; Vatan, Rémi; Reusse, Pascale; Gabellec, Alice; Velmans, Nicolas; Montagne, Catherine; Geffroy Du Coudret, Sophie; Droumaguet, Edith; Merour, Véronique; Enouf, Vincent; Buzelé, Rodolphe; Valence, Marion; Guillotel, Elena; Gagnière, Bertrand; Baidaliuk, Artem; Zhukova, Anna; Tourdjman, Mathieu; Thibault, Vincent; Grolhier, Claire; Pronier, Charlotte; Lescure, François-Xavier; Simon-Loriere, Etienne; Costagliola, Dominique; Van Der Werf, Sylvie; Tattevin, Pierre; Massart, Nicolas.
Afiliación
  • Fillâtre P; Service de Réanimation Polyvalente, CH de Saint-Brieuc, 10 rue Marcel Proust, 22000, Saint-Brieuc, France. Electronic address: pierre.fillatre@armorsante.bzh.
  • Dufour MJ; Service de Biologie Médicale, CH de Lannion, Centre Hospitalier Pierre-le-Damany, 22303, Lannion, France.
  • Behillil S; National Reference Centre for Respiratory Viruses, Molecular Genetics of RNA Viruses, CNRS-UMR 3569, University of Paris, Institut Pasteur, Paris, France.
  • Vatan R; Service de Médecine Interne, CH de Lannion, Centre Hospitalier Pierre-le-Damany, 22303, Lannion, France; Service de Maladies Infectieuses, CH de Saint-Brieuc, 10 rue Marcel Proust, 22000, Saint-Brieuc, France.
  • Reusse P; Service de Gériatrie, CH de Lannion, Centre Hospitalier Pierre-le-Damany, 22303, Lannion, France.
  • Gabellec A; Service de Gériatrie, CH de Lannion, Centre Hospitalier Pierre-le-Damany, 22303, Lannion, France.
  • Velmans N; Service de Médecine Interne, CH de Lannion, Centre Hospitalier Pierre-le-Damany, 22303, Lannion, France.
  • Montagne C; Service d'Imagerie Médicale, CH de Lannion, Centre Hospitalier Pierre-le-Damany, 22303, Lannion, France.
  • Geffroy Du Coudret S; Service de Pneumologie, CH de Lannion, Centre Hospitalier Pierre-le-Damany, 22303, Lannion, France.
  • Droumaguet E; Département d'Informatique Médicale, CH de Lannion, Centre Hospitalier Pierre-le-Damany, 22303, Lannion, France.
  • Merour V; Plateforme de Surveillance Continue, CH de Lannion, Centre Hospitalier Pierre-le-Damany, 22303, Lannion, France.
  • Enouf V; National Reference Centre for Respiratory Viruses, Molecular Genetics of RNA Viruses, CNRS-UMR 3569, University of Paris, Institut Pasteur, Paris, France; Mutualized Platform of Microbiology, Pasteur International Bioresources Network, Institut Pasteur, Paris, France.
  • Buzelé R; Service de Maladies Infectieuses, CH de Saint-Brieuc, 10 rue Marcel Proust, 22000, Saint-Brieuc, France.
  • Valence M; Service de Maladies Infectieuses, CH de Saint-Brieuc, 10 rue Marcel Proust, 22000, Saint-Brieuc, France.
  • Guillotel E; Service de Biologie Médicale, CH de Saint-Brieuc, 10, rue Marcel Proust, 22000, Saint-Brieuc, France.
  • Gagnière B; Santé Publique France, French National Public Health Agency, Cellule Bretagne, Rennes, France.
  • Baidaliuk A; Evolutionary Genomics of RNA Viruses, Institut Pasteur, Paris, France.
  • Zhukova A; Unité Bioinformatique Evolutive & Hub de Bioinformatique et Biostatistique-Département Biologie Computationnelle, USR3756 (C3BI/DBC), Institut Pasteur, Paris, France.
  • Tourdjman M; Santé Publique France, The French Public Health Agency, Saint-Maurice, France.
  • Thibault V; Service de Virologie, CHU de Rennes, 2, rue Henri le Guilloux, 35000, Rennes, France.
  • Grolhier C; Service de Virologie, CHU de Rennes, 2, rue Henri le Guilloux, 35000, Rennes, France.
  • Pronier C; Service de Virologie, CHU de Rennes, 2, rue Henri le Guilloux, 35000, Rennes, France.
  • Lescure FX; Department of Infectious and Tropical Diseases, Assistance Publique-Hôpitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France; Infections Antimicrobials Modelling Evolution (IAME), UMR 1137, University of Paris, Paris, France.
  • Simon-Loriere E; Evolutionary Genomics of RNA Viruses, Institut Pasteur, Paris, France.
  • Costagliola D; Sorbonne Université, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique (IPLESP), Paris, France.
  • Van Der Werf S; National Reference Centre for Respiratory Viruses, Molecular Genetics of RNA Viruses, CNRS-UMR 3569, University of Paris, Institut Pasteur, Paris, France.
  • Tattevin P; Service de Maladie Infectieuse et de Réanimation Médicale, CHU de Rennes, 2, rue Henri le Guilloux, 35000, Rennes, France.
  • Massart N; Service de Réanimation Polyvalente, CH de Saint-Brieuc, 10 rue Marcel Proust, 22000, Saint-Brieuc, France.
Clin Microbiol Infect ; 28(2): 298.e9-298.e15, 2022 Feb.
Article en En | MEDLINE | ID: mdl-34627988
OBJECTIVES: In early January 2021 an outbreak of nosocomial cases of coronavirus disease 2019 (COVID-19) emerged in Western France; RT-PCR tests were repeatedly negative on nasopharyngeal samples but positive on lower respiratory tract samples. Whole-genome sequencing (WGS) revealed a new variant, currently defining a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage B.1.616. In March, the WHO classified this as a 'variant under investigation' (VUI). We analysed the characteristics and outcomes of COVID-19 cases related to this new variant. METHODS: Clinical, virological, and radiological data were retrospectively collected from medical charts in the two hospitals involved. We enrolled those inpatients with: (a) positive SARS-CoV-2 RT-PCR on a respiratory sample, (b) seroconversion with anti-SARS-CoV-2 IgG/IgM, or (c) suggestive symptoms and typical features of COVID-19 on a chest CT scan. Cases were categorized as B.1.616, a variant of concern (VOC), or unknown. RESULTS: From 1st January to 24th March 2021, 114 patients fulfilled the inclusion criteria: B.1.616 (n = 39), VOC (n = 32), and unknown (n = 43). B.1.616-related cases were older than VOC-related cases (81 years, interquartile range (IQR) 73-88 versus 73 years, IQR 67-82, p < 0.05) and their first RT-PCR tests were rarely positive (6/39, 15% versus 31/32, 97%, p < 0.05). The B.1.616 variant was independently associated with severe disease (multivariable Cox model HR 4.0, 95%CI 1.5-10.9) and increased lethality (28-day mortality 18/39 (46%) for B.1.616 versus 5/32 (16%) for VOC, p = 0.006). CONCLUSION: We report a nosocomial outbreak of COVID-19 cases related to a new variant, B.1.616, which is poorly detected by RT-PCR on nasopharyngeal samples and is associated with high lethality.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: SARS-CoV-2 / COVID-19 Tipo de estudio: Observational_studies / Prognostic_studies / Risk_factors_studies Límite: Humans País/Región como asunto: Europa Idioma: En Revista: Clin Microbiol Infect Asunto de la revista: DOENCAS TRANSMISSIVEIS / MICROBIOLOGIA Año: 2022 Tipo del documento: Article Pais de publicación: Reino Unido
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: SARS-CoV-2 / COVID-19 Tipo de estudio: Observational_studies / Prognostic_studies / Risk_factors_studies Límite: Humans País/Región como asunto: Europa Idioma: En Revista: Clin Microbiol Infect Asunto de la revista: DOENCAS TRANSMISSIVEIS / MICROBIOLOGIA Año: 2022 Tipo del documento: Article Pais de publicación: Reino Unido