1. A new SARS-CoV-2 variant poorly detected by RT-PCR on nasopharyngeal samples, with high lethality: an observational study
- Author
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Fillâtre, Pierre, Dufour, Marie-José, Behillil, Sylvie, Vatan, Remi, Reusse, Pascale, Gabellec, Alice, Velmans, Nicolas, Montagne, Catherine, Du Coudret, Sophie Geffroy, Droumaguet, Edith, Merour, Véronique, Enouf, Vincent, Buzele, Rodolphe, Valence, Marion, Guillotel, Elena, Gagniere, Bertrand, Baidaliuk, Artem, Zhukova, Anna, Tourdjman, Mathieu, Thibault, V., Grolhier, Claire, Pronier, Charlotte, Lescure, François-Xavier, Simon-Loriere, Etienne, Costagliola, Dominique, Van Der Werf, Sylvie, Tattevin, Pierre, Massart, Nicolas, CHU de Saint-Brieuc, Centre hospitalier Pierre Le Damany - Lannion, Centre hospitalier de Lannion, Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses (GMV-ARN (UMR_3569 / U-Pasteur_2)), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Centre National de Référence des virus des infections respiratoires (dont la grippe) - National Reference Center Virus Influenzae [Paris] (CNR - laboratoire coordonnateur), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Pasteur International Bioresources network (PIBNet), Santé publique France - French National Public Health Agency [Saint-Maurice, France], Génomique évolutive des virus à ARN - Evolutionary genomics of RNA viruses, Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, CHU Pontchaillou [Rennes], Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Université Sorbonne Paris Nord, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), ARN régulateurs bactériens et médecine (BRM), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), None, We thank Olivia Da Conceicao and Cylia Imekhlaf for their help in collecting data from patients' charts. We would like to thank all the healthcare workers, public health employees, and scientists involved in the COVID-19 response to this outbreak. We acknowledge the authors, originating and submitting laboratories of the sequences from GISAID (Supplementary Material Table S2). We avoided any direct analysis of genomic data not submitted as part of this paper and used this genomic data only as background. This work used the computational and storage services (Maestro cluster) provided by the IT department at Institut Pasteur, Paris., ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), Centre National de Référence des virus des infections respiratoires (dont la grippe) - National Reference Center Virus Influenzae [Paris] (CNR), Jonchère, Laurent, Virus et Interférence ARN - Viruses and RNA Interference, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris], Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Université Sorbonne Paris Nord, Morphogenèse du cœur - Heart morphogenesis (Imagine - Institut Pasteur U1163), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )
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SARS-CoV-2 variants ,Reverse Transcriptase Polymerase Chain Reaction ,SARS-CoV-2 ,[SDV]Life Sciences [q-bio] ,COVID-19 ,Coronavirus infections ,[SDV] Life Sciences [q-bio] ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,Humans ,Original Article ,Severity of illness index / Virology ,France ,[SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology ,COVID-19 / Epidemiology ,Retrospective Studies - Abstract
Objectives In early January 2021, an outbreak of nosocomial cases of COVID-19 emerged in Western France, with RT-PCR tests repeatedly negative on nasopharyngeal samples but positive on lower respiratory tract samples. Whole genome sequencing (WGS) revealed a new variant, currently defining a novel SARS-CoV-2 lineage: B.1.616. In March, WHO classified this variant as ‘under investigation’ (VUI). We analyzed 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 inpatients with either: i) positive SARS-CoV-2 RT-PCR on a respiratory sample; ii) seroconversion with anti-SARS-CoV-2 IgG/IgM; iii) suggestive symptoms and typical features of COVID-19 on a chest CT scan. Cases were categorized as either: i) B.1.616; ii) variant of concern (VOC); iii) unknown. Results From January 1st to March 24th, 2021, 114 patients fulfilled 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], vs 73 years IQR [67-82], P, Graphical abstract Image 1
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- 2022