| Title: |
A new SARS-CoV-2 variant poorly detected by RT-PCR on nasopharyngeal samples, with high lethality: an observational study |
| Authors: |
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 |
| Contributors: |
Centre hospitalier de Saint-Brieuc Hôpital Yves Le Foll (CH Saint-Brieuc); Groupement Hospitalier Territoire d'Armor (GHT Armor); 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; Centre Hospitalier Universitaire de Rennes CHU Rennes = Rennes University Hospital Pontchaillou; 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) |
| Source: |
ISSN: 1198-743X. |
| Publisher Information: |
HAL CCSD; Elsevier for the European Society of Clinical Microbiology and Infectious Diseases |
| Publication Year: |
2022 |
| Collection: |
Université de Rennes 1: Publications scientifiques (HAL) |
| Subject Terms: |
COVID-19 / Epidemiology; Coronavirus infections; SARS-CoV-2 variants; Severity of illness index / Virology; [SDV]Life Sciences [q-bio]; [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology |
| Description: |
International audience ; 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. |
| Document Type: |
article in journal/newspaper |
| Language: |
English |
| Relation: |
info:eu-repo/semantics/altIdentifier/pmid/34627988; PUBMED: 34627988 |
| DOI: |
10.1016/j.cmi.2021.09.035 |
| Availability: |
https://hal.science/hal-03373018; https://hal.science/hal-03373018v1/document; https://hal.science/hal-03373018v1/file/Fillatre%20et%20al-2021-A%20new%20SARS-CoV-2%20variant%20poorly%20detected%20by%20RT-PCR%20on%20nasopharyngeal%20samples.pdf; https://doi.org/10.1016/j.cmi.2021.09.035 |
| Rights: |
http://creativecommons.org/licenses/by-nc/ ; info:eu-repo/semantics/OpenAccess |
| Accession Number: |
edsbas.536F6C8 |
| Database: |
BASE |