A New SARS-CoV-2 Variant Poorly Detected by RT-PCR on Nasopharyngeal Samples, with High Lethality

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Background: 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 patients with at least one of the following: 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 chest CT scan. Cases were categorized as either: i) B.1.616; ii) variant of concern (VOC); iii) unknown.Findings: From January 1st to March 24th, 2021, 114 patients fulfilled the inclusion criteria: B.1.616 (n=34), VOC (n=32), and unknown (n=48). B.1.616-related cases were older than VOC-related cases (81 years [73-88], vs 73 years [67-82], P Interpretation: We report a nosocomial outbreak of COVID-19 cases related to a new variant, B.1.616, poorly detected by RT-PCR on nasopharyngeal samples, with high lethality.Funding Statement: None. SW lab is funded by Institut Pasteur, CNRS, Université de Paris, Santé publique France, Labex IBEID (ANR-10-LABX- 62-IBEID), REACTing (Research & Action Emerging Infectious Diseases), and by the H2020 project 101003589 (RECOVER).Declaration of Interests: SW has patents issued and pending for SARS-associated coronavirus diagnostics. All other authors declare no competing interestsEthics Approval Statement: The French infectious diseases society ethics committee (Comité d’Éthique de la Recherche en Maladies Infectieuses et Tropicales, CER-MIT) approved the study (N° COVID 2021-06). Written informed consent was waived.