A new SARS-CoV-2 variant poorly detected by RT-PCR on nasopharyngeal samples, with high lethality: an observational study

Publié le 7 octobre 2021
Mis à jour le 24 juillet 2023

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

Auteur : Fillâtre Pierre, Dufour Marie-José, Behillil Sylvie, Vatan Remi, Reusse Pascale, Gabellec Alice, Velmans Nicolas, Montagne Catherine, Geffroy Du Coudret Sophie, Droumaguet Edith, Merour Véronique, Enouf Vincent, Buzele Rodolphe, Valence Marion, Guillotel Elena, Gagniere 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
Clinical Microbiology and Infection, 2022, vol. 28, n°. 2, p. 1-8