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A new SARS-CoV-2 variant with high lethality poorly detected by RT-PCR on nasopharyngeal samples

Clin Microbiol Infect

Fillâtre P, Dufour MJ, Behillil S, Vatan R, Reusse P, Gabellec A, Velmans N, Montagne C, Geffroy Du Coudret S, Droumaguet E, Merour V, Enouf V, Buzelé R, Valence M, Guillotel E, Gagnière B, Baidaliuk A, Zhukova A, Tourdjman M, Thibault V, Grolhier C, Pronier C, Lescure FX, Simon-Loriere E, Costagliola D, Van Der Werf S, Tattevin P, Massart N.

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.

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