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© Research
Publication : Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases

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

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases - 07 Oct 2021

Fillâtre P, Dufour MJ, Behillil S, Vatan R, Reusse P, Gabellec A, Velmans N, Montagne C, Du Coudret SG, Droumaguet E, Merour V, Enouf V, Buzele R, Valence M, Guillotel E, Gagniere 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,

Link to Pubmed [PMID] – 34627988

Link to DOI – S1198-743X(21)00565-610.1016/j.cmi.2021.09.035

Clin Microbiol Infect 2021 Oct; ():

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.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.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<0.05) and their first RT-PCR tests were rarely positive (6/39, 15% vs 31/32, 97%, P<0.05). 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, vs. 5/32 (16%) for VOC, P=0.006.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.

https://pubmed.ncbi.nlm.nih.gov/34627988