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A new SARS-CoV-2 variant poorly detected by RT-PCR on nasopharyngeal samples, with high lethality: an observational study
- Source :
- Clinical Microbiology and Infection, Clinical Microbiology and Infection, 2022, 28 (2), pp.298.e9-298.e15. ⟨10.1016/j.cmi.2021.09.035⟩, Clinical Microbiology and Infection, Elsevier for the European Society of Clinical Microbiology and Infectious Diseases, 2021, ⟨10.1016/j.cmi.2021.09.035⟩
- Publication Year :
- 2022
- Publisher :
- HAL CCSD, 2022.
-
Abstract
- 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<br />Graphical abstract Image 1
- Subjects :
- SARS-CoV-2 variants
Reverse Transcriptase Polymerase Chain Reaction
SARS-CoV-2
[SDV]Life Sciences [q-bio]
COVID-19
Coronavirus infections
[SDV] Life Sciences [q-bio]
[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology
Humans
Original Article
Severity of illness index / Virology
France
[SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology
COVID-19 / Epidemiology
Retrospective Studies
Subjects
Details
- Language :
- English
- ISSN :
- 1198743X and 14690691
- Database :
- OpenAIRE
- Journal :
- Clinical Microbiology and Infection, Clinical Microbiology and Infection, 2022, 28 (2), pp.298.e9-298.e15. ⟨10.1016/j.cmi.2021.09.035⟩, Clinical Microbiology and Infection, Elsevier for the European Society of Clinical Microbiology and Infectious Diseases, 2021, ⟨10.1016/j.cmi.2021.09.035⟩
- Accession number :
- edsair.pmid.dedup....43b239e5b6420967431acfdf4c224505