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A new SARS-CoV-2 variant with high lethality poorly detected by RT-PCR on nasopharyngeal samples: an observational study
- Source :
- Clinical Microbiology and Infection. 28:298.e9-298.e15
- Publication Year :
- 2022
- Publisher :
- Elsevier BV, 2022.
-
Abstract
- Objectives 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. Methods Clinical, virological, and radiological data were retrospectively collected from medical charts in the two hospitals involved. We enrolled those inpatients with: (a) positive SARS-CoV-2 RT-PCR on a respiratory sample, (b) seroconversion with anti-SARS-CoV-2 IgG/IgM, or (c) suggestive symptoms and typical features of COVID-19 on a chest CT scan. Cases were categorized as B.1.616, a variant of concern (VOC), or unknown. Results From 1st January to 24th March 2021, 114 patients fulfilled the 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 versus 73 years, IQR 67–82, p Conclusion We report a nosocomial outbreak of COVID-19 cases related to a new variant, B.1.616, which is poorly detected by RT-PCR on nasopharyngeal samples and is associated with high lethality.
- Subjects :
- Microbiology (medical)
0303 health sciences
medicine.medical_specialty
business.industry
Outbreak
General Medicine
3. Good health
03 medical and health sciences
0302 clinical medicine
Infectious Diseases
Real-time polymerase chain reaction
medicine.anatomical_structure
Interquartile range
Internal medicine
Severity of illness
medicine
Observational study
030212 general & internal medicine
Seroconversion
Respiratory system
10. No inequality
business
030304 developmental biology
Respiratory tract
Subjects
Details
- ISSN :
- 1198743X
- Volume :
- 28
- Database :
- OpenAIRE
- Journal :
- Clinical Microbiology and Infection
- Accession number :
- edsair.doi...........8cb03eeb91a536d01e510b5d182b7355