Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69–V70, France, August to December 2020
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Abstract
We report the strategy leading to the first detection of variant of concern 202012/01 (VOC) in France (21 December 2020). First, the spike (S) deletion H69–V70 (ΔH69/ΔV70), identified in certain SARS-CoV-2 variants including VOC, is screened for. This deletion is associated with a S-gene target failure (SGTF) in the three-target RT-PCR assay (TaqPath kit). Subsequently, SGTF samples are whole genome sequenced. This approach revealed mutations co-occurring with ΔH69/ΔV70 including S:N501Y in the VOC.
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Because sequencing samples were unavailable, virus-strain characterization relied on PCR data alone.
“Samples were not available for sequencing, and virus-strain characterization was based on PCR data alone.12”
From Safety and Efficacy of NVX-CoV2373 Covid-19 Vaccine (2021) · cites this paper as [12]
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“In the meantime, a similar approach has been adopted in the United Kingdom where the frequency of SGTF is used as a proxy for estimating and monitoring the spread of the VOC 202012/01 [14,20].”
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- Authors
- Bal, A., Destras, G., Gaymard, A., Stefic, K., Marlet, J., Eymieux, S., Regue, H., Semanas, Q., d’Aubarede, C., Billaud, G., Laurent, F., Gonzalez, C., Mekki, Y., Valette, M., Bouscambert, M., Gaudy-Graffin, C., Lina, B., Morfin, F., Josset, L., & the COVID-Diagnosis HCL Study Group
- Affiliations
- Lyon 1 Université (FR)
- CIRI, Centre International de Recherche en Infectiologie, Team VirPath, Univ Lyon, Inserm,
- Service de Bactériologie-Virologie-Hygiène, CHRU de Tours, France; INSERM U1259, Université de Tours, Tours, France
- Université de Tours (FR)
- Hospices Civils de Lyon (FR)
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France
- Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associé au Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- Corresponding author
- Josset, Laurence
- ORCID
- Venue
- Eurosurveillance
- Published
- 2021-01-21
- Volume
- 26
- Issue
- 3
- Pages
- 2100008
- ISSN
- 1025-496X (ISSN-L)
- 1560-7917
- PMC
- PMC7848679
- OpenAlex
- W3121161162
- Cited by
- 212
- References
- 17
- Citations by year
- 2026: 1 · 2025: 2 · 2024: 15 · 2023: 14 · 2022: 73 · 2021: 106 · 2020: 1
- FWCI
- 16.63
- Type
- journal article
- Language
- en
- Open access
- diamond
- doi.org
- Locations
- Eurosurveillance (publishedVersion, cc-by)
- medRxiv (acceptedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- HAL (submittedVersion)
- HAL (submittedVersion, other-oa)
- Funders
- Hospices Civils de Lyon
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 detection and testing
- Health Sciences › Medicine › Infectious Diseases › COVID-19 Clinical Research Studies
- Keywords
- SARS-CoV-2, S-gene target failure, RT-PCR testing, whole genome sequencing, N501Y mutation
- MeSH terms
- COVID-19, SARS-CoV-2, Base Sequence, France, Humans, Genome, Viral, Sequence Deletion, Spike Glycoprotein, Coronavirus
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