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

Bal, Antonin; Destras, Grégory; Gaymard, Alexandre; Stéfic, Karl; Marlet, Julien; Eymieux, Sébastien; Regue, Hadrien; Semanas, Quentin; d’Aubarede, Constance; Billaud, Geneviève; Laurent, Frédéric; González, Claudia; Mekki, Yahia; Valette, Martine; Bouscambert, Maude; Gaudy‐Graffin, Catherine; Lina, Bruno; Morfin, Florence; Josset, Laurence

doi:10.2807/1560-7917.es.2021.26.3.2100008

Cited by 199 publications

(189 citation statements)

References 15 publications

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“…The SARS-CoV-2 variant 20I/501Y.V1 (501Y.V1) contains a deletion at position 69-70 of the spike (S) protein in the target region of the ThermoFisher TaqPath PCR probe targeting the S gene that leads to a loss of amplification [2]. In December 2020, the first variants with S-gene target failure (SGTF) were detected in France through the use of the TaqPath RT-PCR (Scientific TaqPath COVID-19 Combo Kit, Thermo Fisher, Waltham, United States (US)).…”

Section: A Nationwide Survey Of 501yv1 In Francementioning

confidence: 99%

Early assessment of diffusion and possible expansion of SARS-CoV-2 Lineage 20I/501Y.V1 (B.1.1.7, variant of concern 202012/01) in France, January to March 2021

et al. 2021

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The emergence of SARS-CoV-2 variant 20I/501Y.V1 (VOC-202012/1 or GR/501Y.V1) is concerning given its increased transmissibility. We reanalysed 11,916 PCR-positive tests (41% of all positive tests) performed on 7–8 January 2021 in France. The prevalence of 20I/501Y.V1 was 3.3% among positive tests nationwide and 6.9% in the Paris region. Analysing the recent rise in the prevalence of 20I/501Y.V1, we estimate that, in the French context, 20I/501Y.V1 is 52–69% more transmissible than the previously circulating lineages, depending on modelling assumptions.

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Section: A Nationwide Survey Of 501yv1 In Francementioning

confidence: 99%

Early assessment of diffusion and possible expansion of SARS-CoV-2 Lineage 20I/501Y.V1 (B.1.1.7, variant of concern 202012/01) in France, January to March 2021

et al. 2021

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“…This COVID-19 detection kit combines RT-PCR on the Orf1ab, N and S genes. Failure of detection of the S-gene in combination with detection of SARS-CoV-2 RNA for the Orf1ab and N-genes is indicative for the HV69-70 deletion in spike (S gene Target Failure, SGTF) (78). In addition, the presence of the asparagine to tyrosine mutation at spike protein position 501 (N501Y) was detected by the VirSNiP N501Y assay (TIB Molbiol A23063T) according to the instructions of the manufacturer.…”

Section: Rt-pcr Assays For the Detection Of Snps Associated With Sars-cov-2 Vocmentioning

confidence: 99%

SARS-CoV-2 variants of concern partially escape humoral but not T cell responses in COVID-19 convalescent donors and vaccine recipients

et al. 2021

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The emergence of SARS-CoV-2 variants harboring mutations in the spike (S) protein has raised concern about potential immune escape. Here, we studied humoral and cellular immune responses to wild type SARS-CoV-2 and the B.1.1.7 and B.1.351 variants of concern in a cohort of 121 BNT162b2 mRNA-vaccinated health care workers (HCW). Twenty-three HCW recovered from mild COVID-19 disease and exhibited a recall response with high levels of SARS-CoV-2-specific functional antibodies and virus-specific T cells after a single vaccination. Specific immune responses were also detected in seronegative HCW after one vaccination, but a second dose was required to reach high levels of functional antibodies and cellular immune responses in all individuals. Vaccination-induced antibodies cross-neutralized the variants B.1.1.7 and B.1.351, but the neutralizing capacity and Fc-mediated functionality against B.1.351 was consistently 2- to 4-fold lower than to the homologous virus. In addition, peripheral blood mononuclear cells were stimulated with peptide pools spanning the mutated S regions of B.1.1.7 and B.1.351 to detect cross-reactivity of SARS-CoV-2-specific T cells with variants. Importantly, we observed no differences in CD4+ T-cell activation in response to variant antigens, indicating that the B.1.1.7 and B.1.351 S proteins do not escape T-cell-mediated immunity elicited by the wild type S protein. In conclusion, this study shows that some variants can partially escape humoral immunity induced by SARS-CoV-2 infection or BNT162b2 vaccination, but S-specific CD4+ T-cell activation is not affected by the mutations in the B.1.1.7 and B.1.351 variants.

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“…Over the course of the pandemic, several genetic variants of concern have appeared and rapidly increased in frequency. The effects of these mutations remain unclear but there is concern that these variants may alter virus phenotype, affect detection and escape immune responses [1][2][3][4][5][6][7][8][9][10] .…”

Section: Introductionmentioning

confidence: 99%

“…Several variants of concern, including the B.1.1.7 variant first identified in the UK, have a characteristic six nucleotide deletion in the spike gene (S1Δ69-70) that appears likely to be an effective target for detection by nucleic acid testing. Detection of these variants currently requires observation of the dropout of fluorescence from a spike-targeted primer-probe set during qPCR 1 . However, screening using the absence of a signal is prone to falsely label samples near the limit of detection or assay failures as variants and performing qPCR requires costly RT-qPCR machines.…”

Section: Introductionmentioning

confidence: 99%

Molecular beacons allow specific RT-LAMP detection of B.1.1.7 variant SARS-CoV-2

Sherrill-Mix

Duyne

Bushman

2021

Preprint

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Over the course of the COVID-19 pandemic, several SARS-CoV-2 genetic variants of concern have appeared and spread throughout the world. Detection and identification of these variants is important to understanding and controlling their rapid spread. Current detection methods for a particularly concerning variant, B.1.1.7, require expensive qPCR machines and depend on the absence of a signal rather than a positive indicator of variant presence. Here we report an assay using a pair of molecular beacons paired with reverse transcription loop mediated amplification to allow isothermal amplification from saliva to specifically detect B.1.1.7 and other variants which contain a characteristic deletion in the gene encoding the viral spike protein. This assay is specific, affordable and allows multiplexing with other SARS-CoV-2 LAMP primer sets.

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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

Cited by 199 publications

References 15 publications

Early assessment of diffusion and possible expansion of SARS-CoV-2 Lineage 20I/501Y.V1 (B.1.1.7, variant of concern 202012/01) in France, January to March 2021

Early assessment of diffusion and possible expansion of SARS-CoV-2 Lineage 20I/501Y.V1 (B.1.1.7, variant of concern 202012/01) in France, January to March 2021

SARS-CoV-2 variants of concern partially escape humoral but not T cell responses in COVID-19 convalescent donors and vaccine recipients

Molecular beacons allow specific RT-LAMP detection of B.1.1.7 variant SARS-CoV-2

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