The SARS-CoV-2 B.1.351 lineage (VOC β) is outgrowing the B.1.1.7 lineage (VOC α) in some French regions in April 2021

Roquebert, Bénédicte; Trombert‐Paolantoni, Sabine; Haïm-Boukobza, Stéphanie; Lecorché, Emmanuel; Verdurme, Laura; Foulongne, Vincent; Sofonea, Mircea T.; Alizon, Samuel

doi:10.2807/1560-7917.es.2021.26.23.2100447

Cited by 26 publications

(26 citation statements)

References 14 publications

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“…The estimated transmission advantages of 79% (95% CI: 52-110%) the Delta variant over the Alpha variant are in line with that estimated in the UK [7] and from the analysis of the number of variant sequences in the GISAID database [17]. Consistent with our earlier findings from April 2021 [13], we also find that Beta/ Gamma/Eta variants have a transmission advantage over the Alpha variant.…”

Section: Discussionsupporting

confidence: 90%

“…In these three regions, we also found a significant transmission advantage of the Delta variant over the Beta/Gamma/Eta variants (Figure 1B). Finally, consistently with our previous results [13], we find that Beta/ Gamma/Eta variants have a significant, but smaller, transmission advantage over the Alpha variant in these regions (Figure 1C). Transmission advantages tend to decrease with time (Supplementary Figure S3), which could be linked to a delay in collecting the cases or a change in selection pressures.…”

Section: Transmission Advantagessupporting

confidence: 92%

“…Using a multinomial regression model [13], we found that samples bearing the L452R mutation but not the E484K or the E484Q mutation (consistent with the Delta variant), tended to increase in the Hauts-de-France, Îlede-France, Normandie, and Provence-Alpes-Côte d'Azur regions compared with our reference, which were samples lacking the three mutations, consistent with the Alpha variant (Table ).…”

Section: Variant-screening Test Resultsmentioning

confidence: 58%

“…In scenarios A and C, the vaccine rollout is assumed to result in a 66% coverage of the whole population on In the model, screening tests consistent with an Alpha variant are the reference for the RRR. See [13] for details about the methods used.…”

Section: Modelling Epidemic Scenariosmentioning

confidence: 99%

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Rapid spread of the SARS-CoV-2 Delta variant in some French regions, June 2021

et al. 2021

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We analysed 9,030 variant-specific RT-PCR tests performed on SARS-CoV-2-positive samples collected in France between 31 May and 21 June 2021. This analysis revealed rapid growth of the Delta variant in three of the 13 metropolitan French regions and estimated a +79% (95% confidence interval: 52–110%) transmission advantage compared with the Alpha variant. The next weeks will prove decisive and the magnitude of the estimated transmission advantages of the Delta variant could represent a major challenge for public health authorities.

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Section: Discussionsupporting

confidence: 90%

Section: Transmission Advantagessupporting

confidence: 92%

Section: Variant-screening Test Resultsmentioning

confidence: 58%

Section: Modelling Epidemic Scenariosmentioning

confidence: 99%

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Rapid spread of the SARS-CoV-2 Delta variant in some French regions, June 2021

et al. 2021

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“…SARS-CoV-2 N501Y.V1 and N501Y.V2 lineages rapidly replaced the original strain, suggesting the mutations of these variants may be related to increased transmissibility. Preliminary studies have shown that N501Y.V1 and N501Y.V2 lineages have high transmission efficiency and immune escape from neutralizing antibodies than the original strain ( Galloway et al., 2021 ; Hoffmann et al., 2021 ; Roquebert et al., 2021 ). However, the transmission properties and biological characteristics of these variants remain elusive.…”

Section: Introductionmentioning

confidence: 99%

Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity

Tang

Gao

et al. 2021

Front. Cell. Infect. Microbiol.

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SARS-coronavirus 2 (SARS-CoV-2), pathogen of coronavirus disease 2019 (COVID-19), is constantly evolving to adapt to the host and evade antiviral immunity. The newly emerging variants N501Y.V1 (B.1.1.7) and N501Y.V2 (B.1.351), first reported in the United Kingdom and South Africa respectively, raised concerns due to the unusually rapid global spread. The mutations in spike (S) protein may contribute to the rapid spread of these variants. Here, with a vesicular stomatitis virus (VSV)-based pseudotype system, we demonstrated that the pseudovirus bearing N501Y.V2 S protein has higher infection efficiency than pseudovirus with wildtype (WT) and D614G S protein. Moreover, pseudovirus with N501Y.V1 or N501Y.V2 S protein has better thermal stability than WT and D614G, suggesting these mutations of variants may increase the stability of SARS-CoV-2 S protein and virion. However, the pseudovirus bearing N501Y.V1 or N501Y.V2 S protein has similar sensitivity to inhibitors of protease and endocytosis with WT and D614G. These findings could be of value in preventing the spread of virus and developing drugs for emerging SARS-CoV-2 variants.

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Comparison of three molecular diagnostic assays for SARS‐CoV‐2 detection: Evaluation of analytical sensitivity and clinical performance

Kim

Yoon

Lim

et al. 2022

Clinical Laboratory Analysis

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Background Currently, SARS‐CoV‐2 RNA detection using real‐time reverse‐transcription PCR (rRT‐PCR) is the standard diagnostic test for COVID‐19 infection. Various rRT‐PCR assays are currently used worldwide, targeting different genes of the SARS‐CoV‐2. Here, we compared the analytical sensitivity and clinical performance (sensitivity and specificity) of Allplex SARS‐CoV‐2/FluA/FluB/RSV assay (Seegene), Standard M nCoV real‐time detection kit (SD Biosensor), and U‐TOP COVID‐19 detection kit (Seasun Biomaterials) for SARS‐CoV‐2 detection. Methods Two hundred and forty‐nine nasopharyngeal swab samples were evaluated to compare the clinical performance of the rRT‐PCR assays. For the analytical performance evaluation, two RNA controls with known viral loads—SARS‐CoV‐2 RNA control and SARS‐COV‐2 B.1.351 RNA control—were used to investigate the potential impact of SARS‐CoV‐2 variants, particularly the B.1.351 lineage. Results Limits of detection ranged from 650 to 1300 copies/ml for rRT‐PCR assays, and the mean differences in cycle threshold (Ct) values of the two RNA controls were within 1.0 for each target in the rRT‐PCR assays (0.05–0.73), without any prominent Ct value shift or dropouts in the SARS‐COV‐2 B.1.351 RNA control. Using the consensus criterion as the reference standard, 89 samples were positive, whereas 160 were negative. The overall clinical performance of rRT‐PCR assays was comparable (sensitivity 98.88%–100%; specificity 99.38%–100%), whereas the sensitivities of each target gene were more variable. Conclusions The three rRT‐PCR assays showed comparable analytical sensitivity and clinical performance. The analytical and clinical sensitivities of each target gene were influenced more by the primer and probe design than the target gene itself.

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The SARS-CoV-2 B.1.351 lineage (VOC β) is outgrowing the B.1.1.7 lineage (VOC α) in some French regions in April 2021

Cited by 26 publications

References 14 publications

Rapid spread of the SARS-CoV-2 Delta variant in some French regions, June 2021

Rapid spread of the SARS-CoV-2 Delta variant in some French regions, June 2021

Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity

Comparison of three molecular diagnostic assays for SARS‐CoV‐2 detection: Evaluation of analytical sensitivity and clinical performance

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