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:10.1101/2020.11.10.20228528

Cited by 58 publications

(61 citation statements)

References 16 publications

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“…The H69-V70 variant in the UK 14,15 actually involves multiple mutations (Extended Data Table 2). The deletion itself has occurred spontaneously in multiple groups (Fig.…”

Section: Resultsmentioning

confidence: 99%

Progressing adaptation of SARS-CoV-2 to humans

Konishi

2020

Preprint

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The second and subsequent waves of coronavirus disease 2019 (COVID-19) have caused problems worldwide 1. Here, using an objective analytical method 2, we present the changes that occurred in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative virus of COVID-19, over time. The virus has mutated in three major directions, resulting in three groups to date. Analysis of the basic structure of the group of viruses was completed by April and shared across all continents. However, the virus continued to mutate independently in each country after the borders were closed. In particular, the virus mutated before the occurrence of the second and subsequent peaks. It seems that the mutations conferred higher infectivity to the virus, because of which the virus overcame previously effective protection and caused second waves of the disease. Currently, each country may possess such a unique, stronger variant. Some of them slowly entered other countries and caused epidemics. These viruses could also serve as sources of further mutations by exchanging parts of the genome, which could create variants with superior infectivity.

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“…The H69-V70 variant in the UK 14,15 actually involves multiple mutations (Extended Data Table 2). The deletion itself has occurred spontaneously in multiple groups (Fig.…”

Section: Resultsmentioning

confidence: 99%

Progressing adaptation of SARS-CoV-2 to humans

Konishi

2020

Preprint

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“…Here we report a novel RT-qPCR test to differentiate the B. [25][26][27][28] , which are mistakenly identified as B.1. The SGTF assays only became useful proxies when the variant spread and became more dominant in late November when the assays then detected over 90% of the variant 30 .…”

Section: Discussionmentioning

confidence: 99%

Surveillance of SARS-CoV-2 lineage B.1.1.7 in Slovakia using a novel, multiplexed RT-qPCR assay

Kovacova

Boršová

Paul

et al. 2021

Preprint

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The recent emergence of a novel variant of SARS-CoV-2 called lineage B.1.1.7 has sparked global alarm due to evidence of increased transmissibility, mortality, and uncertainty about vaccine efficacy, thus accelerating worldwide efforts to detect and track the variant. Current approaches to detect the B.1.1.7 variant include sequencing and molecular tests that contain a target assay that fails or results in reduced sensitivity towards the B.1.1.7 variant. Since many countries lack a robust genomic surveillance program and the failed target assays detect multiple unrelated variants that contain similar mutations as B.1.1.7, there is an urgent need to develop molecular tests that can accurately and rapidly identify the B.1.1.7 variant. We have developed a room temperature-stable, multiplexed RT-qPCR test that readily differentiates the B.1.1.7 variant from the most common SARS-CoV-2 variants. The test consists of two assays that target either the common SARS-CoV-2 spike gene or the two deletions in the spike gene (ΔH69/ΔV70 and ΔY144) that are present in the B.1.1.7 variant. Moreover, a simple relative comparison of the Ct values of the two assays permits not only identification of the B.1.1.7 variant but also its differentiation from other variants that harbor only the ΔH69/ΔV70 deletion. Each assay is multiplexed with a human RNase P internal control to assess RNA extraction and assay performance. This test can easily be implemented in diagnostic labs to rapidly scale B.1.1.7 surveillance efforts and is particularly useful in countries with high prevalence of variants possessing only the ΔH69/ΔV70 deletion because current strategies using target failure assays incorrectly identify these as putative B.1.1.7 variants.

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“…Indeed, they have become predominant in England (20I/501Y.V1) [1] and were detected in South Africa (20H/501Y.V2) [2] and Brazil [3]. The 20I/501Y.V1 variant has started to spread worldwide including in France [4]. It has been reported as 50-74% more transmissible than preexisting strains, suspected to evade anti-spike antibodies [1], and it caused a reinfection [5].…”

Section: Textmentioning

confidence: 99%

Implementation of an in-house real-time reverse transcription-PCR assay to detect the emerging SARS-CoV-2 N501Y variants

Bedotto

Fournier

Houhamdi

et al. 2021

Preprint

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The real-time detection of emerging SARS-CoV-2 variants is critical to manage patients appropriately, and monitor and assess their epidemiological and clinical features. Sequencing is not a feasible comprehensive detection strategy considering the very large number of SARS-CoV-2 cases in our current setting. SARS-CoV-2 variants currently of greatest concern carry the N501Y substitution within the spike receptor binding domain. They have become predominant in England (20I/501Y.V1) and were detected in South Africa (20H/501Y.V2), Brazil and dozens of other countries worldwide. The 20I/501Y.V1 variant has started to spread worldwide including in France. It has been reported as 50-74% more transmissible than preexisting strains, suspected to evade anti-spike antibodies, and it caused a reinfection. We have implemented an in-house one-step real-time reverse transcription-PCR (qPCR) assay that specifically detects SARS-CoV-2 N501Y. It was found reliable to detect specifically the N501Y substitution and preliminarily allowed estimating 20I/501Y.V1 variant prevalence to 4% among our current SARS-CoV-2 diagnoses since January.

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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 58 publications

References 16 publications

Progressing adaptation of SARS-CoV-2 to humans

Progressing adaptation of SARS-CoV-2 to humans

Surveillance of SARS-CoV-2 lineage B.1.1.7 in Slovakia using a novel, multiplexed RT-qPCR assay

Implementation of an in-house real-time reverse transcription-PCR assay to detect the emerging SARS-CoV-2 N501Y variants

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