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2020 年 8 月至 12 月法国用于鉴定 202012/01 关注变异株和其他具有刺突缺失 H69-V70 的变异株的两步策略

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.

机构信息

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.

These authors contributed equally to this article.

出版信息

Euro Surveill. 2021 Jan;26(3). doi: 10.2807/1560-7917.ES.2021.26.3.2100008.

DOI:10.2807/1560-7917.ES.2021.26.3.2100008
PMID:33478625
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7848679/
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.

摘要

我们报告了在法国首次检测到 202012/01 变异株（VOC）的策略（2020 年 12 月 21 日）。首先，筛选出某些 SARS-CoV-2 变异株中存在的刺突（S）缺失 H69-V70（ΔH69/ΔV70），包括 VOC。这种缺失与三靶 RT-PCR 检测（TaqPath 试剂盒）中的 S 基因靶标失败（SGTF）有关。随后，对 SGTF 样本进行全基因组测序。该方法揭示了与 ΔH69/ΔV70 同时发生的突变，包括 VOC 中的 S:N501Y。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/16b8/7848679/41e5d1ea48ce/2100008-f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/16b8/7848679/94219c9d5ecc/2100008-f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/16b8/7848679/41e5d1ea48ce/2100008-f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/16b8/7848679/94219c9d5ecc/2100008-f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/16b8/7848679/41e5d1ea48ce/2100008-f2.jpg

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[1]
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本文引用的文献

[1]
Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape.

Science. 2021-3-12

[2]
Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation.

Virus Evol. 2020-10-5

[3]
Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants.

Elife. 2020-10-28

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Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding.

Cell. 2020-8-11

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A neutralizing human antibody binds to the N-terminal domain of the Spike protein of SARS-CoV-2.

Science. 2020-6-22

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Antibody cocktail to SARS-CoV-2 spike protein prevents rapid mutational escape seen with individual antibodies.

Science. 2020-6-15

[7]
Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino acid deletion in nsp2 (Asp268del).

Clin Microbiol Infect. 2020-7

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