Mutation-Specific SARS-CoV-2 PCR Screen: Rapid and Accurate Detection of Variants of Concern and the Identification of a Newly Emerging Variant with Spike L452R Mutation
Mutation-Specific SARS-CoV-2 PCR Screen: Rapid and Accurate Detection of Variants of Concern and the Identification of a Newly Emerging Variant with Spike L452R Mutation
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DOI：
10.1128/jcm.00926-21
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发表时间：
2021-08-01
影响因子：
9.4
通讯作者：
Leber, Amy L.
中科院分区：
文献类型：
--
作者：
Wang, Huanyu;Jean, Sophonie;Leber, Amy L.
传染性更强和/或毒性更强的严重急性呼吸综合征冠状病毒 2 (SARS-CoV-2) 变种 (VOC) 的出现引发了密集的基因组监测，这种监测成本高昂且难以长期维持。为了解决这个问题，我们开发了一套基于四种多重突变特异性 PCR 的检测方法，可在当天报告，可检测五种 VOC 和三种感兴趣的变体 (VOI)，如美国疾病控制和预防中心 2021 年 3 月指南 (https://www.cdc.gov/coronavirus/2019-ncov/) 中的定义。将筛选结果与全基因组测序 (WGS) 进行比较，结果显示，使用尖峰 (S) 突变 S-N501Y、S-E484K 和 S-H69-V70del 检测，B.1.1.7 (n = 25) 和 P.1 (n = 5) 变体的菌株分型具有 100% 的一致性。 S-L450R 检测旨在检测 B.1.427/429 VOC，还鉴定出了新出现的多重突变 B.1.526.1 变体的多个分离株，该变体目前在美国东部迅速增加。 PCR 方法可以很容易地在临床实验室中采用，提供快速筛查方法，以便及早发现新出现的变异，并有效地对病例进行分类以进行全基因组测序。
The emergence of more transmissible and/or more virulent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC) has triggered intensive genomic surveillance, which is costly and difficult to sustain operationally over the long term. To address this problem, we developed a set of four multiplex mutation-specific PCR-based assays with same-day reporting that can detect five VOC and three variants of interest (VOI), as defined in the March 2021 guidelines from the U.S. Centers for Disease Control and Prevention (https://www.cdc.gov/coronavirus/2019-ncov/). The screening results were compared to the whole-genome sequencing (WGS) and showed 100% concordance for strain typing for B.1.1.7 (n = 25) and P.1 (n = 5) variants using spike (S) mutation S-N501Y, S-E484K, and S-H69-V70del assays. The S-L450R assay, designed to detect the B.1.427/429 VOC, also identified multiple isolates of a newly emerging multiply mutated B.1.526.1 variant that is now rapidly increasing in the eastern United States. PCR approaches can be easily adopted in clinical laboratories, providing rapid screening methods to allow early detection of newly emergent variants and to efficiently triage cases for full genomic sequencing.