Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2.
Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2.
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DOI：
10.1371/journal.pbio.3001236
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发表时间：
2021-05
期刊：
影响因子：
9.8
通讯作者：
Grubaugh ND
中科院分区：
文献类型：
--
作者：
Vogels CBF;Breban MI;Ott IM;Alpert T;Petrone ME;Watkins AE;Kalinich CC;Earnest R;Rothman JE;Goes de Jesus J;Morales Claro I;Magalhães Ferreira G;Crispim MAE;Brazil-UK CADDE Genomic Network;Singh L;Tegally H;Anyaneji UJ;Network for Genomic Surveillance in South Africa;Hodcroft EB;Mason CE;Khullar G;Metti J;Dudley JT;MacKay MJ;Nash M;Wang J;Liu C;Hui P;Murphy S;Neal C;Laszlo E;Landry ML;Muyombwe A;Downing R;Razeq J;de Oliveira T;Faria NR;Sabino EC;Neher RA;Fauver JR;Grubaugh ND
随着严重急性呼吸综合征冠状病毒2型(SARS-CoV-2)变异株的出现，可能增加传播率和/或导致免疫反应逃逸，迫切需要对循环谱系进行有针对性的监测。研究发现，在英国首次发现的B.1.1.7(也是501Y.V1)变异体可以通过Thermo Fisher TaqPath新冠肺炎聚合酶链式反应分析偶然检测到，因为这些病毒中的一个关键缺失，即SpikeΔ69-70，将导致“Spike基因靶标失败”结果。然而，SGTF的结果对B.1.1.7并不是决定性的，而且这种检测方法不能检测到其他缺乏尖峰Δ69-70的关注变种(VOC)，例如在南非检测到的B.1.351(也是501Y.V2)和最近在巴西检测到的P.1(也是501Y.V3)。我们在所有3个变异体中都发现了ORF1a基因(ORF1a-Δ3675-3677)的缺失，这在其他SARS-CoV-2谱系中尚未被广泛检测到。以ORF1aΔ3675-3677为主要靶标，以SpikeΔ69-70为鉴别指标，设计并验证了一种检测SARS-CoV-2 VOC的开放源码聚合酶链式反应方法。我们的检测方法可以在世界各地的实验室中快速部署，以加强对B.1.1.7、B.1.351和P.1局部出现和传播的监测。对SARS-CoV-2变种的监测非常重要，但测序并不总是实用或负担得起的。这项研究提出了一种能够区分目前流行的不同SARS-CoV-2变异株的多重定量聚合酶链式反应。
With the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants that may increase transmissibility and/or cause escape from immune responses, there is an urgent need for the targeted surveillance of circulating lineages. It was found that the B.1.1.7 (also 501Y.V1) variant, first detected in the United Kingdom, could be serendipitously detected by the Thermo Fisher TaqPath COVID-19 PCR assay because a key deletion in these viruses, spike Δ69–70, would cause a “spike gene target failure” (SGTF) result. However, a SGTF result is not definitive for B.1.1.7, and this assay cannot detect other variants of concern (VOC) that lack spike Δ69–70, such as B.1.351 (also 501Y.V2), detected in South Africa, and P.1 (also 501Y.V3), recently detected in Brazil. We identified a deletion in the ORF1a gene (ORF1a Δ3675–3677) in all 3 variants, which has not yet been widely detected in other SARS-CoV-2 lineages. Using ORF1a Δ3675–3677 as the primary target and spike Δ69–70 to differentiate, we designed and validated an open-source PCR assay to detect SARS-CoV-2 VOC. Our assay can be rapidly deployed in laboratories around the world to enhance surveillance for the local emergence and spread of B.1.1.7, B.1.351, and P.1. Surveillance for SARS-CoV-2 variants is very important, but sequencing is not always practical or affordable. This study presents a multiplex qPCR that is able to distinguish among different SARS-CoV-2 variants of concern that are currently circulating.
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DOI：
10.1126/science.abg3055
发表时间：
2021-04-09
期刊：
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DOI：
10.15585/mmwr.mm7003e2
发表时间：
2021-01-22
期刊：
MMWR. Morbidity and mortality weekly report
影响因子：
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通讯作者：
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