Identifying SARS-CoV-2 Variants of Concern through Saliva-Based RT-qPCR by Targeting Recurrent Mutation Sites.
Identifying SARS-CoV-2 Variants of Concern through Saliva-Based RT-qPCR by Targeting Recurrent Mutation Sites.
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DOI：
10.1128/spectrum.00797-22
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发表时间：
2022-06-29
影响因子：
3.7
通讯作者：
Dean D
中科院分区：
文献类型：
--
作者：
Ham RE;Smothers AR;Che R;Sell KJ;Peng CA;Dean D
SARS-CoV-2致病变种(VOCs)继续对公众健康构成威胁，这就需要一种实时监测战略来补充全基因组测序。因此，我们研究了竞争性探针RT-qPCR检测SARS-CoV-2 VOCs中发现的六个突变位点的有效性，并在用合成RNA验证了检测后，对阳性唾液样本进行了这些检测。与全基因组测序结果比较，SΔ69-70和ORF1aΔ3675-3677的准确率分别为93.6%和68.00%。K417T、E484K、E484Q、L452R的SNP检测准确率分别为99.20%、96.40%、99.60%和96.80%。最后，我们在2021年12月7日至22日期间对345个阳性唾液样本进行了OMICRON特异性突变检测，并能够快速识别OMICRON在南卡罗来纳州北部的快速传播。我们的工作流程展示了一种低成本、实时筛查VOCs人群的新方法。重要性令人关注的SARS-CoV-2变异体及其许多亚类可以通过其基因序列中存在的突变来表征。这些突变可以提供选择性优势，如增加传播性和抗体逃避，这会影响公共卫生建议，如口罩强制要求、检疫要求和治疗方案。我们的RT-qPCR工作流程允许通过针对相关变种之间共享的共同突变位点和检测目标位置存在的单核苷酸来鉴定SARS-CoV-2阳性唾液样本的毒株。这一鉴别诊断系统可以快速有效地识别多种SARS-CoV-2毒株，从而为未来的公共卫生监测提供更多的信息。
SARS-CoV-2 variants of concern (VOCs) continue to pose a public health threat which necessitates a real-time monitoring strategy to complement whole genome sequencing. Thus, we investigated the efficacy of competitive probe RT-qPCR assays for six mutation sites identified in SARS-CoV-2 VOCs and, after validating the assays with synthetic RNA, performed these assays on positive saliva samples. When compared with whole genome sequence results, the SΔ69-70 and ORF1aΔ3675-3677 assays demonstrated 93.60 and 68.00% accuracy, respectively. The SNP assays (K417T, E484K, E484Q, L452R) demonstrated 99.20, 96.40, 99.60, and 96.80% accuracies, respectively. Lastly, we screened 345 positive saliva samples from 7 to 22 December 2021 using Omicron-specific mutation assays and were able to quickly identify rapid spread of Omicron in Upstate South Carolina. Our workflow demonstrates a novel approach for low-cost, real-time population screening of VOCs. IMPORTANCE SARS-CoV-2 variants of concern and their many sublineages can be characterized by mutations present within their genetic sequences. These mutations can provide selective advantages such as increased transmissibility and antibody evasion, which influences public health recommendations such as mask mandates, quarantine requirements, and treatment regimens. Our RT-qPCR workflow allows for strain identification of SARS-CoV-2 positive saliva samples by targeting common mutation sites shared between variants of concern and detecting single nucleotides present at the targeted location. This differential diagnostic system can quickly and effectively identify a wide array of SARS-CoV-2 strains, which can provide more informed public health surveillance strategies in the future.
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影响因子：
9.4
作者：
Griesemer SB;Van Slyke G;Ehrbar D;Strle K;Yildirim T;Centurioni DA;Walsh AC;Chang AK;Waxman MJ;St George K
通讯作者：
St George K
影响因子：
8.8
作者：
Meng B;Kemp SA;Papa G;Datir R;Ferreira IATM;Marelli S;Harvey WT;Lytras S;Mohamed A;Gallo G;Thakur N;Collier DA;Mlcochova P;COVID-19 Genomics UK (COG-UK) Consortium;Duncan LM;Carabelli AM;Kenyon JC;Lever AM;De Marco A;Saliba C;Culap K;Cameroni E;Matheson NJ;Piccoli L;Corti D;James LC;Robertson DL;Bailey D;Gupta RK
通讯作者：
Gupta RK
影响因子：
14.2
作者：
Pasomsub, E.;Watcharananan, S. P.;Phuphuakrat, A.
通讯作者：
Phuphuakrat, A.
影响因子：
4.5
作者：
Crawford DC;Williams SM
通讯作者：
Williams SM
影响因子：
5.3
作者：
Duchene, Sebastian;Featherstone, Leo;Baele, Guy
通讯作者：
Baele, Guy