Evaluation of Swab-Seq as a scalable, sensitive assay for community surveillance of SARS-CoV-2 infection.
Evaluation of Swab-Seq as a scalable, sensitive assay for community surveillance of SARS-CoV-2 infection.
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DOI：
10.1038/s41598-022-06901-5
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发表时间：
2022-02-23
影响因子：
4.6
通讯作者：
Cusanovich DA
中科院分区：
文献类型：
--
作者：
Kang H;Allison S;Spangenberg A;Carr T;Sprissler R;Halonen M;Cusanovich DA
持续的SARS-CoV-2大流行和随后对病毒检测的需求导致了扩大诊断实验室工作以及确保收集和处理样本的基本供应方面的问题。这促使科学界努力建立更可扩展、资源密集度更低且成本更低的改进方案。一种这样的开发努力已经产生了称为“Swab-Seq”的测定，如此命名是因为它最初被开发用于干燥的鼻拭子样品。现有的金标准检测由从鼻咽（NP）拭子中提取的RNA组成，该拭子进行定量逆转录聚合酶链反应（qRT-PCR）。Swab-Seq将此方法用于下一代测序读数。通过将这种修改与无提取采样技术相结合，Swab-Seq实现了高可扩展性，每个样本的低成本和合理的周转时间。我们通过使用传统的NP拭子检测从有症状和无症状个体采集的样本，评价了该检测在社区监测环境中的有效性。此外，我们还评估了无提取采样技术（唾液和含盐漱口液样本）。我们发现该检测试剂盒与qRT-PCR检测试剂盒一样具有临床敏感性，适用于多种样品类型，并且能够轻松地同时容纳数百个样品。因此，我们提供独立的Swab-Seq验证，并扩展其在样品类型和样品稳定性方面的实用性。这种类型的测定极大地扩展了适合当前和潜在未来需求的无症状个体的常规、非侵入性、重复检测的可能性。
The ongoing SARS-CoV-2 pandemic and subsequent demand for viral testing has led to issues in scaling diagnostic lab efforts and in securing basic supplies for collection and processing of samples. This has motivated efforts by the scientific community to establish improved protocols that are more scalable, less resource intensive, and less expensive. One such developmental effort has resulted in an assay called “Swab-Seq”, so named because it was originally developed to work with dry nasal swab samples. The existing gold standard test consists of RNA extracted from a nasopharyngeal (NP) swab that is subjected to quantitative reverse transcription polymerase chain reaction (qRT-PCR). Swab-Seq adapts this method to a next-generation sequencing readout. By pairing this modification with extraction-free sampling techniques, Swab-Seq achieves high scalability, low cost per sample, and a reasonable turnaround time. We evaluated the effectiveness of this assay in a community surveillance setting by testing samples collected from both symptomatic and asymptomatic individuals using the traditional NP swab. In addition, we evaluated extraction-free sampling techniques (both saliva and saline mouth gargle samples). We found the assay to be as clinically sensitive as the qRT-PCR assay, adaptable to multiple sample types, and able to easily accommodate hundreds of samples at a time. We thus provide independent validation of Swab-Seq and extend its utility regarding sample type and sample stability. Assays of this type greatly expand the possibility of routine, noninvasive, repeated testing of asymptomatic individuals suitable for current and potential future needs.
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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：
9.3
作者：
Srivatsan, Sanjay;Heidl, Sarah;Starita, Lea M.
通讯作者：
Starita, Lea M.
影响因子：
4.4
作者：
Fu Y;Wu PH;Beane T;Zamore PD;Weng Z
通讯作者：
Weng Z
DOI：
10.1016/j.medj.2020.12.010
发表时间：
2021-03-12
期刊：
Med (New York, N.Y.)
影响因子：
--
作者：
Vogels CBF;Watkins AE;Harden CA;Brackney DE;Shafer J;Wang J;Caraballo C;Kalinich CC;Ott IM;Fauver JR;Kudo E;Lu P;Venkataraman A;Tokuyama M;Moore AJ;Muenker MC;Casanovas-Massana A;Fournier J;Bermejo S;Campbell M;Datta R;Nelson A;Yale IMPACT Research Team;Dela Cruz CS;Ko AI;Iwasaki A;Krumholz HM;Matheus JD;Hui P;Liu C;Farhadian SF;Sikka R;Wyllie AL;Grubaugh ND
通讯作者：
Grubaugh ND
影响因子：
46.9
作者：
Bray, Nicolas L.;Pimentel, Harold;Pachter, Lior
通讯作者：
Pachter, Lior