Genetics & Biotechnology Lab, Ryan Institute, National University of Ireland Galway, Galway, Republic of Ireland.
Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, United Kingdom.
Microbiol Spectr. 2022 Dec 21;10(6):e0222922. doi: 10.1128/spectrum.02229-22. Epub 2022 Nov 21.
RT-PCR tests based on RNA extraction from nasopharyngeal swabs (NPS) are promoted as the "gold standard" for SARS-CoV-2 detection. However, the use of saliva samples offers noninvasive self-collection more suitable for high-throughput testing. This study evaluated performance of the TaqPath COVID-19 Fast PCR Combo kit 2.0 assay for detection of SARS-CoV-2 in raw saliva relative to a lab-developed direct RT-PCR test (SalivaDirect-based PCR, SDB-PCR) and an RT-PCR test based on RNA extraction from NPS. Saliva and NPS samples were collected from symptomatic and asymptomatic individuals (N = 615). Saliva samples were tested for SARS-CoV-2 using the TaqPath COVID-19 Fast PCR Combo kit 2.0 and the SDB-PCR, while NPS samples were tested by RT-PCR in RNA extracts according to the Irish national testing system. TaqPath COVID-19 Fast PCR Combo kit 2.0 detected SARS-CoV-2 in 52 saliva samples, of which 51 were also positive with the SDB-PCR. Compared to the NPS "gold standard" biospecimen method, 49 samples displayed concordant results, while three samples (35<Ct<37) were positive on raw saliva. Among the negative samples, 10 discordant cases were found with the TaqPath COVID-19 Fast PCR Combo kit 2.0 (PPA-83.05%; NPA-99.44%), compared to the RNA extraction-based NPS method, performing similarly to the SDB-PCR (PPA-84.75%; NPA-99.63%). The direct RT-PCR testing of saliva samples shows high concordance with the NPS extraction-based method for SARS-CoV-2 detection, and therefore provides a cost-effective and highly scalable system for high-throughput COVID-19 rapid-testing. The scale of the COVID-19 pandemic highlighted the need for viral diagnostic systems that are accurate and could be deployed at large population scales. Large-scale diagnostic or surveillance testing of large numbers of people requires collection of infected biological samples that is easy and rapid. Here, we demonstrate that raw saliva samples can be easily collected and tested by RT-PCR assays. Indeed, we find that direct testing of raw saliva by two different RT-PCR assays is as accurate (if not more accurate) than nasal swab-based RT-PCR testing. We present a cost-effective and highly scalable system for high-throughput COVID-19 rapid-testing.
基于鼻咽拭子 (NPS) 中 RNA 提取的 RT-PCR 检测被推广为 SARS-CoV-2 检测的“金标准”。然而，唾液样本的使用提供了更适合高通量检测的非侵入性自我采集。本研究评估了 TaqPath COVID-19 Fast PCR Combo kit 2.0 检测试剂盒在原始唾液中检测 SARS-CoV-2 的性能，与实验室开发的直接 RT-PCR 检测 (SalivaDirect-based PCR，SDB-PCR) 和基于 NPS 中 RNA 提取的 RT-PCR 检测进行比较。从有症状和无症状个体 (N=615) 中采集了唾液和 NPS 样本。使用 TaqPath COVID-19 Fast PCR Combo kit 2.0 和 SDB-PCR 检测唾液样本中的 SARS-CoV-2，而 NPS 样本则根据爱尔兰国家检测系统在 RNA 提取物中进行 RT-PCR 检测。TaqPath COVID-19 Fast PCR Combo kit 2.0 在 52 份唾液样本中检测到 SARS-CoV-2，其中 51 份也与 SDB-PCR 呈阳性。与 NPS“金标准”生物样本方法相比，49 个样本的结果一致，而 3 个样本 (35<Ct<37) 在原始唾液中呈阳性。在阴性样本中，与 TaqPath COVID-19 Fast PCR Combo kit 2.0 相比，10 个样本存在不一致 (PPA-83.05%；NPA-99.44%)，与基于 RNA 提取的 NPS 方法相比，与 SDB-PCR 的性能相似 (PPA-84.75%；NPA-99.63%)。唾液样本的直接 RT-PCR 检测与 NPS 提取法检测 SARS-CoV-2 具有高度一致性，因此为高通量 COVID-19 快速检测提供了一种具有成本效益和高度可扩展的系统。SARS-CoV-2 检测的准确且可在大人群规模上部署的病毒诊断系统的需求。对大量人群进行大规模诊断或监测测试需要采集易于快速采集的感染性生物样本。在这里，我们证明了可以通过 RT-PCR 检测容易地采集和测试原始唾液样本。事实上，我们发现两种不同的 RT-PCR 检测方法直接检测原始唾液与基于鼻拭子的 RT-PCR 检测一样准确（如果不是更准确的话）。我们提出了一种具有成本效益和高度可扩展的系统，用于高通量 COVID-19 快速检测。
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