Clinical Performance of Direct RT-PCR Testing of Raw Saliva for Detection of SARS-CoV-2 in Symptomatic and Asymptomatic Individuals

Abstract

RT-qPCR tests based on RNA extraction from nasopharyngeal swab samples are promoted as the “gold standard” for SARS-CoV-2 detection. However, self-collected saliva samples offer a non-invasive alternative more suited to high-throughput testing. This study evaluated the performance of 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-qPCR test (SalivaDirect-based PCR) and a RT-qPCR test based on RNA extraction from NPS samples. Both 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 SalivaDirect-based PCR, while RNA extracts from NPS samples were tested by RT-qPCR according to the Irish national testing system. The TaqPath™ COVID-19 Fast PCR detected SARS-CoV-2 in 52 saliva samples, of which 51 were also positive with the SalivaDirect-based PCR. 49 samples displayed concordant results with the NPS extraction-based method, while three samples were positive on raw saliva. Among the negative samples, 10 discordant cases were found with the TaqPath COVID-19 Fast PCR (PPA–85.7%; NPA–99.5%), when compared to the RNA extraction-based NPS method, performing similarly to the SalivaDirect-based PCR (PPA-87.5%; NPA-99.5%). The direct RT-qPCR testing of saliva samples shows high concordance with NPS extraction-based method for SARS-CoV-2 detection, providing a cost-effective and highly-scalable system for high-throughput COVID-19 rapid-testing.