Validation and implementation of a direct RT-qPCR method for rapid screening of SARS-CoV-2 infection by using non-invasive saliva samples

Brotons, Pedro; Perez-Argüello, Amaresh; Launes, Cristian; Torrents, Francesc; Subirats, Maria Pilar; Saucedo, Jesica; Claverol, Joana; Garcia-Garcia, Juan Jose; Rodas, Gil; Fumado, Vicky; Jordan, Iolanda; Gratacos, Eduard; Bassat, Quique; Muñoz-Almagro, Carmen

Objective: To validate and implement an optimised screening method for detection of SARS-CoV-2 RNA combining use of self-collected raw saliva samples, single-step heat-treated virus inactivation and RNA extraction, and direct RT-qPCR. Methods: 3-phased study conducted in Barcelona (Spain) in June-October, 2020, including: i) analytical validation against standard RT-qPCR in saliva samples; ii) diagnostic validation against standard RT-qPCR using paired saliva-nasopharyngeal samples obtained from asymptomatic teenagers and adults in a sports academy; and iii) pilot screening of asymptomatic health workers in a tertiary hospital. Results: Phase i) Detection yield of the new method was comparable to that of standard RT-qPCR. Phase ii) Diagnostic sensitivity and specificity values in 303 self-collected saliva samples were 95.7% (95% CI, 79.0-99.2%) and 100.0% (95% CI, 98.6-100.0 %), respectively. Phase iii) Only 17 (0.6%) of saliva samples self-collected by 2,709 participants without supervision were invalid. Rapid analytical workflow by the new method (up to 384 batched samples processable in <2 hours) yielded 24 (0.9%) positive results in the remainder 2,692 saliva samples. Paired nasopharyngeal specimens were all positive by standard RT-qPCR.. Conclusions: Direct RT-qPCR on self-collected raw saliva is a simple, rapid, and accurate method with potential to be scaled up for enhanced SARS-CoV-2 community-wide screening.