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

ABSTRACT

BackgroundThere is an urgent need to curb COVID-19 pandemic through early identification of asymptomatic but infectious cases. We aimed 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 and findingsThe study was conducted in Sant Joan de Deu University Hospital (Barcelona, Spain), 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 young and older adults in a youth sports academy; and iii) high throughput pilot screening of asymptomatic health workers and other staff in the study site. The proposed method had comparable analytical performance to standard RT-qPCR in saliva. Diagnostic validation included saliva samples self-collected with supervision by 173 participants during 9-12 weeks and nasopharyngeal samples collected from them. At baseline, all participants (100.0%) were negative for SARS-CoV-2 in both paired saliva-nasopharyngeal samples. In the following weeks, standard RT-qPCR yielded 23 positive results in nasopharyngeal samples whereas paired saliva specimens yielded 22 (95.7%) positive and one inconclusive result. A total of 2,709 participants engaged in the pilot screening, with high rate of participation (83.4% among health workers). Only 17 (0.6%) of saliva samples self-collected by participants in an unsupervised manner were invalid. Saliva was positive in 24 (0.9%) out of 2,692 valid specimens and inconclusive in 27 (1.0%). All 24 saliva-positive participants and 4 with saliva inconclusive results were positive by standard RT-qPCR in nasopharyngeal samples. The pilot showed potential for rapid analytical workflow (up to 384 batched samples can be processed in <2 hours). ConclusionDirect 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.