SARS-Cov-2 Viral Load in Nasal Swab and Raw Saliva Samples from COVID-19 Patients

Author(s): Yue Qiu, Ling Lu, Andrew Lu, Dexiang Gao, Patrick McGrath, Chann Han, Igor Kogut, Bob Blomquist, Xin Yao, Jose P. Zevallos, Shi-Long Lu, Brian L Harry

Testing of raw saliva is an accessible and cost-effective technology for viral detection. Real-time quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) remains the foundation of microbial detection due to its scalability and superior assay performance. Variability in RT-qPCR testing, however, is a major challenge for assessing viral load, which has implications for transmission risk and clinical care. We hypothesized that RNA extraction is not necessary for accurate quantitation of SARS-CoV-2 viral load in raw saliva. In this longitudinal prospective cohort study, we developed an extraction-free RT-qPCR assay for detection of SARS-CoV-2 in saliva and monitored viral load until convalescence in COVID-19 patients. Comparison of 231 matched anterior nares swab and saliva samples showed that extraction-free testing of saliva has equivalent assay performance compared to that of RNA extracts from either anterior nares or saliva. Although higher viral loads were observed in the nasal cavity compared to the oral cavity, clinical sensitivity for SARS-CoV-2 was equivalent between both nasal swab and saliva samples. Extraction-free testing of a combination specimen consisting of both nasal swab and saliva is also demonstrated. Comparison of RT-qPCR and droplet digital PCR (ddPCR) revealed that cycle threshold (Ct) values between 20 and 30 correlated well with viral loads between 10 and 1,500 copies/µL in saliva. The large dynamic range of viral load in nasal swabs prevented accurate viral load assessment by RT-qPCR. In summary, extraction-free saliva testing can facilitate high-throughput laboratory testing for SARS-CoV-2 and viral load monitoring.