SalivaDirect: Simple and sensitive molecular diagnostic test for SARS-CoV-2 surveillance

Vogels, Chantal B.F.; Watkins, Anne E.; Harden, Christina A.; Brackney, Doug; Shafer, Jared; Wang, Jianhui; Caraballo, Cesar; Kalinich, Chaney C; Ott, Isabel; Fauver, Joseph R.; Kudo, Eriko; Lu, Peiwen; Venkataraman, Arvind; Tokuyama, Maria; Moore, Adam J; Muenker, M. Catherine; Casanovas-Massana, Arnau; Fournier, John; Bermejo, Santos; Campbell, Melissa; Datta, Rupak; Nelson, Allison; Team, - Yale IMPACT Research; Cruz, Charles Dela; Ko, Albert; Iwasaki, Akiko; Krumholz, Harlan M.; Matheus, JD; Hui, Pei; Liu, Chen; Farhadian, Shelli; Sikka, Robby; Wyllie, Anne L; Grubaugh, Nathan

Current bottlenecks for improving accessibility and scalability of SARS-CoV-2 testing include diagnostic assay costs, complexity, and supply chain shortages. To resolve these issues, we developed SalivaDirect, which received Emergency Use Authorization (EUA) from the U.S. Food and Drug Administration on August 15th, 2020. The critical component of our approach is to use saliva instead of respiratory swabs, which enables non-invasive frequent sampling and reduces the need for trained healthcare professionals during collection. Furthermore, we simplified our diagnostic test by (1) not requiring nucleic acid preservatives at sample collection, (2) replacing nucleic acid extraction with a simple proteinase K and heat treatment step, and (3) testing specimens with a dualplex quantitative reverse transcription PCR (RT-qPCR) assay. We validated SalivaDirect with reagents and instruments from multiple vendors to minimize the risk for supply chain issues. Regardless of our tested combination of reagents and instruments from different vendors, we found that SalivaDirect is highly sensitive with a limit of detection of 6-12 SARS-CoV-2 copies/L. When comparing SalivaDirect to paired nasopharyngeal swabs using the authorized ThermoFisher Scientific TaqPath COVID-19 combo kit, we found high agreement in testing outcomes (>94%). In partnership with the National Basketball Association (NBA) and Players Association, we conducted a large-scale (n = 3,779) SalivaDirect usability study and comparison to standard nasal/oral tests for asymptomatic and presymptomatic SARS-CoV-2 detection. From this cohort of healthy NBA players, staff, and contractors, we found that 99.7% of samples were valid using our saliva collection techniques and a 89.5% positive and >99.9% negative test agreement to swabs, demonstrating that saliva is a valid and noninvasive alternative to swabs for large-scale SARS-CoV-2 testing. SalivaDirect is a flexible and inexpensive ($1.21-$4.39/sample in reagent costs) option to help improve SARS-CoV-2 testing capacity. Register to become a designated laboratory to use SalivaDirect under our FDA EUA on our website: publichealth.yale.edu/salivadirect/.