Sensitive detection and quantification of SARS-CoV-2 in saliva

• Published in: Scientific reports Vol. 11; no. 1; pp. 12425 - 12
• Main Authors: Abasiyanik, Mustafa Fatih, Flood, Blake, Lin, Jing, Ozcan, Sefika, Rouhani, Sherin J., Pyzer, Athalia, Trujillo, Jonathan, Zhen, Chaojie, Wu, Ping, Jumic, Stephen, Wang, Andrew, Gajewski, Thomas F., Wang, Peng, Hartley, Madeline, Ameti, Bekim, Niemiec, Rachael, Fernando, Marian, Mishra, Vasudha, Savage, Peter, Aydogan, Bulent, Bethel, Cindy, Matushek, Scott, Beavis, Kathleen G., Agrawal, Nishant, Segal, Jeremy, Tay, Savaş, Izumchenko, Evgeny
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 14.06.2021; Nature Publishing Group; Nature Portfolio
• Subjects: 631/1647; 692/53; 692/699/255; Adult; COVID-19; COVID-19 - diagnosis; COVID-19 - virology; Female; Humanities and Social Sciences; Humans; Male; Microbiology; Middle Aged; multidisciplinary; Nucleic acids; Polymerase chain reaction; Reagent Kits, Diagnostic; Real-Time Polymerase Chain Reaction; Reverse Transcriptase Polymerase Chain Reaction; Reverse transcription; RNA, Viral - analysis; RNA, Viral - genetics; RNA, Viral - metabolism; Saliva; Saliva - virology; SARS-CoV-2 - genetics; SARS-CoV-2 - isolation & purification; Science; Science (multidisciplinary); Severe acute respiratory syndrome coronavirus 2; Viral Load
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-021-91835-7

Saliva has significant advantages as a test medium for detection of SARS-CoV-2 infection in patients, such as ease of collection, minimal requirement of supplies and trained personnel, and safety. Comprehensive validation in a large cohort of prospectively collected specimens with unknown SARS-CoV-2 status should be performed to evaluate the potential and limitations of saliva-based testing. We developed a saliva-based testing pipeline for detection of SARS-CoV-2 nucleic acids using real-time reverse transcription PCR (RT-PCR) and droplet digital PCR (ddPCR) readouts, and measured samples from 137 outpatients tested at a curbside testing facility and 29 inpatients hospitalized for COVID-19. These measurements were compared to the nasal swab results for each patient performed by a certified microbiology laboratory. We found that our saliva testing positively detects 100% (RT-PCR) and 93.75% (ddPCR) of curbside patients that were identified as SARS-CoV-2 positive by the Emergency Use Authorization (EUA) certified nasal swab testing assay. Quantification of viral loads by ddPCR revealed an extremely wide range, with 1 million-fold difference between individual patients. Our results demonstrate for both community screening and hospital settings that saliva testing reliability is on par with that of the nasal swabs in detecting infected cases, and has potential for higher sensitivity when combined with ddPCR in detecting low-abundance viral loads that evade traditional testing methods.