Validation of Snort-spit Saliva in Detecting COVID-19 Using RT-PCR and Rapid Antigen Detection Test Ryner Jose D. Carrillo, MD, MSc (Clin Epid),* 1,2 Abigail D. Sarmiento, MD,* 1 Mark Anthony C. Ang, MD, MoS, 1,2 Michelle H. Diwa, MD, 1,2 Cecille C. Dungog, MD, PhD, 1 Daniel I. Tan, MD, 1 Jan Alexis C. Lacuata, MD, 1 Jacob Ephraim D. Salud, MD, 1 Ramon Antonio B. Lopa, MD, 1,2 John Mark S. Velasco, MD, MPH, MSc, DTM&H, 3 Regina P. Berba, MD, MSc 1,2 and Charlote M. Chiong, MD, PhD, 1,2,3 1 Philippine General Hospital, University of the Philippines Manila 2 College of Medicine, University of the Philippines Manila 3 National Institutes of Health, University of the Philippines Manila ABSTRACT Objectve. To determine the diagnostc accuracy of self-collected snorted and spit saliva in detectng COVID-19 using RT-PCR (ssRT-PCR) and lateral fow antgen test (ssLFA) versus nasopharyngeal swab RT-PCR (npRT-PCR). Methods. One hundred ninety-seven symptomatc subjects for COVID-19 testng in a tertary hospital underwent snort-spit saliva self-collecton for RT-PCR and antgen testng and nasopharyngeal swab for RT-PCR as reference. Positvity rates, agreement, sensitvity, specifcity, and likelihood ratos were estmated. Results. Estmated prevalence of COVID-19 using npRT-PCR was 9% (exact 95% CI of 5.5% - 14.1%). A higher positvity rate of 13% in the ssRT-PCR assay suggested possible higher viral RNA in the snort-spit samples. There was 92.9% agreement between ssRT-PCR and npRT-PCR (exact 95% CI of 88.4% to 96.1%; Cohen’s Kappa of 0.6435). If npRT-PCR will be assumed as reference standard, the estmated Sensitvity was 83.3% (exact 95% CI of 60.8% to 94.2%), Specifcity 93.9% (exact 95% CI of 89.3% to 96.5%), Positve predictve value of 57.7% (exact 95% CI of 38.9% to 74.5%), Negatve predictve value of 98.2% (exact 95% CI of 95% to 99.4%), positve likelihood rato of 3.65 (95% CI of 7.37 to 24.9), negatve likelihood rato of 0.178 (95% CI of 0.063 to 0.499). There was 84.84% agreement (95% exact CI of 79.1% to 89.5%; Cohen’s Kappa of 0.2356) between ssLFAvs npRT-PCR, sensitvity of 38.9% (exact 95% CI of 20.3% to 61.4%), specifcity of 89.4% (exact 95% CI of 84.1% to 93.1%), PPV of 26.9% (95% CI of 13.7% to 46.1%), NPV of 93.6% (exact 95% CI of 88.8% to 96.4%), LR+ of 3.67 (95% CI of 1.79 - 7.51), LR – of 0.68 (95% CI of 0.47 - 0.99). Conclusion. Our data showed that snort-spit saliva RT-PCR testng had acceptable diagnostc performance characteristcs and can potentally be used as an alternatve to the standard nasopharyngeal/oropharyngeal swab RT-PCR test for COVID-19 in certain situatons. However, our data also showed that snort-spit saliva antgen testng using lateral fow assay did not ofer acceptable performance. Key Words: SARS-CoV-2, reverse transcripton polymerase chain reacton, saliva INTRODUCTION In the era of COVID-19 or SARS-CoV-2 pandemic, determining infection and infectivity by viral RNA reverse transcription polymerase chain reaction (RT-PCR) has been the diagnostic method of choice. Studies have tested diferent samples- nasopharyngeal (NP) or oropharyngeal (OP) swabs, bronchial lavage, whole saliva, and deep throat saliva. Te nasopharyngeal swab RT-PCR has been considered by the World Health Organization as the sample type of choice for diagnostics 1 . However, the collection of NP specimens can be regarded as invasive and causes discomfort *Dr. Carrillo and Dr. Sarmiento share primary authorship for this manuscript. Corresponding author: Ryner Jose D. Carrillo, MD, MSc (Clin Epid) Philippine General Hospital University of the Philippines Manila Taf Avenue, Ermita Manila 1000, Philippines Email: rdcarrillo@up.edu.ph VOL. 55 NO. 2 2021 211 ORIGINAL ARTICLE