Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs

Anne Louise Wyllie; John Fournier; Arnau Casanovas-Massana; Melissa Campbell; Maria Tokuyama; Pavithra Vijayakumar; Bertie Geng; M. Catherine Muenker; Adam J. Moore; Chantal B. F. Vogels; Mary E. Petrone; Isabel M. Ott; Peiwen Lu; Alice Lu-Culligan; Jonathan Klein; Arvind Venkataraman; Rebecca Earnest; Michael Simonov; Rupak Datta; Ryan Handoko; Nida Naushad; Lorenzo R. Sewanan; Jordan Valdez; Elizabeth B. White; Sarah Lapidus; Chaney C. Kalinich; Xiaodong Jiang; Daniel J. Kim; Eriko Kudo; Melissa Linehan; Tianyang Mao; Miyu Moriyama; Ji Eun Oh; Annsea Park; Julio Silva; Eric Song; Takehiro Takahashi; Manabu Taura; Orr-El Weizman; Patrick Wong; Yexin Yang; Santos Bermejo; Camila Odio; Saad B. Omer; Charles S. Dela Cruz; Shelli Farhadian; Richard A. Martinello; Akiko Iwasaki; Nathan D. Grubaugh; Albert I. Ko

As temporal SARS-CoV-2 diagnostic testing from nasopharyngeal swabs is reported to be variable 2,3 , we tested longitudinal nasopharyngeal and saliva samples from inpatients to determine which sample type provided more consistent results. From 22 participants with multiple nasopharyngeal swabs and 12 participants with multiple saliva samples, we found that SARS-CoV-2 titers generally decreased in both sample types following the reported date of symptom onset ( Fig. 2a ). Our nasopharyngeal swab results are consistent with previous reports of variable SARS-CoV-2 titers and results 2,3 : we found 5 instances where a participant's nasopharyngeal swab was negative for SARS-CoV-2 followed by a positive result during the next collection (5/33 repeats, 33%; Fig. 2b ). In longitudinal saliva collections from 12 patients, however, there were no instances in which a sample tested negative and was later followed by a positive result. As true negative test results are important for clinicians to track patient improvements and for decisions regarding discharges, our data suggests that saliva is a more consistent sample type than nasopharyngeal swabs for monitoring temporal changes in SARS-CoV-2 titers. (a) Longitudinal SARS-CoV-2 titers from saliva or nasopharyngeal swabs are shown as days since symptom onset. Each circle represents a separate sample, which are connected to additional samples from the same patient by a dashed line. Our assay detection limits for SARS-CoV-2 using the US CDC "N1" assay is at cycle threshold 38, which corresponds to 5,610 virus copies/mL of sample (shown as dotted line and grey area). ( b ) The data are also shown by sampling moment (sequential collection time) to highlight the differences in virus titers between collection points. All of the data used to generate this figure, including the raw cycle thresholds, can be found in Supplementary Data 1 .