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

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

Rapid and accurate SARS-CoV-2 diagnostic testing is essential for controlling the ongoing COVID-19 pandemic. The current gold standard for COVID-19 diagnosis is real-time RT-PCR detection of SARS-CoV-2 from nasopharyngeal swabs. Low sensitivity, exposure risks to healthcare workers, and global shortages of swabs and personal protective equipment, however, necessitate the validation of new diagnostic approaches. Saliva is a promising candidate for SARS-CoV-2 diagnostics because (1) collection is minimally invasive and can reliably be self-administered and (2) saliva has exhibited comparable sensitivity to nasopharyngeal swabs in detection of other respiratory pathogens, including endemic human coronaviruses, in previous studies. To validate the use of saliva for SARS-CoV-2 detection, we tested nasopharyngeal and saliva samples from confirmed COVID-19 patients and self-collected samples from healthcare workers on COVID-19 wards. When we compared SARS-CoV-2 detection from patient-matched nasopharyngeal and saliva samples, we found that saliva yielded greater detection sensitivity and consistency throughout the course of infection. Furthermore, we report less variability in self-sample collection of saliva. Taken together, our findings demonstrate that saliva is a viable and more sensitive alternative to nasopharyngeal swabs and could enable at-home self-administered sample collection for accurate large-scale SARS-CoV-2 testing.