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

Original Article: 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, Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs, MedRxiv pre-print, Aprile 2020.

Author of summary: Mirella Vivoli Vega; Reviewer: Bernadette Basilico

Original Article Published on April 22nd, 2020

The study shows that saliva represents a reliable and more sensitive alternative to nasopharyngeal swabs and could enable self-administered sample collection for accurate large-scale SARS-CoV-2 testing.

Efforts to control SARS-CoV-2 pandemic depend on accurate and rapid diagnostic tests. These tests should also be sensitive in detecting asymptomatic infections to reduce transmission, consistent to monitor disease progression and scalable to inform local and national public health policies, such as when social distancing measures can be safely relaxed. Nasopharyngeal swabs often do not meet these criteria, as they show a relatively poor sensitivity in detecting SARS-CoV-2 in the early stages of infection and inconsistent during serial testing. On the other hand, saliva sampling is an appealing alternative to nasopharyngeal swab, since collecting saliva is non-invasive and easy to self-administer.

Methods.

44 inpatients, SARS-CoV-2 positive through the nasopharyngeal swab, and with severe symptoms were recruited. From this cohort, 121 specimens were analyzed using both saliva and nasopharyngeal swabs. Using the MagMAX Viral/Pathogen Nucleic Acid Isolation kit, containing the specific primers for N1 and N2, the researchers performed the RT-PCR, and calculated the viral titers (number of viruses / mL) only for the N1 set. Samples were classified as positive for SARS-CoV-2 when both N1 and N2 primer-probe sets were detected <38 Ct. The human RNase P (RP) was used as an extraction control. Virus copies were quantified using a 10-fold dilution standard curve of RNA transcripts that we previously generated.

In addition, they enrolled 98 asymptomatic healthcare workers and collected saliva and/or nasopharyngeal swabs every 2.9 days and analyzed by PCR.

Results.

  • From positive samples of inpatients (46 with nasopharyngeal swab and 37 with saliva) it has emerged that the mean virus titers from saliva were about 5⨉ higher than nasopharyngeal swabs. Comparison between 38 positive samples showed that SARS-CoV-2 titers from saliva were significantly higher than nasopharyngeal swabs.
  • The authors found 5 instances where a participant’s nasopharyngeal swab was negative for SARS-CoV-2 followed by a positive result during the next collection, whereas in saliva collections from 12 patients there were no instances in which a sample tested negative and was later followed by a positive result.
  • For 2 of 98 asymptomatic health workers, who were negative by nasopharyngeal swabs, saliva tested positive upon repeat testing 2 days later.  The limited data supports that saliva may be more sensitive for detecting asymptomatic or pre-symptomatic infections; however, a larger sample size is needed to confirm.

Conclusions. The sensitivity of SARS-CoV-2 detection from saliva is comparable, if not superior to nasopharyngeal swabs in early hospitalization and is more consistent during extended hospitalization and recovery. Moreover, the detection of SARS-CoV-2 from the saliva of 2 asymptomatic healthcare workers despite negative matched nasopharyngeal swabs suggests that saliva may also be a viable alternative for identifying mild or subclinical infections. A saliva SARS-CoV-2 detection assay has already gained approval through the FDA, but to meet the growing testing demands, these findings need an immediate validation and implementation.

About the Author

Federico Forneris
Federico Forneris, PhD in Biochemistry and Structural Biology, is Principal Investigator of the Armenise-Harvard Laboratory of Structural Biology at the University of Pavia, Italy

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