Saliva or Nasopharyngeal Swab Specimens for Detection of SARS-CoV-2.
Author(s): Wyllie AL, Fournier J, Casanovas-Massana A, Campbell M, Tokuyama M, Vijayakumar P, Warren JL, Geng B, Muenker MC, Moore AJ, Vogels CBF, Petrone ME, Ott IM, Lu P, Venkataraman A, Lu-Culligan A, Klein J, Earnest R, Simonov M, Datta R, Handoko R, Naushad N, Sewanan LR, Valdez J, White EB, Lapidus S, Kalinich CC, Jiang X, Kim DJ, Kudo E, Linehan M, Mao T, Moriyama M, Oh JE, Park A, Silva J, Song E, Takahashi T, Taura M, Weizman OE, Wong P, Yang Y, Bermejo S, Odio CD, Omer SB, Dela Cruz CS, Farhadian S, Martinello RA, Iwasaki A, Grubaugh ND, Ko AI
Publication: N Engl J Med, 2020, Vol. 383, Page 1283-1286
PubMed ID: 32857487 PubMed Review Paper? No
Purpose of Paper
This paper compared viral loads of SARS-CoV-2, the virus that causes the novel 2019 coronavirus disease (COVID, COVID-19, COVID19), in matched self-collected saliva specimens with healthcare worker–collected nasopharyngeal swab specimens over a 78-day timecourse from onset of symptoms. Matched self-collected saliva and nasopharyngeal specimens from asymptomatic healthcare workers were also compared for detection of SARS-CoV-2 RNA.
Conclusion of Paper
A higher percentage of self-collected saliva specimens were positive for up to 10 days after diagnosis than matched healthcare worker-collected nasopharyngeal swab specimens. Further, self-collected saliva specimens had higher and less variable SARS-CoV-2 RNA copy numbers. While the saliva specimen from 13 of 495 asymptomatic healthcare workers tested positive for SARS-CoV-2 RNA, SARS-CoV-2 was positive in only 2 of the 9 matched nasopharyngeal swab specimens. Overall, there was less variation in SARS-CoV-2 RNA levels in saliva than nasopharyngeal swab specimens which the authors attributed to sampling technique.
Studies
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Study Purpose
This study compared viral loads of SARS-CoV-2, the virus that causes the novel 2019 coronavirus disease (COVID, COVID-19, COVID19), in matched self-collected saliva specimens with healthcare worker–collected nasopharyngeal swab specimens over a 78-day timecourse from onset of symptoms. Matched self-collected saliva and nasopharyngeal specimens from asymptomatic healthcare workers were also compared for detection of SARS-CoV-2 RNA. Specimens were collected every 3 days from 70 patients aged 13-91 y (41 males, 29 females; mean age=61.4 y) previously diagnosed with SARS-CoV-2 infection by nasopharyngeal and/or oropharyngeal swab. Saliva was self-collected by patients by repeatedly spitting into a sterile urine cup until roughly a third full of liquid. Nasopharyngeal swab specimens were then collected by healthcare-workers by passing a flexible, mini-tip swab through the patient's nostril to the posterior nasopharynx with slow rotation while removing and then placement in a tube containing sterile viral transport media. All specimens were stored at room temperature and transported to the lab within 5 h and tested within 12 h of collection. As part of a screening study on asymptomatic cases, 495 healthcare workers aged 22-74 years (105 males, 390 females; mean age=37.6 y) self-collected a nasopharyngeal swab and a saliva sample every three days for up to 84 days or until testing positive for SARS-CoV-2. Specimens were stored at +4°C until being transported to the lab. Viral RNA was extracted using the MagMAX Viral/Pathogen Nucleic Acid Isolation Kit and viral loads were quantified by real-time qRT-PCR using primer/probe sets for the 2019-nCoV_N1 and 2019-nCoV_N2 and the human RNase P as an extraction control. Specimens were classified as positive for SARS-CoV-2 when both N1 and N2 primer-probe sets were detected <38 CTs.
Summary of Findings:
A higher percentage of saliva specimens were positive than nasopharyngeal swab specimens at 1 to 5 days after diagnosis (81% versus 71%, respectively) and up to 10 days after diagnosis (data not provided). SARS-CoV-2 RNA copy numbers were higher in self-collected saliva specimens than matched healthcare worker-collected nasopharyngeal swab specimens (5.58 versus 4.93 mean log copies mL, P<0.001). Of the 495 asymptomatic healthcare workers tested, 13 had saliva specimens that tested positive for SARS-CoV-2 RNA but only 2 of the 9 matched nasopharyngeal swab specimens tested positive. Overall, there was less variation in SARS-CoV-2 RNA levels in saliva than nasopharyngeal swab specimens (standard deviation 0.98 virus RNA copies/mL versus 2.01 virus RNA copies/mL, respectively) which the authors attributed to sampling technique.
Biospecimens
Preservative Types
- None (Fresh)
Diagnoses:
- Pneumonia/Respiratory Infection
Platform:
Analyte Technology Platform RNA Real-time qRT-PCR Pre-analytical Factors:
Classification Pre-analytical Factor Value(s) Biospecimen Acquisition Biospecimen location Saliva
Nasopharynx
Real-time qRT-PCR Specific Targeted nucleic acid SARS-CoV-2
Biospecimen Acquisition Time of biospecimen collection 78-day timecourse from onset of symptoms
Biospecimen Acquisition Method of cell acquisition Healthcare worker–collected swabs
Self-collected saliva