Saliva is a promising alternative specimen for the detection of SARS-CoV-2 in children and adults

Yee, Rebecca; Truong, Thao; Pannaraj, Pia S.; Eubanks, Natalie; Gai, Emily; Jumarang, Jaycee; Turner, Lauren; Peralta, Ariana; Lee, Yesun; Bard, Jennifer T Dien

doi:10.1101/2020.10.25.20219055

Cited by 33 publications

(55 citation statements)

References 24 publications

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“…Our results also revealed that at the early stages of the infection, saliva sampling had a lower sensitivity to detect viral RNA compared to other sampling methods. Although some recent studies have shown similar results to ours, there are also other studies suggesting that saliva samples are compatible with the results of nasopharyngeal samples starting from the early period of the disease ( Azzi et al, 2020 , To et al, 2020 , Pasomsub et al, 2020 , Kam et al, 2020 ; Chong et al, 2020 , Jamal et al, 2020 ; Kim et al, 2020 ; Kojima et al, 2020 ; Yokota et al, 2020 , Yee et al, 2020 ; Santos et al, 2020 ). Some researchers suggest that saliva sampling can allow for an efficient, relatively inexpensive surveillance system however, they also point to the need for pilot studies ( Fogarty et al, 2020 , Medeiros da Silva et al, 2020 ).…”

Section: Discussionsupporting

confidence: 91%

Does sampling saliva increase detection of SARS-CoV-2 by RT-PCR? Comparing saliva with oro-nasopharyngeal swabs

Doğan

Kose

Ağaoğlu

et al. 2021

Journal of Virological Methods

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Section: Discussionsupporting

confidence: 91%

Does sampling saliva increase detection of SARS-CoV-2 by RT-PCR? Comparing saliva with oro-nasopharyngeal swabs

Doğan

Kose

Ağaoğlu

et al. 2021

Journal of Virological Methods

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“…On the basis of our selection criteria, 127 of those studies were excluded and 23 studies 21 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 met our inclusion criteria ( table ). Of these, 14 studies were from the USA, 21 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 four were from European countries, 60 , 61 , 62 , 63 two were from Eastern Mediterranean countries, 64 , 65 and the rest were from Canada, 66 India, 67 and China. 68 7973 individuals with suspected SARS-CoV-2 infection, who were mostly symptomatic outpatients presenting to dedicated testing sites or emergency departments, were included from the 23 eligible studies.…”

Section: Resultsmentioning

confidence: 99%

Diagnostic performance of different sampling approaches for SARS-CoV-2 RT-PCR testing: a systematic review and meta-analysis

Tsang

et al. 2021

The Lancet Infectious Diseases

207

184

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Background The comparative performance of different clinical sampling methods for diagnosis of SARS-CoV-2 infection by RT-PCR among populations with suspected infection remains unclear. This meta-analysis aims to systematically compare the diagnostic performance of different clinical specimen collection methods. Methods In this systematic review and meta-analysis, we systematically searched PubMed, Embase, MEDLINE, Web of Science, medRxiv, bioRxiv , SSRN, and Research Square from Jan 1, 2000, to Nov 16, 2020. We included original clinical studies that examined the performance of nasopharyngeal swabs and any additional respiratory specimens for the diagnosis of SARS-CoV-2 infection among individuals presenting in ambulatory care. Studies without data on paired samples, or those that only examined different samples from confirmed SARS-CoV-2 cases were not useful for examining diagnostic performance of a test and were excluded. Diagnostic performance, including sensitivity, specificity, positive predictive value, and negative predictive value, was examined using random effects models and double arcsine transformation. Findings Of the 5577 studies identified in our search, 23 studies including 7973 participants with 16 762 respiratory samples were included. Respiratory specimens examined in these studies included 7973 nasopharyngeal swabs, 1622 nasal swabs, 6110 saliva samples, 338 throat swabs, and 719 pooled nasal and throat swabs. Using nasopharyngeal swabs as the gold standard, pooled nasal and throat swabs gave the highest sensitivity of 97% (95% CI 93–100), whereas lower sensitivities were achieved by saliva (85%, 75–93) and nasal swabs (86%, 77–93) and a much lower sensitivity by throat swabs (68%, 35–94). A comparably high positive predictive value was obtained by pooled nasal and throat (97%, 90–100) and nasal swabs (96%, 87–100) and a slightly lower positive predictive value by saliva (93%, 88–97). Throat swabs have the lowest positive predictive value of 75% (95% CI 45–96). Comparably high specificities (range 97–99%) and negative predictive value (range 95–99%) were observed among different clinical specimens. Comparison between health-care-worker collection and self-collection for pooled nasal and throat swabs and nasal swabs showed comparable diagnostic performance. No significant heterogeneity was observed in the analysis of pooled nasal and throat swabs and throat swabs, whereas moderate to substantial heterogeneity ( I 2 ≥30%) was observed in studies on saliva and nasal swabs. Interpretation Our review suggests that, compared with the gold standard of nasopharyngeal swabs, pooled nasal and throat swabs offered the best diagnostic performance of the alternative sampling approaches for diagnosis of SARS-CoV-2 infection in ambulatory care. Saliva and nasal swabs gave comparable and very good diagnostic performance and are clinically...

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“…The FDA has moved rapidly to authorize hundreds of molecular tests for Emergency Use during the COVID-19 pandemic and has dramatically expanded access to testing (32). However, the number of tests authorized for alternative specimen types such as oral fluid or saliva which can provide easy, high-throughput access to regular testing, has remained small (33), despite these specimen types being shown to be highly effective (15, 34, 35, 36, 37). And in fact there still remains no test authorized for use in asymptomatic screening using saliva or oral fluid.…”

Section: Discussionmentioning

confidence: 99%

Post-Disease Divergence in SARS-CoV-2 RNA Detection between Nasopharyngeal, Anterior Nares and Saliva/Oral Fluid Specimens - Significant Implications for Policy & Public Health

Turner¹,

Vandenberg²,

Vi³

et al. 2021

Preprint

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BackgroundPatients have been shown to shed SARS-CoV-2 viral RNA in nasopharyngeal (NP) specimens for over 100 days after resolution of clinical disease (1, 2). How this relates to anterior nares and oral fluid specimens has not previously been investigated.MethodsWe prospectively collected oral fluid, anterior nares, NP swab and serum specimens from 1,326 individuals at 2 “drive-through” testing locations. The Curative SARS-CoV-2 Assay (Curative Assay)(3) on oral fluid and anterior nares specimens was compared to the EURORealTime SARS-CoV-2 Assay (EuroRT Assay)(4) on anterior nares and NP specimens. Viral culture and IgG serology were used to assess infectious potential and stage of disease.Additionally we investigated differences in viral RNA detection between specimen types, both early (< 21 days) and late (> 21 days) in SARS-CoV-2 infection, by using an employee surveillance program with daily SARS-CoV-2 testing to precisely determine infection date, even without symptoms. We prospectively collected oral fluid, anterior nares and NP swab specimens from 165 subjects with early infections and 22 subjects with late infections. Specimens were tested using the Curative Assay with the “high-sensitivity” Hologic Aptima SARS-CoV-2 Assay (Hologic Assay)(5) on an NP swab used as the comparator. Late infection specimens were also tested with EuroRT and Zymo Quick SARS-CoV-2 rRT-PCR Kit (Zymo) (6) Assays.ResultsThe “drive-through” study showed similar sensitivities of oral fluid and anterior nares specimens on the Curative Assay to anterior nares specimens tested with the EuroRT Assay. However NP specimens tested with the same EuroRT assay produced 20-30% more positives. Incorporating viral culture and serology data to exclude NP RT-PCR positives that are not infectious or late in the course of disease showed a Positive Percent Agreement (PPA) for of 98.2% and 96.2% and Negative Percent Agreement (NPA) of 97.6% and 98.1% for anterior nares and oral fluid specimens, respectively.Within 21 days of infection, the Curative Assay showed a PPA and NPA of 100% and 100%, respectively for oral fluid; of 100% and 99% respectively for anterior nares; and of 98.2% and 99.0%, respectively in nasopharyngeal specimens compared to an NP specimen on the Hologic Assay. 29 positives were asymptomatic and showed 100% PPA and 100% NPA for all specimen types. After 21 days from infection onset, significant divergence between NP and other specimen types occurred on all 4 assays. Out of 22 paired sample sets, 18, 13, 8 and 4 NP specimens were positive on the Curative, Zymo, Hologic and EuroRT assays, respectively, compared to only 3, 2, 0 and 1 positive anterior nares specimens. Only one oral fluid sample was positive in both the Curative and Zymo assays.ConclusionsWe used a unique population to show significant divergence between NP specimens and anterior nares or oral fluid specimens >21 days from SARS-CoV-2 infection, which appears to be biological variation and is independent of assay used. This has significant public health implications for the use of NP specimens in community testing programs and policy implications for evaluation of novel specimen types and tests where the use of NP swabs as a comparator may say more about the study population than the assay or specimen type to be evaluated and may unnecessarily limit access to testing.

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Saliva is a promising alternative specimen for the detection of SARS-CoV-2 in children and adults

Cited by 33 publications

References 24 publications

Does sampling saliva increase detection of SARS-CoV-2 by RT-PCR? Comparing saliva with oro-nasopharyngeal swabs

Does sampling saliva increase detection of SARS-CoV-2 by RT-PCR? Comparing saliva with oro-nasopharyngeal swabs

Diagnostic performance of different sampling approaches for SARS-CoV-2 RT-PCR testing: a systematic review and meta-analysis

Post-Disease Divergence in SARS-CoV-2 RNA Detection between Nasopharyngeal, Anterior Nares and Saliva/Oral Fluid Specimens - Significant Implications for Policy & Public Health

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