Pooled Saliva Specimens for SARS-CoV-2 Testing

Abstract

We evaluated saliva (SAL) specimens for SARS-CoV-2 RT-PCR testing by comparison of 459 prospectively paired nasopharyngeal (NP) or mid-turbinate (MT) swabs from 449 individuals with the aim of using saliva for asymptomatic screening. Samples were collected in a drive-through car line for symptomatic individuals (N=380) and in the emergency department (ED) (N=69). The percent positive and negative agreement of saliva compared to nasopharyngeal swab were 81.1% (95% CI: 65.8% – 90.5%) and 99.8% (95% CI: 98.7% – 100%), respectively. The sensitivity increased to 90.0% (95% CI: 74.4% – 96.5%) when considering only samples with moderate to high viral load (Cycle threshold (Ct) for the NP <=34). Pools of five saliva specimens were also evaluated on three platforms: bioMérieux NucliSENS easyMAG with ABI 7500Fast (CDC assay), Hologic Panther Fusion, and Roche COBAS 6800. The median loss of signal upon pooling was 2-4 Ct values across the platforms. The sensitivity of detecting a positive specimen in a pool compared with testing individually was 100%, 93%, and 95% for CDC 2019-nCoV Real-Time RT-PCR, Panther Fusion® SARS-CoV-2 assay, and cobas® SARS-CoV-2 test respectively, with decreased sample detection trending with lower viral load. We conclude that although pooled saliva testing, as collected in this study, is not quite as sensitive as NP/MT testing, saliva testing is adequate to detect individuals with higher viral loads in an asymptomatic screening program, does not require swabs or viral transport media for collection, and may help to improve voluntary screening compliance for those individuals averse to various forms of nasal collections.

Diagnosis of SARS-Cov-2 Infection by RT-PCR Using Specimens Other Than Naso- and Oropharyngeal Swabs: A Systematic Review and Meta-Analysis

“…Overall, twenty-one studies had low risk of bias (63.6%) [ 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 35 , 38 , 39 , 40 , 41 , 42 , 43 ], eleven raised some concerns (33.3%) [ 21 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 36 ] and one had high risk of bias (3.0%) [ 37 ] ( Figure 2 ) (fully detailed in Supplementary S3 , pp. 12).…”

“…Therefore, as a diagnostic specimen, "saliva" deserves a particular attention, and several considerations need to be taken into account. Firstly, most studies accounted for salivary samples circumscribed to the oral region (anterior to the throat) [ 12 , 13 , 15 , 20 , 22 , 26 , 30 , 33 , 34 , 35 , 37 , 38 , 39 , 40 , 42 ], while the remaining studies analyzed DTS/POS with or without pre-throat saliva [ 25 , 27 , 29 , 32 , 41 , 43 ]. This fact is very important as the salivary characteristics and the collection method differ, and the DTS/POS may contain samples other than the oropharyngeal region (naso-pharyngeal or laryngeal-pharyngeal) [ 55 ].…”

“…Aiming at simplifying the sample collection procedure, so that the average person could perform self-sampling, alternative specimens have been tested for the detection of SARS-CoV-2, namely sputum, saliva, tears/conjunctival swab (CS), feces, rectal swab, urine, breast milk, and semen [ 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 ]. To the best of our knowledge, until now, just one protocol for saliva testing, the SalivaDirect, has been approved by a public health authority, the United States Food and Drug Administration (FDA) [ 44 ].…”

Evaluation of sample pooling for SARS-CoV-2 RNA detection in nasopharyngeal swabs and salivas on the Roche Cobas 6800

“…Various pooling strategies have been developed since the beginning of the COVID-19 pandemic [ [4] , [5] , [6] , [7] , [8] ]. While the need for pooling is clear, the impact on sensitivity varies among studies and depending on the size of the pool and the platform and assay used.…”

“…We have previously shown that there were no differences in performance between symptomatic and asymptomatic patients and high viral loads could be detected in saliva of asymptomatic or pre-symptomatic patients, further supporting the potential use of saliva pool testing [ 3 ]. In their study, Barat et al evaluated pooled saliva testing in pools of five using two commercial assays (Panther Fusion and Roche Cobas 6800) [ 4 ]. The authors reported a sensitivity of at least 90% for all three methods with the Roche Cobas showing a sensitivity of 94% similar to results from our study with a 6 samples pool size.…”