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 percent positive agreement 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 average loss of signal upon pooling was 2-3 Ct values across the platforms. The sensitivity of detecting a positive specimen in a pool compared with testing individually was 94%, 90%, and 94% 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.

RT-PCR Screening Tests for SARS-CoV-2 with Saliva Samples in Asymptomatic People: Strategy to Maintain Social and Economic Activities while Reducing the Risk of Spreading the Virus

“…Other studies have demonstrated the usefulness of pooled sample testing for evaluating saliva samples. [48][49][50] Because the demand for screening large numbers of people is increasing, we have started comparing the sensitivities of pooled-sample testing and individual testing at Keio University. The results of the pooled-sample testing are beyond the scope of this paper, and the results we describe in the following section were obtained from individual RT-qPCR testing.…”

Evaluation of an Automated High-Throughput Liquid-Based RNA Extraction Platform on Pooled Nasopharyngeal or Saliva Specimens for SARS-CoV-2 RT-PCR

“…However, saliva has been used during the COVID-19 pandemic because of the high sen-sitivity and the ease of specimen collection [20,21,23]. Barat et al has evaluated pooled saliva testing using a MBTE platform for TNA extraction [11]. In our current study, we showed that the benefit of the LRE was most notable for pooled saliva specimens, in which the positive rate was higher for LRE than that of MBTE (88.3% vs. 81.7%).…”

“…During the COVID-19 pandemic, large scale testing for SARS-CoV-2 has been implemented as one of the public health measures to identify patients for early treatment and isolation to prevent further transmission [3]. Because the current diagnostic capacity cannot cope with the large number of specimens, pooled testing has been advocated [11,19]. This study showed that the LRE automated system has similar performance for NPS and better performance for saliva than MBTE in pooled specimens.…”

“…During a typical SARS-CoV-2 RT-PCR-based diagnostic workflow, viral total nucleic acid (TNA) or RNA is extracted and purified using solid phase capture-and-release methods with magnetic beads or spin columns [11]. In these strategies, the ionic strength is increased to selectively bind nucleic acid to solid silica substrates, and later decreased to elute the RNA into a purified solution.…”

“…In this study, we compared the detection rates of SARS-CoV-2 RT-PCR using an automated LRE platform against a magnetic-bead based extraction (MBTE) platform. We specifically assessed nasopharyngeal swab and saliva specimens since both specimen types are now used for pooled testing [11,19].…”