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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.

SUBMITTER: Barat B

PROVIDER: S-EPMC7553188 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Routine testing for SARS-CoV-2 is rare for institutes of higher education due to prohibitive costs and supply chain delays. During spring 2021, we routinely tested all residential students 1 to 2 times per week using pooled, RNA-extraction-free, reverse transcription quantitative PCR (RT-qPCR) testing of saliva at a cost of $0.43/sample with same-day results. The limit of detection was 500 copies/ml on individual samples, and analysis indicates 1,000 and 2,500 copies/ml in pools of 5 and 10, respectively, which is orders of magnitude more sensitive than rapid antigen tests. Importantly, saliva testing flagged 83% of semester positives (43,884 tests administered) and was 95.6% concordant with nasopharyngeal diagnostic results (69.0% concordant on the first test when the nucleocapsid gene (N1) cycle threshold (CT) value was >30). Moreover, testing reduced weekly cases by 59.9% in the spring despite far looser restrictions, allowing for more normalcy while eliminating outbreaks. We also coupled our testing with a survey to clarify symptoms and transmissibility among college-age students. While only 8.5% remained asymptomatic throughout, symptoms were disparate and often cold-like (e.g., only 37.3% developed a fever), highlighting the difficulty with relying on symptom monitoring among this demographic. Based on reported symptom progression, we estimate that we removed 348 days of infectious individuals by routine testing. Interestingly, viral load (CT value) at the time of testing did not affect transmissibility (R2 = 0.0085), though those experiencing noticeable symptoms at the time of testing were more likely to spread the virus to close contacts (31.6% versus 14.3%). Together, our findings support routine testing for reducing the spread of SARS-CoV-2. Implementation of cost- and resource-efficient approaches should receive strong consideration in communities that lack herd immunity. IMPORTANCE This study highlights the utility of routine testing for SARS-CoV-2 using pooled saliva while maintaining high sensitivity of detection (under 2,500 copies/ml) and rapid turnaround of high volume (up to 930 samples in 8 h by two technicians and one quantitative PCR [qPCR] machine). This pooled approach allowed us to test all residential students 1 to 2 times per week on our college campus during the spring of 2021 and flagged 83% of our semester positives. Most students were asymptomatic or presented with symptoms mirroring common colds at the time of testing, allowing for removal of infectious individuals before they otherwise would have sought testing. To our knowledge, the total per-sample consumable cost of $0.43 is the lowest to date. With many communities still lagging in vaccination rates, routine testing that is cost-efficient highlights the capacity of the laboratory's role in controlling the spread of SARS-CoV-2.

Project description:BackgroundSARS-CoV-2 is a novel coronavirus discovered in December 2019 and is currently the cause of the global COVID-19 pandemic. A critical aspect of fighting this pandemic is to obtain accurate and timely test results so that patients who have tested positive for COVID-19 can be identified and isolated to reduce the spread of the virus. Research has shown that saliva is a promising candidate for SARS-CoV-2 diagnostics because its collection is minimally invasive and can be reliably self-administered. However, little research has been conducted on saliva testing and SARS-CoV-2 self-sampling (SARS-CoV-2SS) in Sub-Saharan Africa.ObjectiveThe primary objective of this study is to comparatively evaluate the clinical sensitivity and specificity of nasal and oral samples self-collected by individuals for SARS-CoV-2 testing against a reference method involving sample collection and testing by a health care professional. The secondary objectives of this study are to evaluate the usability of nasal self-sampling and saliva self-sampling as a sample collection method for SARS-CoV-2 diagnostic testing by using failure mode and error assessment.MethodsParticipants will be recruited from the general population by using various methods, Participants will be screened progressively as they present at the clinical trial sites as well as in primary health care catchment areas in the inner city of Johannesburg, South Africa. In the event that recruitment numbers are low, we will use a mobile van to recruit participants from outlying areas of Johannesburg. We aim to enroll 250 participants into this study in approximately 6 weeks. Two sample types-a self-administered nasal swab and a self-administered saliva sample-will be collected from each participant, and a health care professional will collect a third sample by using a nasopharyngeal swab (ie, the standard reference method).ResultsThis protocol has been approved by the University of the Witwatersrand Human Research Ethics Committee on July 31, 2020 (Protocol number EzCov003). As of May 13, 2021, 120 participants have been enrolled into the study.ConclusionsSARS-CoV-2SS may offer many benefits to individuals, by allowing for initial self-identification of symptoms and collection of samples without involving third parties and potential risk of infection provided the sample can be safely processed via a collection system. The results of this study will provide preliminary data on the acceptability, feasibility, and usability of SARS-CoV-2SS among the general population for its future implementation.International registered report identifier (irrid)DERR1-10.2196/24811.

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Pooled Saliva Specimens for SARS-CoV-2 Testing.

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