Self-collected Saline Gargle Samples as an Alternative to Healthcare Worker Collected Nasopharyngeal Swabs for COVID-19 Diagnosis in Outpatients

Goldfarb, David M.; Tilley, Peter; Al‐Rawahi, Ghada N.; Srigley, Jocelyn A.; Ford, Geoffrey; Pedersen, Heather; Pabbi, Abhilasha; Hannam-Clark, Stephanie; Charles, Marthe; Dittrick, Michelle; Gadkar, Vijay; Pernica, Jeffrey M.; Hoang, Linda

doi:10.1101/2020.09.13.20188334

Cited by 30 publications

(41 citation statements)

References 11 publications

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“…We considered clearing the throat important to sample material from the posterior oropharynx, where SARS-CoV-2 sampling by oropharyngeal swabs is known to be efficient [ 34 , 35 ]. While gargling with saline or buffer solutions has been suggested as a possibility to sample saliva from the deep throat [ 36 , 37 ], we rated this procedure as less operable as the gargling solution would need to be optimized for taste to be accepted by individuals, could not include preservatives and gargling itself may potentially generate aerosols. In addition, gargling is not practicable for many younger children, for whom we particularly sought to create more possibilities for SARS-CoV-2 testing, as NPS collection is often not practical in children.…”

Section: Discussionmentioning

confidence: 99%

High Efficacy of Saliva in Detecting SARS-CoV-2 by RT-PCR in Adults and Children

et al. 2021

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Rising demands for repetitive SARS-CoV-2 screens and mass testing necessitate additional test strategies. Saliva may serve as an alternative to nasopharyngeal swab (NPS) as its collection is simple, non-invasive and amenable for mass- and home testing, but its rigorous validation, particularly in children, is missing. We conducted a large-scale head-to-head comparison of SARS-CoV-2 detection by RT-PCR in saliva and NPS of 1270 adults and children reporting to outpatient test centers and an emergency unit. In total, 273 individuals were tested positive for SARS-CoV-2 in either NPS or saliva. SARS-CoV-2 RT-PCR results in the two specimens showed a high agreement (overall percent agreement = 97.8%). Despite lower viral loads in the saliva of both adults and children, detection of SARS-CoV-2 in saliva fared well compared to NPS (positive percent agreement = 92.5%). Importantly, in children, SARS-CoV-2 infections were more often detected in saliva than NPS (positive predictive value = 84.8%), underlining that NPS sampling in children can be challenging. The comprehensive parallel analysis reported here establishes saliva as a generally reliable specimen for the detection of SARS-CoV-2, with particular advantages for testing children, that is readily applicable to increase and facilitate repetitive and mass testing in adults and children.

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Section: Discussionmentioning

confidence: 99%

High Efficacy of Saliva in Detecting SARS-CoV-2 by RT-PCR in Adults and Children

et al. 2021

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“…We recently showed that self-collected saline mouth rinse/gargle samples had similar performance as NPFS for detection of SARS-CoV-2 in adults and children presenting with outpatient illness (Goldfarb et al, 2020). In the present work, we seek to evaluate this sample type with a simplified process for detecting SARS-CoV-2, without RNA extraction (extraction-free PCR; Fig.…”

Section: Introductionmentioning

confidence: 99%

Gargle-Direct: Extraction-Free Detection of SARS-CoV-2 using Real-time PCR (RT-qPCR) of Saline Gargle Rinse Samples

Tilley

Gadkar

Goldfarb

et al. 2020

Preprint

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Background: Saline mouth rinse/gargle samples have recently been shown to be a suitable option for swab-independent self-collection for SARS-CoV-2 diagnosis. We sought to evaluate a simplified process for direct reverse transcriptase PCR(RT-qPCR) testing of this novel sample type and to compare performance with routine RT-qPCR using automated nucleic acid extraction. Methods: Clinical saline mouth rinse/gargle samples were subjected to automated nucleic acid extraction (standard method), followed by RT-qPCR using three assays including the FDA authorized US-CDCs N1/N2 assay, which was the reference standard for determining sensitivity/specificity. For extraction-free workflow, an aliquot of each gargle sample underwent viral heat inactivation at 65 °C for 20 minutes followed by RT-qPCR testing, without an intermediate extraction step. An in-house validated RT-qPCR lab developed test (LDT), targeting the SARS-CoV-2, S/ORF8 genes (SORP triplex assay) and the N1/N2 US-CDC assay was used to evaluate the extraction-free protocol. To improve the analytical sensitivity, we developed a single-tube hemi-nested (STHN) version of the SORP triplex assay. Results: A total of 38 SARS-CoV-2 positive and 75 negative saline mouth rinse/gargle samples were included in this evaluation. A 100% concordance in detection rate was obtained between the standard method and the extraction-free approach for the SORP assay. An average increase of +2.63 to +5.74 of the cycle threshold (CT) values was observed for both the SORP and N1/N2 assay when extraction-free was compared between the standard method. The average ΔCT [(ΔCT=CT(Direct PCR)-CT(Extracted RNA)], for each of the gene targets were: S (ΔCT= +4.24), ORF8 (ΔCT=+2.63), N1 (ΔCT=+2.74) and N2 (ΔCT=+5.74). The ΔCT for the STHN SORP assay was +1.51 and -2.05 for the S and ORF8 targets respectively, when extracted method was compared to the standard method. Conclusion: Our Gargle-Direct SARS-CoV-2 method is operationally simple, minimizes pre-analytical sample processing and is potentially implementable by most molecular diagnostic laboratories. The empirical demonstration of single-tube hemi-nested RT-qPCR, to specifically address and alleviate the widely-acknowledged problem of reduced analytical sensitivity of detection of extraction-free templates, should help diagnostic laboratories in choosing Gargle-Direct protocol for high-throughput testing.

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“…1,4 One aspect of this debate concerns the occurrence of SARS-CoV-2 infection in children compared to adults. In our study, we detected SARS-CoV-2 infection in 1.42% (95% CI 1.06-1.90%) of study participants at the second round of examinations (10)(11)(12)(13)(14)(15)(16). This prevalence was somewhat less than the screen-detected prevalence of 2.12% in adults, which was observed by a different nationwide population-based study 21 conducted at a similar time frame (12-14 November, 48 out of 2263 tests positive based on nasopharyngeal swabs).…”

Section: Discussionmentioning

confidence: 50%

“…Gargling has been demonstrated to produce comparable sample quality like throat swab samples for other respiratory viruses 11 and has also been applied successfully for the detection of SARS-CoV-2. [12][13][14][15] At the laboratories, sample inactivation, RNA extraction, and RT-qPCR detection of SARS-CoV-2 was performed according to previously established protocols (for details, see Supplementary Material). Gargling samples were analysed in pools with a maximal pool size of 10.…”

Section: Sars-cov-2 Detection By Rt-pcrmentioning

confidence: 99%

Prevalence of RT-qPCR-detected SARS-CoV-2 infection at schools: First results from the Austrian School-SARS-CoV-2 prospective cohort study

Willeit

Krause

Lamprecht

et al. 2021

Preprint

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BackgroundThee is much debate about the role of schools and children in the SARS-CoV-2 pandemic. We aimed to quantify reliably the prevalence of SARS-CoV-2 infections at schools detected with reverse-transcription polymerase-chain-reaction (RT-PCR).MethodsThis nationwide prospective cohort study monitors a representative sample of pupils (grade 1-8) and teachers at Austrian schools throughout the school year 2020/2021. We repeatedly test participants for SARS-CoV-2 infection using a gargling solution and RT-PCR. We herein report on the first two rounds of examinations. We used mixed-effect logistic regression to estimate odds ratios and robust 95% confidence intervals (95% CI).FindingsWe analysed data on 10734 participants from 245 schools (9465 pupils, 1269 teachers). Prevalence of RT-PCR-detected SARS-CoV-2 infection increased from 0.39% at round 1 (95% CI 0.28-0.55%, 29 September-22 October 2020) to 1.42% at round 2 (95% CI 1.06-1.90%, 10-16 November). Odds ratios for SARS-CoV-2 infection were 2.29 (95% CI 1.26-4.17, P=0.007) in regions with >500 vs. ≤500 inhabitants/km2, 1.69 (95% CI 1.42-2.00, P<0.001) for a two-fold higher regional 7-day incidence, and 2.71 (95% CI 1.68-4.39, P<0.001) in pupils at schools with a high/very high vs. low/moderate social deprivation index. Associations of community incidence and social deprivation persisted in multivariable models. There were no differences between age groups, sexes, pupils vs. teachers, or primary (grade 1-4) vs. secondary schools (grade 5-8).InterpretationThis monitoring study in Austrian schools revealed SARS-CoV-2 infection in 0.39%-1.42% of participants and identified associations of regional community incidence and social deprivation with higher prevalence.FundingBMBWF Austria.

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Self-collected Saline Gargle Samples as an Alternative to Healthcare Worker Collected Nasopharyngeal Swabs for COVID-19 Diagnosis in Outpatients

Cited by 30 publications

References 11 publications

High Efficacy of Saliva in Detecting SARS-CoV-2 by RT-PCR in Adults and Children

High Efficacy of Saliva in Detecting SARS-CoV-2 by RT-PCR in Adults and Children

Gargle-Direct: Extraction-Free Detection of SARS-CoV-2 using Real-time PCR (RT-qPCR) of Saline Gargle Rinse Samples

Prevalence of RT-qPCR-detected SARS-CoV-2 infection at schools: First results from the Austrian School-SARS-CoV-2 prospective cohort study

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