Effective bubble-based testing for SARS-CoV-2 using swab-pooling

Bamberger, Nadav; Mor, Orna; Walfisch, Ronen; Fleishon, Shay; Varkovitzky, Itay; Younger, Asaf; Levi, Danit Oz; Kohn, Yishai; Steinberg, David M.; Zeevi, Danny; Erster, Oran; Livneh, Zvi

doi:10.1016/j.cmi.2022.02.016

Cited by 6 publications

(7 citation statements)

References 30 publications

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“…Therefore, the number of individuals per pool is negligible to the swab method as long as it is ensured that all swabs are covered with buffer solution (in the case of this pilot study, the maximum number was 15 swabs). The higher amount of buffer solution compared to a single sample is consistent with the approach of other studies [ 27 , 29 – 31 ]. Accordingly, the laboratory methodology was not re-validated in this pilot study.…”

Section: Discussionsupporting

confidence: 91%

“…Nevertheless, there is an ongoing debate in the scientific community about the optimal number of samples that can be pooled in order to obtain a sufficiently high sensitivity and cost efficiency [ 45 – 47 ]. In a recently published study by Cohen et al, bubble-based swab samples of up to 37 swabs were pooled and tested for SARS-CoV-2 by PCR [ 27 ]. After adjusting for the dilution effect, the expected sensitivity per pool size was calculated.…”

Section: Discussionmentioning

confidence: 99%

“…Up to 15 people gave their lollipop swabs together in one empty sample tube and thereby formed a pool. No fixed number of samples per pool was specified, but rather all persons in a class who were in physical contact with each other were to form one or more pools, depending on the class size (also referred to as pooling-in-a-pod or bubble-based testing [ 27 , 28 ]). The teacher recorded the names of the people who were part of one pool.…”

Section: Methodsmentioning

confidence: 99%

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SARS-CoV-2 surveillance by RT-qPCR-based pool testing of saliva swabs (lollipop method) at primary and special schools—A pilot study on feasibility and acceptability

Kästner

Lücker²,

Sombetzki³

et al. 2022

PLoS ONE

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Background Since the onset of the COVID-19 pandemic, children have been mentally and physically burdened, particularly due to school closures, with an associated loss of learning. Therefore, efficient testing strategies with high sensitivity are necessary to keep schools open. Apart from individual rapid antigen testing, various methods have been investigated, such as PCR-based pool-testing of nasopharyngeal swabs, gargle, or saliva samples. To date, previous validation studies have found the PCR-based saliva swab pool testing method to be an effective screening method, however, the acceptability and feasibility of a widespread implementation in the school-setting among stakeholders has not been comprehensively evaluated. Methods In this pilot study, SARS-CoV-2 saliva swab pool testing of up to 15 swabs per pool was conducted in ten primary and special schools in Mecklenburg-Western Pomerania, Germany, over a period of one month. Thereafter, parents, teachers and school principals of the participating schools as well as the participating laboratories were surveyed about the feasibility and acceptability of this method, its large-scale implementation and challenges. Data were analyzed quantitatively and qualitatively. Results During the study period, 1,630 saliva swab pools were analyzed, of which 22 tested SARS-CoV-2 positive (1.3%). A total of N = 315 participants took part in the survey. Across all groups, the saliva swab pool testing method was perceived as more child-friendly (>87%), convenient (>82%), and easier (>81%) compared to rapid antigen testing by an anterior nasal swab. Over 80% of all participants favored widespread, regular use of the saliva swab method. Conclusion In school settings in particular, a high acceptability of the test method is crucial for a successful SARS-CoV-2 surveillance strategy. All respondents clearly preferred the saliva swab method, which can be used safely without complications in children six years of age and older. Hurdles and suggestions for improvement of an area-wide implementation were outlined.

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Section: Discussionsupporting

confidence: 91%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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SARS-CoV-2 surveillance by RT-qPCR-based pool testing of saliva swabs (lollipop method) at primary and special schools—A pilot study on feasibility and acceptability

Kästner

Lücker²,

Sombetzki³

et al. 2022

PLoS ONE

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“… 1 , 2 As real‐time reverse‐transcription PCR (rtRT‐PCR) is considered the laboratory gold standard for SARS‐CoV‐2 detection, 3 , 4 clinical and reference laboratories could not simply switch to antigen detection to meet the demand for testing. Rather, rtRT‐PCR testing had to be elevated to new, higher levels of throughput and turnaround time, primarily through the use of fully integrated, automated, 5 , 6 and semiautomated high‐throughput systems, 7 pooling of samples, 8 , 9 , 10 logistics, 11 and triage of samples through multiple platforms in simultaneous use.…”

Section: Introductionmentioning

confidence: 99%

Performance of nasopharyngeal swab and saliva in detecting Delta and Omicron SARS‐CoV‐2 variants

Uršič

Kogoj

Šikonja

et al. 2022

Journal of Medical Virology

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A prospective cohort study was conducted during the Delta and Omicron severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) epidemic waves from paired nasopharyngeal swab (NPS or NP swab) and saliva samples taken from 624 participants.The study aimed to assess if any differences among participants from both waves could be observed and if any difference in molecular diagnostic performance could be observed among the two sample types. Samples were transported immediately to the laboratory to ensure the highest possible sample quality without any freezing and thawing steps before processing. Nucleic acids from saliva and NPS were prospectively extracted and SARS-CoV-2 was detected using a real-time reverse-transcription polymerase chain reaction. All observed results were statistically analyzed. Although the results obtained with NP and saliva agreed overall, higher viral loads were observed in NP swabs regardless of the day of specimen collection in both SARS-CoV-2 epidemic waves. No significant difference could be observed between the two epidemic waves characterized by Delta or Omicron SARS-CoV-2. To note, Delta infection resulted in higher viral loads both in NP and saliva and more symptoms, including rhinorrhea, cough, and dyspnea, whereas Omicron wave patients more frequently reported sore throat. An increase in the mean log RNA of SARS-CoV-2 was observed with the number of expressed symptoms in both waves, however, the difference was not significant. Data confirmed that results from saliva were concordant with those from NP swabs, although saliva proved to be a challenging sample with frequent inhibitions that required substantial retesting.

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“…Specific detection of MPX using quantitative PCR (qPCR) is cheaper, faster, and can readily be adjusted for high throughput testing of very large numbers of samples, as was performed during the COVID19 pandemic (Cohen et al 2022). furthermore, this approach can easily distinguish between different MPX strains (Li et al .…”

Section: Introductionmentioning

confidence: 99%

A Multi-Laboratory Evaluation of Commercial Monkeypox Molecular Tests

Erster

Levy

Kabat

et al. 2022

Preprint

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In this report, we describe the first national scale multi-laboratory evaluation of commercial quantitative PCR kits for detection of Monkeypox virus (MPXV) DNA. The objective of this study was to assess the performance of two kits by different diagnostic laboratories across Israel. A panel of 10 standardized samples was tested simultaneously using the Novaplex (15 laboratories) and Bio-Speedy (seven laboratories) kits. An in-house assay based on previously published tests was used as reference. Comparison of the results showed high intra-assay consistency between laboratories, with small variations for most samples. The sensitivity of the two kits was similar to that of the in-house assay, with an analytical detection limit of less than ten copies per reaction. Significant differences were observed, however, in the Cq values and relative fluorescence (RF), between the assays. The RF signal of the in-house and Bio-Speedy assay ranged between 5,000 and 10,000 RFU, while the signal in the Novaplex assay was less than 600 RFU. Due to the kit measurement protocol, the Cq values of the Bio-Speedy kit were 5-7.5 cycles lower than those of the In-house assay. On the contrary, the Cq values of the Novaplex kit were significantly higher than those of the in-house assay, with differences of 3-5 cycles per sample. Our results suggest that while all assays were similar in their overall sensitivity, direct comparison of Cq values between them may be misleading. Additionally, the low fluorescence obtained with the Novaplex kit may be problematic with marginal or high-background samples. Diagnostic laboratories should therefore consider all these aspects when choosing a specific MPX detection assay.

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Effective bubble-based testing for SARS-CoV-2 using swab-pooling

Cited by 6 publications

References 30 publications

SARS-CoV-2 surveillance by RT-qPCR-based pool testing of saliva swabs (lollipop method) at primary and special schools—A pilot study on feasibility and acceptability

SARS-CoV-2 surveillance by RT-qPCR-based pool testing of saliva swabs (lollipop method) at primary and special schools—A pilot study on feasibility and acceptability

Performance of nasopharyngeal swab and saliva in detecting Delta and Omicron SARS‐CoV‐2 variants

A Multi-Laboratory Evaluation of Commercial Monkeypox Molecular Tests

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