Evaluation of Sample Pooling for SARS-CoV-2 Detection in Nasopharyngeal Swab and Saliva Samples with the Idylla SARS-CoV-2 Test

Hofman, Paul; Allègra, Maryline; Salah, Myriam; Benzaquen, Jonathan; Tanga, Virginie; Bordone, Olivier; Fayada, Julien; Long‐Mira, Elodie; Lassalle, Sandra; Lanteri, Elisabeth; Lespinet‐Fabre, Virginie; Brest, Patrick; Mograbi, Baharia; Maniel, Charlotte; Boutros, Jacques; Leroy, Sylvie; Heeke, Simon; Hofman, Véronique; Marquette, Charles‐Hugo

doi:10.1128/spectrum.00996-21

Cited by 3 publications

(1 citation statement)

References 26 publications

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“…Furthermore, when outbreaks occur locally and spread quickly, gene sequencing will not meet the needs of large-scale rapid screening. Presently, several countries and regions have carried out mixed testing of unknown SARS-CoV-2 samples to achieve the goal of rapid screening of positive cases ( Bogere et al, 2021 ; Heaney et al, 2021 ; Hofman et al, 2021 ), which requires a higher sensitivity of testing methods. Our experiments showed that the PCR-CRISPR method could detect 0.1% of target nucleic acids in mixed samples ( Wen et al, 2021 ), providing new insights for large-scale rapid screening of variants ( Figure 3C ).…”

Section: Discussionmentioning

confidence: 99%

Highly Sensitive Detection Method for HV69-70del in SARS-CoV-2 Alpha and Omicron Variants Based on CRISPR/Cas13a

Niu

Han

Dong

et al. 2022

Front. Bioeng. Biotechnol.

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As SARS-CoV-2 variants continue to evolve, identifying variants with adaptive diagnostic tool is critical to containing the ongoing COVID-19 pandemic. Herein, we establish a highly sensitive and portable on-site detection method for the HV69-70del which exist in SARS-CoV-2 Alpha and Omicron variants using a PCR-based CRISPR/Cas13a detection system (PCR-CRISPR). The specific crRNA (CRISPR RNA) targeting the HV69-70del is screened using the fluorescence-based CRISPR assay, and the sensitivity and specificity of this method are evaluated using diluted nucleic acids of SARS-CoV-2 variants and other pathogens. The results show that the PCR-CRISPR detection method can detect 1 copies/μL SARS-CoV-2 HV69-70del mutant RNA and identify 0.1% of mutant RNA in mixed samples, which is more sensitive than the RT-qPCR based commercial SARS-CoV-2 variants detection kits and sanger sequencing. And it has no cross reactivity with ten other pathogens nucleic acids. Additionally, by combined with our previously developed ERASE (Easy-Readout and Sensitive Enhanced) lateral flow strip suitable for CRISPR detection, we provide a novel diagnosis tool to identify SARS-CoV-2 variants in primary and resource-limited medical institutions without professional and expensive fluorescent detector.

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Section: Discussionmentioning

confidence: 99%

Highly Sensitive Detection Method for HV69-70del in SARS-CoV-2 Alpha and Omicron Variants Based on CRISPR/Cas13a

Niu

Han

Dong

et al. 2022

Front. Bioeng. Biotechnol.

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Sample pooling and SARS-CoV-2 assays

Hueda-Zavaleta,

Bardales-Silva,

Minchón-Vizconde

et al. 2024

Features, Transmission, Detection, and Case Studies in COVID-19

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Development and evaluation of three automated media pooling and molecular diagnostic systems for the detection of SARS-CoV-2

Matsumura,

Noguchi,

Shinohara

et al. 2024

Microbiol Spectr

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Pooled testing combined with molecular diagnostics for the detection of SARS-CoV-2 is a promising method that can increase testing capacities and save costs. However, pooled testing is also associated with the risks of decreased test sensitivity and specificity. To perform reliable pooled testing, we developed and validated three automated media pooling and molecular diagnostic systems. These pooling systems (geneLEAD-PS, Panther-PS, and Biomek-PS) comprised existing automated molecular detection platforms, corresponding automated media pooling devices, and laboratory information management systems. Analytical sensitivity analysis and mock sample evaluation were performed, and the obtained data were used to determine the sizes of the pool for the validation study. In the validation study, a total of 2,448, 3,228, and 6,420 upper respiratory samples were used for geneLEAD-PS, Panther-PS, and Biomek-PS, respectively, and the diagnostic performances were compared with the reference RT‒PCR assay. A pool size of 6 for geneLEAD-PS and a pool size of 4 for Panther-PS and Biomek-PS were selected for the validation studies. All three systems showed high positive percent agreement values of ≥90.5% and negative percent agreement values of ≥99.8% for any specimen type. Pooled testing resulted in a 65%–71% reduction in cost per sample. The testing capacities of geneLEAD-PS, Panther-PS, and Biomek-PS were 144 samples in 3 hours, 384 samples in 5.5 hours, and 376 samples in 4 hours, respectively. The developed pooling systems showed robust diagnostic performances and will increase the testing capacities of molecular diagnostic tests while saving costs and may contribute to infection control of COVID-19. IMPORTANCE During the COVID-19 pandemic, there have been surges in demand for accurate molecular diagnostic testing and laboratory supply shortages. Pooled testing combined with highly sensitive molecular testing, which entails mixing multiple samples as a single sample, is a promising approach to increase testing capacities while reducing the use of consumables. However, pooled testing is associated with risks that compromise diagnostic performance, such as false negatives due to dilution of positive samples or false positives due to cross-contamination. To perform reliable pooled testing, three different pooling systems (an automated pooling device, an automated molecular detection platform, and a laboratory information management system) were developed to accurately interpret pooled testing results. These three systems were validated using multiple clinical samples and showed high concordance with individual testing. The developed pooling systems will contribute to increasing reliable molecular testing capacities while using fewer consumables and saving costs.

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Evaluation of Sample Pooling for SARS-CoV-2 Detection in Nasopharyngeal Swab and Saliva Samples with the Idylla SARS-CoV-2 Test

Cited by 3 publications

References 26 publications

Highly Sensitive Detection Method for HV69-70del in SARS-CoV-2 Alpha and Omicron Variants Based on CRISPR/Cas13a

Highly Sensitive Detection Method for HV69-70del in SARS-CoV-2 Alpha and Omicron Variants Based on CRISPR/Cas13a

Sample pooling and SARS-CoV-2 assays

Development and evaluation of three automated media pooling and molecular diagnostic systems for the detection of SARS-CoV-2

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