Comparative Performance of SARS-CoV-2 Detection Assays Using Seven Different Primer-Probe Sets and One Assay Kit

Nalla, Arun Kumar; Casto, Amanda M.; Huang, Meei Li; Perchetti, Garrett A.; Sampoleo, Reigran; Shrestha, Lasata; Wei, Yulun; Zhu, Haiying; Jerome, Keith R.; Greninger, Alexander L.

doi:10.1128/jcm.00557-20

Cited by 428 publications

(294 citation statements)

References 4 publications

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“…Participants who had a positive nasopharyngeal (NP) swab as part of routine clinical care were recruited for enrollment into the Hospitalized and Ambulatory Adults with Respiratory Viral Infections (HAARVI) study at the University of Washington. These clinical samples were established to be COVID-19-positive via testing at the University of Washington’s Virology lab ( 3 ). Paired conventional and dry mid-nasal swabs were then self-collected via Seattle Flu Study (SFS) home self-swab kits delivered to participants’ homes within 1-2 days after they had tested positive, and returned via delivery service at ambient temperature ( 4, 5 ).…”

Section: Resultsmentioning

confidence: 99%

SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing

Srivatsan

Heidl

Pfau

et al. 2020

Preprint

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The urgent need for massively scaled clinical or surveillance testing for SARS-CoV-2 has necessitated a reconsideration of the methods by which respiratory samples are collected, transported, processed and tested. Conventional testing for SARS-CoV-2 involves collection of a clinical specimen with a nasopharyngeal swab, storage of the swab during transport in universal transport medium (UTM), extraction of RNA, and quantitative reverse transcription PCR (RT-qPCR). As testing has scaled across the world, supply chain challenges have emerged across this entire workflow. Here we sought to evaluate how eliminating the UTM storage and RNA extraction steps would impact the results of molecular testing. Using paired mid-turbinate swabs self-collected by 11 individuals with previously established SARS-CoV-2 positivity, we performed a comparison of conventional (swab → UTM → RNA extraction → RT-qPCR) vs. simplified (direct elution from dry swab → RT-qPCR) protocols. Our results suggest that dry swabs eluted directly into a simple buffered solution (TE) can support molecular detection of SARS-CoV-2 via endpoint RT-qPCR without substantially compromising sensitivity. Although further confirmation with a larger sample size and variation of other parameters is necessary, these results are encouraging for the possibility of a simplified workflow that could support massively scaled testing for COVID-19 control. ResultsBased on prior literature ( 1 , 2 ) and the fact that dry swabs are employed for SARS-CoV-2 testing outside of the United States , we know that swabs collected and transported without transport media are amenable to subsequent nucleic acid detection-based diagnostics. We hypothesized that elution of dry swabs directly into a Tris-EDTA (TE) buffer would be compatible with RT-qPCR, i.e. skipping conventional RNA extraction altogether. TE's lower salt Seattle Flu Study Investigators Principal Investigators:

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Section: Resultsmentioning

confidence: 99%

SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing

Srivatsan

Heidl

Pfau

et al. 2020

Preprint

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“…Therefore, in‐house clinical validations upon implementation of novel RT‐PCR kits need to be conducted. Thus far, several studies have been devoted to this topic, but the majority of them assessed these products using different kits 9‐12 . Only a study by Shen et al evaluated the same Sansure PCR kit that we evaluated, 10 and they found sensitivity, specificity, PPV, NPV, and kappa values of 95.00%, 87.50%, 95.00%, 87.50%, and 0.825, respectively, for the Sansure PCR kit (Lot No.…”

Section: Discussionmentioning

confidence: 99%

Comparison of the diagnostic efficacy between two PCR test kits for SARS‐CoV‐2 nucleic acid detection

Liu

Ren

et al. 2020

Clinical Laboratory Analysis

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Background To compare the diagnostic efficacy between two different real‐time reverse transcription polymerase chain reaction (RT‐PCR) test kits for severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) nucleic acid detection and provide references for laboratories. Methods Throat swab samples from 18 hospitalized patients were clinically diagnosed with coronavirus disease 2019 (COVID‐19) and 100 hospitalized patients without COVID‐19 were collected. SARS‐CoV‐2 nucleic acid was detected in throat swab samples with RT‐PCR test kits from Sansure Biotech Inc (Hunan, China) and Shanghai BioGerm Medical Biotechnology Co., Ltd.(Shanghai, China). The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and kappa value were analyzed, and three parallel tests were performed with three weakly positive samples. Results The sensitivity, specificity, PPV, NPV, and kappa value of the Sansure PCR kit were 0.833, 1.000, 1.000, 0.971, and 0.894, respectively, and the sensitivity, specificity, PPV, NPV, and kappa value of the BioGerm PCR kit were 0.944, 1.000, 1.000, 0.990, and 0.966, respectively. For the three parallel tests, the coefficient of variation value of the BioGerm PCR kit in all three samples was the smallest for both the ORF1ab and N gene. Conclusion The detection efficacy of the BioGerm PCR kit for SARS‐CoV‐2 nucleic acid detection was relatively higher than that of the Sansure PCR kit.

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“…The study found high specificity among all primer sets and variable sensitivity, with the CDC N2 and the Germany E-gene sets being more sensitive than others. 11 Another study (in preprint) examined the sensitivity and efficiency of four 12 Other studies have also compared the US CDC N1 and N2 against commercial test kits, reporting similar specificity with variable sensitivity. 13,14 To accelerate testing capacity, the US Food and Drug Administration (FDA) released updated guidance on February 29, 2020, opening up the production of diagnostic kits to state laboratories, laboratories certified under Clinical Laboratory Improvement Amendments (CLIA), and commercial diagnostic developers.…”

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confidence: 99%

COVID‐19 Clinical Diagnostics and Testing Technology

2020

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Given the global nature of the coronavirus disease 2019 (COVID‐19) pandemic, the need for disease detection and expanding testing capacity remains critical priorities. This review discusses the technological advances in testing capability and methodology that are currently used or in development for detecting the novel coronavirus. We describe the current clinical diagnostics and technology, including molecular and serological testing approaches, for severe acute respiratory syndrome‐coronavirus 2 (SARS‐CoV‐2) testing as well as address their advantages and limitations. Nucleic acid amplification technology for molecular diagnostics remains the gold standard for virus detection. We highlight alternative molecular detection techniques used for developing novel COVID‐19 diagnostics on the horizon. Antibody response against SARS‐CoV‐2 remains poorly understood and proper validation of serology tests is necessary to demonstrate their accuracy and clinical utility. In order to bring the pandemic under control, we must speed up the development of rapid and widespread testing through improvements in clinical diagnostics and testing technology as well as access to these tools.

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Comparative Performance of SARS-CoV-2 Detection Assays Using Seven Different Primer-Probe Sets and One Assay Kit

Cited by 428 publications

References 4 publications

SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing

SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing

Comparison of the diagnostic efficacy between two PCR test kits for SARS‐CoV‐2 nucleic acid detection

COVID‐19 Clinical Diagnostics and Testing Technology

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