Comparison of Four Molecular
            <i>In Vitro</i>
            Diagnostic Assays for the Detection of SARS-CoV-2 in Nasopharyngeal Specimens

Wei, Zhen; Manji, Ryhana; Smith, E O; Berry, Gregory J.

doi:10.1128/jcm.00743-20

Cited by 128 publications

(74 citation statements)

References 13 publications

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“…Nearly 80% of the infected individuals are either asymptomatic or have mild symptoms leading to difficulties to diagnose this disease. COVID-19 has high human-to-human transmission rates (R0 = 2.0 -2.5), and is stable in aerosols and on surfaces, presenting a challenge to mitigation and emphasizing the urgent need for a more rapid, accessible and accurate diagnostic assays (5). SARS-CoV-2 virus is detected in various human sampling sources including respiratory and fecal, but testing has been validated for PCR primarily of nasal, nasopharyngeal, and oropharyngeal specimens.…”

Section: Introductionmentioning

confidence: 99%

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Performance of Abbott ID NOW COVID-19 rapid nucleic acid amplification test in nasopharyngeal swabs transported in viral media and dry nasal swabs, in a New York City academic institution

Basu

Zinger

Inglima

et al. 2020

Preprint

102

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word count=237)The recent emergence of the SARS-CoV-2 pandemic has posed formidable challenges for clinical laboratories seeking reliable laboratory diagnostic confirmation. The swift advance of the crisis in the United States has led to Emergency Use Authorization (EUA) facilitating the availability of molecular diagnostic assays without the more rigorous scrutiny to which tests are normally subjected to prior to FDA approval. The need to identify the COVID-19 positive cases quickly and accurately has propelled the release of a variety of assays intended to meet the urgent demand.Several Nucleic Acid Amplification Tests (NAAT) platforms are currently available. Our laboratory currently uses two real time RT-PCR platforms, the Roche Cobas SARS-CoV2 and the Cepheid Xpert Xpress SARS-CoV-2. Both platforms demonstrate comparable performance; however the run times for each assay are 3.5 hours and 45 minutes, respectively. In search for a platform with shorter turnaround time, we sought to evaluate the recently released Abbott ID NOW COVID-19 assay which is capable of producing positive results in as little as 5 minutes. We present here the result comparisons between Abbot ID NOW COVID-19 and Cepheid Xpert Xpress SARS-CoV-2 using nasopharyngeal swabs transported in VTM as well as dry nasal swabs for the Abbott assay. Regardless of method of collection and sample type, Abbot ID NOW COVID-19 missed a third of the samples detected positive by Cepheid Xpert Xpress when using NP swabs in VTM and over 48% when using dry nasal swabs.

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Section: Introductionmentioning

confidence: 99%

“…(EUA) (5,6). The initiative to expand and accelerate testing has eased the usual scrutiny that new assays would normally undergo prior to release.…”

Section: Introductionmentioning

confidence: 99%

Performance of Abbott ID NOW COVID-19 rapid nucleic acid amplification test in nasopharyngeal swabs transported in viral media and dry nasal swabs, in a New York City academic institution

Basu

Zinger

Inglima

et al. 2020

Preprint

102

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“…The majority of the SARS-CoV-2 NAAT tests available today are based on real time reverse transcription polymerase chain reaction (RT-PCR) methods, including the BioFire Diagnostics COVID-19 test (BioFire) and the Hologic Panther Fusion SARS-CoV-2 assay (Fusion) evaluated in the present study. Clinical comparative data have been obtained for the Fusion assay ( 6, 7, 8, 9 ), but to our knowledge there have been no comparative studies of the BioFire assay. Recently, Hologic has developed a second NAAT, the Aptima SARS-CoV-2 assay (Aptima), which has been submitted to the Food and Drug Administration (FDA) for Emergency Use Authorization (EUA); this NAAT is based on target capture and transcription-mediated amplification (TMA) technologies and is run on the Panther instrument.…”

Section: Introductionmentioning

confidence: 99%

Analytical and Clinical Comparison of Three Nucleic Acid Amplification Tests for SARS-CoV-2 Detection

Smith

Wei

Manji

et al. 2020

Preprint

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“…As shown in Table 1, these platforms compared very well for both UTM and sputum/tracheal aspirates. Similarly, Zehn et al also demonstrated an overall strong correlation between the Diasorin, GenMark and CDC assays (5). For their study they obtained a kappa score analysis of 0.96, while our correlations between the platforms ranged from 0.92 – 0.97 and 0.88 – 0.99 using Pearson’s r and chi-square analysis respectively.…”

Section: Methodsmentioning

confidence: 85%

Comparison of the NeuMoDX, Diasorin Simplexa, Cepheid and Roche CDC SARS-CoV 2 EUA assays using nasopharyngeal/nasal swabs in universal transport media (UTM) and sputum and tracheal aspirates

Tibbetts

Callahan

Rofoo

et al. 2020

Preprint

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14In March 2019 the outbreak of SARS-CoV 2 was officially defined as a pandemic by the World 15 Health Organization and shortly after, the United States Food and Drug Administration (FDA) 16 granted Emergency Use Authorization (EUA) to the Centers for Disease Control (CDC) for 17 reverse transcription polymerase chain reaction (rtPCR) molecular testing for the detection of the 18 SARS-CoV-2 virus from NP swabs. Since then, EUA with relaxed regulations were granted to 19 numerous manufacturers and clinical microbiology laboratories to implement in-house testing 20 assays with nasopharyngeal swabs (NP) and subsequently additional specimen types. Because of 21 supply chain shortages leading to competition for reagents, sustaining any significant volume of 22 testing soon became problematic. As a countermeasure, within several weeks the Henry Ford 23 Microbiology Laboratory validated 4 different rtPCR assays and multiple specimen types using 24 NeuMoDX, Diasorin Simplexa, Cepheid and Roche platforms. The purpose of this study was to 25 analyze the analytic sensitivity of these rtPCR assays with NP/nasal swabs and sputum/tracheal 26 aspirates. Qualitative analytic agreement between the 4 platforms for NP/nasal swabs ranged 27 95% -100% overall with no statistically significant difference in threshold cT values. Similar 28 results were obtained with the sputum/tracheal aspirates. These data demonstrate the high 29 accuracy and reproducibility in detection of SARS-CoV 2 between the rtPCR assays performed 30 on 4 different platforms with numerous specimen types. 31 million total cases and 96,526 deaths have been reported within the United States 35 (https://www.worldometers.info/coronavirus/#countries, accessed 5/22/2020). 36SARS-CoV-2 is a member of the betacoronavirus clade of the Coronaviridae family and is more 37 closely related to SARS-CoV-1 and MERS, which share a common zoonotic origin (1). 38However, SARS-CoV-2 does share some similarities to the alphacoronavirus clade, which 39 typically cause up to 30% of common colds and some gastrointestinal diseases (1). 40Coronaviruses are small (120 nm diameter), spherical virons surrounded by the spike or "S" 41 receptor binding proteins, resulting in a "corona" appearance in electron microscopic images. 42Genomically, these virons consist of 27-34 kb of single-stranded, positive-sense RNA encoding 43 ~ 16 non-structural proteins and 5 structural proteins: spike (S), nucleocapsid (N), a 44 phosphoprotein (M), hemagglutinin/esterase (HE), and a non-glycosylated membrane protein (E) 45 (1). The HE protein is only found in the betacoronavirus clade and is functionally analogous to 46 the HE gene found in Influenza C virus (1). 47SARS-CoV-2 viral loads have been demonstrated to peak within 1 week of symptom onset and 48 that the spectrum of shedding can vary considerably based on the severity of illness. Therefore, it 49 is crucial for diagnostic assays to use highly sensitive molecular methods to detect SARS-CoV-2 50 across a broad spectrum of viral loads ...

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Comparison of Four Molecular In Vitro Diagnostic Assays for the Detection of SARS-CoV-2 in Nasopharyngeal Specimens

Abstract: limit 250 words): 17

Cited by 128 publications

References 13 publications

Performance of Abbott ID NOW COVID-19 rapid nucleic acid amplification test in nasopharyngeal swabs transported in viral media and dry nasal swabs, in a New York City academic institution

Performance of Abbott ID NOW COVID-19 rapid nucleic acid amplification test in nasopharyngeal swabs transported in viral media and dry nasal swabs, in a New York City academic institution

Analytical and Clinical Comparison of Three Nucleic Acid Amplification Tests for SARS-CoV-2 Detection

Comparison of the NeuMoDX, Diasorin Simplexa, Cepheid and Roche CDC SARS-CoV 2 EUA assays using nasopharyngeal/nasal swabs in universal transport media (UTM) and sputum and tracheal aspirates

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