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Clinical evaluation of a multiplex real-time RT-PCR assay for detection of SARS-CoV-2 in individual and pooled upper respiratory tract samples.
Laverack, Melissa; Tallmadge, Rebecca L; Venugopalan, Roopa; Cronk, Brittany; Zhang, XiuLin; Rauh, Rolf; Saunders, Amy; Nelson, William M; Plocharczyk, Elizabeth; Diel, Diego G.
  • Laverack M; Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell COVID-19 Testing Laboratory, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, USA.
  • Tallmadge RL; Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell COVID-19 Testing Laboratory, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, USA.
  • Venugopalan R; Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell COVID-19 Testing Laboratory, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, USA.
  • Cronk B; Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell COVID-19 Testing Laboratory, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, USA.
  • Zhang X; Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell COVID-19 Testing Laboratory, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, USA.
  • Rauh R; Tetracore Inc., Rockville, MD, USA.
  • Saunders A; Tetracore Inc., Rockville, MD, USA.
  • Nelson WM; Tetracore Inc., Rockville, MD, USA.
  • Plocharczyk E; Cayuga Medical Center, Cayuga Health System, Ithaca, NY, USA.
  • Diel DG; Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell COVID-19 Testing Laboratory, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, USA. dgdiel@cornell.edu.
Arch Virol ; 166(9): 2551-2561, 2021 Sep.
Article in English | MEDLINE | ID: covidwho-1309044
ABSTRACT
The aim of this study was to identify and validate a sensitive, high-throughput, and cost-effective SARS-CoV-2 real-time RT-PCR assay to be used as a surveillance and diagnostic tool for SARS-CoV-2 in a university surveillance program. We conducted a side-by-side clinical evaluation of a newly developed SARS-CoV-2 multiplex assay (EZ-SARS-CoV-2 Real-Time RT-PCR) with the commercial TaqPath COVID-19 Combo Kit, which has an Emergency Use Authorization from the FDA. The EZ-SARS-CoV-2 RT-PCR incorporates two assays targeting the SARS-CoV-2 N gene, an internal control targeting the human RNase P gene, and a PCR inhibition control in a single reaction. Nasopharyngeal (NP) and anterior nares (AN) swabs were tested as individuals and pools with both assays and in the ABI 7500 Fast and the QuantStudio 5 detection platforms. The analytical sensitivity of the EZ-SARS-CoV-2 RT-PCR assay was 250 copies/ml or approximately 1.75 genome copy equivalents per reaction. The clinical performance of the EZ-SARS-CoV-2 assay was evaluated using NP and AN samples tested in other laboratories. The diagnostic sensitivity of the assay ranged between 94 and 96% across the detection platforms, and the diagnostic specificity was 94.06%. The positive predictive value was 94%, and the negative predictive value ranged from 94 to 96%. Pooling five NP or AN specimens yielded 93% diagnostic sensitivity. The overall agreement between these SARS-CoV-2 RT-PCR assays was high, supported by a Cohen's kappa value of 0.93. The EZ-SARS-CoV-2 RT-PCR assay performance attributes of high sensitivity and specificity with AN sample matrix and pooled upper respiratory samples support its use in a high-throughput surveillance testing program.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: RNA, Viral / Multiplex Polymerase Chain Reaction / Coronavirus Nucleocapsid Proteins / COVID-19 Nucleic Acid Testing / SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Experimental Studies / Observational study / Prognostic study Limits: Humans Language: English Journal: Arch Virol Year: 2021 Document Type: Article Affiliation country: S00705-021-05148-1

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Full text: Available Collection: International databases Database: MEDLINE Main subject: RNA, Viral / Multiplex Polymerase Chain Reaction / Coronavirus Nucleocapsid Proteins / COVID-19 Nucleic Acid Testing / SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Experimental Studies / Observational study / Prognostic study Limits: Humans Language: English Journal: Arch Virol Year: 2021 Document Type: Article Affiliation country: S00705-021-05148-1