Evaluation of PCR cycle threshold values by patient population with the quidel lyra SARS-CoV-2 assay

Robert F. Potter; Brooj Abro; Charles S. Eby; Carey Ann D. Burnham; Neil W. Anderson; Bijal A. Parikh

doi:10.1016/j.diagmicrobio.2021.115387

Evaluation of PCR cycle threshold values by patient population with the quidel lyra SARS-CoV-2 assay

Robert F. Potter, Brooj Abro, Charles S. Eby, Carey Ann D. Burnham, Neil W. Anderson, Bijal A. Parikh

Research output: Contribution to journal › Article › peer-review

2 Scopus citations

Abstract

The Lyra SARS-CoV-2 assay was the primary method for molecular testing performed at Barnes-Jewish Healthcare System in St. Louis, Missouri during the initial COVID-19 surge from mid-March to late-April 2020. We performed a retrospective analysis of 1,043 positive Lyra SARS-CoV-2 results during these 36 days to investigate associations between cycle threshold (C_T) value and patient characteristics. Total RNA were extracted from NP or OP swabs using either the EasyMag or KingFisher automated extraction systems and quantified with RotorGene Q (Qiagen) or Applied Biosystems 7500 Fast Dx thermocyclers respectively. Notably, we found lower a significant median lower C_T for samples tested on the KingFisher-ABI 7500 fastDX (KF/ABI) system compared to the EasyMag/RotorGene (EM/RGQ) platform. Since 77.5% of our tests were ran on the EM/RGQ pipeline we then perform additional analysis on these values and found that C _T values in outpatient care settings compared to samples obtained in the emergency department or inpatient had significantly lower C _T values. These collective findings suggests a difference in viral load amongst various patient populations.

Original language	English
Article number	115387
Journal	Diagnostic Microbiology and Infectious Disease
Volume	101
Issue number	2
DOIs	https://doi.org/10.1016/j.diagmicrobio.2021.115387
State	Published - Oct 2021

Keywords

Clinical virology
Molecular assays
SARS-CoV-2

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title = "Evaluation of PCR cycle threshold values by patient population with the quidel lyra SARS-CoV-2 assay",

abstract = "The Lyra SARS-CoV-2 assay was the primary method for molecular testing performed at Barnes-Jewish Healthcare System in St. Louis, Missouri during the initial COVID-19 surge from mid-March to late-April 2020. We performed a retrospective analysis of 1,043 positive Lyra SARS-CoV-2 results during these 36 days to investigate associations between cycle threshold (CT) value and patient characteristics. Total RNA were extracted from NP or OP swabs using either the EasyMag or KingFisher automated extraction systems and quantified with RotorGene Q (Qiagen) or Applied Biosystems 7500 Fast Dx thermocyclers respectively. Notably, we found lower a significant median lower CT for samples tested on the KingFisher-ABI 7500 fastDX (KF/ABI) system compared to the EasyMag/RotorGene (EM/RGQ) platform. Since 77.5% of our tests were ran on the EM/RGQ pipeline we then perform additional analysis on these values and found that C T values in outpatient care settings compared to samples obtained in the emergency department or inpatient had significantly lower C T values. These collective findings suggests a difference in viral load amongst various patient populations.",

keywords = "Clinical virology, Molecular assays, SARS-CoV-2",

author = "Potter, {Robert F.} and Brooj Abro and Eby, {Charles S.} and Burnham, {Carey Ann D.} and Anderson, {Neil W.} and Parikh, {Bijal A.}",

note = "Funding Information: We thank the Molecular Infectious Disease Lab of Barnes-Jewish Hospital for their tireless efforts in running SARS-CoV-2 tests and their help in compiling the data. No external funding was obtained to support this study. Publisher Copyright: {\textcopyright} 2021",

year = "2021",

month = oct,

doi = "10.1016/j.diagmicrobio.2021.115387",

language = "English",

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journal = "Diagnostic Microbiology and Infectious Disease",

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AU - Burnham, Carey Ann D.

AU - Anderson, Neil W.

AU - Parikh, Bijal A.

N1 - Funding Information: We thank the Molecular Infectious Disease Lab of Barnes-Jewish Hospital for their tireless efforts in running SARS-CoV-2 tests and their help in compiling the data. No external funding was obtained to support this study. Publisher Copyright: © 2021

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AB - The Lyra SARS-CoV-2 assay was the primary method for molecular testing performed at Barnes-Jewish Healthcare System in St. Louis, Missouri during the initial COVID-19 surge from mid-March to late-April 2020. We performed a retrospective analysis of 1,043 positive Lyra SARS-CoV-2 results during these 36 days to investigate associations between cycle threshold (CT) value and patient characteristics. Total RNA were extracted from NP or OP swabs using either the EasyMag or KingFisher automated extraction systems and quantified with RotorGene Q (Qiagen) or Applied Biosystems 7500 Fast Dx thermocyclers respectively. Notably, we found lower a significant median lower CT for samples tested on the KingFisher-ABI 7500 fastDX (KF/ABI) system compared to the EasyMag/RotorGene (EM/RGQ) platform. Since 77.5% of our tests were ran on the EM/RGQ pipeline we then perform additional analysis on these values and found that C T values in outpatient care settings compared to samples obtained in the emergency department or inpatient had significantly lower C T values. These collective findings suggests a difference in viral load amongst various patient populations.

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Evaluation of PCR cycle threshold values by patient population with the quidel lyra SARS-CoV-2 assay

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