tetano
Editor, Senior Moderator
J Clin Virol
. 2020 May 8;129:104427.
doi: 10.1016/j.jcv.2020.104427. Online ahead of print.
Comparison of a Laboratory-Developed Test Targeting the Envelope Gene With Three Nucleic Acid Amplification Tests for Detection of SARS-CoV-2
Philip L Bulterys[SUP] 1 [/SUP], Natasha Garamani[SUP] 1 [/SUP], Bryan Stevens[SUP] 2 [/SUP], Malaya K Sahoo[SUP] 1 [/SUP], ChunHong Huang[SUP] 1 [/SUP], Catherine A Hogan[SUP] 2 [/SUP], James Zehnder[SUP] 1 [/SUP], Benjamin A Pinsky[SUP] 3 [/SUP]
Affiliations
Abstract
Background: Numerous nucleic acid amplification tests, including real-time, reverse transcription PCR (rRT-PCR) and isothermal amplification methods, have been developed to detect SARS-CoV-2 RNA, including many that have received emergency use authorization (EUA). There is a need to assess their test performance relative to one another.
Objectives: The aim of this study was to compare the test performance of a high complexity laboratory-developed rRT-PCR EUA from Stanford Health Care (SHC) targeting the SARS-CoV-2 envelope (E) gene with other tests: the Atila isothermal amplification assay targeting the nucleocapsid (N) gene and open reading frame 1ab (ORF1ab), the Altona E and spike (S) multiplex, real-time RT-PCR, and the US Centers for Disease Control and Prevention (CDC) N1 and N2 rRT-PCRs.
Study design: A diagnostic comparison study was performed by testing nasopharyngeal samples from persons under investigation for coronavirus disease 2019 (COVID-19). Assay performance was assessed by percent agreement and Cohen's kappa coefficient.
Results: Positive percent agreement with the SHC EUA reference assay was 82.8 % (95 % confidence interval (CI) 65.0 to 92.9) for Atila, 86.7 % (95 % CI 69.7 to 95.3) for the Altona E and S targets, and 86.7 % (95 % CI 69.7 to 95.3) and 90.0 % (95 % CI 73.6 to 97.3), for the CDC N1 and N2 targets, respectively. All assays demonstrated 100 % negative percent agreement. Kappa coefficients ranged from 0.86 to 0.92, indicating excellent agreement.
Conclusions: Performance was comparable among the SARS-CoV-2 nucleic acid amplification methods tested, with a limited number of discrepancies observed in specimens with low viral loads.
Keywords: COVID-19; Coronavirus; Diagnostics; SARS-CoV-2.
. 2020 May 8;129:104427.
doi: 10.1016/j.jcv.2020.104427. Online ahead of print.
Comparison of a Laboratory-Developed Test Targeting the Envelope Gene With Three Nucleic Acid Amplification Tests for Detection of SARS-CoV-2
Philip L Bulterys[SUP] 1 [/SUP], Natasha Garamani[SUP] 1 [/SUP], Bryan Stevens[SUP] 2 [/SUP], Malaya K Sahoo[SUP] 1 [/SUP], ChunHong Huang[SUP] 1 [/SUP], Catherine A Hogan[SUP] 2 [/SUP], James Zehnder[SUP] 1 [/SUP], Benjamin A Pinsky[SUP] 3 [/SUP]
Affiliations
- PMID: 32535398
- PMCID: PMC7207111
- DOI: 10.1016/j.jcv.2020.104427
Abstract
Background: Numerous nucleic acid amplification tests, including real-time, reverse transcription PCR (rRT-PCR) and isothermal amplification methods, have been developed to detect SARS-CoV-2 RNA, including many that have received emergency use authorization (EUA). There is a need to assess their test performance relative to one another.
Objectives: The aim of this study was to compare the test performance of a high complexity laboratory-developed rRT-PCR EUA from Stanford Health Care (SHC) targeting the SARS-CoV-2 envelope (E) gene with other tests: the Atila isothermal amplification assay targeting the nucleocapsid (N) gene and open reading frame 1ab (ORF1ab), the Altona E and spike (S) multiplex, real-time RT-PCR, and the US Centers for Disease Control and Prevention (CDC) N1 and N2 rRT-PCRs.
Study design: A diagnostic comparison study was performed by testing nasopharyngeal samples from persons under investigation for coronavirus disease 2019 (COVID-19). Assay performance was assessed by percent agreement and Cohen's kappa coefficient.
Results: Positive percent agreement with the SHC EUA reference assay was 82.8 % (95 % confidence interval (CI) 65.0 to 92.9) for Atila, 86.7 % (95 % CI 69.7 to 95.3) for the Altona E and S targets, and 86.7 % (95 % CI 69.7 to 95.3) and 90.0 % (95 % CI 73.6 to 97.3), for the CDC N1 and N2 targets, respectively. All assays demonstrated 100 % negative percent agreement. Kappa coefficients ranged from 0.86 to 0.92, indicating excellent agreement.
Conclusions: Performance was comparable among the SARS-CoV-2 nucleic acid amplification methods tested, with a limited number of discrepancies observed in specimens with low viral loads.
Keywords: COVID-19; Coronavirus; Diagnostics; SARS-CoV-2.