Rapid adaptation and continuous performance evaluation of SARS‐CoV‐2 envelope gene (E‐gene) real‐time RT‐PCR assays to support the hospital surge in test demand

Ho, Yolanda Iok Ieng; Wong, April S. Y.; Leung, Eddie Chi Man; Wong, River Chun Wai; Lai, Robin Kit-Ho

doi:10.1002/jmv.26660

Cited by 3 publications

(1 citation statement)

References 8 publications

(12 reference statements)

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“…The in-house-developed COVID-19-nsp10 assay exhibits high sensitivity, with an LOD below 100 copies/mL, and it does not show any cross-reactivity with other common respiratory viruses. The commercial LightMix E-gene assay is commonly used as a reference assay due to its exceptional sensitivity in detecting SARS-CoV-2 [ 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 ], with an LOD of 31.3 copies/mL, as determined in our previous study [ 25 ]. When compared to the validated LightMix E-gene assay as the reference method, our COVID-19-nsp10 assay showed comparable diagnostic performance, with 100% diagnostic sensitivity and specificity using clinical specimens.…”

Section: Discussionmentioning

confidence: 99%

Development and Evaluation of an In-House Real-Time RT-PCR Targeting nsp10 Gene for SARS-CoV-2 Detection

Yip,

Poon,

Leung

et al. 2024

IJMS

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The emergence of SARS-CoV-2 mutations poses significant challenges to diagnostic tests, as these mutations can reduce the sensitivity of commonly used RT-PCR assays. Therefore, there is a need to design diagnostic assays with multiple targets to enhance sensitivity. In this study, we identified a novel diagnostic target, the nsp10 gene, using nanopore sequencing. Firstly, we determined the analytical sensitivity and specificity of our COVID-19-nsp10 assay. The COVID-19-nsp10 assay had a limit of detection of 74 copies/mL (95% confidence interval: 48–299 copies/mL) and did not show cross-reactivity with other respiratory viruses. Next, we determined the diagnostic performance of the COVID-19-nsp10 assay using 261 respiratory specimens, including 147 SARS-CoV-2-positive specimens belonging to the ancestral strain and Alpha, Beta, Gamma, Delta, Mu, Eta, Kappa, Theta and Omicron lineages. Using a LightMix E-gene RT-PCR assay as the reference method, the diagnostic sensitivity and specificity of the COVID-19-nsp10 assay were found to be 100%. The median Cp values for the LightMix E-gene RT-PCR and our COVID-19-nsp10 RT-PCR were 22.48 (range: 12.95–36.60) and 25.94 (range 16.37–36.87), respectively. The Cp values of the COVID-19-nsp10 RT-PCR assay correlated well with those of the LightMix E-gene RT-PCR assay (Spearman’s ρ = 0.968; p < 0.0001). In conclusion, nsp10 is a suitable target for a SARS-CoV-2 RT-PCR assay.

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Section: Discussionmentioning

confidence: 99%

Development and Evaluation of an In-House Real-Time RT-PCR Targeting nsp10 Gene for SARS-CoV-2 Detection

Yip,

Poon,

Leung

et al. 2024

IJMS

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Application of digital PCR to determine the reliability of Xpert Xpress SARS-CoV-2 assay with envelope (E) gene negative and nucleocapsid (N2) gene positive results

Wong

et al. 2022

Diagnostic Microbiology and Infectious Disease

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Optimizing testing regimes for the detection of COVID-19 in children and older adults

Chauhan

Soni

Jain

2021

Expert Review of Molecular Diagnostics

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Introduction: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection is a major pandemic and continuously emerging due to unclear prognosis and unavailability of reliable detection tools. Older adults are more susceptible to COVID-19 than children showing mature Angiotensin-Converting Enzyme 2 (ACE2), low concentration of immune targets, and comorbid conditions. Several detection platforms have been commercialized to date and more are in pipeline, however, the rate of false-positive results and rapid mutation of SARS-CoV-2 is increasing. Additionally, physiological, and geographical variations of affected individuals are also calling for diagnostic methods optimization. Areas Covered: Extensive information related to the optimization and usefulness of SARS-CoV-2 diagnostic methods based on sensitivity and specificity as definitive and feasible investigative tools is discussed. Moreover, an option of combining laboratory diagnostic methods to improve diagnostic strategies is also proposed and discussed in the comparative section of optimization studies. Expert Opinion: The review article explains the importance of optimization strategies for SARS-CoV-2 detection in children and older adults. There are advancements in COVID-19 detection including CRISPR-based, electrochemical, and optical-based sensing systems. However, the lack of sufficient studies on a comparative evaluation of standardized SARS-CoV-2 diagnostic methods among children and older adults, limit the authentication of commercialized kits.

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Rapid adaptation and continuous performance evaluation of SARS‐CoV‐2 envelope gene (E‐gene) real‐time RT‐PCR assays to support the hospital surge in test demand

Cited by 3 publications

References 8 publications

Development and Evaluation of an In-House Real-Time RT-PCR Targeting nsp10 Gene for SARS-CoV-2 Detection

Development and Evaluation of an In-House Real-Time RT-PCR Targeting nsp10 Gene for SARS-CoV-2 Detection

Application of digital PCR to determine the reliability of Xpert Xpress SARS-CoV-2 assay with envelope (E) gene negative and nucleocapsid (N2) gene positive results

Optimizing testing regimes for the detection of COVID-19 in children and older adults

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