Development of a Novel, Genome Subtraction-Derived, SARS-CoV-2-Specific COVID-19-nsp2 Real-Time RT-PCR Assay and Its Evaluation Using Clinical Specimens
| Autor: | Cyril C. Y. Yip, Kwok-Hung Chan, Tom Wai-Hin Chung, Stephen Kwok-Wing Tsui, Ivan Hung, Jasper Fuk-Woo Chan, Chi-Chun Ho, Anthony Raymond Tam, Helen Shuk-Ying Chan, Zijiao Zou, Kwok-Yung Yuen, Anthony Chin-Ki Ng, Kit-Hang Leung, Kelvin K. W. To, Agnes Yim Fong Fung, Sally C. Y. Wong, Owen Tak-Yin Tsang, Vincent C.C. Cheng |
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| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
0301 basic medicine
genome subtraction viruses clinical evaluation specificity medicine.disease_cause Genome lcsh:Chemistry COVID-19 Testing nsp2 COVID-19-nsp2 assay lcsh:QH301-705.5 Spectroscopy Coronavirus Reverse Transcriptase Polymerase Chain Reaction Subtraction virus diseases General Medicine Computer Science Applications GolayMetaMiner Real-time polymerase chain reaction COVID-19 sensitivity real-time RT-PCR SARS-CoV-2 RNA Viral Coronavirus Infections COVID-19 Vaccines Coronavirus disease 2019 (COVID-19) Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Concordance Pneumonia Viral 030106 microbiology Genome Viral Biology Real-Time Polymerase Chain Reaction Sensitivity and Specificity Article Catalysis Inorganic Chemistry Betacoronavirus 03 medical and health sciences medicine Humans Physical and Theoretical Chemistry Pandemics Molecular Biology Cycle threshold Clinical Laboratory Techniques Organic Chemistry Reproducibility of Results Virology 030104 developmental biology lcsh:Biology (General) lcsh:QD1-999 |
| Zdroj: | International Journal of Molecular Sciences Volume 21 Issue 7 International Journal of Molecular Sciences, Vol 21, Iss 2574, p 2574 (2020) International journal of environmental research and public health, 21(7):2574 |
| ISSN: | 1422-0067 |
| DOI: | 10.3390/ijms21072574 |
| Popis: | The pandemic novel coronavirus infection, Coronavirus Disease 2019 (COVID-19), has affected at least 190 countries or territories, with 465,915 confirmed cases and 21,031 deaths. In a containment-based strategy, rapid, sensitive and specific testing is important in epidemiological control and clinical management. Using 96 SARS-CoV-2 and 104 non-SARS-CoV-2 coronavirus genomes and our in-house program, GolayMetaMiner, four specific regions longer than 50 nucleotides in the SARS-CoV-2 genome were identified. Primers were designed to target the longest and previously untargeted nsp2 region and optimized as a probe-free real-time reverse transcription-polymerase chain reaction (RT-PCR) assay. The new COVID-19-nsp2 assay had a limit of detection (LOD) of 1.8 TCID50/mL and did not amplify other human-pathogenic coronaviruses and respiratory viruses. Assay reproducibility in terms of cycle threshold (Cp) values was satisfactory, with the total imprecision (% CV) values well below 5%. Evaluation of the new assay using 59 clinical specimens from 14 confirmed cases showed 100% concordance with our previously developed COVID-19-RdRp/Hel reference assay. A rapid, sensitive, SARS-CoV-2-specific real-time RT-PCR assay, COVID-19-nsp2, was developed. |
| Databáze: | OpenAIRE |
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