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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.
Yip, Cyril Chik-Yan; Ho, Chi-Chun; Chan, Jasper Fuk-Woo; To, Kelvin Kai-Wang; Chan, Helen Shuk-Ying; Wong, Sally Cheuk-Ying; Leung, Kit-Hang; Fung, Agnes Yim-Fong; Ng, Anthony Chin-Ki; Zou, Zijiao; Tam, Anthony Raymond; Chung, Tom Wai-Hin; Chan, Kwok-Hung; Hung, Ivan Fan-Ngai; Cheng, Vincent Chi-Chung; Tsang, Owen Tak-Yin; Tsui, Stephen Kwok Wing; Yuen, Kwok-Yung.
  • Yip CC; Department of Microbiology, Queen Mary Hospital, HKSAR, Hong Kong, China.
  • Ho CC; Genomics and Bioinformatics Programme, The Chinese University of Hong Kong, HKSAR, Hong Kong, China.
  • Chan JF; State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, HKSAR, Hong Kong, China.
  • To KK; Department of Microbiology, The University of Hong Kong, HKSAR, Hong Kong, China.
  • Chan HS; Department of Clinical Microbiology and Infection, The University of Hong Kong-Shenzhen Hospital, Shenzhen 518053, China.
  • Wong SC; Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, HKSAR, Hong Kong, China.
  • Leung KH; State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, HKSAR, Hong Kong, China.
  • Fung AY; Department of Microbiology, The University of Hong Kong, HKSAR, Hong Kong, China.
  • Ng AC; Department of Clinical Microbiology and Infection, The University of Hong Kong-Shenzhen Hospital, Shenzhen 518053, China.
  • Zou Z; Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, HKSAR, Hong Kong, China.
  • Tam AR; Department of Medicine, Queen Elizabeth Hospital, HKSAR, Hong Kong, China.
  • Chung TW; Department of Pathology, Queen Elizabeth Hospital, HKSAR, Hong Kong, China.
  • Chan KH; Department of Microbiology, The University of Hong Kong, HKSAR, Hong Kong, China.
  • Hung IF; Department of Microbiology, The University of Hong Kong, HKSAR, Hong Kong, China.
  • Cheng VC; Department of Microbiology, The University of Hong Kong, HKSAR, Hong Kong, China.
  • Tsang OT; Department of Microbiology, The University of Hong Kong, HKSAR, Hong Kong, China.
  • Tsui SKW; Department of Medicine, Queen Mary Hospital, HKSAR, Hong Kong, China.
  • Yuen KY; Department of Microbiology, Queen Mary Hospital, HKSAR, Hong Kong, China.
Int J Mol Sci ; 21(7)2020 Apr 08.
Article in English | MEDLINE | ID: covidwho-42099
ABSTRACT
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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Pneumonia, Viral / RNA, Viral / Genome, Viral / Coronavirus Infections / Clinical Laboratory Techniques / Real-Time Polymerase Chain Reaction / Betacoronavirus Type of study: Diagnostic study / Experimental Studies / Observational study / Prognostic study Topics: Long Covid / Vaccines Limits: Humans Language: English Year: 2020 Document Type: Article Affiliation country: IJMS21072574

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Pneumonia, Viral / RNA, Viral / Genome, Viral / Coronavirus Infections / Clinical Laboratory Techniques / Real-Time Polymerase Chain Reaction / Betacoronavirus Type of study: Diagnostic study / Experimental Studies / Observational study / Prognostic study Topics: Long Covid / Vaccines Limits: Humans Language: English Year: 2020 Document Type: Article Affiliation country: IJMS21072574