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Article: 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

TitleDevelopment of a Novel, Genome Subtraction-Derived, SARS-CoV-2-Specific COVID-19-nsp2 Real-Time RT-PCR Assay and Its Evaluation Using Clinical Specimens
Authors
KeywordsSARS-CoV-2
COVID-19
nsp2
real-time RT-PCR
genome subtraction
Issue Date2020
PublisherMolecular Diversity Preservation International. The Journal's web site is located at http://www.mdpi.org/ijms
Citation
International Journal of Molecular Sciences, 2020, v. 21, p. article no. 2574 How to Cite?
AbstractThe 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.
Persistent Identifierhttp://hdl.handle.net/10722/285290
ISSN
2011 Impact Factor: 2.598
PubMed Central ID
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorYip, CCY-
dc.contributor.authorHo, CH-
dc.contributor.authorChan, JFW-
dc.contributor.authorTo, KKW-
dc.contributor.authorChan, HSY-
dc.contributor.authorWong, SCY-
dc.contributor.authorLeung, KH-
dc.contributor.authorFung, AYF-
dc.contributor.authorNg, ACK-
dc.contributor.authorZou, Z-
dc.contributor.authorTam, AR-
dc.contributor.authorChung, TWH-
dc.contributor.authorChan, KH-
dc.contributor.authorHung, IFN-
dc.contributor.authorCheng, VCC-
dc.contributor.authorTsang, OTY-
dc.contributor.authorTsui, SKW-
dc.contributor.authorYuen, KY-
dc.date.accessioned2020-08-18T03:52:04Z-
dc.date.available2020-08-18T03:52:04Z-
dc.date.issued2020-
dc.identifier.citationInternational Journal of Molecular Sciences, 2020, v. 21, p. article no. 2574-
dc.identifier.issn1661-6596-
dc.identifier.urihttp://hdl.handle.net/10722/285290-
dc.description.abstractThe 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.-
dc.languageeng-
dc.publisherMolecular Diversity Preservation International. The Journal's web site is located at http://www.mdpi.org/ijms-
dc.relation.ispartofInternational Journal of Molecular Sciences-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.subjectSARS-CoV-2-
dc.subjectCOVID-19-
dc.subjectnsp2-
dc.subjectreal-time RT-PCR-
dc.subjectgenome subtraction-
dc.titleDevelopment of a Novel, Genome Subtraction-Derived, SARS-CoV-2-Specific COVID-19-nsp2 Real-Time RT-PCR Assay and Its Evaluation Using Clinical Specimens-
dc.typeArticle-
dc.identifier.emailYip, CCY: yipcyril@hku.hk-
dc.identifier.emailHo, CH: hcc604@HKUCC-COM.hku.hk-
dc.identifier.emailChan, JFW: jfwchan@hku.hk-
dc.identifier.emailTo, KKW: kelvinto@hku.hk-
dc.identifier.emailWong, SCY: wcy288@hku.hk-
dc.identifier.emailLeung, KH: khl17@hku.hk-
dc.identifier.emailFung, AYF: agnes_fung@hku.hk-
dc.identifier.emailNg, ACK: nck912@hku.hk-
dc.identifier.emailChan, KH: chankh2@hkucc.hku.hk-
dc.identifier.emailHung, IFN: ivanhung@hkucc.hku.hk-
dc.identifier.emailCheng, VCC: vcccheng@hkucc.hku.hk-
dc.identifier.emailYuen, KY: kyyuen@hkucc.hku.hk-
dc.identifier.authorityYip, CCY=rp01721-
dc.identifier.authorityChan, JFW=rp01736-
dc.identifier.authorityTo, KKW=rp01384-
dc.identifier.authorityChan, KH=rp01921-
dc.identifier.authorityHung, IFN=rp00508-
dc.identifier.authorityYuen, KY=rp00366-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.3390/ijms21072574-
dc.identifier.pmid32276333-
dc.identifier.pmcidPMC7177594-
dc.identifier.scopuseid_2-s2.0-85083206760-
dc.identifier.hkuros312845-
dc.identifier.volume21-
dc.identifier.spagearticle no. 2574-
dc.identifier.epagearticle no. 2574-
dc.identifier.isiWOS:000535574200316-
dc.publisher.placeSwitzerland-

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