SrasV1, 2020, Analysis, bibRecord, 000733

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.

Identifieur interne : 000733 ( 2020/Analysis ); précédent : 000732; suivant : 000734

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.

Source :

International journal of molecular sciences [ 1422-0067 ] ; 2020.

RBID : pubmed:32276333

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.

DOI: 10.3390/ijms21072574
PubMed: 32276333

Affiliations:

Links to Exploration step

pubmed:32276333

Le document en format XML

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<author><name sortKey="Hung, Ivan Fan Ngai" sort="Hung, Ivan Fan Ngai" uniqKey="Hung I" first="Ivan Fan-Ngai" last="Hung">Ivan Fan-Ngai Hung</name>
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<country xml:lang="fr">République populaire de Chine</country>
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<author><name sortKey="Cheng, Vincent Chi Chung" sort="Cheng, Vincent Chi Chung" uniqKey="Cheng V" first="Vincent Chi-Chung" last="Cheng">Vincent Chi-Chung Cheng</name>
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<country xml:lang="fr">République populaire de Chine</country>
<wicri:regionArea>Department of Microbiology, Queen Mary Hospital, HKSAR, Hong Kong</wicri:regionArea>
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<author><name sortKey="Tsang, Owen Tak Yin" sort="Tsang, Owen Tak Yin" uniqKey="Tsang O" first="Owen Tak-Yin" last="Tsang">Owen Tak-Yin Tsang</name>
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<country xml:lang="fr">République populaire de Chine</country>
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<author><name sortKey="Tsui, Stephen Kwok Wing" sort="Tsui, Stephen Kwok Wing" uniqKey="Tsui S" first="Stephen Kwok Wing" last="Tsui">Stephen Kwok Wing Tsui</name>
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<author><name sortKey="Yuen, Kwok Yung" sort="Yuen, Kwok Yung" uniqKey="Yuen K" first="Kwok-Yung" last="Yuen">Kwok-Yung Yuen</name>
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<front><div type="abstract" xml:lang="en">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 TCID<sub>50</sub>
/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.</div>
</front>
</TEI>
<affiliations><list><country><li>République populaire de Chine</li>
</country>
<settlement><li>Sha Tin</li>
</settlement>
<orgName><li>Université chinoise de Hong Kong</li>
</orgName>
</list>
<tree><country name="République populaire de Chine"><noRegion><name sortKey="Yip, Cyril Chik Yan" sort="Yip, Cyril Chik Yan" uniqKey="Yip C" first="Cyril Chik-Yan" last="Yip">Cyril Chik-Yan Yip</name>
</noRegion>
<name sortKey="Chan, Helen Shuk Ying" sort="Chan, Helen Shuk Ying" uniqKey="Chan H" first="Helen Shuk-Ying" last="Chan">Helen Shuk-Ying Chan</name>
<name sortKey="Chan, Jasper Fuk Woo" sort="Chan, Jasper Fuk Woo" uniqKey="Chan J" first="Jasper Fuk-Woo" last="Chan">Jasper Fuk-Woo Chan</name>
<name sortKey="Chan, Kwok Hung" sort="Chan, Kwok Hung" uniqKey="Chan K" first="Kwok-Hung" last="Chan">Kwok-Hung Chan</name>
<name sortKey="Cheng, Vincent Chi Chung" sort="Cheng, Vincent Chi Chung" uniqKey="Cheng V" first="Vincent Chi-Chung" last="Cheng">Vincent Chi-Chung Cheng</name>
<name sortKey="Chung, Tom Wai Hin" sort="Chung, Tom Wai Hin" uniqKey="Chung T" first="Tom Wai-Hin" last="Chung">Tom Wai-Hin Chung</name>
<name sortKey="Fung, Agnes Yim Fong" sort="Fung, Agnes Yim Fong" uniqKey="Fung A" first="Agnes Yim-Fong" last="Fung">Agnes Yim-Fong Fung</name>
<name sortKey="Ho, Chi Chun" sort="Ho, Chi Chun" uniqKey="Ho C" first="Chi-Chun" last="Ho">Chi-Chun Ho</name>
<name sortKey="Hung, Ivan Fan Ngai" sort="Hung, Ivan Fan Ngai" uniqKey="Hung I" first="Ivan Fan-Ngai" last="Hung">Ivan Fan-Ngai Hung</name>
<name sortKey="Leung, Kit Hang" sort="Leung, Kit Hang" uniqKey="Leung K" first="Kit-Hang" last="Leung">Kit-Hang Leung</name>
<name sortKey="Ng, Anthony Chin Ki" sort="Ng, Anthony Chin Ki" uniqKey="Ng A" first="Anthony Chin-Ki" last="Ng">Anthony Chin-Ki Ng</name>
<name sortKey="Tam, Anthony Raymond" sort="Tam, Anthony Raymond" uniqKey="Tam A" first="Anthony Raymond" last="Tam">Anthony Raymond Tam</name>
<name sortKey="To, Kelvin Kai Wang" sort="To, Kelvin Kai Wang" uniqKey="To K" first="Kelvin Kai-Wang" last="To">Kelvin Kai-Wang To</name>
<name sortKey="Tsang, Owen Tak Yin" sort="Tsang, Owen Tak Yin" uniqKey="Tsang O" first="Owen Tak-Yin" last="Tsang">Owen Tak-Yin Tsang</name>
<name sortKey="Tsui, Stephen Kwok Wing" sort="Tsui, Stephen Kwok Wing" uniqKey="Tsui S" first="Stephen Kwok Wing" last="Tsui">Stephen Kwok Wing Tsui</name>
<name sortKey="Wong, Sally Cheuk Ying" sort="Wong, Sally Cheuk Ying" uniqKey="Wong S" first="Sally Cheuk-Ying" last="Wong">Sally Cheuk-Ying Wong</name>
<name sortKey="Yuen, Kwok Yung" sort="Yuen, Kwok Yung" uniqKey="Yuen K" first="Kwok-Yung" last="Yuen">Kwok-Yung Yuen</name>
<name sortKey="Zou, Zijiao" sort="Zou, Zijiao" uniqKey="Zou Z" first="Zijiao" last="Zou">Zijiao Zou</name>
</country>
</tree>
</affiliations>
</record>

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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.

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.

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