Dataset Information

Detection and classification of SARS-CoV-2 using high-resolution melting analysis.

ABSTRACT: Coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has recently posed a significant threat to global public health. The objective of this study was to develop and evaluate a rapid, expandable and sequencing-free high-resolution melting (HRM) approach for the direct detection and classification of SARS-CoV-2. Thirty-one common pathogens that can cause respiratory tract infections were used to evaluate the specificity of the method. Synthetic RNA with serial dilutions was utilized to determine the sensitivity of the method. Finally, the clinical performance of the method was assessed using 290 clinical samples. The one-step multiplex HRM could accurately identify SARS-CoV-2 and differentiate mutations in each marker site within approximately 2 h. For each target, the limit of detection was lower than 10 copies/reaction, and no cross-reactivity was observed among organisms within the specificity testing panel. The method showed good uniformity for SARS-CoV-2 detection with a consistency of 100%. Regarding the clade classification performance, the results showed good concordance compared with sequencing, with the rate of agreement being 95.1% (78/82). The one-step multiplex HRM method is a rapid method for SARS-CoV-2 detection and classification.

SUBMITTER: Sun L

PROVIDER: S-EPMC9111094 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature

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Detection and classification of SARS-CoV-2 using high-resolution melting analysis.

Sun Liying L Xiu Leshan L Zhang Chi C Xiao Yan Y Li Yamei Y Zhang Lulu L Ren Lili L Peng Junping J

Microbial biotechnology 20220301 6

Coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has recently posed a significant threat to global public health. The objective of this study was to develop and evaluate a rapid, expandable and sequencing-free high-resolution melting (HRM) approach for the direct detection and classification of SARS-CoV-2. Thirty-one common pathogens that can cause respiratory tract infections were used to evaluate the specificity of the method ...[more]

PMID: 35233932

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Project description:Coronavirus disease 2019, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), poses a considerable threat to global public health. This study developed and evaluated a rapid, low-cost, expandable, and sequencing-free high-resolution melting (HRM) assay for the direct detection of SARS-CoV-2 variants. A panel of 64 common bacterial and viral pathogens that can cause respiratory tract infections was employed to evaluate our method's specificity. Serial dilutions of viral isolates determined the sensitivity of the method. Finally, the assay's clinical performance was assessed using 324 clinical samples with potential SARS-CoV-2 infection. Multiplex HRM analysis accurately identified SARS-CoV-2 (as confirmed with parallel reverse transcription-quantitative PCR [qRT-PCR] tests), differentiating between mutations at each marker site within approximately 2 h. For each target, the limit of detection (LOD) was lower than 10 copies/reaction (the LOD of N, G142D, R158G, Y505H, V213G, G446S, S413R, F486V, and S704L was 7.38, 9.72, 9.96, 9.96, 9.50, 7.80, 9.33, 8.25, and 8.25 copies/reaction, respectively). No cross-reactivity occurred with organisms of the specificity testing panel. In terms of variant detection, our results had a 97.9% (47/48) rate of agreement with standard Sanger sequencing. The multiplex HRM assay therefore offers a rapid and simple procedure for detecting SARS-CoV-2 variants. IMPORTANCE In the face of the current severe situation of increasing SARS-CoV-2 variants, we developed an upgraded multiplex HRM method for the predominant SARS-CoV-2 variants based on our original research. This method not only could identify the variants but also could be utilized in subsequent detection of novel variants since the assay has great performance in terms of flexibility. In summary, the upgraded multiplex HRM assay is a rapid, reliable, and economical detection method, which could better screen prevalent virus strains, monitor the epidemic situation, and help to develop measures for the prevention and control of SARS-CoV-2.

Dataset Information

Detection and classification of SARS-CoV-2 using high-resolution melting analysis.

Publications

Detection and classification of SARS-CoV-2 using high-resolution melting analysis.

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