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Variant Prediction by Analyzing RdRp/S Gene Double or Low Amplification Pattern in Allplex SARS-CoV-2 Assay
- Title
- Variant Prediction by Analyzing RdRp/S Gene Double or Low Amplification Pattern in Allplex SARS-CoV-2 Assay
- Authors
- So, Min-Kyung; Park, Sholhui; Lee, Kyunghoon; Kim, Soo-Kyung; Chung, Hae-Sun; Lee, Miae
- Ewha Authors
- 이미애; 정혜선; 박설희; 김수경; 이경훈
- SCOPUS Author ID
- 이미애; 정혜선; 박설희; 김수경; 이경훈
- Issue Date
- 2021
- Journal Title
- DIAGNOSTICS
- ISSN
- 2075-4418
- Citation
- DIAGNOSTICS vol. 11, no. 10
- Keywords
- SARS-CoV-2; Allplex SARS-CoV-2 Assay; B.1.671.2; spike gene; amplification curve
- Publisher
- MDPI
- Indexed
- SCIE; SCOPUS
- Document Type
- Article
- Abstract
- The spread of delta variants (B.1.671.2) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a severe global threat. Multiplex real-time PCR is a common method for confirming SARS-CoV-2 infection, however, additional tests, such as whole genomic sequencing, are required to reveal the presence or type of viral mutation. Moreover, applying whole genomic sequencing to all SARS-CoV-2 positive samples is challenging due to time and cost constraints. Here, we report that the double or low amplification curve observed during RNA-dependent RNA polymerase (RdRp) gene/S gene amplification in the Allplex SARS-CoV-2 Assay is related to delta/alpha variants. We analyzed the RdRp/S gene amplification curve using 94 samples confirmed as SARS-CoV-2 infection by the Allplex SARS-CoV-2 Assay from January to August, 2021. These positive samples identified variant types using the Novaplex SARS-CoV-2 Variants I and IV Assays. Overall, 17 samples showing a double curve and 11 samples showing a low amplification pattern were associated with alpha-/delta-type strains with variants in the P681 region. The double or low curve shown in the RdRp gene amplification curve had 100% sensitivity and 100% specificity for diagnosing delta/alpha variants. During the SARS-CoV-2 virus diagnostic RT-PCR test using the Allplex SARS-CoV-2 Assay, we could consider the presence of delta/alpha variants in the samples with double or low amplification curve of the RdRp/S gene channel. This PCR amplification curve abnormality enables rapid and cost-effective variant type prediction during SARS-CoV-2 diagnostic testing in clinical laboratories.</p>
- DOI
- 10.3390/diagnostics11101854
- Appears in Collections:
- 의과대학 > 의학과 > Journal papers
- Files in This Item:
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