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Article

Variant Prediction by Analyzing RdRp/S Gene Double or Low Amplification Pattern in Allplex SARS-CoV-2 Assay

Department of Laboratory Medicine, Ewha Womans University College of Medicine, Seoul 03760, Korea
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Academic Editor: Anna Baraniak
Diagnostics 2021, 11(10), 1854; https://doi.org/10.3390/diagnostics11101854
Received: 21 September 2021 / Revised: 5 October 2021 / Accepted: 5 October 2021 / Published: 8 October 2021
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. View Full-Text
Keywords: SARS-CoV-2; Allplex SARS-CoV-2 Assay; B.1.671.2; spike gene; amplification curve SARS-CoV-2; Allplex SARS-CoV-2 Assay; B.1.671.2; spike gene; amplification curve
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MDPI and ACS Style

So, M.-K.; Park, S.; Lee, K.; Kim, S.-K.; Chung, H.-S.; Lee, M. Variant Prediction by Analyzing RdRp/S Gene Double or Low Amplification Pattern in Allplex SARS-CoV-2 Assay. Diagnostics 2021, 11, 1854. https://doi.org/10.3390/diagnostics11101854

AMA Style

So M-K, Park S, Lee K, Kim S-K, Chung H-S, Lee M. Variant Prediction by Analyzing RdRp/S Gene Double or Low Amplification Pattern in Allplex SARS-CoV-2 Assay. Diagnostics. 2021; 11(10):1854. https://doi.org/10.3390/diagnostics11101854

Chicago/Turabian Style

So, Min-Kyung, Sholhui Park, Kyunghoon Lee, Soo-Kyung Kim, Hae-Sun Chung, and Miae Lee. 2021. "Variant Prediction by Analyzing RdRp/S Gene Double or Low Amplification Pattern in Allplex SARS-CoV-2 Assay" Diagnostics 11, no. 10: 1854. https://doi.org/10.3390/diagnostics11101854

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