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Variant Prediction by Analyzing RdRp/S Gene Double or Low Amplification Pattern in Allplex SARS-CoV-2 Assay
Min-Kyung So1, Sholhui Park1, Kyunghoon Lee1
1Department of Laboratory Medicine, Ewha Womans University College of Medicine, Seoul 03760, Korea.
Diagnostics (Basel, Switzerland)
|October 23, 2021
Summary
Unusual amplification curves in PCR tests can rapidly identify SARS-CoV-2 variants like Delta and Alpha. This method offers a cost-effective way to detect specific mutations during routine diagnostic testing.
Area of Science:
- Virology
- Molecular Biology
- Infectious Diseases
Background:
- The global spread of SARS-CoV-2 variants, such as Delta (B.1.617.2), poses a significant public health challenge.
- Multiplex real-time PCR is standard for SARS-CoV-2 detection, but identifying specific mutations often requires costly and time-consuming whole-genome sequencing.
- Efficient methods for variant identification are crucial for public health surveillance and clinical management.
Purpose of the Study:
- To investigate the correlation between specific amplification curve patterns in the Allplex SARS-CoV-2 Assay and the presence of SARS-CoV-2 variants.
- To determine if PCR amplification curve abnormalities can serve as a rapid and cost-effective indicator for Delta and Alpha variant detection.
Main Methods:
- Analysis of RNA-dependent RNA polymerase (RdRp)/S gene amplification curves from 94 SARS-CoV-2 positive samples using the Allplex SARS-CoV-2 Assay.
- Variant typing of positive samples was performed using Novaplex SARS-CoV-2 Variants I and IV Assays.
- Correlation analysis between observed amplification curve patterns (double or low curve) and identified Alpha/Delta variants.
Main Results:
- A double or low amplification curve in the RdRp/S gene channel was significantly associated with Alpha and Delta variants, particularly those with mutations in the P681 region.
- The presence of a double or low amplification curve demonstrated 100% sensitivity and 100% specificity for identifying Alpha/Delta variants.
- Out of 94 samples, 17 exhibited a double curve and 11 showed a low amplification pattern, both linked to Alpha/Delta strains.
Conclusions:
- Abnormalities in PCR amplification curves (double or low) during routine SARS-CoV-2 testing can be a reliable indicator of Alpha and Delta variant presence.
- This finding allows for rapid, cost-effective variant prediction within clinical laboratories, complementing standard diagnostic workflows.
- The PCR amplification curve pattern offers a valuable tool for early detection and surveillance of concerning SARS-CoV-2 variants.
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