Research Article
Confirming Multiplex RT-qPCR Use in COVID-19 with Next-Generation Sequencing: Strategies for Epidemiological Advantage
Table 3
Comparative detection of VOC classifying mutations with RT-qPCR and NGS-based approaches.
Variant determined by NGS (see Appendix for method).
| Evaluation of Q-PCR-based SARS-CoV-2 variant detection solutions | VOC (n = 67) | Non-VOC (n = 11) | PCR | NGS | PCR | NGS |
| Manufacturer | Catalog # | Reaction | Targets | Variants (WHO label) harboring this mutation | 0 | 0 | 0 | 0 | GT molecular fort collins, CO, USA | 100180 | Reaction-1 | N501Y | Alpha (B.1.1.7), beta (B.1.351), gamma (P.1) | 0 | 0 | 0 | 0 | | | Del69-70 | Alpha (UK, B.1.1.7) | 0 | 0 | 0 | 0 | | Reaction-2 | N501Y | Alpha (B.1.1.7), Beta (B.1.351), gamma (P.1) | 0 | 0 | 0 | 0 | | | E484K | Beta (B.1.351), gamma (P.1) | 1 | 1 | 0 | 0 | | | K417N | Beta (B.1.351), Delta plus | 0 | 0 | 0 | 0 | | | K417T | Gamma (P.1) | 0 | 0 | 0 | 0 | | Reaction - 3 | L452R | Epsilon (B.1.427/B.1.429), Delta (B.1.617.2) | 67 | 67 | 0 | 0 | | | T478K | Delta (B.1.617.2) | 62 | 64 | 0 | 0 | 100172 | Reaction-1 | L452R | Epsilon (B.1.427/B.1.429), Delta (B.1.617.2) | 67 | 67 | 0 | 0 | | | T478K | Delta (B.1.617.2) | 62 | 64 | 0 | 0 |
| Thermo fisher scientific Inc., Waltham, MA, USA | A51819 | Reaction-1 | L452R | B.1.617, B.1.617.1, Delta (B.1.617.2), B.1.617.3, B.1.429 | 63 | 67 | 0 | 0 | A51822 | Reaction-2 | P681R | B.1.617.1, B.1.617.2, B.1.617.3 | 55 | 64 | 0 | 0 |
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