Research Article
Confirming Multiplex RT-qPCR Use in COVID-19 with Next-Generation Sequencing: Strategies for Epidemiological Advantage
Table 2
Data of representative samples (n = 21) sequenced and classified into Delta and non-VOC variants using NGS and RT-qPCR assays.
| Sample | COVID-PCR (Ct values) | % of non-N bases (coverage≥10x) | Median coverage | COVID lineage by NGS | Variant-specific PCR (Ct values) | Lineage by RT-qPCR | (GT molecular) | (Thermo fisher scientific) | N1 | N2 | Next clade | Pango | L452R | T478K | L452R | P681R |
| NTC | Negative | Negative | | | N/A | N/A | Neg | Neg | Neg | Neg | N/A | 665588 | 12.99 | 11.9 | 88.15 | 58 | 21A (elta) | AY.25 | 18.5 | Neg | 20.88 | 25.97 | Delta | 664789 | 28.72 | 27.78 | 99.40 | 221 | 21A (Delta) | AY.3 | 31.81 | 32.6 | 33.97 | 34.37 | Delta | 665660 | 16.71 | 15.64 | 98.45 | 116 | 21A (Delta) | AY.3 | 20.18 | 24.98 | 24.49 | 26.58 | Delta | 664822 | 26.3 | 25.24 | 93.87 | 103 | 21A (Delta) | AY.3 | 20.55 | Neg | 22.18 | 24.87 | Delta | 666013 | 14.5 | 13.98 | 99.36 | 217 | 21A (Delta) | B.1.617.2 | 22.72 | 33.27 | 27.8 | 28.78 | Delta | 665426 | 15.98 | 14.44 | 98.14 | 128 | 21A (Delta) | AY.3 | 18.69 | 25.39 | 23.92 | 25.52 | Delta | 21 | 21.41 | 21.71 | 100.0 | 1340 | 20C | B.1.243 | Neg | Neg | Neg | Neg | Non-VOC | 22 | 25.3 | 26.82 | 100.0 | 2380 | 19A | B.1.574 | Neg | Neg | Neg | Neg | Non-VOC | 23 | 25.35 | 25.04 | 100.0 | 1276 | 20C | B.1.574 | Neg | Neg | Neg | Neg | Non-VOC | 24 | 28.74 | 29.52 | 100.0 | 2618 | 20A | B.1.2 | Neg | Neg | Neg | Neg | Non-VOC | 25 | 19.86 | 20.43 | 100.0 | 229 | 20A | B.1 | Neg | Neg | Neg | Neg | Non-VOC | 26 | 17.33 | 17.64 | 100.0 | 1477 | 20C | B.1.234 | Neg | Neg | Neg | Neg | Non-VOC | 27 | 20.77 | 21.68 | 100.0 | 1092 | 20A | B.1.126 | Neg | Neg | Neg | Neg | Non-VOC | 28 | 19.98 | 20.58 | 100.0 | 1614 | 20C | B.1.602 | Neg | Neg | Neg | Neg | Non-VOC | 29 | 26.99 | 27.61 | 100.0 | 3734 | 20A | B.1 | Neg | Neg | Neg | Neg | Non-VOC | 210 | 33.9 | 32.64 | 100.0 | 1531 | 20C | B.1 | Neg | Neg | Neg | Neg | Non-VOC | 211 | 32.66 | 31.53 | 100.0 | 2485 | 20C | B.1.564 | Neg | Neg | Neg | Neg | Non-VOC | 212 | 33.19 | 35.37 | 100.0 | 2019 | 21A (Delta) | B.1.617.2 | 33.27 | 27.8 | 29.99 | 26.72 | Delta | 213 | 32.29 | 32.86 | 100.0 | 1888 | 21A (Delta) | AY.3 | 25.39 | 23.92 | 22.25 | 29.92 | Delta | 214 | 25.13 | 25.77 | 100.0 | 2618 | 21A (Delta) | B.1.617.2 | 32.32 | 33.12 | 24.93 | 31.56 | Delta | Wuhan-hu1 | 25.26 | 25.89 | 100.00 | 3236 | 19B | A | Neg | Neg | Neg | Neg | Non-VOC |
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