TABLE 4.
Breakdown of amplicon sequencing results by detection and RT-qPCR result
| Amplicon sequencing result | SARS-CoV-2 RT-qPCR (N and Orf1ab) | No. samples | % samples | Cq (mean) | Cq (range) | Estimated copies/reaction (mean) | Estimated copies/sampler (mean) |
|---|---|---|---|---|---|---|---|
| Omicron and Delta variant of concern (VOC) detected (NTD and RBM amplicons sequenced) | Dual loci positive (N and Orf1ab) | 21 | 5.1 | 34.4 | 31.8–38.2 | 596 | 5,960 |
| Single loci positive (N or Orf1ab) | 0 | 0.0 | |||||
| Subtotal | 21 | 5.1 | |||||
| Delta VOC detected (NTD and RBM amplicons sequenced) | Dual loci positive (N and Orf1ab) | 238 | 57.9 | 34.2 | 29.8–39.8 | 788.6 | 7,886 |
| Single loci positive (N or Orf1ab) | 4 | 1.0 | 38.5 | 38.0–39.3 | 16.5 | 165 | |
| Subtotal | 242 | 58.9 | |||||
| Unable to sequence | Dual loci positive (N and Orf1ab) | 73 | 17.8 | 35.3 | 30.5–38.3 | 436 | 4,360 |
| Single loci positive (N or Orf1ab) | 21 | 5.1 | 38.4 | 37.2–40.2 | 31.7 | 317 | |
| Subtotal | 94 | 22.9 | |||||
| VOC detected (only NTD or RBM amplicon sequenced) | Dual loci positive (N and Orf1ab) | 47 | 11.4 | 35.2 | 32.0–38.0 | 343.7 | 3,437 |
| Single loci positive (N or Orf1ab) | 7 | 1.7 | 38.9 | 38.1–41.9 | 21.5 | 215 | |
| Subtotal | 54 | 13.1 | |||||
| Total | 411 | 100.00 | |||||