TABLE 1.
Concordance between Ion AmpliSeq SARS-CoV-2 and reference method
| Specimen number | Ct value | Paragon Genomics CleanPlexa | Ion AmpliSeq SARS-CoV-2 | Avg base coverage depth | Base reads on target | Target base coverage at 100× | Concordance |
|---|---|---|---|---|---|---|---|
| 1 | 29.38 | B.1.2 | B.1.2 | 3,165 | 99.58% | 99.83% | Yes |
| 2 | 27.38 | B.1.427 | B.1.427 | 3,418 | 99.76% | 99.87% | Yes |
| 3 | 26.57 | B.1.240 | B.1.240 | 4,114 | 99.81% | 99.91% | Yes |
| 4 | 25.6 | B.1.1 | B.1.1 | 4,060 | 99.94% | 99.84% | Yes |
| 5 | 27.87 | B.1.429 | B.1.429 | 3,619 | 99.75% | 99.68% | Yes |
| 6 | 24.27 | B.1.1 | B.1.1 | 4,809 | 99.45% | 99.65% | Yes |
| 7 | 23.88 | B.1.1.7 | B.1.1.7 | 4,189 | 99.89% | 99.71% | Yes |
| 8 | 22.83 | P.1.17 | P.1.17 | 4,374 | 99.91% | 99.65% | Yes |
| 9 | 27.33 | AY.20 | AY.20 | 3,834 | 99.55% | 99.32% | Yes |
| 10 | 29.88 | AY.103 | AY.103 | 1,875 | 99.81% | 99.57% | Yes |
| 11 | 28.49 | AY.100 | AY.100 | 2,431 | 99.43% | 98.70% | Yes |
| 12 | 29.11 | AY.26 | AY.26 | 2,248 | 98.54% | 99.41% | Yes |
| 13 | 31.82 | B.1.2 | B.1.2 | 2,631 | 98.52% | 99.82% | Yes |
| 14 | 31.27 | B.1.2 | B.1.2 | 994 | 96.61% | 98.36% | Yes |
| 15 | 30.34 | B.1.429 | B.1.429 | 9,205 | 98.23% | 99.78% | Yes |
| 16 | 30.17c | B.1.429 | B.1.429 | 623 | 94.90% | 95.47% | Yes |
| 17 | 31.45 | B.1.429 | B.1.361 | 4,654 | 99.69% | 99.87% | No |
| 18 | 30.8 | None | B.1.429 | 2,090 | 97.93% | 99.73% | No |
| 19 | 30.34 | B.1.427 | B.1.429 | 454 | 78.76% | 88.26% | Yesb |
| 20 | 18.87 | B.1.427 | B.1.427 | 7,644 | 99.93% | 99.87% | Yes |
| 21 | 25.55 | B.1.427 | B.1.427 | 2,168 | 99.08% | 99.70% | Yes |
| 22 | 31.36c | B | B.1.429 | 3,340 | 91.18% | 99.57% | No |
| 23 | 28.5c | B.1.427 | B.1.429 | 1,690 | 93.30% | 99.05% | Yesb |
| 24 | 15 | B.1.526 | B.1.526 | 1,949 | 99.95% | 99.68% | Yes |
| 25 | 20.64 | P.1 | P.1 | 3,692 | 99.96% | 99.67% | Yes |
| 26 | 27.04 | AY.44 | AY.44 | 2,725 | 99.93% | 99.76% | Yes |
| 27 | 10.82 | BB.2 | BB.2 | 8,006 | 99.95% | 99.57% | Yes |
| 28 | 18.57 | P.1 | P.1 | 10,070 | 99.94% | 99.87% | Yes |
| 29 | 28.11 | B.1.241 | B.1.241 | 1,949 | 99.87% | 99.68% | Yes |
| 30 | 26.81c | B.1.1.239 | B.1.1.239 | 498 | 94.46% | 96.82% | Yes |
| 31 | 15.1 | B.1.1.291 | B.1.1.291 | 9,327 | 99.93% | 99.82% | Yes |
| 32 | 16.62 | B.1.526 | B.1.526 | 8,781 | 99.95% | 99.83% | Yes |
| 33 | 21.33 | B.1.1.7 | B.1.1.7 | 2,633 | 99.04% | 99.23% | Yes |
| 34 | 29.75c | B | B.1.429 | 327 | 79.92% | 90.43% | No |
| 35 | 14.45 | B.1.1.7 | B.1.1.7 | 2,998 | 99.80% | 99.68% | Yes |
| 36 | 19.37 | P.1 | P.1 | 5,640 | 99.77% | 99.62% | Yes |
| 37 | 20.98 | P.1.17 | P.1.17 | 6,679 | 99.79% | 99.83% | Yes |
| 38 | 24.9 | AY.103 | AY.103 | 2,730 | 98.69% | 99.28% | Yes |
| 39 | 19.81 | AY.119 | AY.119 | 3,383 | 99.56% | 98.81% | Yes |
| 40 | 16.67 | AY.116.1 | AY.116.1 | 6,547 | 99.76% | 99.82% | Yes |
| 41 | 17.77 | B.1.637 | B.1.637 | 4,703 | 99.70% | 99.77% | Yes |
| 42 | 18.34 | B.1.526 | B.1.526 | 3,220 | 99.78% | 99.59% | Yes |
| 43 | 20.18 | B.1.1.7 | B.1.1.7 | 3,749 | 99.80% | 99.97% | Yes |
| 44 | 19.59 | B.1.1.7 | B.1.1.7 | 4,018 | 99.79% | 99.83% | Yes |
| 45 | 27.37 | B.1.421 | B.1.421 | 2,039 | 98.76% | 99.66% | Yes |
| 46 | 24.48 | B.1.421 | B.1.421 | 3,585 | 99.73% | 99.40% | Yes |
| 47 | 19.75 | B.1.421 | B.1.421 | 5,402 | 99.79% | 99.80% | Yes |
| 48 | 14.42 | B.1.421 | B.1.421 | 10,677 | 99.75% | 99.91% | Yes |
| 49 | 28.81 | B.1.404 | B.1.404 | 1,315 | 96.18% | 99.62% | Yes |
| 50 | 27.86 | B.1.404 | B.1.404 | 4,447 | 99.80% | 99.54% | Yes |
| 51 | 28.03 | B.1 | B.1.438.4 | 1,136 | 95.45% | 98.43% | Yesb |
| 52 | 27.03 | B.1.399 | B.1.399 | 4,699 | 99.76% | 98.96% | Yes |
| 53 | 17.42 | B.1.399 | B.1.399 | 20,056 | 99.96% | 99.09% | Yes |
| 54 | 14.77 | B.1.399 | B.1.399 | 5,681 | 99.96% | 99.74% | Yes |
| 55 | 25.64 | B | B.1.324 | 1,016 | 98.23% | 99.37% | Yesb |
| 56 | 25.53 | B | B.1.609 | 2,834 | 97.45% | 99.37% | Yesb |
| 57 | 18.71 | B.1.324 | B.1.324 | 8,486 | 99.96% | 99.84% | Yes |
| 58 | 14.06 | B.1.298 | B.1.298 | 4,901 | 99.97% | 100% | Yes |
| 59 | 19.54 | B.1 | B.1.265 | 6,085 | 99.94% | 99.44% | Yesb |
| 60 | 25.76 | B.1.232 | B.1.232 | 3,925 | 99.77% | 99.13% | Yes |
| 61 | 24.19 | B.1.232 | B.1.232 | 3,213 | 97.54% | 99.39% | Yes |
| 62 | 25.9 | B.1.126 | B.1.126 | 3,699 | 99.78% | 98.30% | Yes |
| 63 | 16.35 | B.1.429 | B.1.429 | 9,198 | 99.97% | 99.82% | Yes |
| 64 | 23.84 | B.1.1.7 | B.1.1.7 | 6,214 | 99.95% | 99.98% | Yes |
| 65 | 27.82 | B.1.1.228 | B.1.1.228 | 2,319 | 99.87% | 99.02% | Yes |
| 66 | 29.39 | AY.54 | AY.54 | 2,607 | 99.77% | 99.44% | Yes |
| 67 | 21.89 | BB.2 | BB.2 | 10,089 | 99.89% | 99.78% | Yes |
| 68 | 21.34 | B.1.526 | B.1.526 | 10,482 | 99.97% | 99.73% | Yes |
| 69 | 26.24 | B.1.126 | B.1.126 | 6,545 | 99.71% | 98.51% | Yes |
| 70 | 13.94 | AY.103 | AY.103 | 5,381 | 99.96% | 99.78% | Yes |
| 71 | 14.06 | P.1 | P.1 | 8,572 | 99.95% | 99.93% | Yes |
| 72 | 17.4 | B.1.1.7 | B.1.1.7 | 6,248 | 99.95% | 99.99% | Yes |
| 73 | 14.02 | B.1.1.7 | B.1.1.7 | 17,717 | 99.94% | 100% | Yes |
| 74 | 16.35 | B.1.429 | B.1.429 | 4,951 | 99.95% | 99.79% | Yes |
| 75 | 16.35 | B.1.429 | B.1.429 | 19,243 | 99.94% | 99.96% | Yes |
a
Underlined CleanPlex lineage calls did not pass more stringent QC thresholds.
b
Lineage calling was interpreted as concordant when Pango nomenclatures (e.g., B.1.617.2, AY.X) classified as the same variant based on SIG classification (i.e., Delta) or both Pango nomenclatures are considered a nonvariant that will only be reported out as nonvariant.
c
Samples did not meet QC cutoffs on first attempt. These samples were repeated and pooled with other low titer samples. Low titer was considered Ct >25.5 or approximately 1,000 copies/mL. QC metrics were improved and lineage calls were unchanged. Results are from low titer pooled repeat testing run.