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. 2022 Mar 23;60(4):e02569-21. doi: 10.1128/jcm.02569-21

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.