Preliminary in silico assessment of the specificity of published molecular assays and design of new assays using the available whole genome sequences of 2019-nCoV

SARS-CoV-2 coronavirus nCoV-2019 Diagnostics and Vaccines
23

Updated to 17,446 COVID-19 WGS from GISAID.

Table 1. Results from PSET analysis. The five Noblis assays were compared alongside the four assays from Corman and three assays from the CDC. Along with assays from China, Hong Kong, Thailand, Japan, and France. Each assay was tested using SARS-CoV-2 as the intended target. All off-target hits (TN, PF, FP) are to entries in NCBI BLAST databases (nt, gss, and env_nt).

identifier type targets PT TP FN Percent True PF FP TN
Noblis.12 Probe 2697049 17251 81 114 99.35% 0 0 680
Noblis.40 Probe 2697049 16740 627 79 99.55% 0 1 1420
Noblis.42 Probe 2697049 17338 33 75 99.57% 0 2 1136
Noblis.44 Probe 2697049 17127 48 271 98.45% 0 1 1786
Noblis.57 Probe 2697049 17153 137 156 99.11% 0 1 853
ncov_e_gene Probe 2697049 17297 50 99 99.43% 361 15 53
ncov_n_gene Probe 2697049 17199 143 104 99.40% 0 340 72
ncov_rdrp_1 Probe 2697049 0 17392 54 99.69% 433 105 5967
ncov_rdrp_2 Probe 2697049 2 17389 55 99.68% 2 73 5916
cdc_n1 Probe 2697049 16952 443 51 99.71% 0 2 381
cdc_n2 Probe 2697049 16939 137 370 97.88% 0 1 372
cdc_n3 Probe 2697049 17038 361 47 99.73% 1 353 36
China_N Probe 2697049 13895 241 3310 81.03% 0 2 691
China_ORF1ab Probe 2697049 16202 147 1097 93.71% 1 0 367
France_nCoV_IP2 Probe 2697049 17301 69 76 99.56% 1 0 367
France_nCoV_IP4 Probe 2697049 17308 75 63 99.64% 0 0 1190
HKU-N Probe 2697049 16938 145 363 97.92% 327 33 34
HKU-ORF1b-nsp14 Probe 2697049 17287 83 76 99.56% 324 29 452
Japan_NIID_2019-nCOV_N Probe 2697049 0 17076 370 97.88% 0 0 384
Japan_NIID_WH-1_F24381 Outer 2697049 17178 165 103 99.41% 0 1 601
Japan_NIID_WH-1_F501 Outer 2697049 16964 318 164 99.06% 0 1 370
Japan_NIID_WH-1_F509 Outer 2697049 17110 163 173 99.01% 1 0 369
Japan_NIID_WH-1_Seq_F24383 Outer 2697049 17172 165 109 99.38% 0 0 606
Japan_NIID_WH-1_Seq_F519 Outer 2697049 16948 253 245 98.60% 0 1 369
Japan_WuhanCoV-spk1 Outer 2697049 17208 133 105 99.40% 1 1 594
Thailand_WH-NIC_N Probe 2697049 17216 173 57 99.67% 0 2 375
25

*Updated to 25,181 COVID-19 WGS from GISAID. (*small error in previous post, re-uploaded with correction)

Table 1. Results from PSET analysis. The five Noblis assays were compared alongside the four assays from Corman and three assays from the CDC. Along with assays from China, Hong Kong, Thailand, Japan, and France. Each assay was tested using SARS-CoV-2 as the intended target. All off-target hits (TN, PF, FP) are to entries in NCBI BLAST databases (nt, gss, and env_nt).

identifier type PT TP FN Percent True PF FP TN
Noblis.12 Probe 24952 107 122 99.52% 0 0 680
Noblis.40 Probe 24227 871 83 99.67% 0 1 1420
Noblis.42 Probe 25011 43 127 99.50% 0 2 1136
Noblis.44 Probe 24681 75 425 98.31% 0 1 1786
Noblis.57 Probe 24777 210 194 99.23% 0 1 853
ncov_e_gene Probe 25005 68 108 99.57% 361 15 53
ncov_n_gene Probe 24847 214 120 99.52% 0 340 72
ncov_rdrp_1 Probe 0 25122 59 99.77% 433 105 5967
ncov_rdrp_2 Probe 2 25119 60 99.76% 2 73 5916
cdc_n1 Probe 24582 533 66 99.74% 0 2 381
cdc_n2 Probe 24617 181 383 98.48% 0 1 372
cdc_n3 Probe 24675 399 107 99.58% 1 353 36
China_N Probe 18633 320 6228 75.27% 0 2 691
China_ORF1ab Probe 23801 150 1230 95.12% 1 0 367
France_nCoV_IP2 Probe 24984 106 91 99.64% 1 0 367
France_nCoV_IP4 Probe 24927 180 74 99.71% 0 0 1190
HKU-N Probe 24627 179 375 98.51% 327 33 34
HKU-ORF1b-nsp14 Probe 24942 145 94 99.63% 324 29 452
Japan_NIID_2019-nCOV_N Probe 0 24797 384 98.48% 0 0 384
Japan_NIID_WH-1_F24381 Outer 24762 291 128 99.49% 0 1 601
Japan_NIID_WH-1_F501 Outer 24614 388 179 99.29% 0 1 370
Japan_NIID_WH-1_F509 Outer 24767 227 187 99.26% 1 0 369
Japan_NIID_WH-1_Seq_F24383 Outer 24757 291 133 99.47% 0 0 606
Japan_NIID_WH-1_Seq_F519 Outer 24591 298 292 98.84% 0 1 369
Japan_WuhanCoV-spk1 Outer 24792 259 130 99.48% 1 1 594
Thailand_WH-NIC_N Probe 24878 232 71 99.72% 0 2 375
26

Updated to 30,561 COVID-19 WGS from GISAID.

Table 1. Results from PSET analysis. The five Noblis assays were compared alongside the four assays from Corman and three assays from the CDC. Along with assays from China, Hong Kong, Thailand, Japan, and France. Each assay was tested using SARS-CoV-2 as the intended target. All off-target hits (TN, PF, FP) are to entries in NCBI BLAST databases (nt, gss, and env_nt).

identifier type PT TP FN Percent True PF FP TN
Noblis.12 Probe 30281 139 141 99.54% 0 0 680
Noblis.40 Probe 29454 1013 94 99.69% 0 1 1420
Noblis.42 Probe 30352 60 149 99.51% 0 2 1136
Noblis.44 Probe 30013 95 453 98.52% 0 1 1786
Noblis.57 Probe 30033 267 261 99.15% 0 1 853
ncov_e_gene Probe 30355 81 125 99.59% 361 15 53
ncov_n_gene Probe 30153 266 142 99.54% 0 340 72
ncov_rdrp_1 Probe 0 30483 78 99.74% 433 105 5967
ncov_rdrp_2 Probe 2 30483 76 99.75% 2 73 5916
cdc_n1 Probe 29815 664 82 99.73% 0 2 381
cdc_n2 Probe 29912 249 400 98.69% 0 1 372
cdc_n3 Probe 29996 497 68 99.78% 1 353 36
China_N Probe 22004 375 8182 73.23% 0 2 691
China_ORF1ab Probe 28846 183 1532 94.99% 1 0 367
France_nCoV_IP2 Probe 30343 122 96 99.69% 1 0 367
France_nCoV_IP4 Probe 30271 208 82 99.73% 0 0 1190
HKU-N Probe 29953 218 390 98.72% 327 33 34
HKU-ORF1b-nsp14 Probe 30247 209 105 99.66% 324 29 452
Japan_NIID_2019-nCOV_N Probe 0 30160 401 98.69% 0 0 384
Japan_NIID_WH-1_F24381 Outer 30007 394 160 99.48% 0 1 601
Japan_NIID_WH-1_F501 Outer 29912 437 212 99.31% 0 1 370
Japan_NIID_WH-1_F509 Outer 30075 265 221 99.28% 1 0 369
Japan_NIID_WH-1_Seq_F24383 Outer 30002 391 168 99.45% 0 0 606
Japan_NIID_WH-1_Seq_F519 Outer 29898 320 343 98.88% 0 1 369
Japan_WuhanCoV-spk1 Outer 30039 352 170 99.44% 1 1 594
Thailand_WH-NIC_N Probe 30203 273 85 99.72% 0 2 375
27

Updated to 34,646 COVID-19 WGS from GISAID.

Table 1. Results from PSET analysis. The five Noblis assays were compared alongside the four assays from Corman and three assays from the CDC. Along with assays from China, Hong Kong, Thailand, Japan, and France. Each assay was tested using SARS-CoV-2 as the intended target. All off-target hits (TN, PF, FP) are to entries in NCBI BLAST databases (nt and env_nt).

identifier type PT TP FN Percent True PF FP TN
Noblis.12 Probe 34345 148 153 99.56% 0 0 680
Noblis.40 Probe 33477 1073 96 99.72% 0 1 1420
Noblis.42 Probe 34424 66 156 99.55% 0 2 1136
Noblis.44 Probe 34059 119 468 98.65% 0 1 1786
Noblis.57 Probe 34064 301 281 99.19% 0 1 853
ncov_e_gene Probe 34379 93 174 99.50% 361 15 53
ncov_n_gene Probe 34175 297 174 99.50% 0 340 72
ncov_rdrp_1 Probe 0 34563 83 99.76% 433 105 5967
ncov_rdrp_2 Probe 2 34563 81 99.77% 2 73 5916
cdc_n1 Probe 33786 770 90 99.74% 0 2 381
cdc_n2 Probe 33957 272 417 98.80% 0 1 372
cdc_n3 Probe 33981 536 129 99.63% 1 353 36
China_N Probe 24954 415 9277 73.22% 0 2 691
China_ORF1ab Probe 32864 172 1610 95.35% 1 0 367
France_nCoV_IP2 Probe 34392 140 114 99.67% 1 0 367
France_nCoV_IP4 Probe 34327 233 86 99.75% 0 0 1190
HKU-N Probe 33992 247 407 98.83% 327 33 34
HKU-ORF1b-nsp14 Probe 34317 213 116 99.67% 324 29 452
Japan_NIID_2019-nCOV_N Probe 0 34217 429 98.76% 0 0 384
Japan_NIID_WH-1_F24381 Outer 34037 429 180 99.48% 0 1 601
Japan_NIID_WH-1_F501 Outer 33845 560 241 99.30% 0 1 370
Japan_NIID_WH-1_F509 Outer 34042 301 303 99.13% 1 0 369
Japan_NIID_WH-1_Seq_F24383 Outer 34028 429 189 99.45% 0 0 606
Japan_NIID_WH-1_Seq_F519 Outer 33835 371 440 98.73% 0 1 369
Japan_WuhanCoV-spk1 Outer 34079 380 187 99.46% 1 1 594
Thailand_WH-NIC_N Probe 34261 289 96 99.72% 0 2 375
28

Updated to 39,051 COVID-19 WGS from GISAID.

Table 1. Results from PSET analysis. The five Noblis assays were compared alongside the four assays from Corman and three assays from the CDC. Along with assays from China, Hong Kong, Thailand, Japan, and France. Each assay was tested using SARS-CoV-2 as the intended target. All off-target hits (TN, PF, FP) are to entries in NCBI BLAST databases (nt and env_nt).

identifier type PT TP FN Percent True PF FP TN
Noblis.12 Probe 38711 176 164 99.58% 0 0 680
Noblis.40 Probe 37741 1210 100 99.74% 0 1 1420
Noblis.42 Probe 38796 77 178 99.54% 0 2 1136
Noblis.44 Probe 38391 158 502 98.71% 0 1 1786
Noblis.57 Probe 38355 381 315 99.19% 0 1 853
ncov_e_gene Probe 38740 118 193 99.51% 361 15 53
ncov_n_gene Probe 38441 400 210 99.46% 0 340 72
ncov_rdrp_1 Probe 0 38960 91 99.77% 433 105 5967
ncov_rdrp_2 Probe 2 38960 89 99.77% 2 73 5916
cdc_n1 Probe 37989 958 104 99.73% 0 2 381
cdc_n2 Probe 38168 308 575 98.53% 0 1 372
cdc_n3 Probe 38297 611 143 99.63% 1 353 36
China_N Probe 27528 485 11038 71.73% 0 2 691
China_ORF1ab Probe 37074 248 1729 95.57% 1 0 367
France_nCoV_IP2 Probe 38748 177 126 99.68% 1 0 367
France_nCoV_IP4 Probe 38713 249 89 99.77% 0 0 1190
HKU-N Probe 38159 325 567 98.55% 327 33 34
HKU-ORF1b-nsp14 Probe 38696 232 123 99.69% 324 29 452
Japan_NIID_2019-nCOV_N Probe 0 38461 590 98.49% 0 0 384
Japan_NIID_WH-1_F24381 Outer 38357 475 219 99.44% 0 1 601
Japan_NIID_WH-1_F501 Outer 38119 662 270 99.31% 0 1 370
Japan_NIID_WH-1_F509 Outer 38376 330 345 99.12% 1 0 369
Japan_NIID_WH-1_Seq_F24383 Outer 38347 475 229 99.41% 0 0 606
Japan_NIID_WH-1_Seq_F519 Outer 38137 401 513 98.69% 0 1 369
Japan_WuhanCoV-spk1 Outer 38403 422 226 99.42% 1 1 594
Thailand_WH-NIC_N Probe 38585 356 110 99.72% 0 2 375
29

Updated to 45,665 COVID-19 WGS from GISAID.

Table 1. Results from PSET analysis. The five Noblis assays were compared alongside the four assays from Corman and three assays from the CDC. Along with assays from China, Hong Kong, Thailand, Japan, France, South Korea, and Singapore. 12 New assays added. Each assay was tested using SARS-CoV-2 as the intended target. All off-target hits (TN, PF, FP) are to entries in NCBI BLAST databases (nt and env_nt).

identifier type PT TP FN Percent True PF FP TN
Noblis.12 Probe 45257 202 206 99.55% 0 0 680
Noblis.40 Probe 44122 1407 136 99.70% 0 1 1420
Noblis.42 Probe 45350 94 221 99.52% 0 2 1136
Noblis.44 Probe 44905 199 561 98.77% 0 1 1786
Noblis.57 Probe 44845 431 389 99.15% 0 1 853
ncov_e_gene Probe 45272 145 248 99.46% 361 15 53
ncov_n_gene Probe 44916 486 263 99.42% 0 340 72
ncov_rdrp_1 Probe 0 45528 137 99.70% 433 105 5967
ncov_rdrp_2 Probe 2 45531 132 99.71% 2 73 5916
cdc_n1 Probe 44356 1190 119 99.74% 0 2 381
cdc_n2 Probe 44682 352 631 98.62% 0 1 372
cdc_n3 Probe 44786 715 164 99.64% 1 353 36
China_N Probe 32237 557 12871 71.81% 0 2 691
China_ORF1ab Probe 43473 372 1820 96.01% 1 0 367
France_nCoV_IP2 Probe 45322 196 147 99.68% 1 0 367
France_nCoV_IP4 Probe 45289 275 101 99.78% 0 0 1190
HKU-N Probe 44664 374 627 98.63% 327 33 34
HKU-ORF1b-nsp14 Probe 45224 288 153 99.66% 324 29 452
Japan_NIID_2019-nCOV_N Probe 0 45011 654 98.57% 0 0 384
Japan_NIID_WH-1_F24381 Outer 44867 540 258 99.44% 0 1 601
Japan_NIID_WH-1_F501 Outer 44660 699 306 99.33% 0 1 370
Japan_NIID_WH-1_F509 Outer 44875 401 389 99.15% 1 0 369
Japan_NIID_WH-1_Seq_F24383 Outer 44855 542 268 99.41% 0 0 606
Japan_NIID_WH-1_Seq_F519 Outer 44561 492 612 98.66% 0 1 369
Japan_WuhanCoV-spk1 Outer 44931 466 268 99.41% 1 1 594
Thailand_WH-NIC_N Probe 45043 494 128 99.72% 0 2 375
Chan-N Probe 44758 282 625 98.63% 4 3 353
Chan-ORF1ab Probe 0 45266 399 99.13% 0 5 2
Chan-S Probe 44678 158 829 98.18% 5 0 2
Niu-E Probe 45162 223 280 99.39% 26 359 0
Won-E Outer 2 45443 220 99.52% 0 384 1
Won-N Outer 44620 827 218 99.52% 8 7 358
Won-ORF1ab Outer 45260 242 163 99.64% 5 2 313
Won-S Outer 43872 154 1639 96.41% 5 1 0
Yip-ORF1ab Outer 45075 141 449 99.02% 5 1 1
Young-N Probe 0 45433 232 99.49% 0 5 1
Young-ORF1ab Probe 45408 150 107 99.77% 5 1 0
Young-S Probe 44929 374 362 99.21% 4 1 0
30

Updated to 49,073 COVID-19 WGS from GISAID.

Table 1. Results from PSET analysis. The five Noblis assays were compared alongside the four assays from Corman and three assays from the CDC. Along with assays from China, Hong Kong, Thailand, Japan, France, South Korea, and Singapore. Each assay was tested using SARS-CoV-2 as the intended target. All off-target hits (TN, PF, FP) are to entries in NCBI BLAST databases (nt and env_nt).

identifier type PT TP FN Percent True PF FP TN
Noblis.12 Probe 48626 231 216 99.56% 0 0 680
Noblis.40 Probe 47497 1438 138 99.72% 0 1 1420
Noblis.42 Probe 48706 110 257 99.48% 0 2 1136
Noblis.44 Probe 48260 245 568 98.84% 0 1 1786
Noblis.57 Probe 48176 494 403 99.18% 0 1 853
ncov_e_gene Probe 48666 155 252 99.49% 361 15 53
ncov_n_gene Probe 48275 528 270 99.45% 0 340 72
ncov_rdrp_1 Probe 0 48932 141 99.71% 433 105 5967
ncov_rdrp_2 Probe 2 48937 134 99.73% 2 73 5916
cdc_n1 Probe 47644 1306 123 99.75% 0 2 381
cdc_n2 Probe 48037 378 658 98.66% 0 1 372
cdc_n3 Probe 48149 750 174 99.65% 1 353 36
China_N Probe 34411 599 14063 71.34% 0 2 691
China_ORF1ab Probe 46769 465 1839 96.25% 1 0 367
France_nCoV_IP2 Probe 48702 222 149 99.70% 1 0 367
France_nCoV_IP4 Probe 48664 308 101 99.79% 0 0 1190
HKU-N Probe 47944 475 654 98.67% 327 33 34
HKU-ORF1b-nsp14 Probe 48608 304 161 99.67% 324 29 452
Japan_NIID_2019-nCOV_N Probe 0 48394 679 98.62% 0 0 384
Japan_NIID_WH-1_F24381 Outer 48220 591 262 99.47% 0 1 601
Japan_NIID_WH-1_F501 Outer 48001 756 316 99.36% 0 1 370
Japan_NIID_WH-1_F509 Outer 48212 448 413 99.16% 1 0 369
Japan_NIID_WH-1_Seq_F24383 Outer 48209 592 272 99.45% 0 0 606
Japan_NIID_WH-1_Seq_F519 Outer 47901 516 656 98.66% 0 1 369
Japan_WuhanCoV-spk1 Outer 48293 493 287 99.42% 1 1 594
Thailand_WH-NIC_N Probe 48428 513 132 99.73% 0 2 375
Chan-N Probe 48116 302 655 98.67% 4 3 353
Chan-ORF1ab Probe 0 48594 479 99.02% 0 5 2
Chan-S Probe 48050 179 844 98.28% 5 0 2
Niu-E Probe 48553 234 286 99.42% 26 359 0
Won-E Outer 2 48848 223 99.55% 0 384 1
Won-N Outer 47977 868 228 99.54% 8 7 358
Won-ORF1ab Outer 48630 277 166 99.66% 5 2 313
Won-S Outer 47016 353 1704 96.53% 5 1 0
Yip-ORF1ab Outer 48404 204 465 99.05% 5 1 1
Young-N Probe 0 48825 248 99.49% 0 5 1
Young-ORF1ab Probe 48811 155 107 99.78% 5 1 0
Young-S Probe 48298 400 375 99.24% 4 1 0
31

Updated to 54,429 COVID-19 WGS from GISAID.

Table 1. Results from PSET analysis. The five Noblis assays were compared alongside the four assays from Corman and three assays from the CDC. Along with assays from China, Hong Kong, Thailand, Japan, France, South Korea, and Singapore. Each assay was tested using SARS-CoV-2 as the intended target. All off-target hits (TN, PF, FP) are to entries in NCBI BLAST databases (nt and env_nt).

identifier type PT TP FN Percent True PF FP TN
Noblis.12 Probe 53921 230 278 99.49% 0 0 680
Noblis.40 Probe 52753 1525 151 99.72% 0 1 1420
Noblis.42 Probe 54023 118 288 99.47% 0 2 1136
Noblis.44 Probe 53559 260 610 98.88% 0 1 1786
Noblis.57 Probe 53411 528 490 99.10% 0 1 853
ncov_e_gene Probe 53985 168 276 99.49% 361 15 53
ncov_n_gene Probe 53515 597 317 99.42% 0 340 72
ncov_rdrp_1 Probe 0 54274 155 99.72% 433 105 5967
ncov_rdrp_2 Probe 2 54283 144 99.74% 2 73 5916
cdc_n1 Probe 52801 1481 147 99.73% 0 2 381
cdc_n2 Probe 53269 434 726 98.67% 0 1 372
cdc_n3 Probe 53422 807 200 99.63% 1 353 36
China_N Probe 37416 666 16347 69.97% 0 2 691
China_ORF1ab Probe 51819 432 2178 96.00% 1 0 367
France_nCoV_IP2 Probe 54026 226 177 99.67% 1 0 367
France_nCoV_IP4 Probe 53952 366 111 99.80% 0 0 1190
HKU-N Probe 53129 580 720 98.68% 327 33 34
HKU-ORF1b-nsp14 Probe 53922 338 169 99.69% 324 29 452
Japan_NIID_2019-nCOV_N Probe 0 53681 748 98.63% 0 0 384
Japan_NIID_WH-1_F24381 Outer 53440 689 300 99.45% 0 1 601
Japan_NIID_WH-1_F501 Outer 53229 822 378 99.31% 0 1 370
Japan_NIID_WH-1_F509 Outer 53368 597 464 99.15% 1 0 369
Japan_NIID_WH-1_Seq_F24383 Outer 53418 704 307 99.44% 0 0 606
Japan_NIID_WH-1_Seq_F519 Outer 53109 576 744 98.63% 0 1 369
Japan_WuhanCoV-spk1 Outer 53520 602 307 99.44% 1 1 594
Thailand_WH-NIC_N Probe 53610 661 158 99.71% 0 2 375
Chan-N Probe 53373 342 714 98.69% 4 3 353
Chan-ORF1ab Probe 0 53780 649 98.81% 0 5 2
Chan-S Probe 53251 203 975 98.21% 5 0 2
Niu-E Probe 53864 257 308 99.43% 26 359 0
Won-E Outer 2 54183 244 99.55% 0 384 1
Won-N Outer 53103 1060 266 99.51% 8 7 358
Won-ORF1ab Outer 53961 263 205 99.62% 5 2 313
Won-S Outer 52200 179 2050 96.23% 5 1 0
Yip-ORF1ab Outer 53597 210 622 98.86% 5 1 1
Young-N Probe 0 54150 279 99.49% 0 5 1
Young-ORF1ab Probe 54134 179 116 99.79% 5 1 0
Young-S Probe 53562 464 403 99.26% 4 1 0
32

Updated to 60,164 COVID-19 WGS from GISAID.

Table 1. Results from PSET analysis. The five Noblis assays were compared alongside the four assays from Corman and three assays from the CDC. Along with assays from China, Hong Kong, Thailand, Japan, France, South Korea, and Singapore. Each assay was tested using SARS-CoV-2 as the intended target. All off-target hits (TN, PF, FP) are to entries in NCBI BLAST databases (nt and env_nt).

identifier type PT TP FN Percent True PF FP TN
Noblis.12 Probe 59599 263 302 99.50% 0 0 680
Noblis.40 Probe 58388 1604 172 99.71% 0 1 1420
Noblis.42 Probe 59712 137 315 99.48% 0 2 1136
Noblis.44 Probe 59226 284 654 98.91% 0 1 1786
Noblis.57 Probe 59009 577 578 99.04% 0 1 853
ncov_e_gene Probe 59629 189 346 99.42% 361 15 53
ncov_n_gene Probe 59097 705 362 99.40% 0 340 72
ncov_rdrp_1 Probe 0 59967 197 99.67% 433 105 5967
ncov_rdrp_2 Probe 4 59977 183 99.70% 2 73 5916
cdc_n1 Probe 58220 1790 154 99.74% 0 2 381
cdc_n2 Probe 58905 459 800 98.67% 0 1 372
cdc_n3 Probe 59068 872 224 99.63% 1 353 36
China_N Probe 40973 742 18449 69.34% 0 2 691
China_ORF1ab Probe 57344 469 2351 96.09% 1 0 367
France_nCoV_IP2 Probe 59690 247 227 99.62% 1 0 367
France_nCoV_IP4 Probe 59625 407 132 99.78% 0 0 1190
HKU-N Probe 58744 629 791 98.69% 327 33 34
HKU-ORF1b-nsp14 Probe 59603 363 198 99.67% 324 29 452
Japan_NIID_2019-nCOV_N Probe 0 59342 822 98.63% 0 0 384
Japan_NIID_WH-1_F24381 Outer 58889 922 353 99.41% 0 1 601
Japan_NIID_WH-1_F501 Outer 58852 890 422 99.30% 0 1 370
Japan_NIID_WH-1_F509 Outer 58970 681 513 99.15% 1 0 369
Japan_NIID_WH-1_Seq_F24383 Outer 58862 940 362 99.40% 0 0 606
Japan_NIID_WH-1_Seq_F519 Outer 58727 617 820 98.64% 0 1 369
Japan_WuhanCoV-spk1 Outer 58970 831 363 99.40% 1 1 594
Thailand_WH-NIC_N Probe 59498 280 386 99.36% 0 2 375
Chan-N Probe 59277 722 165 99.73% 4 3 353
Chan-ORF1ab Probe 58987 388 789 98.69% 0 5 2
Chan-S Probe 0 59402 762 98.73% 5 0 2
Niu-E Probe 58801 233 1130 98.12% 26 359 0
Won-E Outer 2 59852 310 99.48% 0 384 1
Won-N Outer 58614 1238 312 99.48% 8 7 358
Won-ORF1ab Outer 59635 283 246 99.59% 5 2 313
Won-S Outer 57705 202 2257 96.25% 5 1 0
Yip-ORF1ab Outer 59189 276 699 98.84% 5 1 1
Young-N Probe 0 59862 302 99.50% 0 5 1
Young-ORF1ab Probe 59817 203 144 99.76% 5 1 0
Young-S Probe 59157 558 449 99.25% 4 1 0
33

Updated to 66,862 COVID-19 WGS from GISAID.

Table 1. Results from PSET analysis. The five Noblis assays were compared alongside the four assays from Corman and three assays from the CDC. Along with assays from China, Hong Kong, Thailand, Japan, France, South Korea, and Singapore. Each assay was tested using SARS-CoV-2 as the intended target. All off-target hits (TN, PF, FP) are to entries in NCBI BLAST databases (nt and env_nt).

identifier type PT TP FN Percent True PF FP TN
Noblis.12 Probe 66251 294 317 99.53% 0 0 680
Noblis.40 Probe 64912 1767 183 99.73% 0 1 1420
Noblis.42 Probe 66354 168 340 99.49% 0 2 1136
Noblis.44 Probe 65850 320 692 98.97% 0 1 1786
Noblis.57 Probe 65576 649 637 99.05% 0 1 853
ncov_e_gene Probe 66264 207 391 99.42% 361 15 53
ncov_n_gene Probe 65616 833 413 99.38% 0 340 72
ncov_rdrp_1 Probe 0 66649 213 99.68% 433 105 5967
ncov_rdrp_2 Probe 4 66661 197 99.71% 2 73 5916
cdc_n1 Probe 64689 2008 165 99.75% 0 2 381
cdc_n2 Probe 65479 547 836 98.75% 0 1 372
cdc_n3 Probe 65653 955 254 99.62% 1 353 36
China_N Probe 44961 938 20963 68.65% 0 2 691
China_ORF1ab Probe 63933 505 2424 96.37% 1 0 367
France_nCoV_IP2 Probe 66352 262 248 99.63% 1 0 367
France_nCoV_IP4 Probe 66287 432 143 99.79% 0 0 1190
HKU-N Probe 65338 695 829 98.76% 327 33 34
HKU-ORF1b-nsp14 Probe 66183 465 214 99.68% 324 29 452
Japan_NIID_2019-nCOV_N Probe 0 65999 863 98.71% 0 0 384
Japan_NIID_WH-1_F24381 Outer 65482 995 385 99.42% 0 1 601
Japan_NIID_WH-1_F501 Outer 65425 962 475 99.29% 0 1 370
Japan_NIID_WH-1_F509 Outer 65511 783 568 99.15% 1 0 369
Japan_NIID_WH-1_Seq_F24383 Outer 65455 1009 398 99.40% 0 0 606
Japan_NIID_WH-1_Seq_F519 Outer 65280 665 917 98.63% 0 1 369
Japan_WuhanCoV-spk1 Outer 65594 873 395 99.41% 1 1 594
Thailand_WH-NIC_N Probe 65891 793 178 99.73% 0 2 375
Chan-N Probe 65579 455 828 98.76% 4 3 353
Chan-ORF1ab Probe 0 66049 813 98.78% 0 5 2
Chan-S Probe 65395 254 1213 98.19% 5 0 2
Niu-E Probe 66120 309 433 99.35% 26 359 0
Won-E Outer 2 66514 346 99.48% 0 384 1
Won-N Outer 64929 1572 361 99.46% 8 7 358
Won-ORF1ab Outer 66276 323 263 99.61% 5 2 313
Won-S Outer 64167 220 2475 96.30% 5 1 0
Yip-ORF1ab Outer 65785 325 752 98.88% 5 1 1
Young-N Probe 0 66540 322 99.52% 0 5 1
Young-ORF1ab Probe 66479 228 155 99.77% 5 1 0
Young-S Probe 65727 657 478 99.29% 4 1 0
34

Updated to 70,850 COVID-19 WGS from GISAID.

Table 1. Results from PSET analysis. The five Noblis assays were compared alongside the four assays from Corman and three assays from the CDC. Along with assays from China, Hong Kong, Thailand, Japan, France, South Korea, and Singapore. Each assay was tested using SARS-CoV-2 as the intended target. All off-target hits (TN, PF, FP) are to entries in NCBI BLAST databases (nt and env_nt).

identifier type PT TP FN Percent True PF FP TN
Noblis.12 Probe 70210 313 327 99.54% 0 0 680
Noblis.40 Probe 68817 1832 201 99.72% 0 1 1420
Noblis.42 Probe 70319 181 350 99.51% 0 2 1136
Noblis.44 Probe 69809 339 702 99.01% 0 1 1786
Noblis.57 Probe 69430 686 734 98.96% 0 1 853
ncov_e_gene Probe 70235 218 397 99.44% 361 15 53
ncov_n_gene Probe 69525 865 460 99.35% 0 340 72
ncov_rdrp_1 Probe 0 70626 224 99.68% 433 105 5967
ncov_rdrp_2 Probe 4 70639 207 99.71% 2 73 5916
cdc_n1 Probe 68548 2121 181 99.74% 0 2 381
cdc_n2 Probe 69391 577 882 98.76% 0 1 372
cdc_n3 Probe 69586 981 283 99.60% 1 353 36
China_N Probe 46971 992 22887 67.70% 0 2 691
China_ORF1ab Probe 67843 529 2478 96.50% 1 0 367
France_nCoV_IP2 Probe 70311 286 253 99.64% 1 0 367
France_nCoV_IP4 Probe 70250 453 147 99.79% 0 0 1190
HKU-N Probe 69244 734 872 98.77% 327 33 34
HKU-ORF1b-nsp14 Probe 70118 512 220 99.69% 324 29 452
Japan_NIID_2019-nCOV_N Probe 0 69939 911 98.71% 0 0 384
Japan_NIID_WH-1_F24381 Outer 69319 1074 457 99.35% 0 1 601
Japan_NIID_WH-1_F501 Outer 69317 1007 526 99.26% 0 1 370
Japan_NIID_WH-1_F509 Outer 69394 836 620 99.12% 1 0 369
Japan_NIID_WH-1_Seq_F24383 Outer 69289 1091 470 99.34% 0 0 606
Japan_NIID_WH-1_Seq_F519 Outer 69178 690 982 98.61% 0 1 369
Japan_WuhanCoV-spk1 Outer 69460 921 469 99.34% 1 1 594
Thailand_WH-NIC_N Probe 69818 829 203 99.71% 0 2 375
Chan-N Probe 69487 489 874 98.77% 4 3 353
Chan-ORF1ab Probe 0 70015 835 98.82% 0 5 2
Chan-S Probe 69291 275 1284 98.19% 5 0 2
Niu-E Probe 70086 325 439 99.38% 26 359 0
Won-E Outer 2 70496 352 99.50% 0 384 1
Won-N Outer 68808 1638 404 99.43% 8 7 358
Won-ORF1ab Outer 70240 337 273 99.61% 5 2 313
Won-S Outer 68057 234 2559 96.39% 5 1 0
Yip-ORF1ab Outer 69750 343 757 98.93% 5 1 1
Young-N Probe 0 70498 352 99.50% 0 5 1
Young-ORF1ab Probe 70452 237 161 99.77% 5 1 0
Young-S Probe 69634 704 512 99.28% 4 1 0
35

Updated to 74,584 COVID-19 WGS from GISAID.

Table 1. Results from PSET analysis. The five Noblis assays were compared alongside the four assays from Corman and three assays from the CDC. Along with assays from China, Hong Kong, Thailand, Japan, France, South Korea, and Singapore. Each assay was tested using SARS-CoV-2 as the intended target. All off-target hits (TN, PF, FP) are to entries in NCBI BLAST databases (nt and env_nt).

identifier type PT TP FN Percent True PF FP TN
Noblis.12 Probe 73921 326 337 99.55% 0 0 680
Noblis.40 Probe 72484 1883 217 99.71% 0 1 1420
Noblis.42 Probe 74005 220 359 99.52% 0 2 1136
Noblis.44 Probe 73498 372 714 99.04% 0 1 1786
Noblis.57 Probe 73100 721 763 98.98% 0 1 853
ncov_e_gene Probe 73942 229 413 99.45% 361 15 53
ncov_n_gene Probe 73151 936 497 99.33% 0 340 72
ncov_rdrp_1 Probe 0 74352 232 99.69% 433 105 5967
ncov_rdrp_2 Probe 5 74367 212 99.72% 2 73 5916
cdc_n1 Probe 72089 2311 184 99.75% 0 2 381
cdc_n2 Probe 73090 599 895 98.80% 0 1 372
cdc_n3 Probe 73257 1017 310 99.58% 1 353 36
China_N Probe 48896 1028 24660 66.94% 0 2 691
China_ORF1ab Probe 71449 552 2583 96.54% 1 0 367
France_nCoV_IP2 Probe 74020 306 258 99.65% 1 0 367
France_nCoV_IP4 Probe 73951 484 149 99.80% 0 0 1190
HKU-N Probe 72935 763 886 98.81% 327 33 34
HKU-ORF1b-nsp14 Probe 73809 549 226 99.70% 324 29 452
Japan_NIID_2019-nCOV_N Probe 0 73656 928 98.76% 0 0 384
Japan_NIID_WH-1_F24381 Outer 73011 1101 472 99.37% 0 1 601
Japan_NIID_WH-1_F501 Outer 72976 1056 552 99.26% 0 1 370
Japan_NIID_WH-1_F509 Outer 73053 882 649 99.13% 1 0 369
Japan_NIID_WH-1_Seq_F24383 Outer 72973 1126 485 99.35% 0 0 606
Japan_NIID_WH-1_Seq_F519 Outer 72850 708 1026 98.62% 0 1 369
Japan_WuhanCoV-spk1 Outer 73162 937 485 99.35% 1 1 594
Thailand_WH-NIC_N Probe 73512 865 207 99.72% 0 2 375
Chan-N Probe 73166 526 892 98.80% 4 3 353
Chan-ORF1ab Probe 0 73737 847 98.86% 0 5 2
Chan-S Probe 72979 286 1319 98.23% 5 0 2
Niu-E Probe 73774 356 454 99.39% 26 359 0
Won-E Outer 2 74216 366 99.51% 0 384 1
Won-N Outer 72467 1682 435 99.42% 8 7 358
Won-ORF1ab Outer 73957 351 276 99.63% 5 2 313
Won-S Outer 71568 240 2776 96.28% 5 1 0
Yip-ORF1ab Outer 73398 396 790 98.94% 5 1 1
Young-N Probe 0 74206 378 99.49% 0 5 1
Young-ORF1ab Probe 74123 253 208 99.72% 5 1 0
Young-S Probe 73193 732 659 99.12% 4 1 0
36

Updated to 78,448 COVID-19 WGS from GISAID.

Table 1. Results from PSET analysis. The five Noblis assays were compared alongside the four assays from Corman and three assays from the CDC. Along with assays from China, Hong Kong, Thailand, Japan, France, South Korea, and Singapore. Each assay was tested using SARS-CoV-2 as the intended target. All off-target hits (TN, PF, FP) are to entries in NCBI BLAST databases (nt and env_nt).

identifier type PT TP FN Percent True PF FP TN
Noblis.12 Probe 77728 353 367 99.53% 0 0 680
Noblis.40 Probe 76308 1912 228 99.71% 0 1 1420
Noblis.42 Probe 77815 251 382 99.51% 0 2 1136
Noblis.44 Probe 77296 394 758 99.03% 0 1 1786
Noblis.57 Probe 76873 740 835 98.94% 0 1 853
ncov_e_gene Probe 77757 241 450 99.43% 361 15 53
ncov_n_gene Probe 76826 1001 621 99.21% 0 340 72
ncov_rdrp_1 Probe 0 78186 262 99.67% 433 105 5967
ncov_rdrp_2 Probe 6 78206 236 99.70% 2 73 5916
cdc_n1 Probe 75749 2467 232 99.70% 0 2 381
cdc_n2 Probe 76688 741 1019 98.70% 0 1 372
cdc_n3 Probe 76988 1051 409 99.48% 1 353 36
China_N Probe 51505 1174 25769 67.15% 0 2 691
China_ORF1ab Probe 75229 569 2650 96.62% 1 0 367
France_nCoV_IP2 Probe 77832 317 299 99.62% 1 0 367
France_nCoV_IP4 Probe 77782 505 161 99.79% 0 0 1190
HKU-N Probe 76513 925 1010 98.71% 327 33 34
HKU-ORF1b-nsp14 Probe 77636 578 234 99.70% 324 29 452
Japan_NIID_2019-nCOV_N Probe 0 77390 1058 98.65% 0 0 384
Japan_NIID_WH-1_F24381 Outer 76797 1124 527 99.33% 0 1 601
Japan_NIID_WH-1_F501 Outer 76694 1098 656 99.16% 0 1 370
Japan_NIID_WH-1_F509 Outer 76776 918 754 99.04% 1 0 369
Japan_NIID_WH-1_Seq_F24383 Outer 76760 1147 541 99.31% 0 0 606
Japan_NIID_WH-1_Seq_F519 Outer 76571 734 1143 98.54% 0 1 369
Japan_WuhanCoV-spk1 Outer 76953 957 538 99.31% 1 1 594
Thailand_WH-NIC_N Probe 77290 899 259 99.67% 0 2 375
Chan-N Probe 76864 559 1025 98.69% 4 3 353
Chan-ORF1ab Probe 0 77546 902 98.85% 0 5 2
Chan-S Probe 76691 310 1447 98.16% 5 0 2
Niu-E Probe 77581 374 493 99.37% 26 359 0
Won-E Outer 2 78050 396 99.50% 0 384 1
Won-N Outer 76166 1736 546 99.30% 8 7 358
Won-ORF1ab Outer 77779 373 296 99.62% 5 2 313
Won-S Outer 75218 251 2979 96.20% 5 1 0
Yip-ORF1ab Outer 77187 409 852 98.91% 5 1 1
Young-N Probe 0 77962 486 99.38% 0 5 1
Young-ORF1ab Probe 77900 326 222 99.72% 5 1 0
Young-S Probe 76962 767 719 99.08% 4 1 0
37

Updated to 81,375 COVID-19 WGS from GISAID.

Table 1. Results from PSET analysis. The five Noblis assays were compared alongside the four assays from Corman and three assays from the CDC. Along with assays from China, Hong Kong, Thailand, Japan, France, South Korea, and Singapore. Each assay was tested using SARS-CoV-2 as the intended target. All off-target hits (TN, PF, FP) are to entries in NCBI BLAST databases (nt and env_nt).

identifier type PT TP FN Percent True PF FP TN
Noblis.12 Probe 80629 375 371 99.54% 0 0 680
Noblis.40 Probe 79217 1929 229 99.72% 0 1 1420
Noblis.42 Probe 80711 279 385 99.53% 0 2 1136
Noblis.44 Probe 80193 416 766 99.06% 0 1 1786
Noblis.57 Probe 79696 795 884 98.91% 0 1 853
ncov_e_gene Probe 80662 253 460 99.43% 361 15 53
ncov_n_gene Probe 79688 1040 647 99.20% 0 340 72
ncov_rdrp_1 Probe 0 81109 266 99.67% 433 105 5967
ncov_rdrp_2 Probe 6 81129 240 99.71% 2 73 5916
cdc_n1 Probe 78614 2517 244 99.70% 0 2 381
cdc_n2 Probe 79527 773 1075 98.68% 0 1 372
cdc_n3 Probe 79854 1095 426 99.48% 1 353 36
China_N Probe 53206 1218 26951 66.88% 0 2 691
China_ORF1ab Probe 78024 586 2765 96.60% 1 0 367
France_nCoV_IP2 Probe 80744 326 305 99.63% 1 0 367
France_nCoV_IP4 Probe 80688 521 166 99.80% 0 0 1190
HKU-N Probe 79290 1012 1073 98.68% 327 33 34
HKU-ORF1b-nsp14 Probe 80555 585 235 99.71% 324 29 452
Japan_NIID_2019-nCOV_N Probe 0 80250 1125 98.62% 0 0 384
Japan_NIID_WH-1_F24381 Outer 79663 1175 537 99.34% 0 1 601
Japan_NIID_WH-1_F501 Outer 79542 1149 684 99.16% 0 1 370
Japan_NIID_WH-1_F509 Outer 79641 953 781 99.04% 1 0 369
Japan_NIID_WH-1_Seq_F24383 Outer 79624 1200 551 99.32% 0 0 606
Japan_NIID_WH-1_Seq_F519 Outer 79428 769 1178 98.55% 0 1 369
Japan_WuhanCoV-spk1 Outer 79824 1003 548 99.33% 1 1 594
Thailand_WH-NIC_N Probe 80166 938 271 99.67% 0 2 375
Chan-N Probe 79664 622 1089 98.66% 4 3 353
Chan-ORF1ab Probe 0 80465 910 98.88% 0 5 2
Chan-S Probe 79578 317 1480 98.18% 5 0 2
Niu-E Probe 80483 387 505 99.38% 26 359 0
Won-E Outer 2 80967 406 99.50% 0 384 1
Won-N Outer 79037 1767 571 99.30% 8 7 358
Won-ORF1ab Outer 80690 385 300 99.63% 5 2 313
Won-S Outer 77946 263 3166 96.11% 5 1 0
Yip-ORF1ab Outer 80055 433 887 98.91% 5 1 1
Young-N Probe 0 80875 500 99.39% 0 5 1
Young-ORF1ab Probe 80786 362 227 99.72% 5 1 0
Young-S Probe 79676 802 897 98.90% 4 1 0
38

Updated to 155,090 COVID-19 WGS from GISAID.

Table 1. Results from PSET analysis. The five Noblis assays were compared alongside the four assays from Corman and three assays from the CDC. Along with assays from China, Hong Kong, Thailand, Japan, France, South Korea, and Singapore. Each assay was tested using SARS-CoV-2 as the intended target. All off-target hits (TN, PF, FP) are to entries in NCBI BLAST databases (nt and env_nt).

identifier type PT TP FN Percent True PF FP TN
Noblis.12 Probe 151389 3124 577 99.63% 0 0 680
Noblis.40 Probe 151690 2939 461 99.70% 0 1 1420
Noblis.42 Probe 153741 685 664 99.57% 0 2 1136
Noblis.44 Probe 152825 1123 1142 99.26% 0 1 1786
Noblis.57 Probe 151126 1667 2297 98.52% 0 1 853
ncov_e_gene Probe 153740 484 866 99.44% 361 15 53
ncov_n_gene Probe 149783 3679 1628 98.95% 0 340 72
ncov_rdrp_1 Probe 0 154278 812 99.48% 433 105 5967
ncov_rdrp_2 Probe 8 154308 774 99.50% 2 73 5916
cdc_n1 Probe 150613 4099 378 99.76% 0 2 381
cdc_n2 Probe 149756 3617 1717 98.89% 0 1 372
cdc_n3 Probe 152268 2067 755 99.51% 1 353 36
China_N Probe 89180 3746 62164 59.92% 0 2 691
China_ORF1ab Probe 149836 960 4294 97.23% 1 0 367
France_nCoV_IP2 Probe 153767 779 544 99.65% 1 0 367
France_nCoV_IP4 Probe 153580 1190 320 99.79% 0 0 1190
HKU-N Probe 151013 2353 1724 98.89% 327 33 34
HKU-ORF1b-nsp14 Probe 152940 1810 340 99.78% 324 29 452
Japan_NIID_2019-nCOV_N Probe 0 153281 1809 98.83% 0 0 384
Japan_NIID_WH-1_F24381 Outer 151755 1856 1479 99.05% 0 1 601
Japan_NIID_WH-1_F501 Outer 152321 1804 965 99.38% 0 1 370
Japan_NIID_WH-1_F509 Outer 151285 2736 1069 99.31% 1 0 369
Japan_NIID_WH-1_Seq_F24383 Outer 151705 1890 1495 99.04% 0 0 606
Japan_NIID_WH-1_Seq_F519 Outer 151813 1536 1741 98.88% 0 1 369
Japan_WuhanCoV-spk1 Outer 152152 1440 1498 99.03% 1 1 594
Thailand_WH-NIC_N Probe 152416 2258 416 99.73% 0 2 375
Chan-N Probe 150115 3213 1762 98.86% 4 3 353
Chan-ORF1ab Probe 2 153697 1391 99.10% 0 5 2
Chan-S Probe 152099 677 2314 98.51% 5 0 2
Niu-E Probe 152976 1191 923 99.40% 26 359 0
Won-E Outer 5 154304 781 99.50% 0 384 1
Won-N Outer 149757 3865 1468 99.05% 8 7 358
Won-ORF1ab Outer 153513 745 832 99.46% 5 2 313
Won-S Outer 147646 679 6765 95.64% 5 1 0
Yip-ORF1ab Outer 152311 1110 1669 98.92% 5 1 1
Young-N Probe 0 154189 901 99.42% 0 5 1
Young-ORF1ab Probe 151420 2980 690 99.56% 5 1 0
Young-S Probe 150084 2610 2396 98.46% 4 1 0
40

Updated to 429,535 COVID-19 WGS from GISAID.

Table 1. Results from PSET analysis. The five Noblis assays were compared alongside the four assays from Corman and three assays from the CDC. Along with assays from China, Hong Kong, Thailand, Japan, France, South Korea, and Singapore. Each assay was tested using SARS-CoV-2 as the intended target. All off-target hits (TN, PF, FP) are to entries in NCBI BLAST databases (nt and env_nt). *edited 2/2 to include 5 additional assays.

Assay type PT TP FN Percent True PF FP TN
Noblis.12 Probe 418132 9890 1513 99.65% 0 0 680
Noblis.40 Probe 422357 6189 989 99.77% 0 1 1420
Noblis.42 Probe 425135 3027 1373 99.68% 0 2 1136
Noblis.44 Probe 423566 3726 2243 99.48% 0 1 1786
Noblis.57 Probe 420120 4728 4687 98.91% 0 1 853
ncov_e_gene Probe 425568 1533 2434 99.43% 361 15 53
ncov_n_gene Probe 412931 12717 3887 99.10% 0 340 72
ncov_rdrp_1 Probe 0 427853 1682 99.61% 433 105 5967
ncov_rdrp_2 Probe 15 428021 1499 99.65% 2 73 5916
cdc_n1 Probe 413781 14665 1089 99.75% 0 2 381
cdc_n2 Probe 413697 12867 2971 99.31% 0 1 372
cdc_n3 Probe 415446 12633 1456 99.66% 1 353 36
China_N Probe 250112 23943 155480 63.80% 0 2 691
China_ORF1ab Probe 417104 3245 9186 97.86% 1 0 367
France_nCoV_IP2 Probe 424068 3058 2409 99.44% 1 0 367
France_nCoV_IP4 Probe 423557 5197 781 99.82% 0 0 1190
HKU-N Probe 416560 9882 3093 99.28% 327 33 34
HKU-ORF1b-nsp14 Probe 425082 3616 837 99.81% 324 29 452
Japan_NIID_2019-nCOV_N Probe 0 426277 3258 99.24% 0 0 384
Japan_NIID_WH-1_F24381 Outer 421243 5282 3010 99.30% 0 1 601
Japan_NIID_WH-1_F501 Outer 422571 4379 2585 99.40% 0 1 370
Japan_NIID_WH-1_F509 Outer 419030 7716 2789 99.35% 1 0 369
Japan_NIID_WH-1_Seq_F24383 Outer 421039 5450 3046 99.29% 0 0 606
Japan_NIID_WH-1_Seq_F519 Outer 418816 4946 5773 98.66% 0 1 369
Japan_WuhanCoV-spk1 Outer 423033 3482 3020 99.30% 1 1 594
Thailand_WH-NIC_N Probe 420302 8063 1170 99.73% 0 2 375
Chan-N Probe 414334 11996 3205 99.25% 4 3 353
Chan-ORF1ab Probe 5 424942 4588 98.93% 0 5 2
Chan-S Probe 420124 3359 6052 98.59% 5 0 2
Niu-E Probe 422447 4543 2545 99.41% 26 359 0
Won-E Outer 6 427327 2202 99.49% 0 384 1
Won-N Outer 416703 9242 3590 99.16% 8 7 358
Won-ORF1ab Outer 425905 2027 1603 99.63% 5 2 313
Won-S Outer 411918 2402 15215 96.46% 5 1 0
Yip-ORF1ab Outer 421949 3155 4431 98.97% 5 1 1
Young-N Probe 1 428083 1451 99.66% 0 5 1
Young-ORF1ab Probe 420062 8220 1253 99.71% 5 1 0
Young-S Probe 367410 13478 48647 88.67% 4 1 0
C1_COV_ORF1a Probe 411789 6109 11637 97.29% 0 0 0
C2_COV_ORF1b Probe 417280 10607 1648 99.62% 0 0 0
C3_COV_ORF3a Probe 385590 31374 12571 97.07% 0 0 0
C4_COV_ORF8 Probe 371318 51082 7135 98.34% 0 0 0
C5_COV_S_gene Probe 421619 5116 2800 99.35% 0 0 0
41

Updated to 466,524 COVID-19 WGS from GISAID.

Table 1. Results from PSET analysis. The five Noblis assays were compared alongside the four assays from Corman and three assays from the CDC. Along with assays from China, Hong Kong, Thailand, Japan, France, South Korea, and Singapore. Each assay was tested using SARS-CoV-2 as the intended target. All off-target hits (TN, PF, FP) are to entries in NCBI BLAST databases (nt and env_nt). *edited 2/2 to include 5 additional assays.

Assay PT TP FN Percent True PF FP TN
Noblis.12 454125 10499 1900 99.59% 0 0 680
Noblis.40 458704 6644 1176 99.75% 0 1 1420
Noblis.42 461350 3393 1781 99.62% 0 2 1136
Noblis.44 459680 4097 2747 99.41% 0 1 1786
Noblis.57 455564 5232 5728 98.77% 0 1 853
ncov_e_gene 461926 1752 2846 99.39% 361 15 53
ncov_n_gene 448606 13640 4278 99.08% 0 340 72
ncov_rdrp_1 0 464006 2518 99.46% 433 105 5967
ncov_rdrp_2 16 464254 2254 99.52% 2 73 5916
cdc_n1 449212 15919 1393 99.70% 0 2 381
cdc_n2 449423 13796 3305 99.29% 0 1 372
cdc_n3 448548 16074 1902 99.59% 1 353 36
China_N 263858 28328 174338 62.63% 0 2 691
China_ORF1ab 452935 3603 9986 97.86% 1 0 367
France_nCoV_IP2 460117 3537 2870 99.38% 1 0 367
France_nCoV_IP4 459488 5955 1081 99.77% 0 0 1190
HKU-N 452261 10734 3529 99.24% 327 33 34
HKU-ORF1b-nsp14 461355 3951 1218 99.74% 324 29 452
Japan_NIID_2019-nCOV_N 0 462783 3741 99.20% 0 0 384
Japan_NIID_WH-1_F24381 456883 5750 3891 99.17% 0 1 601
Japan_NIID_WH-1_F501 458829 4663 3032 99.35% 0 1 370
Japan_NIID_WH-1_F509 455000 8305 3219 99.31% 1 0 369
Japan_NIID_WH-1_Seq_F24383 456677 5914 3933 99.16% 0 0 606
Japan_NIID_WH-1_Seq_F519 454746 5480 6298 98.65% 0 1 369
Japan_WuhanCoV-spk1 458563 4051 3910 99.16% 1 1 594
Thailand_WH-NIC_N 456149 8902 1473 99.68% 0 2 375
Chan-N 449760 13098 3666 99.21% 4 3 353
Chan-ORF1ab 5 461374 5145 98.90% 0 5 2
Chan-S 455718 3978 6828 98.54% 5 0 2
Niu-E 458497 5053 2974 99.36% 26 359 0
Won-E 7 463939 2578 99.45% 0 384 1
Won-N 452543 10040 3941 99.16% 8 7 358
Won-ORF1ab 461759 2445 2320 99.50% 5 2 313
Won-S 447723 2713 16088 96.55% 5 1 0
Yip-ORF1ab 458076 3477 4971 98.93% 5 1 1
Young-N 1 464658 1865 99.60% 0 5 1
Young-ORF1ab 456396 8564 1564 99.66% 5 1 0
Young-S 392575 15258 58691 87.42% 4 1 0
C1_COV_ORF1a 447079 6777 12668 97.28% 0 0 0
C2_COV_ORF1b 452758 11713 2053 99.56% 0 0 0
C3_COV_ORF3a 415896 37202 13426 97.12% 0 0 0
C4_COV_ORF8 397705 60858 7961 98.29% 0 0 0
C5_COV_S_gene 457226 5598 3700 99.21% 0 0 0
42

Updated to 507,323 COVID-19 WGS from GISAID.

Table 1. Results from PSET analysis. The five Noblis assays were compared alongside the four assays from Corman and three assays from the CDC. Along with assays from China, Hong Kong, Thailand, Japan, France, South Korea, and Singapore. Each assay was tested using SARS-CoV-2 as the intended target. All off-target hits (TN, PF, FP) are to entries in NCBI BLAST databases (nt and env_nt). *edited 2/2 to include 5 additional assays.

assay PT TP FN Percent True PF FP TN
Noblis.12 494230 11101 1992 99.61% 0 0 680
Noblis.40 499141 6954 1228 99.76% 0 1 1420
Noblis.42 501587 3845 1891 99.63% 0 2 1136
Noblis.44 499889 4450 2984 99.41% 0 1 1786
Noblis.57 495554 5690 6079 98.80% 0 1 853
ncov_e_gene 502382 1902 3039 99.40% 361 15 53
ncov_n_gene 488006 14617 4700 99.07% 0 340 72
ncov_rdrp_1 0 504677 2646 99.48% 433 105 5967
ncov_rdrp_2 16 504957 2350 99.54% 2 73 5916
cdc_n1 488471 17396 1456 99.71% 0 2 381
cdc_n2 488978 14940 3405 99.33% 0 1 372
cdc_n3 488204 17106 2013 99.60% 1 353 36
China_N 279059 31342 196922 61.18% 0 2 691
China_ORF1ab 492603 4055 10665 97.90% 1 0 367
France_nCoV_IP2 500117 3999 3207 99.37% 1 0 367
France_nCoV_IP4 498969 7209 1145 99.77% 0 0 1190
HKU-N 491804 11889 3630 99.28% 327 33 34
HKU-ORF1b-nsp14 501877 4181 1265 99.75% 324 29 452
Japan_NIID_2019-nCOV_N 0 503471 3852 99.24% 0 0 384
Japan_NIID_WH-1_F24381 496921 6295 4107 99.19% 0 1 601
Japan_NIID_WH-1_F501 499044 5044 3235 99.36% 0 1 370
Japan_NIID_WH-1_F509 494915 8978 3430 99.32% 1 0 369
Japan_NIID_WH-1_Seq_F24383 496682 6491 4150 99.18% 0 0 606
Japan_NIID_WH-1_Seq_F519 494624 6040 6659 98.69% 0 1 369
Japan_WuhanCoV-spk1 498900 4290 4133 99.19% 1 1 594
Thailand_WH-NIC_N 495941 9848 1534 99.70% 0 2 375
Chan-N 489511 14036 3776 99.26% 4 3 353
Chan-ORF1ab 6 501750 5567 98.90% 0 5 2
Chan-S 495106 4758 7459 98.53% 5 0 2
Niu-E 498719 5429 3175 99.37% 26 359 0
Won-E 7 504559 2757 99.46% 0 384 1
Won-N 492335 10637 4351 99.14% 8 7 358
Won-ORF1ab 502141 2742 2440 99.52% 5 2 313
Won-S 487318 3020 16985 96.65% 5 1 0
Yip-ORF1ab 498221 3849 5253 98.96% 5 1 1
Young-N 1 505333 1989 99.61% 0 5 1
Young-ORF1ab 496665 8997 1661 99.67% 5 1 0
Young-S 411307 16905 79111 84.41% 4 1 0
C1_COV_ORF1a 485703 7396 14224 97.20% 0 0 0
C2_COV_ORF1b 492279 12891 2153 99.58% 0 0 0
C3_COV_ORF3a 450634 41962 14727 97.10% 0 0 0
C4_COV_ORF8 417307 81555 8461 98.33% 0 0 0
C5_COV_S_gene 496985 6416 3922 99.23% 0 0 0
43

Updated to 565,366 COVID-19 WGS from GISAID.

Table 1. Results from PSET analysis. The five Noblis assays were compared alongside the four assays from Corman and three assays from the CDC. Along with assays from China, Hong Kong, Thailand, Japan, France, South Korea, and Singapore. Each assay was tested using SARS-CoV-2 as the intended target. All off-target hits (TN, PF, FP) are to entries in NCBI BLAST databases (nt and env_nt). *edited 2/2 to include 5 additional assays.

assay PT TP FN Percent True PF FP TN
Noblis.12 550666 12329 2371 99.58% 0 0 680
Noblis.40 556093 7876 1397 99.75% 0 1 1420
Noblis.42 557860 4643 2863 99.49% 0 2 1136
Noblis.44 555976 5236 4154 99.27% 0 1 1786
Noblis.57 550426 6426 8514 98.49% 0 1 853
ncov_e_gene 559501 2135 3730 99.34% 361 15 53
ncov_n_gene 543949 15931 5486 99.03% 0 340 72
ncov_rdrp_1 0 560329 5037 99.11% 433 105 5967
ncov_rdrp_2 16 560651 4699 99.17% 2 73 5916
cdc_n1 542650 19854 2862 99.49% 0 2 381
cdc_n2 542621 17193 5552 99.02% 0 1 372
cdc_n3 543000 19063 3303 99.42% 1 353 36
China_N 301247 39356 224763 60.24% 0 2 691
China_ORF1ab 547989 4790 12587 97.77% 1 0 367
France_nCoV_IP2 556064 4682 4620 99.18% 1 0 367
France_nCoV_IP4 554800 8835 1731 99.69% 0 0 1190
HKU-N 545445 14138 5783 98.98% 327 33 34
HKU-ORF1b-nsp14 558319 4608 2439 99.57% 324 29 452
Japan_NIID_2019-nCOV_N 0 559362 6004 98.94% 0 0 384
Japan_NIID_WH-1_F24381 551867 7153 6346 98.88% 0 1 601
Japan_NIID_WH-1_F501 555798 5516 4052 99.28% 0 1 370
Japan_NIID_WH-1_F509 551045 10081 4240 99.25% 1 0 369
Japan_NIID_WH-1_Seq_F24383 551598 7371 6397 98.87% 0 0 606
Japan_NIID_WH-1_Seq_F519 548791 6863 9712 98.28% 0 1 369
Japan_WuhanCoV-spk1 554212 4769 6385 98.87% 1 1 594
Thailand_WH-NIC_N 551265 11160 2941 99.48% 0 2 375
Chan-N 543747 15662 5957 98.95% 4 3 353
Chan-ORF1ab 9 558836 6521 98.85% 0 5 2
Chan-S 550675 5931 8760 98.45% 5 0 2
Niu-E 555439 6058 3869 99.32% 26 359 0
Won-E 7 561958 3401 99.40% 0 384 1
Won-N 548247 12021 5098 99.10% 8 7 358
Won-ORF1ab 557321 3243 4802 99.15% 5 2 313
Won-S 543572 3507 18287 96.77% 5 1 0
Yip-ORF1ab 554920 4405 6041 98.93% 5 1 1
Young-N 1 562014 3351 99.41% 0 5 1
Young-ORF1ab 553503 9608 2255 99.60% 5 1 0
Young-S 442944 19378 103044 81.77% 4 1 0
C1_COV_ORF1a 541039 8523 15804 97.20% 0 0 0
C2_COV_ORF1b 547608 14381 3377 99.40% 0 0 0
C3_COV_ORF3a 497339 51945 16082 97.16% 0 0 0
C4_COV_ORF8 449151 105492 10723 98.10% 0 0 0
C5_COV_S_gene 551794 7443 6129 98.92% 0 0 0
44

Updated to 612,842 COVID-19 WGS from GISAID.

Table 1. Results from PSET analysis. The five Noblis assays were compared alongside the four assays from Corman and three assays from the CDC. Along with assays from China, Hong Kong, Thailand, Japan, France, South Korea, and Singapore. Each assay was tested using SARS-CoV-2 as the intended target. All off-target hits (TN, PF, FP) are to entries in NCBI BLAST databases (nt and env_nt). *edited 2/2 to include 5 additional assays.

assay PT TP FN Percent True PF FP TN
Noblis.12 596946 13235 2661 99.57% 0 0 680
Noblis.40 602916 8385 1541 99.75% 0 1 1420
Noblis.42 604096 5144 3602 99.41% 0 2 1136
Noblis.44 602167 5733 4942 99.19% 0 1 1786
Noblis.57 593816 7120 11906 98.06% 0 1 853
ncov_e_gene 606416 2315 4111 99.33% 361 15 53
ncov_n_gene 589936 17083 5823 99.05% 0 340 72
ncov_rdrp_1 0 604088 8754 98.57% 433 105 5967
ncov_rdrp_2 16 604437 8389 98.63% 2 73 5916
cdc_n1 586474 21564 4804 99.22% 0 2 381
cdc_n2 587540 18886 6416 98.95% 0 1 372
cdc_n3 587035 20532 5275 99.14% 1 353 36
China_N 318368 45327 249147 59.35% 0 2 691
China_ORF1ab 592185 5331 15326 97.50% 1 0 367
France_nCoV_IP2 600416 5429 6997 98.86% 1 0 367
France_nCoV_IP4 600711 10173 1958 99.68% 0 0 1190
HKU-N 590470 15731 6641 98.92% 327 33 34
HKU-ORF1b-nsp14 603677 4979 4186 99.32% 324 29 452
Japan_NIID_2019-nCOV_N 0 606145 6697 98.91% 0 0 384
Japan_NIID_WH-1_F24381 595210 7927 9705 98.42% 0 1 601
Japan_NIID_WH-1_F501 602499 6049 4294 99.30% 0 1 370
Japan_NIID_WH-1_F509 596590 11765 4487 99.27% 1 0 369
Japan_NIID_WH-1_Seq_F24383 594996 8081 9765 98.41% 0 0 606
Japan_NIID_WH-1_Seq_F519 594146 7711 10985 98.21% 0 1 369
Japan_WuhanCoV-spk1 597924 5169 9749 98.41% 1 1 594
Thailand_WH-NIC_N 595999 11955 4888 99.20% 0 2 375
Chan-N 588910 17108 6824 98.89% 4 3 353
Chan-ORF1ab 14 605287 7541 98.77% 0 5 2
Chan-S 596453 7013 9376 98.47% 5 0 2
Niu-E 601941 6656 4245 99.31% 26 359 0
Won-E 7 609067 3768 99.39% 0 384 1
Won-N 594453 12997 5392 99.12% 8 7 358
Won-ORF1ab 600687 3632 8523 98.61% 5 2 313
Won-S 589287 3934 19621 96.80% 5 1 0
Yip-ORF1ab 601244 4865 6733 98.90% 5 1 1
Young-N 1 607495 5346 99.13% 0 5 1
Young-ORF1ab 600138 10183 2521 99.59% 5 1 0
Young-S 465509 21589 125744 79.48% 4 1 0
C1_COV_ORF1a 586139 9589 17114 97.21% 0 0 0
C2_COV_ORF1b 591979 15595 5268 99.14% 0 0 0
C3_COV_ORF3a 534775 61016 17051 97.22% 0 0 0
C4_COV_ORF8 471704 127922 13216 97.84% 0 0 0
C5_COV_S_gene 595102 8416 9324 98.48% 0 0 0