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

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