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 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