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 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