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 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