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

PSET results updated with new 2019-nCoV genomes; 655 total genomes. Just using the subset of genomes on GISAID marked as high quality sampled from humans. Sequence IDs tested in this analysis listed here: 655_ids.zip (1.4 KB)

Previous Noblis assays showed some false negatives due to Ns, sequence gaps, and in one case the assay’s position at the very start of the genome. These have been replaced with five new assays generated at a later date using 96 complete genomes. The Noblis.57 assay and the German ncov_e_gene assay each have one FN that’s due to a stretch of Ns. All other assays still performing very well in silico against new sequences.

Table 1. Results from PSET analysis. The five Noblis assays were compared alongside the four assays from Corman and three assays from the CDC. Each assay was tested using 2019-nCoV (655 genomes) as the intended target. All off-target hits (TN, PF, FP) are to entries in NCBI BLAST databases (nt, gss, and env_nt).

identifier provider PT TP TN PF FP FN
Noblis.12 Noblis 653 2 2 0 0 0
Noblis.40 Noblis 635 20 316 0 0 0
Noblis.42 Noblis 655 0 275 0 0 0
Noblis.44 Noblis 655 0 277 0 0 0
Noblis.57 Noblis 654 0 359 0 0 1
ncov_e_gene Corman et al 651 3 42 353 15 1
ncov_n_gene Corman et al 652 3 55 0 339 0
ncov_rdrp_1 Corman et al 0 655 75 433 87 0
ncov_rdrp_2 Corman et al 1 654 526 1 66 0
cdc_n1 CDC 647 8 363 0 0 0
cdc_n2 CDC 653 2 361 0 0 0
cdc_n3 CDC 628 27 17 0 346 0

Figure 1. Map of the SARS-CoV-2 genome (NCBI Accession: MN908947.3) with assay signature locations (created using DNA Features Viewer Python library). Noblis assays in red, Corman assays in blue, CDC assays in purple, and gene regions in green.