BioLaboro: A bioinformatics system for detecting molecular assay signature erosion and designing new assays in response to emerging and reemerging pathogens

Mitchell Holland; Daniel Negrón; Shane Mitchell; Nate Dellinger; Mychal Ivancich; Tyler Barrus; Sterling Thomas; Katharine W. Jennings; Bruce Goodwin; Shanmuga Sozhamannan

Ninety six complete SARS-CoV-2 whole genome sequences were downloaded from the GISAID 282 and uploaded to BioLaboro as a custom database. These 96 genomes were used as our reference 283 set and EPI_ISL_404253 (Genbank ID: MN988713.1) was used as the algorithmic reference 284 . CC-BY-NC-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.08.031963 doi: bioRxiv preprint sequence. The algorithmic reference sequence was first split into k-mers of 50 bps each using a 285 sliding window of 1 bp, which amounted to 29,833 k-mers to be evaluated with the conserved 286 sequence detection algorithm. BioVelocity found 79% (23,542) of these k-mers to be conserved 287 in all 96 of the SARS-CoV-2 genomes. The conserved k-mers were then evaluated to determine 288 overlapping segments and were combined into 96 conserved contigs. These contigs were next 289 evaluated with BioVelocity's signature sequence detection algorithm. The contigs were split into Table 5 . In the second phase, Primer3 was used to identify potential primer pairs and probes for 302 generating new PCR detection assays as described above for BOMV. There were 330 primer 303 sets created from the signatures which were assigned a penalty score to facilitate comparison of 304 the results. Primer sets were sorted by lowest penalty score and five potential assays were chosen 305 . CC-BY-NC-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.08.031963 doi: bioRxiv preprint manually in order to distribute potential candidates across the genome. These assays were then 306 formatted and sent to the final step for validation using PSET. Primer sets sent to PSET are 307 shown in Table 6 . 308 Table 6 Legend: The five new assays identified by Primer3 ranked by lowest penalty score. The