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

Using next generation sequencing, the whole genome sequence (WGS) of SARS-CoV-2 134 are continuously being released and shared (306 complete genomes as of March 09, 2020) with 135 the entire research community through Global Initiative on Sharing All Influenza Data (GISAID) 136 [31]. The release of WGS allowed us to test the BioLaboro pipeline (described in this study) to 137 evaluate currently used diagnostic assays and to rapidly design new assays. 138 In a previous study, we described a bioinformatics tool called PSET (PCR signature 139 erosion tool) and used it to show in silico, confirmed with wet lab work, the effectiveness of 140 existing Ebolavirus diagnostic assays against a large number of sequences available at that time 141 [32]. The phrase "signature erosion" used here signifies potential false-positive or false-negative 142 results in PCR assays due to mutations in the primers, probe, or amplicon target sequences (PCR 143 signatures). Signature erosion could also mean failure of medical countermeasures; for example, 144 a change in the genomic sequence resulting in an amino acid change that could potentially alter 145 the efficacy of sequence-based therapeutics [33, 34] . 146 In this study, we describe an expanded bioinformatics pipeline called BioLaboro in which 147 we have integrated several tools: BioVelocity®, Primer3 and PSET for end-to-end analysis of 148 outbreak pathogen genome sequences to evaluate existing PCR assay efficacy against the new 149 sequences, and to identify unique signature regions (BioVelocity), design PCR assays to these