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 the in silico methods described here, only two of the 30 EBOV rRT-PCR assays evaluated 396 against BOMV target sequences met our criteria for successful detection and neither showed 397 perfect matches. For ongoing biosurveillance, we recommend wet lab testing and validation of 398 the rRT-PCR assays described here to ensure detection of BOMV. 399 We also tested the BioLaboro pipeline with available SARS-CoV-2 viral genomes and The copyright holder for this preprint (which was not peer-reviewed) is the .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 contains less than 10 SNPs with the exception of one having 25. None of the variations impact 412 the diagnostic assay signatures. However, real-time monitoring of these assays against WGS as 413 they become available, will enable rapid identification of signature erosion if it occurs and 414 generation of new assays as needed. The newly designed assays we have described here need to 415 be validated in wet lab testing and with appropriate clinical matrices to determine their 416 performance. However, we have demonstrated that the BioLaboro pipeline can be used 417 effectively and rapidly to validate available assays and to design new assays using genome 418 sequences of newly emerging pathogens.