Rice University computer scientist Todd Treangen and his bioinformatics group are collaborating with Great Basin Scientific, a molecular diagnostics company, to optimize the design and computational evaluation of molecular detection assays for the SARS-CoV-2 viral RNA, the pathogen that causes COVID-19. The aim of the co-development partnership is to streamline development and commercialization of robust and genetically stable COVID-19 testing.

Treangen, an assistant professor of computer science in Rice’s George R. Brown School of Engineering, is co-lead of COV-IRT, the COVID-19 International Research Team, which recently held its 2nd international symposium on the latest COVID-19 breakthroughs.

The Treangen lab COVID-19 diagnostics team, led by PhD student Nicolae Sapoval, postdoctoral scientist Leo Elworth and Treangen, has developed novel bioinformatics software called OliVar, which allows researchers and assay developers to automate and design assays that target regions of the virus genome that have the lowest frequency of mutation. The software aids in designing high-quality molecular detection assays specifically targeted to the regions of high genomic stability. The ability to identify stable genomic regions helps ensure test longevity and robustness for viral genomes that mutate often and evolve rapidly in nature. Additional OliVar team members include software engineer Bryce Kille and PhD students Yunxi Liu and Yilei Fu.

"This exciting collaboration with Great Basin will allow for computational methods and software developed in my research group to directly contribute to fast, sensitive, and affordable detection and monitoring of SARS-CoV-2 and emerging pathogens," Treangen said.

Great Basin is using primer and probe designs generated in silico using Olivar to further optimize, test, validate and incorporate into the Great Basin SARS-CoV-2 Direct Test, an RT-PCR based test that detects SARS-CoV-2 RNA directly from upper respiratory patient specimens. The Great Basin SARS-CoV-2 Direct Test is in late-stage development, and the company is expected to submit the test to the Food and Drug Administration later this year for Emergency Use Approval authorization.