COVID-19 Genome Sequencing Response MSU-MI-SAPPHIRE (Year 3)

Michigan State University’s MI-SAPPHIRE effort, a multi-institutional, state-supported initiative created by the Michigan Department of Health and Human Services with federal funding from the U.S. Centers for Disease Control and Prevention to bolster Michigan’s capacity to respond to COVID-19 and future pathogens. MSU’s role leverages institutional strengths—the Genomics Core at the Research Technology Support Facility, the Veterinary Diagnostic Laboratory, the Early Detection Program (EDP) known as the Spartan Spit Kit, and interdisciplinary collaborations across campus—to expand viral surveillance, sequencing, and bioinformatics capabilities. With an MSU MI-SAPPHIRE award of $1.87 million, DiRita and colleagues will perform whole-genome sequencing of SARS-CoV-2 from positive saliva samples identified through the EDP, rather than sending those samples out to the state. This shift increases in-state sequencing capacity and enables more rapid and comprehensive monitoring of variant emergence in the MSU community and beyond. The project intentionally broadens the sample base: sequencing will include samples from medically underserved communities in collaboration with ongoing CDC-funded work, samples from immunocompromised patients accessed through health system partnerships, and viral genomes from animals sequenced with the Veterinary Diagnostic Laboratory.

Those diverse sample sources will improve understanding of viral sequence diversity and the evolutionary dynamics that generate novel variants. DiRita frames the effort as expanding knowledge of viral sequence diversity and building infrastructure that keeps pace with rapid pathogen evolution. The MI-SAPPHIRE program at MSU is designed not only to detect and sequence more viruses but also to ensure the state can analyze, interpret, and disseminate the growing volume of genomic data. A complementary MI-SAPPHIRE grant of $2.5 million, shared between MSU and Spectrum Health, allocates roughly $600,000 toward developing computational resources and tools—bioinformatics capacity—that will help Michigan make the most of its sequencing data. M

The MSU MI-SAPPHIRE work emphasizes building a statewide network of university expertise so that Michigan’s public health system can rapidly identify and respond to emerging pathogens. By situating sequencing capacity within MSU and connecting it with community partners, hospitals, and veterinary diagnostics, DiRita and collaborators are creating a more resilient surveillance ecosystem that supports quicker variant detection, deeper evolutionary insight, and improved readiness for the next pathogen.