UC Davis

Influenza A virus remains a critical public health threat due to the emergence of novel strains, low vaccination rates, and antiviral resistance, necessitating the development of novel broad-spectrum therapeutics. One promising approach involves manipulating defective viral genomes (DVGs) produced during influenza replication. These DVGs, through defective interference (DI), reduce the abundance of standard viral genomes (SVGs), thereby decreasing viral yield in a strain-independent manner and leading to milder clinical outcomes. While research has traditionally focused on viral factors influencing DVG production, recent studies have shifted attention to host cell factors. Our research demonstrates that host cell metabolism significantly influences DVG production. By manipulating host anabolic signaling with alpelisib—an inhibitor of host PI3Kα—we observed significantly altered responses in the production of DVGs and non-infectious virions in a strain-specific manner (H1N1/H3N2). This finding was partially facilitated by our development of a novel cluster-forming assay to simultaneously titrate infectious and non-infectious viral particles with high throughput and improved precision. Furthermore, a screen of various metabolites and signaling molecules identified adenosine and insulin as potent inducers of DVG production, while TCA cycle inhibitors and the purine analog favipiravir increased total viral genome production. Cyanobacterial extracts also elicited significant alterations in DVG production, particularly in A/H3N2 infections. These findings underscore the extensive scope of host-virus metabolic signaling crosstalk and the potential to target host metabolic pathways to influence influenza infection severity in a DVG-dependent manner. Our study advances the understanding of DVG production mechanisms and highlights novel antiviral intervention strategies, including targeting PI3K-AKT and Ras-MAPK signaling pathways, TCA cycle metabolism, purine-pyrimidine metabolism, and cyanotherapeutic approaches. This research not only reveals the host's role in viral genome interactions but also opens new avenues for the development of broad-spectrum influenza therapeutics.