Influenza A deletion-containing viral genome production is altered by metabolites, metabolic signaling molecules, and cyanobacterial extracts

RNA virus infections generate abundant non-standard viral genomes that have been associated with milder clinical outcomes, leading to research into harnessing them as novel antivirals. We recently showed that altering host cell metabolism away from pro-growth pathways using alpelisib increased the production of influenza A nonstandard viral genomes (specifically deletion-containing viral genomes, DelVGs). To uncover more drugs that could induce increased DelVGs, we subjected influenza infections (A/H1N1 and A/H3N2) to a screen of metabolites, metabolic signaling molecules, and cyanobacterium-derived biologics, and quantified DelVGs and total viral genomes using long-read sequencing. We show that metabolites and signaling molecules of host cell central carbon metabolism can significantly alter DelVG production early in influenza A infection. Adenosine emerged as a potent inducer of defective viral genomes, significantly amplifying DelVG production across both subtypes. Insulin had similar effects, albeit subtype-specific, predominantly enhancing polymerase segment DelVGs in A/H3N2 infections. Tricarboxylic acid (TCA) cycle inhibitors, 4-octyl itaconate and UK5099, along with the purine analog favipiravir, increased total viral genome production across subtypes. Cyanobacterial extracts primarily affected DelVGs and total viral genome production in A/H3N2 infections, with a specific, almost complete shutdown of influenza antigenic segments. These results suggest new avenues for antiviral intervention, including host metabolic pathways (PI3K-AKT, Ras-MAPK pathways, TCA, and purine-pyrimidine) and cyanotherapeutics that affect DelVG production. Our study advances our fundamental understanding of DelVG production mechanisms and highlights the potential of targeting host metabolism to develop broad-spectrum influenza therapeutics.