Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice

Tchitchek, Nicolas; Eisfeld, Amie J; Tisoncik-Go, Jennifer; Josset, Laurence; Gralinski, Lisa E; Bécavin, Christophe; Tilton, Susan C; Webb-Robertson, Bobbie-Jo; Ferris, Martin T; Totura, Allison L; Li, Chengjun; Neumann, Gabriele; Metz, Thomas O; Smith, Richard D; Waters, Katrina M; Baric, Ralph; Kawaoka, Yoshihiro; Katze, Michael G

We report that the wild-type and mutant viruses differentially regulate a common set of transcripts and proteins, demonstrating a large degree of overlap in the host response among the different strain and dosage conditions. Regardless of the virus genetic change, we show that the host response is mainly impacted by the magnitude of gene expression and the speed at which these changes occur for this core set of transcripts, as opposed to transcriptomic differences explained by each specific mutation. We identified three main eigentranscripts associated with host immune mechanisms, including metabolic cellular processes and T cell signaling pathways, and three main eigenproteins associated with host antiviral defenses. Through a new geometric representation method and two criteria (the magnitude and velocity coefficients), we were able to visualize and quantify the magnitude and velocity kinetic effects of the host response to wild-type and mutant H5N1 VN1203 viruses, which were influenced by both the infection dosage and specific modifications to key H5N1 virulence determinants. Intriguingly, two newly generated H5N1 VN1203 mutant viruses, VN1203-PB1F2del and VN1203-NS1trunc, had the most distinct profiles, with apparent displacement relative to all other viruses at 2 dpi and 1 dpi, respectively. The divergent kinetic effects occurred mostly at early timepoints (between days 1 and 2 post-infection), and we observed analogous kinetic effects with different doses of low pathogenicity 2009 pandemic H1N1 influenza virus (CA04-WT). Importantly, we demonstrate that the magnitude and velocity kinetic effects were associated with clinical disease severity and virus replication. Specifically, mouse weight loss correlated with the magnitude of the host response, and infectious viral particle production at a given time point correlated with the velocity of the host response at the next time-point.