Destabilized adaptive influenza variants critical for innate immune system escape are potentiated by host chaperones

The threat of viral pandemics demands a comprehensive understanding of evolution at the host–pathogen interface. Here, we show that the accessibility of adaptive mutations in influenza nucleoprotein at fever-like temperatures is mediated by host chaperones. Particularly noteworthy, we observe that the Pro283 nucleoprotein variant, which (1) is conserved across human influenza strains, (2) confers resistance to the Myxovirus resistance protein A (MxA) restriction factor, and (3) critically contributed to adaptation to humans in the 1918 pandemic influenza strain, is rendered unfit by heat shock factor 1 inhibition–mediated host chaperone depletion at febrile temperatures. This fitness loss is due to biophysical defects that chaperones are unavailable to address when heat shock factor 1 is inhibited. Thus, influenza subverts host chaperones to uncouple the biophysically deleterious consequences of viral protein variants from the benefits of immune escape. In summary, host proteostasis plays a central role in shaping influenza adaptation, with implications for the evolution of other viruses, for viral host switching, and for antiviral drug development.
Host chaperones enable the influenza virus to evade the host’s innate immune response by ameliorating the biophysically deleterious consequences of adaptive mutations (such as the nucleoprotein Pro283 variant that strengthened the 1918 pandemic strain).
Author summary Viruses, such as influenza, evade the host immune response by mutating frequently. However, these adaptive amino acid substitutions are often biophysically deleterious and can thus increase the propensity for viral proteins to misfold and hamper viral replication. Host protein folding factors called chaperones interact extensively with viral proteins, like influenza nucleoprotein, and are thus poised to potentiate the fitness of biophysically defective, adaptive variants. Here, we directly test this hypothesis by quantitatively profiling the mutational tolerance of influenza nucleoprotein in host cells with reduced chaperone levels. We find that chaperones indeed increase the accessibility of destabilized adaptive nucleoprotein variants, with an especially strong effect at fever-like temperatures. We observe that the destabilized Pro283 nucleoprotein variant, which is universally conserved across human influenza strains and enables evasion of the Myxovirus resistance protein A (MxA) innate immunity restriction factor, is rendered unfit in a chaperone-depleted host environment. Together, these data show that host chaperones critically impact viral adaptation and may serve as targets for antiviral therapeutic adjuvants.