Influenza NS1 protein is the main viral protein counteracting host innate immune responses, allowing the virus to efficiently replicate in interferon (IFN)-competent systems. In this manuscript, we analyzed NS1 protein variability within influenza A (IAV) H3N2 viruses infecting humans during the 2012/2013 season. We also evaluated the impact of the mutations on the ability of NS1 proteins to inhibit the host innate immune responses and general gene expression. Surprisingly, a previously unidentified mutation in the double stranded (ds)RNA-binding domain (I64T) decreased NS1-mediated general inhibition of host protein synthesis, by decreasing its interaction with the cleavage and polyadenylation specificity factor 30 (CPSF30), leading to increased innate immune responses after viral infection. Notably, a recombinant A/Puerto Rico/8/34 H1N1 virus encoding the H3N2 NS1-T64 protein was highly attenuated in mice, most likely because of its ability to induce higher antiviral IFN responses at early times after infection, and because this virus is highly sensitive to the IFN-induced antiviral state. Interestingly, using Peripheral Blood Mononuclear Cells (PBMCs) collected at the acute visit (days 2-3 after infection), we show that the subject infected with the NS1-T64 attenuated virus has diminished responses to interferon and to interferon induction, suggesting why this subject could be infected with this highly IFN-sensitive virus. These data demonstrate the importance of influenza virus surveillance to identify new mutations in the NS1 protein affecting its ability to inhibit innate immune responses, and as a consequence, the pathogenicity of the virus.

IMPORTANCE:

Influenza A and B viruses are one of the most common causes of respiratory infections in humans, causing 1 billion infections, and between 300,000 and 500,000 deaths annually. Influenza virus surveillance to identify new mutations in the NS1 protein affecting innate immune responses, and as a consequence, the pathogenicity of the circulating viruses is highly relevant. Here, we analyzed amino acid variability in the NS1 proteins from human seasonal viruses, and the effect of the mutations in innate immune responses and virus pathogenesis. A previously unidentified mutation in the dsRNA-binding domain decreased NS1-mediated general inhibition of host protein synthesis and the interaction of the protein with CPSF30. This mutation led to increased innate immune responses after viral infection, augmented IFN-sensitivity and virus attenuation in mice. Interestingly, using PBMCs, the subject infected with the virus encoding the attenuating mutation induced decreased antiviral responses, suggesting why this subject could be infected with this virus.