Pathogenic Influenza Viruses and Coronaviruses Utilize Similar and Contrasting Approaches To Control Interferon-Stimulated Gene Responses

Menachery, Vineet D.; Eisfeld, Amie J.; Schäfer, Alexandra; Josset, Laurence; Sims, Amy C.; Proll, Sean; Fan, Shufang; Li, Chengjun; Neumann, Gabriele; Tilton, Susan C.; Chang, Jean; Gralinski, Lisa E.; Long, Casey; Green, Richard; Williams, Christopher M.; Weiss, Jeffrey; Matzke, Melissa M.; Webb-Robertson, Bobbie-Jo; Schepmoes, Athena A.; Shukla, Anil K.; Metz, Thomas O.; Smith, Richard D.; Waters, Katrina M.; Katze, Michael G.; Kawaoka, Yoshihiro; Baric, Ralph S.

Examination of individual protein expression patterns also confirmed these trends. Although most ISGs are absent in mock samples, two detectable proteins were expressed at basal levels: STAT1 and PKR. H5N1-VN1203 infection had reduced protein expression of both STAT1 (27.4% decrease at 24 hpi) and PKR (28.5% decrease at 18 hpi) relative to that of mock; similarly, MERS-CoV reduced the protein level of STAT1 (15.8% decrease at 18 to 24 hpi) and PKR (20.2% decrease at 18 to 24 hpi) (see Fig. S1B ). In contrast, both proteins were significantly increased following both H1N1-09 and SARS-CoV infection; however, the increase occurred only at late times (Ͼ30 hpi) for SARS-CoV, contrasting that for H1N1-09. Further examination of individual ISGs found a consistent linkage between mRNA expression (see Fig. S1B , solid line) and protein abundance (dotted line). For H1N1-09, mRNA upregulation by 3 to 7 hpi corresponded to parallel protein production 7 to 12 h later for ISGs; representative kinetics for MX1, OAS2, and IFIT family members are shown (see Fig. S1C ). A similar mRNA/protein kinetic relationship was observed for SARS-CoV, showing delayed RNA induction, which allowed viral replication to peak prior to ISG protein production (see Fig. S1D ). For both H5N1-VN1203 and MERS-CoV, this analysis was excluded due to insufficient detectable data to produce a representative curve. Together, the proteomics data validated the RNA expression results and confirmed unique strategies to control the ISG response between different viral strains and families.