Probing the unfolded protein response to mouse hepatitis virus coronavirus infection through RNA sequencing and ribosome profiling

Coronaviruses (CoVs) are enveloped, positive-sense RNA viruses with an unusually large RNA genome and a unique replication strategy. They cause important diseases in mammals and birds ranging from enteritis in cows and pigs and upper respiratory disease in chickens, to potentially lethal human respiratory infections. Here, we apply ribosome profiling and parallel RNA sequencing to analyse global changes in host cell transcriptome and translatome upon infection with mouse hepatitis virus strain A59 (MHV-A59), a model murine coronavirus in the same genus as the human pathogens severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). Amongst differentially-regulated cellular genes, we observed up-regulation of all arms of the unfolded protein response (UPR), including translational activation of transcription factors ATF4, ATF5 and Chop. Polysome profiling of infected-cells revealed an accumulation of empty 80S ribosomes, consistent with increased phosphorylation of eIF2α leading to translational shut-off via inhibited initiation. Ribosomal footprints on phosphorylated-eIF2α-resistant mRNAs revealed unambiguous upstream open reading frame (uORF) occupancy consistent with host maintenance of the UPR. Unexpectedly, an inhibitor of PERK that blocks the UPR and relieves translation inhibition was found to attenuate virus growth suggesting that MHV may subvert the UPR to its own advantage. This study sheds new light on the complex interactions between MHV and host during infection and provides new potential targets for antiviral intervention.