Coronaviruses reprogram the tRNA epitranscriptome to favor viral protein expression.
Coronaviruses genomes are enriched in suboptimal A/U-ending codons, which areassociated with reduced translation efficiency due to limited cognate tRNA availability.How coronavirus efficiently express their proteins despite this limitation remainsunclear. By analyzing their codon usage, we identify four tRNAmodifications -inosine,queuosine,mcm5U/mcm5s2U,and m5C/f5C- as essential fordecoding of suboptimal codons. Notably, SARS-CoV-2 and HCoV-OC43 infections,representing severe and mild human infections, respectively, reprogram thesemodifications to favor viral protein synthesis. Mechanistically, this reprogramming wasdriven by altered expression of the corresponding tRNA modifying enzymes. Sinceboth viruses induced DDR and oxidative stress -known to similarly alterqueuosine,mcm5U/mcm5s2U, and m5C/f5C modifications to favor expression of stressresponse proteins- our findings support that coronavirus genomes have adapted tothe tRNA modification landscape under stress conditions. Overall, coronavirusesorchestrate a codon-specific reprogramming of the host tRNA modification landscape,highlighting a conserved strategy that optimizes translation efficiency and represents apromising target for pan-coronavirus antiviral therapy development.