Translational adaptation of human viruses to the tissues they infect

Xavier Hernandez-Alias; Martin Schaefer; Luis Serrano

To estimate the adaptation of each protein to the tRNA-based codon efficiencies of each tissue, we computed their SDA 2 (Sup. Table 5 ). For that purpose, we matched each virus to the tRNAs of their tissues of infection (Sup. Table 5 ). In concordance with our hypothesis, based on current viral annotations (VOGdb, vogdb.org), we observed a small but highly significant shift in SDA between structural and replication proteins in all but hepatocyteinfecting viruses (Fig. 4A) . However, the proteomes of this latter group are poorly annotated at the viral orthology database VOGdb, and separation between classes is often hindered by the polyprotein structure of their genomes 39 . Similarly, we performed a Gene Set Enrichment Analysis to identify which Virus Orthologous Groups (VOGs) were enriched in high-SDA or low-SDA proteins (Fig. 4B) . As determined by current annotations 39 , top-VOGs mostly contained replication-related early proteins, whereas bottom-VOGs had structural late functions.