Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences

Bahir, Iris; Fromer, Menachem; Prat, Yosef; Linial, Michal

The similarity between the codon and amino acid preferences of human-infecting viruses and a wide variety of host organisms (Figure 4 ) may reflect the non-unique definition for virus strains that are associated with broad taxonomical host groups. We thus compiled a set of representative viruses derived from an organism-level view of the hosts (Figure 2 , level A), where, in this setting, only viruses that uniquely infect a defined host species are included. The 30 hosts infected by virus representatives unique to their respective hosts are listed in Table I . Most viruses are represented with 41000 codons for each host and 10 of the viruses are supported by 420 000 codons (see Supplementary Table S2) . A comparison of the codon usage among the viruses themselves is shown ( Figure 5A ), indicating enormous variability between viral genomes. Note that the colors in the various matrices range from blue (high similarity) to red The Vir  Ho analysis shows the L 2 distances between viruses and hosts. Note that this matrix is not symmetric and that the x-and y-axes show the hosts (Ho) and the viruses (Vir), respectively. Source data is available for this figure at www.nature.com/msb. Figure 5B ), the internal variability in the groups of mammals, plants, and insects was relatively low (especially among the mammal hosts). Nonetheless, among the 10 bacterial hosts tested, the variability is very high (dominated by red color).