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

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

As we did not find virus-to-host adaptation of GC content with respect to the entire taxonomical spectrum, we proceeded to test the codon usage distances for all pairs of virus and host ( Figure 6B ); the similarity of the viruses toward their specific hosts (the diagonal of the matrix in Figure 6B ) is also summarized in Table II . The adaptation among the bacterial set is very prominent, especially in light of the extreme differences among the different bacterial hosts themselves ( Figure 5B ; Supplementary information S1). In fact, each bacterial virus shows a very different pattern relative to all other bacterial viruses. In addition, significant levels of resemblance are evident among the different plant viruses and their hosts. However, the strongest signal observed is the resemblance of human viruses to all mammalian hosts; at the same time, these viruses remain rather different from any of the other mammalian viruses ( Figure 5A ). Furthermore, the strong similarity of the codon usage of human viruses to all 11 mammalian hosts reaches substantially farther into the taxonomic realm, approaching the insect and bird host species as well (Supplementary Table S3 ). Interestingly, the viruses that actually infect birds do not show strong adaptation to their hosts (based on viruses that infect chickens). We have shown that human viruses show an unexpected similarity to a broad range of host taxonomical groups, including mammals, avians, most insects, and some plants. Among all tested mammals, only human and rat viruses share strong resemblance in their codon usage profiles. However, owing to the relatively weak support for rat-infecting viruses (i.e., few proteins, narrower virus representatives), we will focus only on the adaptation of human viruses.