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

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

As an illustrative example ( Figure 2 ), we depict the viruses that infect mammals (excluding humans and other primates). Critically, these mappings account both for the virus under study and its hosts, with respect to the underlying host taxonomical tree. There are 10 host organisms that are infected by 17 viruses. These 17 viruses are represented by 7 types of viruses ( Figure 2 , V1-V7) that are identical in terms of their defined host range. We show that for the case in which the host-species level is considered (level A), only a restricted virus-to-host mapping can be applied. However, higher taxonomical views (levels B, C, or D) are consistent with a mapping of additional viruses. All further analyses herein will follow such a mapping (see Materials and methods). Note that resolving the ambiguity of assignment of viruses to their hosts is a fundamental precondition for studying virus-host evolution on a large scale.