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

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

Ambiguity in virus-to-host mappings in publicly available databases often reflects missing information regarding a specific host. For example, a virus may be assigned to several hosts described at various levels of the species taxonomical tree (e.g., rodents, primates, and insects). However, only rarely do members of the same virus genus infect hosts differing above the level of class (e.g., mammals), phylum (e.g., chordata), or regnum (e.g., animals). An example of such an uncommon case is the Iridoviridae family (dsDNA viruses), which infects frog, snakes, insects, and fish. To overcome the ambiguities resulting from virus-host assignments, we adopt a mapping that focuses on the host taxonomical level of interest, which then groups together viruses that infect a unique group of hosts at that particular level.