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

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

In addition, shifts in hosts have huge implications on human health and on the world economy, for example, zoonotic epidemics. Known examples of naturally occurring host-virus shifts are the introduction of HIV-1 to humans in the early 1950s and the shift in the SARS (CoV) virus that crossed over to infect humans only very recently. The worldwide threat of influenza-based epidemics, such as the transmission of avian flu (Influenza A virus, H5N1) to humans and the latest outbreak of swine influenza (H1N1, April 2009) in Mexico, is heightened by the rapid evolution of the Influenza virus witnessed during the last decade; recently, H3N2 and H3N8 were introduced from humans to pigs and from horses to dogs, respectively (Campitelli et al, 1997) . It is likely that the domestication and close interaction between humans, rats, and farm animals for thousands of years has led to the evolution of viruses that infect humans and are adapted toward a broad range of hosts. The similarities in codon usage and amino acid composition that we have observed in this work can somewhat relate to the potential for zoonosis. Although, as discussed above, these molecular properties are neither necessary nor sufficient conditions for host shifts, our analysis can nevertheless contribute to a framework that would permit analysis of the potential of certain viruses to adapt to new host species.