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

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

Studying the evolution of viral codon usage and amino acid preferences in view of their hosts is fundamental in developing strategies for managing viral infections in the scope of human health, agriculture, and the environment. Insight into such phenomena was used in the laboratory, for example, when unfavorable codon pairs of capsid poxvirus proteins were injected into infected mice, resulting in virus attenuation (Coleman et al, 2008) . Similarly, neuroattenuated phenotype was associated with codon preference deoptimization in polioviruses (Mueller et al, 2006) . In a common vaccination practice, a live, attenuated virus is produced by adaptation to a new host, thereby eliminating its virulence to humans. As we have found that human-infecting viruses have conserved and unique codon usages, we propose that a fine-tuning of codon deoptimization may allow the alteration of tissue tropism and virulence attenuation.