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

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

Host range, tissue specificity, and codon usage similarity It is known that a change in only a few amino acids of viral proteins can lead to a shift in the host infectivity range. Such a shift occurs through a genetic adaptation process that overcomes the hurdles of viral entry and replication in a new cellular environment. FX174 bacteriophage, which normally grows on E. coli, was switched to infect Salmonella, where this shift was attributed to only a very few mutations (2-3) in the major capsid gene (Crill et al, 2000) . This phenomenon is not unique to bacterial viruses, as this has occurred in canine parvovirus, which appeared in the late 1970s as a variant of a feline parvovirus. The host shift was attributed to only two to three substitutions (Truyen et al, 1995) . A shift in host recognition was also shown in the case of HIV-1, where a single mutation in the envelope gene was sufficient to alter cell specificity (Rambaut et al, 2004) . In all these strategies, virus-host shift is based on modifications in the virus receptor recognition step. However, it has been shown that host range is not entirely dependent on the initial recognition stage (McFadden, 2005) .