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

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

Here, we found similar codon usages among viruses, hosts, and for virus-host pairs. Similarity in codon usage in different viruses can somewhat be explained by the occurrence of lateral gene transfer (LGT) and other modes of genetic material exchange. Accordingly, recent recombination events between the host and the virus may leave behind similar codon frequencies. Yet we do not believe this phenomenon to be a major determinant in codon usage adaptation as (i) it is unlikely that the codon usage of some functional groups but not of the entire proteome will show differences in the patterns observed ( Figure 7C ); (ii) there is no evidence that among the mammals we tested here some are more likely to be affected by LGT than others, yet human viruses show a significantly different pattern than other mammals; (iii) different classes of viruses (class I-VII) have similar adaptation trends, despite substantial differences in the potential for the exchange of genetic material with the host in RNA and DNA viruses. Thus, although it is unlikely that LGT dominates the observed resemblance of codon usage between eukaryotic viruses and their hosts, this does not hold for bacteria and archaea, which are exposed to high frequencies of LGT events.