It is well-documented that codon usage biases affect gene translational efficiency; however, it is less known if viruses share their host’s codon usage motifs. We determined that human-infecting viruses share similar codon usage biases as proteins that are expressed in tissues the viruses infect. By performing 7,052,621 pairwise comparisons of genes from humans versus genes from 113 viruses that infect humans, we determined which codon usage motifs were most highly correlated. We found that 16 viruses averaged a significant correlation in codon usage with over 500 human genes per viral gene, 58 viruses were highly correlated with an average of at least 100 human genes per viral gene, and 37 viruses were significantly correlated with an average of at least one human gene per viral gene at an alpha level of 7.09 x (0.05 alpha / 7,052,621 comparisons). Only two viruses were not highly correlated with an average of one human gene per viral gene. While relatively few of the interactions were previously documented, the high statistical correlations suggest that researchers may be able to determine which tissues a virus is most likely to infect by analyzing codon usage biases.
B. Miller, J., Hippen, A. A., M. Wright, S., Morris, C., & G. Ridge, P. (2017). Human viruses have codon usage biases that match highly expressed proteins in the tissues they infect. Biomedical Genetics and Genomics, 2(2). https://doi.org/10.15761/bgg.1000134