Comparative genomics of hepatitis A virus, hepatitis C virus, and hepatitis E virus provides insights into the evolutionary history of Hepatovirus species

Wassenaar, Trudy M.; Jun, Se-Ran; Robeson, Michael; Ussery, David W.

Since Dexler and colleagues had proposed that rodent HAV species F I G U R E 2 Codon usage wheel plots of HCV, HEV, and HAV, compared with human codon usage. The viral codon usage shown is a calculated average of (a) 6 HCV genomes representing genotypes 1a, 2a, 3a, 4a, 5a and 6a', (b) 9 HEV genomes of genotypes 1-4 of human, swine and rabit origines, and (c) 6 HAV genomes of genotypes IA, IB, IIA, IIB, IIIA and IIIB. Panel (d) shows the HAV codon usage for those amino acids used at frequencies >45% only. The codons are sorted for amino acids, with, from top clockwise, amino acids with 2, 3, 4, and 6 codons. Nonvariable amino acids are excluded (Table 1) . The latter (African sheath-tailed bat) is widespread in Africa and prefers a diet of beetles and lepidopterans (McWilliam, 1987) . Both investigated bat hepatovirus species had a codon usage extremely similar to that of the other analyzed hepatovirus species ( Figure A3 panel a) . Thus, possibly the selection mechanism proposed for HAV that resulted in de-optimized codon use for its human host also applies to these other hepatoviruses that replicate in other mammalian hosts.