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.

The three viral species HAV, HCV, and HEV are not phylogenetically related. Separate phylogenetic trees were produced for the three viral species, with 134 HAV genomes, 2,542 HCV genomes, and 557 HEV genomes, as shown in Figure 1 . All trees were drawn to scale, to illustrate the much lower genomic diversity of HAV compared with the other two species. The trees for HCV and HEV were collapsed at 90% identity for graphical representation. The HAV branches remained un-collapsed, since the shown branches per genotype all have a similarity >90%. The genomic diversity of HEV is higher than that of HAV but lower than that of HCV, as illustrated by the branch lengths of the trees. The produced HAV tree is in good agreement with previously published data (Vaughan et al., 2014) , although we did not include simian serotypes IV to VI. Our HCV tree that was based on 2,542 genomes is also mostly in agreement with previous publications that used smaller datasets. A neighbor joining (NJ) tree based on 162 genome sequences (Jackowiak et al., 2014) already identified a relationship between genotype 1 (Gt1) and Gt4, which is also visible in Figure 1 ; these two genotypes have evolved later than the other genotypes (Preciado et al., 2014) . The relationship between Gt2 and Gt7 was also noted before. However, our data produced a better resolution of genotypes than the NJ tree published by Jackowiak and colleagues. An ML tree based on 129 genome sequences (Smith et al., 2014) also did not fully resolve the branch of Gt1 and Gt4 with respect to the other genotypes. It is unclear on what data the tree shown in a review article (Preciado et al., 2014) was based, in which Gt1 and Gt4 were separated. In our tree, the branch leading to Gt1 and Gt4 is placed between Gt3 and Gt6/Gt8. Upon closer investigation of HCV genomes for which a subtype was specified in their Genbank annotation, only a few annotations did not match the current nomenclature, all of which were given a genotype before standardization of the nomenclature (Tokita et al., 1996) . This illustrates that historical Genbank annotations must be interpreted with caution. The six genotypes of HEV are also well resolved in Figure 1 , but the subtypes within these genotypes are not.