Molecular evolution of hepatitis A virus: a new classification based on the complete VP1 protein

Abstract

Hepatitis A virus (HAV) is a positive-stranded RNA virus in the genus Hepatovirus in the family Picornaviridae So far, analysis of the genetic variability of HAV has been based on two discrete regions, the VP1/2A junction and the VP1 N terminus. In this report, we determined the nucleotide and deduced amino acid sequences of the complete VP1 gene of 81 strains from France, Kosovo, Mexico, Argentina, Chile, and Uruguay and compared them with the sequences of seven strains of HAV isolated elsewhere. Overall strain variation in the complete VP1 gene was found to be as high as 23.7% at the nucleotide level and 10.5% at the amino acid level. Different phylogenetic methods revealed that HAV sequences form five distinct and well-supported genetic lineages. Within these lineages, HAV sequences clustered by geographical origin only for European strains. The analysis of the complete VP1 gene allowed insight into the mode of evolution of HAV and revealed the emergence of a novel variant with a 15-amino-acid deletion located on the VP1 region where neutralization escape mutations were found. This could be the first antigenic variant of HAV so far identified.

FIG. 1.

Consensus phylogenetic tree constructed for representative human picornaviruses. The tree was constructed by neighbor-joining and p-distance methods. The numbers at nodes represent the percentages of 500 bootstrap pseudoreplicates. The bar indicates genetic distance. Abbreviations: CA, coxsackie A virus; EV, enterovirus; CB, coxsackie B virus; E, echovirus; FMDV, foot-and-mouth disease virus; EMCV, encephalomyocarditis virus.

FIG. 2.

Phylogenetic analysis of the complete VP1 region using the two-parameter model of Kimura. The numbers at nodes indicate bootstrap percentages after 1,000 replications of bootstrap sampling. Genotypes and subgenotypes are indicated at nodes. The bar indicates genetic distance.

FIG. 3.

Neighbor-joining phylogenetic tree of the VP1/2A region using the two-parameter model of Kimura. Genotypes and subgenotypes are shown at nodes for strains reported previously. The numbers at the nodes indicate bootstrap percentages after 1,000 replications of bootstrap sampling. The bar indicates genetic distance.

FIG. 4.

Scheme representing the 15-amino-acid deletion within the VP1 protein of the Uru-3 strain. Neutralization escape mutations are circled.

FIG. 5.

Profiles of synonymous (blue line) and nonsynonymous (red line) distances between different HAV genetic lineages. Sequences from strains Chile-6 (subgenotype IA) and MBB (subgenotype IB) (A), strains Chile-6 (subgenotype IA) and P27 (subgenotype IIIA) (B), and strains MBB (subgenotype IB) and P27 (subgenotype IIIA) (C). The x axis depicts the window number, and the y axis depicts distance.

FIG. 6.

Profiles of synonymous (blue line) and nonsynonymous (red line) distances within different HAV genetic lineages. Sequences from strains Uru-5 and and Chile-6 (subgenotype IA) (A), strains HM-175 and MBB (subgenotype IB) (B), and strains GA76 and P27 (subgenotype IIIA) (C). For further details, see the legend to Fig. 5.