Family: Picornaviridae
Genus: Hepatovirus
Distinguishing features
The genus is distinguished on the basis of genetic characters. In contrast to those of other picornaviruses, protein 1A of hepatoviruses is extremely small (16–27 aa). Protein 1A of hepatitis A virus (HAV) does not appear to be myristoylated at its N-terminus (Tesar et al., 1993). A significant fraction of RNA containing particles possess uncleaved 1AB. Immature HAV may contain uncleaved 1D-2A (pX) precursor protein (Anderson and Ross 1990, Wang et al., 2015, Graff et al., 1999). HAV is non-cytopathogenic and egress of virus is poorly understood, but particles are released within membranous structures ("cloaked particle", "enveloped HAV", eHAV) containing one to four virions with processed 1AB and uncleaved pX (Feng et al., 2013). Membranes are thought to be removed when eHAV is shed through the bilary tract into intestine. During final morphogenesis step, pX is cleaved off VP1 by an unknown host protease.
Virion
Morphology
No surface morphology is visible by EM. The crystal structure of HAV has been resolved (Wang et al., 2015).
Physicochemical and physical properties
Viruses are very stable, resistant to acid pH and elevated temperatures (60°C for 10 min). Buoyant density in CsCl is 1.32–1.34 g cm-3.
Nucleic acid
Genome (Cohen et al., 1987b, Cohen et al., 1987a, Anthony et al., 2015, Drexler et al., 2015, Yu et al., 2016): c. 7,487 nt (5′-UTR: c. 734 nt; ORF: 6,684–6,693, nt; 3′-UTR: 53–59 nt).
Although the IRES is distantly related to the type II IRES, it has been designated as type III. The 5′-UTR contains a 5′-terminal hairpin, two putative pseudoknots, and a short (c. 40 nt) pyrimidine-rich (i.e. not a pure poly-C) tract upstream of the IRES. The cre is located in the 3D region. Nucleotide sequence identity between different HAV strains is generally greater than 80%.
Genome organization and replication
Genome layout:
VPg+5′-UTRIRES-III-[1A-1B-1C-1D-2A/2B-2C/3A-3B-3C-3D]-3′-UTR-poly(A)
The deduced polyprotein is of 2,227–2,230 amino acids. The 2A protein has unknown function. The primary cleavage of the polyprotein occurs at the 2A/2B junction, and is catalyzed by 3Cpro. The 1D/2A cleavage may be directed by an unknown cellular protease, or the VP1 protein may be subject to C-terminal trimming as in cardioviruses. Replication in cell culture occurs slowly, with little CPE, and with low yields of virus compared to most other picornaviruses. The IRES differs from those of other picornaviruses in that its activity is dependent on intact eIF-4G.
Biology
HAV infects epithelial cells of the small intestine and hepatocytes of primates. Virus is predominantly replicated within the liver, excreted via the bile and present in feces in high titer. Viral shedding is maximal shortly before the onset of clinical signs of hepatitis, which probably represents immunopathologically-mediated liver injury. Clinical manifestations are fever, jaundice, light stools, abdominal pain, and occasionally diarrhea. HAV generally establishes a persistent infection when inoculated on to any of a wide range of primate cells in vitro, but persistent infection does not occur in vivo, and the viruses are not associated with chronic hepatitis. HAVs can be divided into two distinct biotypes that are phylogenetically distinct and have different preferred hosts (all species of primates: humans, chimpanzees, owl monkeys and marmosets, for one biotype, versus green monkeys and cynomolgus monkeys for the other). These two biotypes share cross-reacting antigens, but have biotype-specific epitopes that can be distinguished by monoclonal antibodies. Little biological data are available on hepatoviruses B-I; RNA of these viruses have been detected in fecal samples, liver and other tissue samples of various mammals (seals, woodchucks, various bat species, hedgehogs, rodents, shrews and tupajas).
Phylogenetic analysis has been used to identify groups within species as follows: Hepatovirus A – 5 genotypes (HAV-IA, IB, IIA, IIB, IIIA and IIIB in humans, IV and V in primates), Hepatovirus B - 1 genotype (HepV-B1), Hepatovirus C – 1 genotype (HepV-C1), Hepatovirus D – 2 genotypes (HepV-D1, -D2), Hepatovirus E – 1 genotype (HepV-E1), Hepatovirus F – 3 genotypes (HepV-F1, -F2, -F3), Hepatovirus G – 2 genotypes (HepV-G1, -G2), Hepatovirus H – 3 genotypes (HepV-H1 to -H3) and Hepatovirus I – 1 genotype (HepV-I1). Human variants of HAV display some differences in geographical distributions and risk group associations. Clinical outcomes of infection with different HAV genotypes, where investigated, are similar.
Antigenicity
Members of Hepatovirus A belong to a single serotype and are highly conserved in their antigenic properties. Most antibodies are directed against a single, conformationally defined immunodominant antigenic site that is comprised of aa residues of the VP3 and VP1 proteins on the surface of the virion. eHAV which circulates in host blood is protected from neutralization by a cell-derived envelope. No serological data are available on hepatoviruses B-I.
Derivation of names
Hepatovirus-: from Greek hepatos, "liver"
Species demarcation criteria
Members of a species of the genus Hepatovirus:
- are less than 30% divergent in polyprotein amino acid sequence
- are less than 30% divergent in P1 amino acid sequence
- are less than 30% divergent in 2C+3CD amino acid sequence
- share a common genome organization
The divergence (number of differences per site between sequences) of members of different Hepatovirus species ranges from 0.18–0.40 for P1 and 0.19–0.49 for 3CD.