Hepeviridae


Hepeviridae

Chapter Contents

Hepeviridae: The Family

Hepeviridae: Member Taxa

Hepeviridae: Supporting Information

  • Authors - Corresponding author: M. A. Purdy (mup3@cdc.gov)
  • Resources - Sequence alignments and tree files
  • References - Literature cited

Citation

A summary of this ICTV online (10th) report chapter has been published as an ICTV Virus Taxonomy Profile article in the Journal of General Virology, and should be cited when referencing this online chapter as follows:

Purdy, M.A., Harrison, T.J., Jameel, S., Meng, X-J., Okamoto, H., Van der Poel, W.H.M., Smith, D.B. and ICTV Report Consortium, 2017, ICTV Virus Taxonomy Profile: HepeviridaeJournal of General Virology, 98: 26452646.

Summary

The Hepeviridae includes enterically-transmitted, small, non-enveloped positive-sense RNA viruses. Members of the family are assigned to two genera and five species. Members of the Piscihepevirus genus infect trout and members of the Orthohepevirus genus infect mammals and birds. The species Orthohepevirus A includes hepatitis E virus (HEV), which is usually responsible for self-limited acute hepatitis in humans and several mammalian species, but may become chronic in immunocompromised humans. Extrahepatic manifestations of Guillain-Barré syndrome, neuralgic amyotrophy, glomerulonephritis, and pancreatitis have been described in a proportion of HEV cases. The species Orthohepevirus B includes avian HEV that causes hepatitis-splenomegaly syndrome in chickens.

Table 1.Hepeviridae. Characteristics of the family Hepeviridae.

Characteristic

Description

Typical member

hepatitis E virus Burma (M73218), species Orthohepevirus A, genus Orthohepevirus,

Virion

Non-enveloped, 27–34 nm diameter with a single capsid protein

Genome

6.4-7.2 kb capped positive-sense monopartite RNA containing 3 open reading frames

Replication

Occurs in association with the host endoplasmic reticulum.

Translation

From genomic (ORF1) and subgenomic (ORF2 and ORF3) capped RNA

Host range

Mammals (Orthohepevirus A, C and D), birds (Orthohepevirus B) and trout (Piscihepevirus)

Taxonomy

two genera

Virion

Morphology

Virions of HEV are icosahedral, non-enveloped, spherical particles with a diameter of approximately 27–34 nm (Figure 1.Hepeviridae). Spikes and indentations can be seen on electron micrographs (EM) of virions (Bradley 1990). The capsid is formed from capsomeres consisting of homodimers of a single capsid protein, forming the virus shell. Each capsid protein contains three linear domains forming distinct structural elements: S (the continuous capsid), P1 (three-fold protrusions), and P2 (two-fold spikes). Neutralizing epitopes have been found in the P2 domain. Each domain contains a putative polysaccharide-binding site that may interact with cellular receptors. Native T=3 capsids contain flat dimers, with less curvature than those of T=1 virus-like particles (Figure 2.Hepeviridae) (Mori and Matsuura 2011). Virion particles of avian HEV (Figure 3.Hepeviridae) revealed by negative staining EM of bile samples from chickens with hepatitis–splenomegaly syndrome are similar in size and morphology to HEV (Haqshenas et al., 2001).

Figure 1.Hepeviridae. Negative contrast electron micrograph of hepatitis E virus virions from a case stool collected in Nepal. (A) virion and (B) empty capsid. The bar represents 100nm (photo from M. Purdy).

Figure 2.Hepeviridae. Structure of the hepatitis E virus-like particle (VLP) (T=1). (A) Crystal structure of hepatitis E virus VLP. The three domains, S, P1 and P2 are colored blue, yellow and red, respectively. The VLP is positioned in a standard orientation with the 3 2-fold icosahedral symmetry axes aligned along the vertical, horizontal, and viewing directions, respectively. (B) Cryo-EM reconstruction at 14 Å resolution. The surface is coloured by radial depth cue from blue, yellow, to red. (C) Hepatitis E virus VLP with only the S domain. (D) VLP with S and P1 domains. (E) VLP with P1 and P2 domains (from (Guu et al., 2009) with permission).

Figure 3.Hepeviridae. Electron micrograph of 30–35 nm diameter particles of avian hepatitis E virus. Virus particles were detected from a bile sample of a chicken with hepatitis–splenomegaly syndrome. Bar=100 nm (from (Haqshenas et al., 2001) with permission from the Microbiology Society).

Physicochemical and physical properties

Members of the Orthohepevirus genus have virion buoyant densities of 1.35 to 1.40 g cm−3 in CsCl and 1.29 g cm−3 in glycerol and potassium tartrate gradients. The virion S20,w is 183S. Virions are sensitive to low-temperature storage (between −70°C and +8°C) and iodinated disinfectants (Bradley 1990). The virion of HEV is more heat-labile than that of hepatitis A virus (HAV): HEV was about 50% inactivated at 56°C, but 1% infectivity remained after 60 min at this temperature; no infectivity was detected after heating at 66°C or 70°C for 1 h. (Emerson et al., 2005). Liver suspensions containing avian HEV remained infectious after treatment with chloroform and ether but lost infectivity after incubating at 56°C for 1 h or 37°C for 6 h. Viral infectivity in liver suspensions was reduced 1000-fold after treatment with 0.05% Tween-20, 0.1% NP40 and 0.05% formalin (Meng et al., 2006). Properties of members of the Piscihepevirus genus have not been investigated.

Nucleic acid

The genome of members of the Hepeviridae is a linear, positive-sense, ssRNA molecule of approximately 6.6 - 7.2 kb, with a 5′-m7G cap structure and a 3′-poly(A) tail.

Proteins

Virions are constructed from a major capsid protein (CP) encoded by the second open reading frame (ORF2). The CP binds to surface heparin sulfate proteoglycans (HSPGs) on liver cells (Kalia et al., 2009) and may be proteolytically processed. A small immunoreactive protein (113-114 amino acids, 12.5 kDa) encoded by the third ORF (ORF3) has been identified and shown to exhibit multiple functions associated with virion morphogenesis, egress and viral pathogenesis. Recently, the ORF3 polypeptide has been shown to share several structural features with class I viroporins (Ding et al., 2017). Non-structural proteins encoded by the first major ORF (ORF1) have limited similarity with the “alpha-like supergroup” of viruses and contain domains consistent with a methyltransferase, papain-like cysteine protease, macro domain, RNA helicase and RNA-dependent RNA polymerase (Cao and Meng 2012). Some of these predicted enzymatic properties have been confirmed experimentally (Karpe and Lole 2010, Parvez 2015, Mahilkar et al., 2016).

A hypervariable region lies between the protease and helicase domains. The hypervariable region contains two subregions; the amino-terminal half of this region consists of a variable length polypeptide with host species-specific sequence conservation, which is unique to Hepeviridae (Kelly et al., 2016) and may be responsible for host specificity (Lara et al., 2014). The carboxyl-terminal half consists of an intrinsically-disordered polypeptide with a high frequency of proline residues (Kelly et al., 2016, Purdy 2012). The translational and post-translational processing of the non-structural polyprotein remain unresolved. In particular, it remains unclear whether the non-structural polyprotein functions as a single protein with multiple functional domains or whether it is proteolytically cleaved into smaller proteins with distinct enzymatic activities.

Lipids

Although HEV is shed in faeces as a non-enveloped virus there is evidence that, like HAV, HEV can hijack host membranes on assembly and exit. Possession of a host-derived envelope may allow the virus to circulate in a patient’s blood escaping detection by neutralizing antibodies (Yin et al., 2016).

Carbohydrates

Evidence for glycosylation of the major CP has been reported following its expression in mammalian cells (Jameel et al., 1996). The CP sequence contains three potential sites for N-linked glycosylation and a signal peptide sequence at its N terminus (Zafrullah et al., 1999). Mutations within Orthohepevirus A CP glycosylation sites prevent the formation of infectious virus particles, although the lethal effect is due to altered protein structure rather than elimination of glycosylation (Graff et al., 2008).

Genome organization and replication

The RNA genome of members of the Hepeviridae is organized into three ORFs, with the non-structural proteins encoded toward the 5′ end of the genome and the structural protein(s) toward the 3′ end. Capped genomic RNA of an Orthohepevirus B isolate has been shown to be infectious for chickens (Huang et al., 2005) and that of Orthohepevirus A for pigs, rhesus monkeys and chimpanzees (Panda et al., 2000, Emerson et al., 2001, Huang et al., 2005). The 5′-untranslated region (UTR) is up to 34 nt in length among members of Orthohepevirus A, but is 100 nt in cutthroat trout virus (Piscihepevirus A). A 5′-methylguanine cap structure has been identified at the 5′ end of the HEV genome and plays a role in the initiation of virus replication (Ahmad et al., 2011). The 3′-UTR of HEV contains a cis-reactive element (Emerson et al., 2001) as does a central region of ORF2 (Emerson et al., 2013). The 3′ end of the genome is also polyadenylated.

In all members of the Hepeviridae, ORF1 encodes a non-structural polyprotein, followed by ORF2 that encodes the CP, and an overlapping reading frame, ORF3 which encodes a small phosphoprotein of 113–114 aa with a multifunctional C-terminal region (Figure 4.Hepeviridae). A bicistronic subgenomic mRNA encoding both ORF2 and ORF3 proteins has been identified (Graff et al., 2006). Isolates have been described from chronically infected individuals that contain an insertion of host-derived sequences such as human ribosomal protein S17 within the ORF1 hypervariable region that confers a growth advantage in cultured hepatoma cells (Shukla et al., 2011, Nguyen et al., 2012). 

Figure 4.Hepeviridae. Genome organization of members of Hepeviridae. Schematic diagrams are shown for cutthroat trout virus (Piscihepevirus A), human hepatitis E virus (Orthohepevirus A), avian hepatitis E virus (Orthohepevirus B), rat hepatitis E virus (Orthohepevirus C), bat hepatitis E virus (Orthohepevirus D) and unassigned isolates from moose, kestrel and little egret. The diagram shows a short 5′ non-coding region (NCR), a 3′ NCR, and three ORFs. ORF1 encodes non-structural proteins including putative functional domains MT, methytransferase; P, a putative papain-like cysteine protease; HUD, Hepeviridae unique domain also called the Z domain (Kelly et al., 2016); PP, a hypervariable polyproline region that is dispensable for virus infectivity; Hel, helicase; RdRp, RNA-dependent RNA polymerase (Kelly et al., 2016, Koonin et al., 1992). ORF2 (green) encodes capsid protein and ORF3 (brown) encodes a small phosphoprotein with a multi-functional C-terminal region. ORF2 and ORF3 overlap each other but neither overlaps ORF1.

Replication of HEV is not well understood. The viral RdRp associates with the host endoplasmic reticulum (ER) through residues 4449-5109 encoding a predicted transmembrane domain to begin replicating the viral genome. It appears that replication involves temporal separation and alternating cycles of positive- and negative-sense RNAs to produce capsid, ORF3 protein, ORF1 polypeptide, and new genomes, resulting in the generation of progeny virions (Varma et al., 2011).

Biology

Hepevirus infection occurs by the faecal-oral route for Orthohepevirus A and Orthohepevirus B, and is usually associated with a self-resolving mild, acute infection of the liver. More recently, chronic hepatitis E has become a significant clinical problem in immunosuppressed individuals especially in solid organ transplant recipients. Transmission can occur through contaminated water, consumption of raw/undercooked meats or faeces from infected animals, and rarely through blood transfusions. Little is known about the mode of transmission or pathology for other species in the family.

Genus demarcation criteria

Members of different genera differ in host range with piscihepeviruses only known from fish, while orthohepeviruses have been isolated from a wide range of mammals and birds. Members of the two genera also differ in phylogenetic relationships observed for comparisons between three conserved regions within ORF1. These relationships are mirrored in sequence distance between representatives of each genus with inter-genus amino p-distances greater than 0.6 compared to intra-genus p-distances of less than 0.5 (Smith et al., 2014). Members of the same genus all share similar genome organisation: in orthohepeviruses ORF3 overlaps the 5′-end of ORF2 while in piscihepeviruses the overlap is more central (Batts et al., 2011).

Derivation of names

Hepe: from hepatitis E virus.

Phylogenetic relationships

The family includes two genera whose members are phylogenetically distinct; the genus Orthohepevirus includes four species that are phylogenetically distinct and have different host ranges (Figure 5.Hepeviridae). Only one species has been described in the genus Piscihepevirus.

Figure 5.Hepeviridae. Phylogenetic trees for members of the Orthohepevirus genus. Maximum likelihood trees for amino acid distances were created using MEGA 6 (Tamura et al., 2013) with the Le and Gascuel substitution model with frequencies (Le and Gascuel 2008) and 4 gamma rate categories. Partial amino acid deletion was allowed using a 90% coverage cutoff. 1000 bootstrap replicates were used. Branches supported by > 80% of bootstrap replicates are indicated. (A) ORF1 sequences from assigned and unassigned Orthohepevirus species were used with regions between 485-776 aa and 923-931 aa (numbered with reference to the ORF1 polyprotein of M73218) removed from the analysis due to indels within these regions. (B) Complete ORF2 sequences. Sequences are identified by their accession ID and host. Orthohepevirus A sequences are additionally identified by genotype. Orthohepevirus species are denoted by their species names. Unclassified viruses are denoted by the host from which they were first isolated.

Similarity with other taxa

HEV is similar to members of the family Caliciviridae based on the superficial structural morphology as revealed by EM, and its genome organization (Bradley 1990). However, members of the two families show little detectable sequence homology and the cap structure at the 5′ end of the HEV genome is absent in caliciviruses. HEV shows highest, but limited, amino acid sequence similarity in its replicative enzymes with Rubella virus and alphaviruses of the family Togaviridae and with plant furoviruses. The capping enzyme, helicase and replicase of HEV have properties very similar to those of viruses within the “alphavirus-like supergroup” (Kelly et al., 2016). 

Related, Unclassified Viruses

Virus name

NCBI taxon ID

Accession number

hepelivirus

1229326

JQ898340, KM407530

bivalve hepelivirus G

1926998

KX158876