Review of Hepatitis E Virus in Rats: Evident Risk of Species Orthohepevirus C to Human Zoonotic Infection and Disease

Abstract

Hepatitis E virus (HEV) (family Hepeviridae) is one of the most common human pathogens, causing acute hepatitis and an increasingly recognized etiological agent in chronic hepatitis and extrahepatic manifestations. Recent studies reported that not only are the classical members of the species Orthohepevirus A (HEV-A) pathogenic to humans but a genetically highly divergent rat origin hepevirus (HEV-C1) in species Orthohepevirus C (HEV-C) is also able to cause zoonotic infection and symptomatic disease (hepatitis) in humans. This review summarizes the current knowledge of hepeviruses in rodents with special focus of rat origin HEV-C1. Cross-species transmission and genetic diversity of HEV-C1 and confirmation of HEV-C1 infections and symptomatic disease in humans re-opened the long-lasting and full of surprises story of HEV in human. This novel knowledge has a consequence to the epidemiology, clinical aspects, laboratory diagnosis, and prevention of HEV infection in humans.

Keywords: cross-species transmission; hepatitis; hepatitis E virus; hepevirus; human; orthohepevirus; rat; reservoir; rodent; zoonosis.

Figure 1

Schematic genome organization of rodent origin hepeviruses in species Orthohepevirus C and closely related, unassigned rodent hepeviruses. (A) The genome representation, (B) the significant nucleotide signals, and (C) the prediction of secondary RNA structural elements in rodent hepeviruses are presented. The alignment of the subgenomic RNA promoter sequence region (black dotted line), including the cis-reactive site (CRE) (red dotted line) and the transcription initiation site (TSS) (green dotted line), are highlighted. The consensus nucleotide Logo is generated from the alignment [49]. The internal ribosome entry site (IRES)-like, internal stem-loop (ISL)1/ISL2, CRE secondary RNA structural elements were predicted by ViennaRNA Web Service using the RNAfold server [50]. Open reading frame (ORF)4 is not present in all members of the orthohepevirus C.

Figure 2

Schematic organization of the encoded polyproteins (ORF1, ORF2, and ORF3) and the putative (ORF4) protein in rodent origin hepevirus genome. The ORF1 is coding the non-structural proteins, sequentially the MT-Y: methyltransferase domain; PCP: papain-like cysteine protease domain; HVR: hypervariable region; PPR: poly-proline region; X: macro domain; Hel: helicase enzyme; RdRp: RNA-dependent RNA polymerase. The amino acid (aa) number positions are based on reference HEV-1 Burma strain. The conserved aa motifs in each ORFs were analyzed by GeneDoc using 65–80% aa conservation level set-up. The conserved aa is colored by black, the different aa is highlighted by red, and x means any aa in the motifs of rodent hepevirus ORF1. The S-, P1-, and P2 domains of ORF2-encoded viral capsid protein and the two main domains with the potential immunodominant region in ORF3-encoded protein are also identifiable in rodent hepeviruses. The immunodominant sites are emphasized by red, blue, and green dotted lines. The putative ORF4 in rodent hepevirus is not homologous with ORF4 of species Orthohepevirus A, but the conserved aa motifs are presented in the figure. The comparative analysis was based on the reference HEV-1 Burma strain (M73218), but other references, HEV-1 strain, Xinjiang (L08816), and strain Sar-55 (AF444002), were also involved in the analysis. Complete HEV-C1 strains used in this analysis: ratIDE079F (AB847305), ratELOMB-131 (LC145325), ratELOMB-187SF (AB847307), Vietnam-105 (JX120573), LCK-3110 (MG813927), ratESUMBAWA-140L (LC225389), ratESOLO-014SF (AB847306), ratIDE113F (AB847309), HEV 17/1683 (MK050105), rat/Mu09/0685/DEU/2010 (JN167537), R63 (GU345042), R68 (GU345043), rat/Mu09/0434/DEU/2010 (JN167538), LA-B350 (KM516906), ratESOLO-006SF (AB847308), GZ95 (MH729810), GZ481 (MH729811); HEV-C2: HEV-4351 (AB890001), FRHEV4 (JN998606), the putative HEV-“C3”: RdHEVAc14/LiJiang/2015 (MG020022), RdHEVAc86/LiJiang/2015 (MG020023), the putative HEV-“C4”: RdHEVEm40/LuXi/2014 (MG020024), RdHEVEm67/LuXi/2014 (MG020025) and novel unassigned hepeviruses: AlgSwe2012 (KF951328), Yunnan-2013 (KR905549), RtCm-HEV/XJ2016 (KY432903), RtCb-HEV/HeB2014 (KY432899), RtMg-HEV/XJ2016 (KY432902), RtEi-HEV/SX2016 (KY432904), RtCl-HEV/GZ2016 (KY432905), RtMr-HEV/HLJ2016 (KY432901), kestrel/MR22/2014/HUN (KU670940), 1 (MG021328). The partial capsid coding (ORF2) nucleotide sequence of strain NorwayRat/rat08-HEV/HUN/2018 (MT847624) was also involved into the analysis.

Figure 3

The phylogenetic reconstruction of hepeviruses. Phylogenetic trees are generated based on the (A) ORF1-encoded non-structural polyprotein (left) and (B) ORF2-encoded capsid protein (right) sequences and each tree are rooted to piscihepevirus A (Piscihepevirus) srain Heenan88 (HQ731075). Each phylogenetic tree is focusing on the analysis of the rodent origin HEV-C1 (magenta), HEV-C2 (pink) sequences in Orthohepevirus C (red) complementing with the currently unassigned rodent-borne hepevirus sequences. The putative HEV-“C3” and HEV-“C4” clades in Orthohepevirus C are also highlighted. The rodent hepeviruses are marked with black dot, while rodent origin HEV-C1 in human infections are highlighted by white dot. The reported (potential) source of infection of hepeviruses are shown next to the lineages. The phylogenetic subtrees are compressed based representative genotypes in Orthohepevirus A. The following sequences are used in subtree HEV-1: AY230202, MH918640, AY204877, X98292, L08816, D11092, LC225387, M73218, JF443721, FJ457024; HEV-2: MH809516, KX578717; HEV-3: FJ705359, KP294371, FJ998008, MF959764, LC260517, MF959765, KU513561, MK390971, JQ013794, JQ953664, AB301710, AP003430, KT633715, AF082843, AY115488, AB369689, AB369687, EU723512, EU360977, AB290313, AB248521, JQ026407, AF455784, FJ906895; HEV-4: DQ450072, AB108537, MK410048, AB369688, AB220974, AB074915, KU356182, KF736234, AB197673, AY723745, AJ272108, LC428039, DQ279091; HEV-5: AB573435; HEV-6: AB856243, AB602441; HEV-7: KJ496144, KJ496143; HEV-8: MH410176, KX387867, KX387865. The evolutionary analyses were conducted in MEGA X [71], and phylogenetic trees were inferred by using the Maximum Likelihood method and Jukes-Cantor model [72]. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site.

Figure 4

Cluster analysis of hepeviruses based on the complete nucleotide sequences of open reading Figure 1 (ORF1). (A) Plot A represents the distribution of representative hepevirus species in Hepeviridae, and (B) Plot B focuses on the distribution of rodent origin hepeviruses. Piscihepevirus A (purple), Orthohepevirus A (green), B (gold), C (red), and D (blue) and currently unassigned (yellow and black) species in Plot A and Plot B, respectively, are K-means clustered together [73]. The rodent origin hepevirus clusters in Orthohepevirus C, HEV-C1 (magenta), HEV-C2 (brown), and two novel clusters, HEV-“C3” (yellow) and HEV-“C4” (orange), are shown in Plot B. Briefly, a total of 101 and 40 complete coding sequence (CDS) of ORF1 sequences in Plot A and Plot B, respectively, are aligned by MEGA using codon based ClustalW alignment method and analyzed by R using seqinr, msa, cluster, factoextra, and randomColoR packages. An identity matrix of pairwise distances from aligned nucleotide sequences was calculated. The matrix scaled and the optimal number of clusters and the means (centres) of each cluster were estimated. The R algorithm code could be provided on request.