Identification of a Novel Hepatitis E Virus Genotype 3 Strain Isolated from a Chronic Hepatitis E Virus Infection in a Kidney Transplant Recipient in Switzerland

Wang, Bo; Harms, Dominik; Hofmann, Jörg; Ciardo, Diana; Kneubühl, Agnes; Bock, C.‐Thomas

doi:10.1128/genomea.00345-17

Cited by 15 publications

(19 citation statements)

References 11 publications

(11 reference statements)

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“…DE/15-0031 consisted of 7,227 nt, excluding the poly(A) tail at the 3= terminus, and contained the three HEV ORFs with 1,705 (ORF1), 661 (ORF2), and 123 (ORF3) aa. The genomic features of the HEV variant SW/16-0282 have been described recently (36). The genomic regions of identified HEV-3 strains are described in Table 3.…”

Section: Resultsmentioning

confidence: 99%

Comprehensive Molecular Approach for Characterization of Hepatitis E Virus Genotype 3 Variants

et al. 2018

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Autochthonous hepatitis E virus genotype 3 (HEV-3) infections in industrialized countries are more frequent than previously assumed. HEV-3 is zoonotic and the causal pathogen of chronic hepatitis E. According to the latest classification of the family , 10 designated HEV-3 subtypes (HEV-3a to HEV-3j) and 7 unassigned HEV-3 subtypes are proposed. In order to identify and characterize the HEV-3 variants in circulation, we developed a molecular approach combining a sensitive HEV-specific real-time reverse transcription-PCR (RT-PCR) targeting the overlapping region of HEV ORF2 and ORF3 (the ORF2/3 region) and two newly designed consensus nested RT-PCRs targeting the HEV ORF1 and ORF2 genes, respectively. Since complete genome sequences are required for new HEV-3 subtype assignment, we implemented a straightforward approach for full-length HEV-3 genome amplification. Twenty-nine human serum samples and six human feces samples from chronic hepatitis E patients were selected for evaluation of the system. Viral loads ranged from 1 × 10 to 1.9 × 10 copies/ml of serum and from 1.8 × 10 to 1 × 10 copies/g of feces. Sequence and phylogenetic analyses of partial ORF1 and ORF2 sequences showed that HEV strains had considerable genetic diversity and clustered into the HEV-3c (29/35), HEV-3e (2/35), HEV-3f (2/35), and unassigned HEV-3 (2/35) subtypes. Moreover, from these strains, three full-length HEV-3 genome sequences were generated and characterized. DE/15-0030 represents a typical HEV-3c strain (95.7% nucleotide identity to wbGER27), while DE/15-0031 and SW/16-0282 have <89.2% homology to known HEV-3 strains and are phylogenetically divergent, indicating novel HEV-3 subtypes. In summary, our approach will significantly facilitate the detection, quantification, and determination of HEV-3 strains and will thus help to improve molecular diagnostics and our knowledge of HEV diversity and evolution.

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Section: Resultsmentioning

confidence: 99%

Comprehensive Molecular Approach for Characterization of Hepatitis E Virus Genotype 3 Variants

et al. 2018

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“…HEV-3 and HEV-4 are zoonotic viruses that are highly prevalent in porcine species and may be transmitted to humans by the consumption of pig liver and meat ( 2 ). HEV is also present in Switzerland ( 3 , 4 ); however, aside from a single full-length sequence that was published recently ( 5 ), no further information on the diversity of HEV strains is available.…”

Section: Genome Announcementmentioning

confidence: 99%

“…Alignment of the reads to full-length hepatitis E virus genomes using the SeqMan NGen software (DNAStar [Lasergene, Madison, WI, USA]) revealed best match to the recently published Swiss HEV-3 strain SW/16-0282 (GenBank accession no. KY780957 [ 5 ]). The consensus sequences of the alignments were near full length, with only 39 and 69 nucleotide gaps in the open reading frame 2 (ORF2) region for the fecal sample and the sausage sample, respectively.…”

Section: Genome Announcementmentioning

confidence: 99%

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Complete Genome Sequences of Two Swiss Hepatitis E Virus Isolates from Human Stool and Raw Pork Sausage

et al. 2017

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“…Sequence analysis and genome assembly were carried out with Geneious version 10.0.5 (Biomatters Limited, Auckland, New Zealand) as previously described (Wang et al 2017a;. Pairwise distances of complete genome nt and concatenated ORF1/ORF2 aa sequences were analysed using SSE as recommended by ICTV Hepeviridae Study Group (Simmonds 2012;Smith et al 2014).…”

Section: Sequence Analysismentioning

confidence: 99%

Chevrier’s Field Mouse (Apodemus chevrieri) and Père David’s Vole (Eothenomys melanogaster) in China Carry Orthohepeviruses that form Two Putative Novel Genotypes Within the Species Orthohepevirus C

Wang

Zhou

et al. 2018

Virol. Sin.

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Hepatitis E virus (HEV) is the prototype of the family Hepeviridae and the causative agent of common acute viral hepatitis. Genetically diverse HEV-related viruses have been detected in a variety of mammals and some of them may have zoonotic potential. In this study, we tested 278 specimens collected from seven wild small mammal species in Yunnan province, China, for the presence and prevalence of orthohepevirus by broad-spectrum reverse transcription (RT)-PCR. HEV-related sequences were detected in two rodent species, including Chevrier's field mouse (Apodemus chevrieri, family Muridae) and Père David's vole (Eothenomys melanogaster, family Cricetidae), with the infection rates of 29.20% (59/202) and 7.27% (4/55), respectively. Further four representative full-length genomes were generated: two each from Chevrier's field mouse (named RdHEVAc14 and RdHEVAc86) and Père David's vole (RdHEVEm40 and RdHEVEm67). Phylogenetic analyses and pairwise distance comparisons of whole genome sequences and amino acid sequences of the gene coding regions showed that orthohepeviruses identified in Chinese Chevrier's field mouse and Père David's vole belonged to the species Orthohepevirus C but were highly divergent from the two assigned genotypes: HEV-C1 derived from rat and shrew, and HEV-C2 derived from ferret and possibly mink. Quantitative real-time RT-PCR demonstrated that these newly discovered orthohepeviruses had hepatic tropism. In summary, our work discovered two putative novel genotypes orthohepeviruses preliminarily named HEV-C3 and HEV-C4 within the species Orthohepevirus C, which expands our understanding of orthohepevirus infection in the order Rodentia and gives new insights into the origin, evolution, and host range of orthohepevirus.

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Identification of a Novel Hepatitis E Virus Genotype 3 Strain Isolated from a Chronic Hepatitis E Virus Infection in a Kidney Transplant Recipient in Switzerland

Cited by 15 publications

References 11 publications

Comprehensive Molecular Approach for Characterization of Hepatitis E Virus Genotype 3 Variants

Comprehensive Molecular Approach for Characterization of Hepatitis E Virus Genotype 3 Variants

Complete Genome Sequences of Two Swiss Hepatitis E Virus Isolates from Human Stool and Raw Pork Sausage

Chevrier’s Field Mouse (Apodemus chevrieri) and Père David’s Vole (Eothenomys melanogaster) in China Carry Orthohepeviruses that form Two Putative Novel Genotypes Within the Species Orthohepevirus C

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