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

ABSTRACT We present here the full-length genome sequences of two hepatitis E virus genotype 3 (HEV-3) isolates from a human stool sample from a patient with acute hepatitis and a raw sausage containing pig liver. Sequence analysis implies that Swiss HEV isolates may form a novel subgroup of HEV-3 viruses.

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

Journal of Clinical Microbiology ◽

10.1128/jcm.01686-17 ◽

2018 ◽

Vol 56 (5) ◽

Cited By ~ 7

Author(s):

Bo Wang ◽

Dominik Harms ◽

C. Patrick Papp ◽

Sandra Niendorf ◽

Sonja Jacobsen ◽

...

Keyword(s):

Chronic Hepatitis ◽

Hepatitis E Virus ◽

Phylogenetic Analyses ◽

Hepatitis E ◽

Full Length ◽

Molecular Approach ◽

Genotype 3 ◽

Genome Sequences ◽

Virus Genotype ◽

Pcr Targeting

ABSTRACT 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 Hepeviridae , 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 4 to 1.9 × 10 10 copies/ml of serum and from 1.8 × 10 4 to 1 × 10 12 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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Analysis of the full-length genome of hepatitis E virus isolates obtained from wild boars in Japan

Journal of General Virology ◽

10.1099/vir.0.81394-0 ◽

2005 ◽

Vol 86 (12) ◽

pp. 3321-3326 ◽

Cited By ~ 40

Author(s):

Tsutomu Nishizawa ◽

Masaharu Takahashi ◽

Kazunori Endo ◽

Shinji Fujiwara ◽

Nobuo Sakuma ◽

...

Keyword(s):

Hepatitis E Virus ◽

Hepatitis E ◽

Full Length ◽

Partial Sequence ◽

Genotype 3 ◽

Entire Genome ◽

Wild Boars ◽

Full Length Sequence ◽

Full Length Genome ◽

Virus Isolates

Two (2·3 %) of 87 wild-caught boars in Japan had detectable hepatitis E virus (HEV) RNA. The two boar HEV isolates (wbJTS1 and wbJYG1) obtained in the present study and a previously reported isolate (wbJSG1) whose partial sequence had been determined were sequenced over the entire genome. The wbJSG1, wbJTS1 and wbJYG1 isolates comprised 7225 or 7226 nt, excluding the poly(A) tail, and segregated into genotype 3. They differed by 8·5–11·2 % from each other and by 8·6–18·4 % from 17 reported genotype 3 HEV isolates, including one boar isolate, in the full-length sequence. When compared with 191 reported genotype 3 HEV isolates whose partial sequences were known, these three boar isolates were closer to Japanese isolates than to isolates of non-Japanese origin (89·2±2·6 vs 85·9±2·2 %; P<0·0001). A proportion of wild boars in Japan are infected with markedly heterogeneous HEV strains that are indigenous to Japan and may serve as reservoirs of HEV.

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Complete Genome Sequence of Hepatitis E Virus Genotype 3 Obtained from a Chronically Infected Individual in Uruguay

Microbiology Resource Announcements ◽

10.1128/mra.00367-21 ◽

2021 ◽

Vol 10 (22) ◽

Author(s):

Florencia Cancela ◽

Yanina Panzera ◽

Victoria Mainardi ◽

Solange Gerona ◽

Natalia Ramos ◽

...

Keyword(s):

Genome Sequence ◽

Hepatitis E Virus ◽

Reference Strain ◽

Acute Viral Hepatitis ◽

Infected Individual ◽

Hepatitis E ◽

Genotype 3 ◽

Virus Genotype ◽

Sequence Identity ◽

Full Length Genome

Hepatitis E is a leading cause of acute viral hepatitis worldwide. We report the full-length genome sequence of an HEV-3 strain obtained from a chronically infected patient from Uruguay. This strain shared only 86% nucleotide sequence identity with the most closely related reference strain belonging to subtype 3m.

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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

Genome Announcements ◽

10.1128/genomea.00345-17 ◽

2017 ◽

Vol 5 (20) ◽

Cited By ~ 7

Author(s):

Bo Wang ◽

Dominik Harms ◽

Jörg Hofmann ◽

Diana Ciardo ◽

Agnes Kneubühl ◽

...

Keyword(s):

Chronic Hepatitis ◽

Transplant Recipient ◽

Kidney Transplant ◽

Hepatitis E Virus ◽

Kidney Transplant Recipient ◽

Hepatitis E ◽

Genotype 3 ◽

Virus Genotype ◽

Causal Pathogen ◽

Full Length Genome

ABSTRACT Hepatitis E virus genotype 3 (HEV-3) is the causal pathogen of chronic hepatitis E. We report here the full-length genome sequence of an HEV-3 strain, isolated from a kidney transplant recipient in Switzerland (SW/16-0282). This HEV-3 strain showed less than 88% homology compared to known strains, suggesting a new HEV-3 strain.

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Classification of the Zoonotic Hepatitis E Virus Genotype 3 Into Distinct Subgenotypes

Frontiers in Microbiology ◽

10.3389/fmicb.2020.634430 ◽

2021 ◽

Vol 11 ◽

Author(s):

Florence Nicot ◽

Chloé Dimeglio ◽

Marion Migueres ◽

Nicolas Jeanne ◽

Justine Latour ◽

...

Keyword(s):

Molecular Epidemiology ◽

Hepatitis E Virus ◽

Hepatitis E ◽

Genotype 3 ◽

Genome Sequences ◽

Virus Genotype ◽

Subtype Classification ◽

Reference Sequences ◽

Epidemiology Studies

Hepatitis E virus (HEV) genotype 3 is the most common genotype linked to HEV infections in Europe and America. Three major clades (HEV-3.1, HEV-3.2, and HEV-3.3) have been identified but the overlaps between intra-subtype and inter-subtype p-distances make subtype classification inconsistent. Reference sequences have been proposed to facilitate communication between researchers and new putative subtypes have been identified recently. We have used the full or near full-length HEV-3 genome sequences available in the Genbank database (April 2020; n = 503) and distance analyses of clades HEV-3.1 and HEV-3.2 to determine a p-distance cut-off (0.093 nt substitutions/site) in order to define subtypes. This could help to harmonize HEV-3 genotyping, facilitate molecular epidemiology studies and investigations of the biological and clinical differences between HEV-3 subtypes.

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