Comprehensive Molecular Approach for Characterization of Hepatitis E Virus Genotype 3 Variants
| Autor: | Sonja Jacobsen, Sven Pischke, Heiner Wedermeyer, Marc Lütgehetmann, Dominik Harms, Sandra Niendorf, Bo Wang, C. Patrick Papp, C.-Thomas Bock, Jörg Hofmann |
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| Rok vydání: | 2018 |
| Předmět: |
Serum
0301 basic medicine Microbiology (medical) Genotype viruses Sequence Homology Biology Real-Time Polymerase Chain Reaction medicine.disease_cause Genome Homology (biology) Feces 03 medical and health sciences Hepatitis E virus Virology medicine Cluster Analysis Humans Gene Phylogeny Genetics Genetic diversity Phylogenetic tree Reverse Transcriptase Polymerase Chain Reaction virus diseases Genetic Variation Sequence Analysis DNA Viral Load Molecular diagnostics digestive system diseases Hepatitis E 030104 developmental biology Viral load |
| Zdroj: | Journal of Clinical Microbiology. 56 |
| ISSN: | 1098-660X 0095-1137 |
| Popis: | 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 |
| Databáze: | OpenAIRE |
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