|
1
|
Zhang F, Xu LD, Wu S, Wang B, Xu P, Huang YW. Deciphering the hepatitis E virus ORF1: Functional domains, protein processing, and patient-derived mutations. Virology 2025; 603:110350. [PMID: 39675187 DOI: 10.1016/j.virol.2024.110350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2024] [Revised: 11/25/2024] [Accepted: 12/05/2024] [Indexed: 12/17/2024]
Abstract
Hepatitis E virus (HEV) is a major cause of acute and chronic hepatitis in humans. The HEV open reading frames (ORF1) encodes a large non-structural protein essential for viral replication, which contains several functional domains, including helicase and RNA-dependent RNA polymerase. A confusing aspect is that, while RNA viruses typically encode large polyproteins that rely on their enzymatic activity for processing into functional units, the processing of the ORF1 protein and the mechanisms involved remain unclear. The ORF1 plays a pivotal role in the viral life cycle, thus mutations in this region, especially those occurring under environmental pressures such as during antiviral drug treatment, could significantly affect viral replication and survival. Here, we summarize the recent advances in the functional domains, processing, and mutations of ORF1. Gaining a deeper understanding of HEV biology, particularly focusing on ORF1, could facilitate the development of new strategies to control HEV infections.
Collapse
Affiliation(s)
- Fei Zhang
- Department of Hepatobiliary and Pancreatic Surgery and Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311215, China; MOE Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Ling-Dong Xu
- Department of Hepatobiliary and Pancreatic Surgery and Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China; MOE Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China; Laboratory Animal Center, Zhejiang University, Hangzhou, 310058, China
| | - Shiying Wu
- MOE Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China; College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Bin Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, 510642, China
| | - Pinglong Xu
- Department of Hepatobiliary and Pancreatic Surgery and Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311215, China; MOE Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China.
| | - Yao-Wei Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, 510642, China.
| |
Collapse
|
|
2
|
Kim DH, Kim DY, Kim JH, Lim KB, Cho AY, Lee JB, Park SY, Song CS, Lee SW, Lee DH, Kim DG, Choi IS. Utility of hypervariable region in hepatitis E virus for genetic evolution analysis and epidemiological studies. J Gen Virol 2025; 106. [PMID: 39937581 DOI: 10.1099/jgv.0.002080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2025] Open
Abstract
Clinical and experimental studies have advanced our understanding of hepatitis E virus (HEV) infection; however, translating the findings to improve prevention and clinical outcomes remains challenging. Phylogenetic analyses of HEV show inconsistencies due to variations in the nucleotide regions studied. This study examined specific HEV regions to facilitate comprehensive molecular and phylogenetic analyses by examining the complete genome and commonly studied partial genome regions. We compared topological similarities between phylogenetic trees and evaluated evolutionary divergence using base substitutions and pairwise distances. The hypervariable region (HVR) showed the closest topology (Robinson-Foulds, Jaccard Robinson-Foulds and clustering information) to the complete genome and a higher mutation rate, resulting in longer branch lengths and clearer genotypic distinctions. Pairwise analysis revealed greater intra- and intergenotypic diversity in the HVR than in other regions. The higher base substitution rate and longer branch lengths of HVR suggest its key role in genotype evolution. Classifying HEV using HVR instead of the other partial genomic regions can reveal subtypes that more accurately reflect the genetic characteristics of HEV. Future research could focus on HVRs to better compare clinical symptoms and genetic features of HEV.
Collapse
Affiliation(s)
- Dong-Hwi Kim
- Department of Infectious Diseases, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Seoul 05029, Gwangjin-gu, Republic of Korea
| | - Da-Yoon Kim
- Department of Infectious Diseases, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Seoul 05029, Gwangjin-gu, Republic of Korea
| | - Jae-Hyeong Kim
- Department of Infectious Diseases, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Seoul 05029, Gwangjin-gu, Republic of Korea
| | - Kyu-Beom Lim
- Department of Infectious Diseases, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Seoul 05029, Gwangjin-gu, Republic of Korea
| | - Andrew Y Cho
- Department of Infectious Diseases, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Seoul 05029, Gwangjin-gu, Republic of Korea
| | - Joong-Bok Lee
- Department of Infectious Diseases, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Seoul 05029, Gwangjin-gu, Republic of Korea
- Konkuk University Zoonotic Diseases Research Center, Konkuk University, 120 Neungdong-ro, Seoul 05029, Gwangjin-gu, Republic of Korea
| | - Seung-Yong Park
- Department of Infectious Diseases, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Seoul 05029, Gwangjin-gu, Republic of Korea
- Konkuk University Zoonotic Diseases Research Center, Konkuk University, 120 Neungdong-ro, Seoul 05029, Gwangjin-gu, Republic of Korea
| | - Chang-Seon Song
- Department of Infectious Diseases, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Seoul 05029, Gwangjin-gu, Republic of Korea
- Konkuk University Zoonotic Diseases Research Center, Konkuk University, 120 Neungdong-ro, Seoul 05029, Gwangjin-gu, Republic of Korea
| | - Sang-Won Lee
- Department of Infectious Diseases, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Seoul 05029, Gwangjin-gu, Republic of Korea
- Konkuk University Zoonotic Diseases Research Center, Konkuk University, 120 Neungdong-ro, Seoul 05029, Gwangjin-gu, Republic of Korea
| | - Dong-Hun Lee
- Department of Infectious Diseases, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Seoul 05029, Gwangjin-gu, Republic of Korea
- Konkuk University Zoonotic Diseases Research Center, Konkuk University, 120 Neungdong-ro, Seoul 05029, Gwangjin-gu, Republic of Korea
| | - Do-Geun Kim
- Korea Brain Research Institute (KBRI), Daegu, Republic of Korea
- Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
| | - In-Soo Choi
- Department of Infectious Diseases, College of Veterinary Medicine, Konkuk University, 120 Neungdong-ro, Seoul 05029, Gwangjin-gu, Republic of Korea
- Konkuk University Zoonotic Diseases Research Center, Konkuk University, 120 Neungdong-ro, Seoul 05029, Gwangjin-gu, Republic of Korea
- KU Center for Animal Blood Medical Science, Konkuk University, 120 Neungdong-ro, Seoul 05029, Gwangjin-gu, Republic of Korea
| |
Collapse
|
|
3
|
Ruiz-Ponsell L, Monastiri A, López-Roig M, Sauleda S, Bes M, Mentaberre G, Escobar-González M, Costafreda MI, López-Olvera JR, Serra-Cobo J. Endemic maintenance of human-related hepatitis E virus strains in synurbic wild boars, Barcelona Metropolitan Area, Spain. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 955:176871. [PMID: 39395489 DOI: 10.1016/j.scitotenv.2024.176871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Revised: 10/08/2024] [Accepted: 10/09/2024] [Indexed: 10/14/2024]
Abstract
Hepatitis E virus (HEV), shared by humans, domestic animals, and wildlife, is an emerging global public health threat. Because wild boars are a major reservoir of HEV, the new zoonotic interfaces resulting from wild boar population increase and synurbization significantly contribute to increasing the risk of zoonotic transmission of HEV. This study characterizes HEV strains of synurbic wild boars and assesses their relationship with sympatric human and domestic swine HEV strains. We analyzed the faeces of 312 synurbic wild boars collected from 2016 to 2021 in the Barcelona Metropolitan Area (BMA), where there is a high density of wild boars, and found 7 HEV-positive samples among those collected between 2019 and 2020. The molecular analysis of these isolates, along with 6 additional wild boar HEV isolates from a previous study, allowed us to establish a close phylogenetic relationship between these HEV strains and human HEV isolates from sympatric blood donors and domestic pigs from Catalonia. HEV-positive wild boar samples belonged to piglet, juvenile and yearling individuals, but not adults, indicating the endemic maintenance of HEV in the wild boar population of the BMA by naïve young individuals. All wild boar HEV isolates in this study classified within HEV genotype 3. The results show, for the first time, a close molecular similarity between the HEV strains endemically maintained by the synurbic wild boars in the BMA and citizens from the same area and period. The data could also indicate that HEV infection presents a seasonal and interannual variability in wild boars of BMA. Further investigation is required to unveil the HEV transmission routes between synurbic wild boars and sympatric citizens. These findings can serve in other synurbic wildlife-human interfaces throughout the world.
Collapse
Affiliation(s)
| | - Abir Monastiri
- Universitat de Barcelona, Barcelona, Spain; Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Spain
| | - Marc López-Roig
- Universitat de Barcelona, Barcelona, Spain; Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Spain
| | - Sílvia Sauleda
- Banc de Sang i Teixits de Catalunya, Barcelona, Spain; Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Bes
- Banc de Sang i Teixits de Catalunya, Barcelona, Spain; Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Gregorio Mentaberre
- Wildlife Ecology and Health Group, Barcelona, Spain; Universitat de Lleida, Lleida, Spain
| | - María Escobar-González
- Wildlife Ecology and Health Group, Barcelona, Spain; Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Barcelona, Spain
| | - Maria I Costafreda
- Universitat de Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Institut de Recerca en Nutrició i Seguretat Alimentària (INSA), Santa Coloma de Gramanet, Spain.
| | - Jorge R López-Olvera
- Wildlife Ecology and Health Group, Barcelona, Spain; Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Barcelona, Spain
| | - Jordi Serra-Cobo
- Universitat de Barcelona, Barcelona, Spain; Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Spain
| |
Collapse
|
|
4
|
Hakze-van der Honing RW, Franz E, van der Poel WH, Coipan CE. Utility of various genome lengths in diversity and evolution analyses of Hepatitis E virus. Virus Res 2024; 347:199429. [PMID: 38960004 PMCID: PMC11296050 DOI: 10.1016/j.virusres.2024.199429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/28/2024] [Accepted: 06/30/2024] [Indexed: 07/05/2024]
Abstract
The aim of this study was to investigate to what extent fragments of the HEV genome could be used for accurate diagnostics and inference of viral population-scale processes. For this, we selected all the published whole genome sequences from the NCBI GenBank and trimmed them to various fragment lengths (ORF1,2,3, ORF1, ORF2, ORF3, 493 nt in ORF2 and 148 nt in ORF2). Each of the fragment lengths was used to infer the richness and diversity of the viral sequence types, typing accuracy, and potential use in phylodynamics. The results obtained from the different fragments were compared. We observed that, generally, the longer the nucleic acid fragment used in typing, the better the accuracy in predicting the viral subtype. However, the dominant HEV subtypes circulating in Europe were relatively well classified even by the 493 nt fragment, with false negative rates as low as 8 in 1000 typed sequences. Most fragments also give comparable results in analyses of population size, albeit with shorter fragments showing a broader 95 % highest posterior density interval and less obvious increase of the viral effective population size. The reconstructed phylogenies of a heterochronous subset indicated a good concordance between all the fragments, with the major clades following similar branching patterns. Furthermore, we have used the HEV sequence data from the Netherlands available in the HEVnet database as a case study for reconstruction of population size changes in the past decades. This data showed that molecular and epidemiological results are concordant and point to an increase in the viral effective population size underlying the observed increase in incidence of acute HEV infection cases. In the absence of whole genome sequencing data, the 493 bp fragment can be used for analyzing HEV strains currently circulating in Europe, as it is informative for describing short term population-scale processes.
Collapse
Affiliation(s)
| | - Eelco Franz
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Wim H.M. van der Poel
- Wageningen University and Research, Houtribweg 39, 8221 RA, Lelystad, the Netherlands
| | - Claudia E. Coipan
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| |
Collapse
|
|
5
|
Orosz L, Sárvári KP, Dernovics Á, Rosztóczy A, Megyeri K. Pathogenesis and clinical features of severe hepatitis E virus infection. World J Virol 2024; 13:91580. [PMID: 38984076 PMCID: PMC11229844 DOI: 10.5501/wjv.v13.i2.91580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/08/2024] [Accepted: 04/15/2024] [Indexed: 06/24/2024] Open
Abstract
The hepatitis E virus (HEV), a member of the Hepeviridae family, is a small, non-enveloped icosahedral virus divided into eight distinct genotypes (HEV-1 to HEV-8). Only genotypes 1 to 4 are known to cause diseases in humans. Genotypes 1 and 2 commonly spread via fecal-oral transmission, often through the consumption of contaminated water. Genotypes 3 and 4 are known to infect pigs, deer, and wild boars, often transferring to humans through inadequately cooked meat. Acute hepatitis caused by HEV in healthy individuals is mostly asymptomatic or associated with minor symptoms, such as jaundice. However, in immunosuppressed individuals, the disease can progress to chronic hepatitis and even escalate to cirrhosis. For pregnant women, an HEV infection can cause fulminant liver failure, with a potential mortality rate of 25%. Mortality rates also rise amongst cirrhotic patients when they contract an acute HEV infection, which can even trigger acute-on-chronic liver failure if layered onto pre-existing chronic liver disease. As the prevalence of HEV infection continues to rise worldwide, highlighting the particular risks associated with severe HEV infection is of major medical interest. This text offers a brief summary of the characteristics of hepatitis developed by patient groups at an elevated risk of severe HEV infection.
Collapse
Affiliation(s)
- László Orosz
- Department of Medical Microbiology, University of Szeged, Szeged 6720, Csongrád-Csanád, Hungary
| | - Károly Péter Sárvári
- Department of Medical Microbiology, University of Szeged, Szeged 6720, Csongrád-Csanád, Hungary
| | - Áron Dernovics
- Department of Medical Microbiology, University of Szeged, Szeged 6720, Csongrád-Csanád, Hungary
| | - András Rosztóczy
- Department of Internal Medicine, Division of Gastroenterology, University of Szeged, Szeged 6725, Csongrád-Csanád, Hungary
| | - Klára Megyeri
- Department of Medical Microbiology, University of Szeged, Szeged 6720, Csongrád-Csanád, Hungary
| |
Collapse
|
|
6
|
Pierce DM, Buchanan FJT, Macrae FL, Mills JT, Cox A, Abualsaoud KM, Ward JC, Ariëns RAS, Harris M, Stonehouse NJ, Herod MR. Thrombin cleavage of the hepatitis E virus polyprotein at multiple conserved locations is required for genome replication. PLoS Pathog 2023; 19:e1011529. [PMID: 37478143 PMCID: PMC10395923 DOI: 10.1371/journal.ppat.1011529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 07/03/2023] [Indexed: 07/23/2023] Open
Abstract
The genomes of positive-sense RNA viruses encode polyproteins that are essential for mediating viral replication. These viral polyproteins must undergo proteolysis (also termed polyprotein processing) to generate functional protein units. This proteolysis can be performed by virally-encoded proteases as well as host cellular proteases, and is generally believed to be a key step in regulating viral replication. Hepatitis E virus (HEV) is a leading cause of acute viral hepatitis. The positive-sense RNA genome is translated to generate a polyprotein, termed pORF1, which is necessary and sufficient for viral genome replication. However, the mechanism of polyprotein processing in HEV remains to be determined. In this study, we aimed to understand processing of this polyprotein and its role in viral replication using a combination of in vitro translation experiments and HEV sub-genomic replicons. Our data suggest no evidence for a virally-encoded protease or auto-proteolytic activity, as in vitro translation predominantly generates unprocessed viral polyprotein precursors. However, seven cleavage sites within the polyprotein (suggested by bioinformatic analysis) are susceptible to the host cellular protease, thrombin. Using two sub-genomic replicon systems, we demonstrate that mutagenesis of these sites prevents replication, as does pharmacological inhibition of serine proteases including thrombin. Overall, our data supports a model where HEV uses host proteases to support replication and could have evolved to be independent of a virally-encoded protease for polyprotein processing.
Collapse
Affiliation(s)
- Danielle M Pierce
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Frazer J T Buchanan
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Fraser L Macrae
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, United Kingdom
| | - Jake T Mills
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Abigail Cox
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Khadijah M Abualsaoud
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
- Department of Laboratory and Blood Bank, Al Mikhwah General Hospital, Al Mikhwah, Saudi Arabia
| | - Joseph C Ward
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Robert A S Ariëns
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, United Kingdom
| | - Mark Harris
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Nicola J Stonehouse
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Morgan R Herod
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| |
Collapse
|
|
7
|
Ju X, Dong L, Ding Q. Hepatitis E Virus Life Cycle. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1417:141-157. [PMID: 37223864 DOI: 10.1007/978-981-99-1304-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Hepatitis E virus (HEV) infects over 20 million people worldwide per year, leading to 30,000-40,000 deaths. In most cases HEV infection in a self-limited, acute illness. However, chronic infections could occur in immunocompromised individuals. Due to scarcity of robust cell culture models in vitro and genetic tractable animal models in vivo, the details of HEV life cycle, as well as its interaction with host cells still remain elusive, which dampens antivirals discovery. In this chapter, we present an update in the HEV infectious cycle steps: entry, genome replication/subgenomic RNA transcription, assembly, and release. Moreover, we discussed the future prospective on HEV research and illustrates important questions urgently to be addressed.
Collapse
Affiliation(s)
- Xiaohui Ju
- School of Medicine, Tsinghua University, Beijing, China
| | - Lin Dong
- School of Medicine, Tsinghua University, Beijing, China
| | - Qiang Ding
- School of Medicine, Tsinghua University, Beijing, China.
| |
Collapse
|
|
8
|
He Q, Zhang Y, Gong W, Zeng H, Wang L. Genetic Evolution of Hepatitis E Virus. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1417:59-72. [PMID: 37223859 DOI: 10.1007/978-981-99-1304-6_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Comparative analysis of the genomic sequences of multiple hepatitis E virus (HEV) isolates has revealed extensive genomic diversity among them. Recently, a variety of genetically distinct HEV variants have also been isolated and identified from large numbers of animal species, including birds, rabbits, rats, ferrets, bats, cutthroat trout, and camels, among others. Furthermore, it has been reported that recombination in HEV genomes takes place in animals and in human patients. Also, chronic HEV infection in immunocompromised individuals has revealed the presence of viral strains carrying insertions from human genes. This paper reviews current knowledge on the genomic variability and evolution of HEV.
Collapse
Affiliation(s)
- Qiyu He
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Yulin Zhang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Wanyun Gong
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Hang Zeng
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Ling Wang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.
| |
Collapse
|
|
9
|
Cancela F, Noceti O, Arbiza J, Mirazo S. Structural aspects of hepatitis E virus. Arch Virol 2022; 167:2457-2481. [PMID: 36098802 PMCID: PMC9469829 DOI: 10.1007/s00705-022-05575-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/04/2022] [Indexed: 12/14/2022]
Abstract
Hepatitis E virus (HEV) is a leading cause of acute hepatitis worldwide. Hepatitis E is an enterically transmitted zoonotic disease that causes large waterborne epidemic outbreaks in developing countries and has become an increasing public-health concern in industrialized countries. In this setting, the infection is usually acute and self-limiting in immunocompetent individuals, although chronic cases in immunocompromised patients have been reported, frequently associated with several extrahepatic manifestations. Moreover, extrahepatic manifestations have also been reported in immunocompetent individuals with acute HEV infection. HEV belongs to the alphavirus-like supergroup III of single-stranded positive-sense RNA viruses, and its genome contains three partially overlapping open reading frames (ORFs). ORF1 encodes a nonstructural protein with eight domains, most of which have not been extensively characterized: methyltransferase, Y domain, papain-like cysteine protease, hypervariable region, proline-rich region, X domain, Hel domain, and RNA-dependent RNA polymerase. ORF2 and ORF3 encode the capsid protein and a multifunctional protein believed to be involved in virion release, respectively. The novel ORF4 is only expressed in HEV genotype 1 under endoplasmic reticulum stress conditions, and its exact function has not yet been elucidated. Despite important advances in recent years, the biological and molecular processes underlying HEV replication remain poorly understood, primarily due to a lack of detailed information about the functions of the viral proteins and the mechanisms involved in host-pathogen interactions. This review summarizes the current knowledge concerning HEV proteins and their biological properties, providing updated detailed data describing their function and focusing in detail on their structural characteristics. Furthermore, we review some unclear aspects of the four proteins encoded by the ORFs, highlighting the current key information gaps and discussing potential novel experimental strategies for shedding light on those issues.
Collapse
Affiliation(s)
- Florencia Cancela
- grid.11630.350000000121657640Sección Virología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Ofelia Noceti
- grid.414402.70000 0004 0469 0889Programa Nacional de Trasplante Hepático y Unidad Docente Asistencial Centro Nacional de Tratamiento Hepatobiliopancreatico. Hospital Central de las Fuerzas Armadas, Montevideo, Uruguay
| | - Juan Arbiza
- grid.11630.350000000121657640Sección Virología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Santiago Mirazo
- grid.11630.350000000121657640Sección Virología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay ,grid.11630.350000000121657640Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay ,Av. Alfredo Navarro 3051, PC 11600 Montevideo, Uruguay
| |
Collapse
|
|
10
|
Pellerin M, Hirchaud E, Blanchard Y, Pavio N, Doceul V. Characterization of a Cell Culture System of Persistent Hepatitis E Virus Infection in the Human HepaRG Hepatic Cell Line. Viruses 2021; 13:406. [PMID: 33806591 PMCID: PMC8001476 DOI: 10.3390/v13030406] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/19/2021] [Accepted: 02/26/2021] [Indexed: 12/12/2022] Open
Abstract
Hepatitis E virus (HEV) is considered as an emerging global health problem. In most cases, hepatitis E is a self-limiting disease and the virus is cleared spontaneously without the need of antiviral therapy. However, immunocompromised individuals can develop chronic infection and liver fibrosis that can progress rapidly to cirrhosis and liver failure. The lack of efficient and relevant cell culture system and animal models has limited our understanding of the biology of HEV and the development of effective drugs for chronic cases. In the present study, we developed a model of persistent HEV infection in human hepatocytes in which HEV replicates efficiently. This HEV cell culture system is based on differentiated HepaRG cells infected with an isolate of HEV-3 derived from a patient suffering from acute hepatitis E. Efficient replication was maintained for several weeks to several months as well as after seven successive passages on HepaRG naïve cells. Moreover, after six passages onto HepaRG, we found that the virus was still infectious after oral inoculation into pigs. We also showed that ribavirin had an inhibitory effect on HEV replication in HepaRG. In conclusion, this system represents a relevant and efficient in vitro model of HEV replication that could be useful to study HEV biology and identify effective antiviral drugs against chronic HEV infection.
Collapse
Affiliation(s)
- Marie Pellerin
- UMR 1161 Virologie, INRAE, ANSES, Ecole Nationale Vétérinaire d’Alfort, Université Paris-Est, 94700 Maisons-Alfort, France; (M.P.); (N.P.)
| | - Edouard Hirchaud
- Agence Nationale de Sécurité Sanitaire, De L’environnement et du Travail (ANSES), Laboratory of Ploufragan-Plouzané-Niort, Viral Genetic and Biosafety (GVB) Unit, 22440 Ploufragan, France; (E.H.); (Y.B.)
| | - Yannick Blanchard
- Agence Nationale de Sécurité Sanitaire, De L’environnement et du Travail (ANSES), Laboratory of Ploufragan-Plouzané-Niort, Viral Genetic and Biosafety (GVB) Unit, 22440 Ploufragan, France; (E.H.); (Y.B.)
| | - Nicole Pavio
- UMR 1161 Virologie, INRAE, ANSES, Ecole Nationale Vétérinaire d’Alfort, Université Paris-Est, 94700 Maisons-Alfort, France; (M.P.); (N.P.)
| | - Virginie Doceul
- UMR 1161 Virologie, INRAE, ANSES, Ecole Nationale Vétérinaire d’Alfort, Université Paris-Est, 94700 Maisons-Alfort, France; (M.P.); (N.P.)
| |
Collapse
|
|
11
|
Yadav KK, Boley PA, Fritts Z, Kenney SP. Ectopic Expression of Genotype 1 Hepatitis E Virus ORF4 Increases Genotype 3 HEV Viral Replication in Cell Culture. Viruses 2021; 13:v13010075. [PMID: 33430442 PMCID: PMC7827316 DOI: 10.3390/v13010075] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/05/2021] [Accepted: 01/05/2021] [Indexed: 02/07/2023] Open
Abstract
Hepatitis E virus (HEV) can account for up to a 30% mortality rate in pregnant women, with highest incidences reported for genotype 1 (gt1) HEV. Reasons contributing to adverse maternal-fetal outcome during pregnancy in HEV-infected pregnant women remain elusive in part due to the lack of a robust tissue culture model for some strains. Open reading frame (ORF4) was discovered overlapping ORF1 in gt1 HEV whose protein expression is regulated via an IRES-like RNA element. To experimentally determine whether gt3 HEV contains an ORF4-like gt1, gt1 and gt3 sequence comparisons were performed between the gt1 and the homologous gt3 sequence. To assess whether ORF4 protein could enhance gt3 replication, Huh7 cell lines constitutively expressing ORF4 were created and used to assess the replication of the Kernow-C1 gt3 and sar55 gt1 HEV. Virus stocks from transfected Huh7 cells with or without ORF4 were harvested and infectivity assessed via infection of HepG2/C3A cells. We also studied the replication of gt1 HEV in the ORF4-expressing tunicamycin-treated cell line. To directly show that HEV transcripts have productively replicated in the target cells, we assessed events at the single-cell level using indirect immunofluorescence and flow cytometry. Despite not naturally encoding ORF4, replication of gt3 HEV was enhanced by the presence of gt1 ORF4 protein. These results suggest that the function of ORF4 protein from gt1 HEV is transferrable, enhancing the replication of gt3 HEV. ORF4 may be utilized to enhance replication of difficult to propagate HEV genotypes in cell culture. IMPORTANCE: HEV is a leading cause of acute viral hepatitis (AVH) around the world. The virus is a threat to pregnant women, particularly during the second and third trimester of pregnancy. The factors enhancing virulence to pregnant populations are understudied. Additionally, field strains of HEV remain difficult to culture in vitro. ORF4 was recently discovered in gt1 HEV and is purported to play a role in pregnancy related pathology and enhanced replication. We present evidence that ORF4 protein provided in trans enhances the viral replication of gt3 HEV even though it does not encode ORF4 naturally in its genome. These data will aid in the development of cell lines capable of supporting replication of non-cell culture adapted HEV field strains, allowing viral titers sufficient for studying these strains in vitro. Furthermore, development of gt1/gt3 ORF4 chimeric virus may shed light on the role that ORF4 plays during pregnancy.
Collapse
Affiliation(s)
- Kush K. Yadav
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center (OARDC), The Ohio State University, Wooster, OH 44691, USA; (K.K.Y.); (P.A.B.)
| | - Patricia A. Boley
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center (OARDC), The Ohio State University, Wooster, OH 44691, USA; (K.K.Y.); (P.A.B.)
| | - Zachary Fritts
- Department of Electrical and Computer Engineering, University of Michigan, Ann Arbor, MI 48105, USA;
| | - Scott P. Kenney
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center (OARDC), The Ohio State University, Wooster, OH 44691, USA; (K.K.Y.); (P.A.B.)
- Correspondence:
| |
Collapse
|
|
12
|
Pallerla SR, Harms D, Johne R, Todt D, Steinmann E, Schemmerer M, Wenzel JJ, Hofmann J, Shih JWK, Wedemeyer H, Bock CT, Velavan TP. Hepatitis E Virus Infection: Circulation, Molecular Epidemiology, and Impact on Global Health. Pathogens 2020; 9:E856. [PMID: 33092306 PMCID: PMC7589794 DOI: 10.3390/pathogens9100856] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/09/2020] [Accepted: 10/16/2020] [Indexed: 12/11/2022] Open
Abstract
Infection with hepatitis E virus (HEV) represents the most common source of viral hepatitis globally. Although infecting over 20 million people annually in endemic regions, with major outbreaks described since the 1950s, hepatitis E remains an underestimated disease. This review gives a current view of the global circulation and epidemiology of this emerging virus. The history of HEV, from the first reported enteric non-A non-B hepatitis outbreaks, to the discovery of the viral agent and the molecular characterization of the different human pathogenic genotypes, is discussed. Furthermore, the current state of research regarding the virology of HEV is critically assessed, and the challenges towards prevention and diagnosis, as well as clinical risks of the disease described. Together, these points aim to underline the significant impact of hepatitis E on global health and the need for further in-depth research to better understand the pathophysiology and its role in the complex disease manifestations of HEV infection.
Collapse
Affiliation(s)
- Srinivas Reddy Pallerla
- Institute of Tropical Medicine, University of Tübingen, 72074 Tübingen, Germany; (S.R.P.); (T.P.V.)
- Vietnamese-German Center for Medical Research (VG-CARE), Hanoi 100000, Vietnam
| | - Dominik Harms
- Division of Viral Gastroenteritis and Hepatitis Pathogens and Enteroviruses, Department of Infectious Diseases, Robert Koch Institute, 13353 Berlin, Germany;
| | - Reimar Johne
- Unit Viruses in Food, Department Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany;
| | - Daniel Todt
- Department of Molecular and Medical Virology, Ruhr University Bochum, 44801 Bochum, Germany; (D.T.); (E.S.)
- European Virus Bioinformatics Center (EVBC), 07743 Jena, Germany
| | - Eike Steinmann
- Department of Molecular and Medical Virology, Ruhr University Bochum, 44801 Bochum, Germany; (D.T.); (E.S.)
| | - Mathias Schemmerer
- Institute of Clinical Microbiology and Hygiene, National Consultant Laboratory for HAV and HEV, University Medical Center Regensburg, 93053 Regensburg, Germany; (M.S.); (J.J.W.)
| | - Jürgen J. Wenzel
- Institute of Clinical Microbiology and Hygiene, National Consultant Laboratory for HAV and HEV, University Medical Center Regensburg, 93053 Regensburg, Germany; (M.S.); (J.J.W.)
| | - Jörg Hofmann
- Institute of Virology, Charité Universitätsmedizin Berlin, Labor Berlin-Charité-Vivantes GmbH, 13353 Berlin, Germany;
| | | | - Heiner Wedemeyer
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, 30623 Hannover, Germany;
- German Center for Infection Research, Partner Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - C.-Thomas Bock
- Institute of Tropical Medicine, University of Tübingen, 72074 Tübingen, Germany; (S.R.P.); (T.P.V.)
- Division of Viral Gastroenteritis and Hepatitis Pathogens and Enteroviruses, Department of Infectious Diseases, Robert Koch Institute, 13353 Berlin, Germany;
| | - Thirumalaisamy P. Velavan
- Institute of Tropical Medicine, University of Tübingen, 72074 Tübingen, Germany; (S.R.P.); (T.P.V.)
- Vietnamese-German Center for Medical Research (VG-CARE), Hanoi 100000, Vietnam
- Faculty of Medicine, Duy Tan University, Da Nang 550000, Vietnam
| |
Collapse
|
|
13
|
Virus-Host Cell Interplay during Hepatitis E Virus Infection. Trends Microbiol 2020; 29:309-319. [PMID: 32828646 PMCID: PMC7437515 DOI: 10.1016/j.tim.2020.07.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/26/2020] [Accepted: 07/22/2020] [Indexed: 12/11/2022]
Abstract
The molecular interplay between cellular host factors and viral proteins is a continuous process throughout the viral life cycle determining virus host range and pathogenesis. The hepatitis E virus (HEV) is a long-neglected RNA virus and the major causative agent of acute viral hepatitis in humans worldwide. However, the mechanisms of liver pathology and clinical disease remain poorly understood for HEV infection. This review summarizes our current understanding of HEV-host cell interactions and highlights experimental strategies and techniques to identify novel host components required for the viral life cycle as well as restriction factors. Understanding these interactions will provide insight into the viral life cycle of HEV and might further help to devise novel therapeutic strategies and antiviral targets.
Collapse
|
|
14
|
LeDesma R, Nimgaonkar I, Ploss A. Hepatitis E Virus Replication. Viruses 2019; 11:E719. [PMID: 31390784 PMCID: PMC6723718 DOI: 10.3390/v11080719] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 07/31/2019] [Accepted: 08/02/2019] [Indexed: 12/19/2022] Open
Abstract
Hepatitis E virus (HEV) is a small quasi-enveloped, (+)-sense, single-stranded RNA virus belonging to the Hepeviridae family. There are at least 20 million HEV infections annually and 60,000 HEV-related deaths worldwide. HEV can cause up to 30% mortality in pregnant women and progress to liver cirrhosis in immunocompromised individuals and is, therefore, a greatly underestimated public health concern. Although a prophylactic vaccine for HEV has been developed, it is only licensed in China, and there is currently no effective, non-teratogenic treatment. HEV encodes three open reading frames (ORFs). ORF1 is the largest viral gene product, encoding the replicative machinery of the virus including a methyltransferase, RNA helicase, and an RNA-dependent RNA polymerase. ORF1 additionally contains a number of poorly understood domains including a hypervariable region, a putative protease, and the so-called 'X' and 'Y' domains. ORF2 is the viral capsid essential for formation of infectious particles and ORF3 is a small protein essential for viral release. In this review, we focus on the domains encoded by ORF1, which collectively mediate the virus' asymmetric genome replication strategy. We summarize what is known, unknown, and hotly debated regarding the coding and non-coding regions of HEV ORF1, and present a model of how HEV replicates its genome.
Collapse
Affiliation(s)
- Robert LeDesma
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ 08544, USA
| | - Ila Nimgaonkar
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ 08544, USA
| | - Alexander Ploss
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ 08544, USA.
| |
Collapse
|
|
15
|
Life cycle and morphogenesis of the hepatitis E virus. Emerg Microbes Infect 2018; 7:196. [PMID: 30498191 PMCID: PMC6265337 DOI: 10.1038/s41426-018-0198-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 11/01/2018] [Accepted: 11/05/2018] [Indexed: 12/19/2022]
Abstract
Hepatitis E virus (HEV) is transmitted primarily via contaminated water and food by the fecal oral route and causes epidemics in developing countries. In industrialized countries, zoonotic transmission of HEV is prevalent. In addition, HEV is the major cause of acute hepatitis in healthy adults and can cause chronic hepatitis in immunocompromised patients, with pregnant HEV-infected women having increased mortality rates of approximately 25%. HEV was once an understudied and neglected virus. However, in recent years, the safety of blood products with respect to HEV has increasingly been considered to be a public health problem. The establishment of HEV infection models has enabled significant progress to be made in understanding its life cycle. HEV infects cells via a receptor (complex) that has yet to be identified. The HEV replication cycle is initiated immediately after the (+) stranded RNA genome is released into the cell cytosol. Subsequently, infectious viral particles are released by the ESCRT complex as quasi-enveloped viruses (eHEVs) into the serum, whereas feces and urine contain only nonenveloped infectious viral progeny. The uncoating of the viral envelope takes place in the biliary tract, resulting in the generation of a nonenveloped virus that is more resistant to environmental stress and possesses a higher infectivity than that of eHEV. This review summarizes the current knowledge regarding the HEV life cycle, viral morphogenesis, established model systems and vaccine development.
Collapse
|
|
16
|
Grierson SS, McGowan S, Cook C, Steinbach F, Choudhury B. Molecular and in vitro characterisation of hepatitis E virus from UK pigs. Virology 2018; 527:116-121. [PMID: 30496912 DOI: 10.1016/j.virol.2018.10.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/18/2018] [Accepted: 10/19/2018] [Indexed: 02/08/2023]
Abstract
Hepatitis E virus (HEV) infection is widespread in the global pig population. Although clinically inapparent in pigs, HEV infection is the cause of Hepatitis E in humans and transmission via the food chain has been established. Following a 2013 study that investigated prevalence of HEV infection in UK slaughter-age pigs samples indicating highest viral load were selected for further characterisation. High throughput sequencing was used to obtain the complete coding sequence from five samples. An in-frame insertion was observed within the HEV hypervariable region in two samples. To interrogate whether this mutation may be the cause of high-level viraemia and faecal shedding as observed in the sampled pigs virus isolation and culture was conducted. Based on viral growth kinetics there was no evidence that these insertions affected replication efficiency in vitro, suggesting as yet undetermined host factors may affect the course of infection and consequently the risk of foodborne transmission.
Collapse
Affiliation(s)
- Sylvia S Grierson
- Animal and Plant Health Agency, Department of Virology, Addlestone, Surrey, UK.
| | - Sarah McGowan
- Animal and Plant Health Agency, Department of Virology, Addlestone, Surrey, UK
| | - Charlotte Cook
- Animal and Plant Health Agency, Department of Epidemiological Sciences, Addlestone, Surrey, UK
| | - Falko Steinbach
- Animal and Plant Health Agency, Department of Virology, Addlestone, Surrey, UK
| | - Bhudipa Choudhury
- Animal and Plant Health Agency, Department of Virology, Addlestone, Surrey, UK
| |
Collapse
|
|
17
|
Smith DB, Simmonds P. Classification and Genomic Diversity of Enterically Transmitted Hepatitis Viruses. Cold Spring Harb Perspect Med 2018; 8:a031880. [PMID: 29530950 PMCID: PMC6120691 DOI: 10.1101/cshperspect.a031880] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Hepatitis A virus (HAV) and hepatitis E virus (HEV) are significant human pathogens and are responsible for a substantial proportion of cases of severe acute hepatitis worldwide. Genetically, both viruses are heterogeneous and are classified into several genotypes that differ in their geographical distribution and risk group association. There is, however, little evidence that variants of HAV or HEV differ antigenically or in their propensity to cause severe disease. Genetically more divergent but primarily hepatotropic variants of both HAV and HEV have been found in several mammalian species, those of HAV being classified into eight species within the genus Hepatovirus in the virus family Picornaviridae. HEV is classified as a member of the species Orthohepevirus A in the virus family Hepeviridae, a species that additionally contains viruses infecting pigs, rabbits, and a variety of other mammalian species. Other species (Orthohepevirus B-D) infect a wide range of other mammalian species including rodents and bats.
Collapse
Affiliation(s)
- Donald B Smith
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, United Kingdom
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, United Kingdom
| |
Collapse
|
|
18
|
Nicot F, Jeanne N, Roulet A, Lefebvre C, Carcenac R, Manno M, Dubois M, Kamar N, Lhomme S, Abravanel F, Izopet J. Diversity of hepatitis E virus genotype 3. Rev Med Virol 2018; 28:e1987. [PMID: 29939461 DOI: 10.1002/rmv.1987] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 05/12/2018] [Accepted: 05/21/2018] [Indexed: 12/27/2022]
Abstract
Hepatitis E virus genotype 3 (HEV-3) can lead to chronic infection in immunocompromised patients, and ribavirin is the treatment of choice. Recently, mutations in the polymerase gene have been associated with ribavirin failure but their frequency before treatment according to HEV-3 subtypes has not been studied on a large data set. We used single-molecule real-time sequencing technology to sequence 115 new complete genomes of HEV-3 infecting French patients. We analyzed phylogenetic relationships, the length of the polyproline region, and mutations in the HEV polymerase gene. Eighty-five (74%) were in the clade HEV-3efg, 28 (24%) in HEV-3chi clade, and 2 (2%) in HEV-3ra clade. Using automated partitioning of maximum likelihood phylogenetic trees, complete genomes were classified into subtypes. Polyproline region length differs within HEV-3 clades (from 189 to 315 nt). Investigating mutations in the polymerase gene, distinct polymorphisms between HEV-3 subtypes were found (G1634R in 95% of HEV-3e, G1634K in 56% of HEV-3ra, and V1479I in all HEV-3efg, clade HEV-3ra, and HEV-3k strains). Subtype-specific polymorphisms in the HEV-3 polymerase have been identified. Our study provides new complete genome sequences of HEV-3 that could be useful for comparing strains circulating in humans and the animal reservoir.
Collapse
Affiliation(s)
- Florence Nicot
- Centre National de Référence du virus de l'hépatite E, Laboratoire de Virologie, Hôpital Purpan, CHU de Toulouse, Toulouse, France
| | - Nicolas Jeanne
- Centre National de Référence du virus de l'hépatite E, Laboratoire de Virologie, Hôpital Purpan, CHU de Toulouse, Toulouse, France
| | - Alain Roulet
- Plateforme Génomique, Centre INRA Occitanie-Toulouse, Castanet-Tolosan, France
| | - Caroline Lefebvre
- Centre National de Référence du virus de l'hépatite E, Laboratoire de Virologie, Hôpital Purpan, CHU de Toulouse, Toulouse, France
| | - Romain Carcenac
- Centre National de Référence du virus de l'hépatite E, Laboratoire de Virologie, Hôpital Purpan, CHU de Toulouse, Toulouse, France
| | - Maxime Manno
- Plateforme Génomique, Centre INRA Occitanie-Toulouse, Castanet-Tolosan, France
| | - Martine Dubois
- Centre National de Référence du virus de l'hépatite E, Laboratoire de Virologie, Hôpital Purpan, CHU de Toulouse, Toulouse, France
| | - Nassim Kamar
- Center of Pathophysiology, Toulouse Purpan, INSERM, U1043, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France.,Service de néphrologie, Dialyse et Transplantation d'Organe, Hôpital Rangueil, CHU de Toulouse, Toulouse, France
| | - Sébastien Lhomme
- Centre National de Référence du virus de l'hépatite E, Laboratoire de Virologie, Hôpital Purpan, CHU de Toulouse, Toulouse, France.,Center of Pathophysiology, Toulouse Purpan, INSERM, U1043, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Florence Abravanel
- Centre National de Référence du virus de l'hépatite E, Laboratoire de Virologie, Hôpital Purpan, CHU de Toulouse, Toulouse, France.,Center of Pathophysiology, Toulouse Purpan, INSERM, U1043, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Jacques Izopet
- Centre National de Référence du virus de l'hépatite E, Laboratoire de Virologie, Hôpital Purpan, CHU de Toulouse, Toulouse, France.,Center of Pathophysiology, Toulouse Purpan, INSERM, U1043, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| |
Collapse
|
|
19
|
Ricci A, Allende A, Bolton D, Chemaly M, Davies R, Fernandez Escamez PS, Herman L, Koutsoumanis K, Lindqvist R, Nørrung B, Robertson L, Ru G, Sanaa M, Simmons M, Skandamis P, Snary E, Speybroeck N, Ter Kuile B, Threlfall J, Wahlström H, Di Bartolo I, Johne R, Pavio N, Rutjes S, van der Poel W, Vasickova P, Hempen M, Messens W, Rizzi V, Latronico F, Girones R. Public health risks associated with hepatitis E virus (HEV) as a food-borne pathogen. EFSA J 2017; 15:e04886. [PMID: 32625551 PMCID: PMC7010180 DOI: 10.2903/j.efsa.2017.4886] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Hepatitis E virus (HEV) is an important infection in humans in EU/EEA countries, and over the last 10 years more than 21,000 acute clinical cases with 28 fatalities have been notified with an overall 10-fold increase in reported HEV cases; the majority (80%) of cases were reported from France, Germany and the UK. However, as infection in humans is not notifiable in all Member States, and surveillance differs between countries, the number of reported cases is not comparable and the true number of cases would probably be higher. Food-borne transmission of HEV appears to be a major route in Europe; pigs and wild boars are the main source of HEV. Outbreaks and sporadic cases have been identified in immune-competent persons as well as in recognised risk groups such as those with pre-existing liver damage, immunosuppressive illness or receiving immunosuppressive treatments. The opinion reviews current methods for the detection, identification, characterisation and tracing of HEV in food-producing animals and foods, reviews literature on HEV reservoirs and food-borne pathways, examines information on the epidemiology of HEV and its occurrence and persistence in foods, and investigates possible control measures along the food chain. Presently, the only efficient control option for HEV infection from consumption of meat, liver and products derived from animal reservoirs is sufficient heat treatment. The development of validated quantitative and qualitative detection methods, including infectivity assays and consensus molecular typing protocols, is required for the development of quantitative microbial risk assessments and efficient control measures. More research on the epidemiology and control of HEV in pig herds is required in order to minimise the proportion of pigs that remain viraemic or carry high levels of virus in intestinal contents at the time of slaughter. Consumption of raw pig, wild boar and deer meat products should be avoided.
Collapse
|
|
20
|
Genotype-Specific Evolution of Hepatitis E Virus. J Virol 2017; 91:JVI.02241-16. [PMID: 28202767 DOI: 10.1128/jvi.02241-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 01/31/2017] [Indexed: 12/20/2022] Open
Abstract
Hepatitis E virus (HEV) is the most common cause of acute viral hepatitis globally. HEV comprises four genotypes with different geographic distributions and host ranges. We utilize this natural case-control study for investigating the evolution of zoonotic viruses compared to single-host viruses, using 244 near-full-length HEV genomes. Genome-wide estimates of the ratio of nonsynonymous to synonymous evolutionary changes (dN/dS ratio) located a region of overlapping reading frames, which is subject to positive selection in genotypes 3 and 4. The open reading frames (ORFs) involved have functions related to host-pathogen interaction, so genotype-specific evolution of these regions may reflect their fitness. Bayesian inference of evolutionary rates shows that genotypes 3 and 4 have significantly higher rates than genotype 1 across all ORFs. Reconstruction of the phylogenies of zoonotic genotypes demonstrates significant intermingling of isolates between hosts. We speculate that the genotype-specific differences may result from cyclical adaptation to different hosts in genotypes 3 and 4.IMPORTANCE Hepatitis E virus (HEV) is increasingly recognized as a pathogen that affects both the developing and the developed world. While most often clinically mild, HEV can be severe or fatal in certain demographics, such as expectant mothers. Like many other viral pathogens, HEV has been classified into several distinct genotypes. We show that most of the HEV genome is evolutionarily constrained. One locus of positive selection is unusual in that it encodes two distinct protein products. We are the first to detect positive selection in this overlap region. Genotype 1, which infects humans only, appears to be evolving differently from genotypes 3 and 4, which infect multiple species, possibly because genotypes 3 and 4 are unable to achieve the same fitness due to repeated host jumps.
Collapse
|
|
21
|
Brown A, Halliday JS, Swadling L, Madden RG, Bendall R, Hunter JG, Maggs J, Simmonds P, Smith DB, Vine L, McLaughlin C, Collier J, Bonsall D, Jeffery K, Dunachie S, Klenerman P, Izopet J, Kamar N, Dalton HR, Barnes E. Characterization of the Specificity, Functionality, and Durability of Host T-Cell Responses Against the Full-Length Hepatitis E Virus. Hepatology 2016; 64:1934-1950. [PMID: 27631819 PMCID: PMC5132006 DOI: 10.1002/hep.28819] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 07/13/2016] [Accepted: 08/17/2016] [Indexed: 12/19/2022]
Abstract
UNLABELLED The interplay between host antiviral immunity and immunopathology during hepatitis E virus (HEV) infection determines important clinical outcomes. We characterized the specificity, functionality, and durability of host T-cell responses against the full-length HEV virus and assessed a novel "Quantiferon" assay for the rapid diagnosis of HEV infection. Eighty-nine volunteers were recruited from Oxford, Truro (UK), and Toulouse (France), including 44 immune-competent patients with acute HEV infection, 18 HEV-exposed immunosuppressed organ-transplant recipients (8 with chronic HEV), and 27 healthy volunteers. A genotype 3a peptide library (616 overlapping peptides spanning open reading frames [ORFs] 1-3) was used in interferon-gamma (IFN-γ) T-cell ELISpot assays. CD4+ /CD8+ T-cell subsets and polyfunctionality were defined using ICCS and SPICE analysis. Quantification of IFN-γ used whole-blood stimulation with recombinant HEV-capsid protein in the QuantiFERON kit. HEV-specific T-cell responses were detected in 41/44 immune-competent HEV exposed volunteers (median magnitude: 397 spot-forming units/106 peripheral blood mononuclear cells), most frequently targeting ORF2. High-magnitude, polyfunctional CD4 and CD8+ T cells were detected during acute disease and maintained to 12 years, but these declined over time, with CD8+ responses becoming more monofunctional. Low-level responses were detectable in immunosuppressed patients. Twenty-three novel HEV CD4+ and CD8+ T-cell targets were mapped predominantly to conserved genomic regions. QuantiFERON testing demonstrated an inverse correlation between IFN-γ production and the time from clinical presentation, providing 100% specificity, and 71% sensitivity (area under the receiver operator characteristic curve of 0.86) for HEV exposure at 0.3 IU/mL. CONCLUSION Robust HEV-specific T-cell responses generated during acute disease predominantly target ORF2, but decline in magnitude and polyfunctionality over time. Defining HEV T-cell targets will be important for the investigation of HEV-associated autoimmune disease. (Hepatology 2016;64:1934-1950).
Collapse
Affiliation(s)
- Anthony Brown
- Peter Medawar Building for Pathogen ResearchUniversity of OxfordOxfordUnited Kingdom
| | - John S. Halliday
- Peter Medawar Building for Pathogen ResearchUniversity of OxfordOxfordUnited Kingdom,The Royal Melbourne HospitalMelbourneVictoriaAustralia
| | - Leo Swadling
- Peter Medawar Building for Pathogen ResearchUniversity of OxfordOxfordUnited Kingdom
| | | | | | | | - James Maggs
- Oxford University Hospitals NHS Foundation TrustOxfordUnited Kingdom
| | - Peter Simmonds
- Peter Medawar Building for Pathogen ResearchUniversity of OxfordOxfordUnited Kingdom,Centre for Immunity, Infection and Evolution, University of EdinburghUnited Kingdom
| | - Donald B. Smith
- Centre for Immunity, Infection and Evolution, University of EdinburghUnited Kingdom
| | - Louisa Vine
- The Royal Cornwall HospitalTruroUnited Kingdom
| | | | - Jane Collier
- Oxford University Hospitals NHS Foundation TrustOxfordUnited Kingdom
| | - David Bonsall
- Peter Medawar Building for Pathogen ResearchUniversity of OxfordOxfordUnited Kingdom
| | - Katie Jeffery
- Oxford University Hospitals NHS Foundation TrustOxfordUnited Kingdom
| | - Susanna Dunachie
- Peter Medawar Building for Pathogen ResearchUniversity of OxfordOxfordUnited Kingdom,Centre for Tropical Medicine & Global HealthUniversity of OxfordOxfordUnited Kingdom
| | - Paul Klenerman
- Peter Medawar Building for Pathogen ResearchUniversity of OxfordOxfordUnited Kingdom,Oxford University Hospitals NHS Foundation TrustOxfordUnited Kingdom,National Institute for Health Research (NIHR)Oxford Biomedical Research CentreOxfordUnited Kingdom
| | | | | | | | - Eleanor Barnes
- Peter Medawar Building for Pathogen ResearchUniversity of OxfordOxfordUnited Kingdom,Oxford University Hospitals NHS Foundation TrustOxfordUnited Kingdom,National Institute for Health Research (NIHR)Oxford Biomedical Research CentreOxfordUnited Kingdom
| |
Collapse
|
|
22
|
The effect of phylogenetic signal reduction on genotyping of hepatitis E viruses of the species Orthohepevirus A. Arch Virol 2016; 162:645-656. [PMID: 27817109 DOI: 10.1007/s00705-016-3135-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 10/25/2016] [Indexed: 12/27/2022]
Abstract
Commonly, hepatitis E virus (HEV) sequences are genotyped phylogenetically using subgenomic sequences. This paper examines this practice with sequences from members of the species Orthohepevirus A. As the length of sequences becomes progressively shorter, the number of identical sequences in an alignment tends to increase; however, these sequences retain their genotypic identity down to 100 nucleotides in length. The best substitution models tend to become less parameterized, bootstrap support decreases, and trees created from short subgenomic fragments are less likely to be isomorphic with trees from longer subgenomic fragments or complete genome sequences. However, it is still possible to correctly genotype sequences using fragments as small as 200 nucleotides. While it is possible to correctly genotype sequences with short subgenomic sequences, the estimates of evolutionary relationships between genotypes degrade to such an extent that sequences below 1600 nucleotides long cannot be used reliably to study these relationships, and comparisons of trees from different subgenomic regions with little or no sequence overlap can be problematic. Subtyping may be done, but it requires a careful examination of the region to be used to ensure that it correctly resolves the subtypes.
Collapse
|
|
23
|
Kelly AG, Netzler NE, White PA. Ancient recombination events and the origins of hepatitis E virus. BMC Evol Biol 2016; 16:210. [PMID: 27733122 PMCID: PMC5062859 DOI: 10.1186/s12862-016-0785-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 09/30/2016] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Hepatitis E virus (HEV) is an enteric, single-stranded, positive sense RNA virus and a significant etiological agent of hepatitis, causing sporadic infections and outbreaks globally. Tracing the evolutionary ancestry of HEV has proved difficult since its identification in 1992, it has been reclassified several times, and confusion remains surrounding its origins and ancestry. RESULTS To reveal close protein relatives of the Hepeviridae family, similarity searching of the GenBank database was carried out using a complete Orthohepevirus A, HEV genotype I (GI) ORF1 protein sequence and individual proteins. The closest non-Hepeviridae homologues to the HEV ORF1 encoded polyprotein were found to be those from the lepidopteran-infecting Alphatetraviridae family members. A consistent relationship to this was found using a phylogenetic approach; the Hepeviridae RdRp clustered with those of the Alphatetraviridae and Benyviridae families. This puts the Hepeviridae ORF1 region within the "Alpha-like" super-group of viruses. In marked contrast, the HEV GI capsid was found to be most closely related to the chicken astrovirus capsid, with phylogenetic trees clustering the Hepeviridae capsid together with those from the Astroviridae family, and surprisingly within the "Picorna-like" supergroup. These results indicate an ancient recombination event has occurred at the junction of the non-structural and structure encoding regions, which led to the emergence of the entire Hepeviridae family. The Astroviridae capsid is also closely related to the Tymoviridae family of monopartite, T = 3 icosahedral plant viruses, whilst its non-structural region is related to viruses of the Potyviridae; a large family of plant-infecting viruses with a flexible filamentous rod-shaped virion. Thus, we identified a separate inter-viral family recombination event, again at the non-structural/structural junction, which likely led to the creation of the Astroviridae. CONCLUSIONS In summary, we have shown that new viral families have been created though recombination at the junction of the genome that encodes non-structural and structural proteins, and such recombination events are implicated in the genesis of important human pathogens; HEV, astrovirus and rubella virus.
Collapse
Affiliation(s)
- Andrew G Kelly
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, Australia
| | - Natalie E Netzler
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, Australia
| | - Peter A White
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, Australia.
| |
Collapse
|
|
24
|
Moon HW, Lee BW, Sung HW, Yoon BI, Kwon HM. Identification and characterization of avian hepatitis E virus genotype 2 from chickens with hepatitis-splenomegaly syndrome in Korea. Virus Genes 2016; 52:738-42. [DOI: 10.1007/s11262-016-1351-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/29/2016] [Indexed: 11/30/2022]
|
|
25
|
Zhang Y, Gong W, Zeng H, Wang L. Genetic Evolution of Hepatitis E Virus. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 948:73-88. [PMID: 27738980 DOI: 10.1007/978-94-024-0942-0_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Comparative analysis of the genomic sequences of multiple hepatitis E virus (HEV) isolates has revealed extensive genomic diversity among them. Recently, a variety of genetically distinct HEV variants have also been isolated and identified from large numbers of animal species, including birds, rabbits, rats, ferrets, bats, cutthroat trout, and camels, among others. Furthermore, it has been reported that recombination in HEV genomes takes place in animals and in human patients. Also, chronic HEV infection in immunocompromised individuals has revealed the presence of viral strains carrying insertions from human genes. This paper reviews the current knowledge on the genomic variability and evolution of HEV.
Collapse
Affiliation(s)
- Yulin Zhang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Wanyun Gong
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Hang Zeng
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Ling Wang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, 38 Xueyuan Road, Haidian District, Beijing, 100191, China.
| |
Collapse
|
|
26
|
Park SJ, Lee BW, Moon HW, Sung HW, Yoon BI, Meng XJ, Kwon HM. Construction of an infectious cDNA clone of genotype 1 avian hepatitis E virus: characterization of its pathogenicity in broiler breeders and demonstration of its utility in studying the role of the hypervariable region in virus replication. J Gen Virol 2015; 96:1015-1026. [PMID: 25593160 DOI: 10.1099/vir.0.000045] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 01/08/2015] [Indexed: 02/07/2023] Open
Abstract
A full-length infectious cDNA clone of the genotype 1 Korean avian hepatitis E virus (avian HEV) (pT11-aHEV-K) was constructed and its infectivity and pathogenicity were investigated in leghorn male hepatoma (LMH) chicken cells and broiler breeders. We demonstrated that capped RNA transcripts from the pT11-aHEV-K clone were translation competent when transfected into LMH cells and infectious when injected intrahepatically into the livers of chickens. Gross and microscopic pathological lesions underpinned the avian HEV infection and helped characterize its pathogenicity in broiler breeder chickens. The avian HEV genome contains a hypervariable region (HVR) in ORF1. To demonstrate the utility of the avian HEV infectious clone, several mutants with various deletions in and beyond the known HVR were derived from the pT11-aHEV-K clone. The HVR-deletion mutants were replication competent in LMH cells, although the deletion mutants extending beyond the known HVR were non-viable. By using the pT11-aHEV-K infectious clone as the backbone, an avian HEV luciferase reporter replicon and HVR-deletion mutant replicons were also generated. The luciferase assay results of the reporter replicon and its mutants support the data obtained from the infectious clone and its derived mutants. To further determine the effect of HVR deletion on virus replication, the capped RNA transcripts from the wild-type pT11-aHEV-K clone and its mutants were injected intrahepatically into chickens. The HVR-deletion mutants that were translation competent in LMH cells displayed in chickens an attenuation phenotype of avian HEV infectivity, suggesting that the avian HEV HVR is important in modulating the virus infectivity and pathogenicity.
Collapse
Affiliation(s)
- Soo-Jeong Park
- Department of Veterinary Microbiology, College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University, Chuncheon, Gangwon 200-701, Republic of Korea
| | - Byung-Woo Lee
- Department of Veterinary Microbiology, College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University, Chuncheon, Gangwon 200-701, Republic of Korea
| | - Hyun-Woo Moon
- Department of Veterinary Microbiology, College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University, Chuncheon, Gangwon 200-701, Republic of Korea
| | - Haan Woo Sung
- Department of Veterinary Microbiology, College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University, Chuncheon, Gangwon 200-701, Republic of Korea
| | - Byung-Il Yoon
- Department of Veterinary Microbiology, College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University, Chuncheon, Gangwon 200-701, Republic of Korea
| | - Xiang-Jin Meng
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061-0913, USA
| | - Hyuk Moo Kwon
- Department of Veterinary Microbiology, College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University, Chuncheon, Gangwon 200-701, Republic of Korea
| |
Collapse
|
|
27
|
Wang S, Wei W, Luo X, Cai X. Genome-wide comparisons of phylogenetic similarities between partial genomic regions and the full-length genome in Hepatitis E virus genotyping. PLoS One 2014; 9:e115785. [PMID: 25542033 PMCID: PMC4277416 DOI: 10.1371/journal.pone.0115785] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 11/26/2014] [Indexed: 01/23/2023] Open
Abstract
Besides the complete genome, different partial genomic sequences of Hepatitis E virus (HEV) have been used in genotyping studies, making it difficult to compare the results based on them. No commonly agreed partial region for HEV genotyping has been determined. In this study, we used a statistical method to evaluate the phylogenetic performance of each partial genomic sequence from a genome wide, by comparisons of evolutionary distances between genomic regions and the full-length genomes of 101 HEV isolates to identify short genomic regions that can reproduce HEV genotype assignments based on full-length genomes. Several genomic regions, especially one genomic region at the 3'-terminal of the papain-like cysteine protease domain, were detected to have relatively high phylogenetic correlations with the full-length genome. Phylogenetic analyses confirmed the identical performances between these regions and the full-length genome in genotyping, in which the HEV isolates involved could be divided into reasonable genotypes. This analysis may be of value in developing a partial sequence-based consensus classification of HEV species.
Collapse
Affiliation(s)
- Shuai Wang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Wei Wei
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Xuenong Luo
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Xuepeng Cai
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- * E-mail:
| |
Collapse
|
|
28
|
Behrendt P, Steinmann E, Manns MP, Wedemeyer H. The impact of hepatitis E in the liver transplant setting. J Hepatol 2014; 61:1418-29. [PMID: 25195557 DOI: 10.1016/j.jhep.2014.08.047] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 08/25/2014] [Accepted: 08/29/2014] [Indexed: 12/27/2022]
Abstract
Hepatitis E virus (HEV) infection has been identified as a cause of graft hepatitis in liver transplant recipients. The true frequency and clinical importance of HEV infections after liver transplantations is a matter of debate. It is proposed that consumption of HEV-contaminated undercooked meat is a main source for HEV infections in developed countries--which might also account for some hepatitis E cases after organ transplantation. However, HEV is also transmitted by transfusion of blood products, likely representing a previously underestimated risk particularly for patients in the transplant setting. HEV infection can take chronic courses in immunocompromised individuals, associated in some cases with rapid progression to cirrhosis within 1-2 years of infection. Diagnosis in transplanted patients is based on HEV RNA testing as antibody assays are not sensitive enough. Selection of immunosuppressive drugs is important as different compounds may influence viral replication and the course of liver disease. Ribavirin has antiviral activity against HEV and should be administered for at least three months in chronically infected individuals; however, treatment failure may occur. HEV infections have also been linked to a variety of extrahepatic manifestations both during and after resolution of infection. In this review we summarize the emerging data on hepatitis E with a particular focus on the importance of HEV infections for liver transplant recipients.
Collapse
Affiliation(s)
- Patrick Behrendt
- Department for Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany; German Center for Infection Research, Hannover, Germany; Twincore, Centre for Experimental and Clinical Infection Research, A Joint Venture Between Medical School Hannover and Helmholtz Centre for Infection Research, Hannover, Germany
| | - Eike Steinmann
- Twincore, Centre for Experimental and Clinical Infection Research, A Joint Venture Between Medical School Hannover and Helmholtz Centre for Infection Research, Hannover, Germany
| | - Michael P Manns
- Department for Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany; German Center for Infection Research, Hannover, Germany
| | - Heiner Wedemeyer
- Department for Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany; German Center for Infection Research, Hannover, Germany.
| |
Collapse
|
|
29
|
Hepatitis E: an old infection with new implications. BLOOD TRANSFUSION = TRASFUSIONE DEL SANGUE 2014; 13:6-17. [PMID: 25369613 DOI: 10.2450/2014.0063-14] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 06/18/2014] [Indexed: 12/24/2022]
|
|
30
|
Johne R, Reetz J, Ulrich RG, Machnowska P, Sachsenröder J, Nickel P, Hofmann J. An ORF1-rearranged hepatitis E virus derived from a chronically infected patient efficiently replicates in cell culture. J Viral Hepat 2014; 21:447-56. [PMID: 24750215 DOI: 10.1111/jvh.12157] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Hepatitis E is an increasingly reported disease in industrialized countries. Studies on the replication cycle of hepatitis E virus (HEV) are hampered due to the lack of efficient and robust cell culture systems for this virus. We describe the successful isolation of HEV derived from a chronically infected kidney transplant patient held under immunosuppressive therapy. Inoculation of serum sample 47832 onto the human lung carcinoma cell line A549 resulted in the replication of the virus as shown by RT-qPCR. This novel human-derived HEV strain is closely related to a wild boar-derived genotype 3 strain, which did not replicate in A549 cells. It carries a 186 nucleotide insertion in the hypervariable ORF1-region, derived from two parts of its ORF1. By passaging of the infected cells, a cell line continuously producing HEV particles was generated as demonstrated by RT-qPCR, immuno-electron microscopy, density gradient centrifugation and immunohistochemistry. Replication of the produced virus was demonstrated after its inoculation onto fresh A549 cells and two consecutive passages, whereas heating at 65 °C for 2 min abolished its infectivity. Several point mutations scattered along the whole genome were present in the HEV strain from the second passage; however, the ORF1 insertion was still present. Previously, cell culture isolation of two other HEV strains carrying insertions in their hypervariable regions, but originating from human ribosomal protein genes, has been described. The findings may indicate that cell culture adaptation of is mostly dependent on the length and position of the insertion, rather than from the sequence itself.
Collapse
Affiliation(s)
- R Johne
- Department of Biological Safety, Federal Institute for Risk Assessment, Berlin, Germany
| | | | | | | | | | | | | |
Collapse
|
|
31
|
Lara J, Purdy MA, Khudyakov YE. Genetic host specificity of hepatitis E virus. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2014; 24:127-39. [PMID: 24667049 PMCID: PMC5745802 DOI: 10.1016/j.meegid.2014.03.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 02/24/2014] [Accepted: 03/16/2014] [Indexed: 01/06/2023]
Abstract
Hepatitis E virus (HEV) causes epidemic and sporadic cases of hepatitis worldwide. HEV genotypes 3 (HEV3) and 4 (HEV4) infect humans and animals, with swine being the primary reservoir. The relevance of HEV genetic diversity to host adaptation is poorly understood. We employed a Bayesian network (BN) analysis of HEV3 and HEV4 to detect epistatic connectivity among protein sites and its association with the host specificity in each genotype. The data imply coevolution among ∼70% of polymorphic sites from all HEV proteins and association of numerous coevolving sites with adaptation to swine or humans. BN models for individual proteins and domains of the nonstructural polyprotein detected the host origin of HEV strains with accuracy of 74-93% and 63-87%, respectively. These findings, taken together with lack of phylogenetic association to host, suggest that the HEV host specificity is a heritable and convergent phenotypic trait achievable through variety of genetic pathways (abundance), and explain a broad host range for HEV3 and HEV4.
Collapse
Affiliation(s)
- James Lara
- Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Michael A Purdy
- Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Yury E Khudyakov
- Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA, USA
| |
Collapse
|
|
32
|
Debing Y, Neyts J. Antiviral strategies for hepatitis E virus. Antiviral Res 2013; 102:106-18. [PMID: 24374149 PMCID: PMC7113752 DOI: 10.1016/j.antiviral.2013.12.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Revised: 12/12/2013] [Accepted: 12/14/2013] [Indexed: 02/08/2023]
Abstract
The hepatitis E virus is a common cause of acute hepatitis. Contrary to hepatitis B and C, hepatitis E is mostly a mild infection, although it has a high mortality in pregnant women and can evolve to chronicity in immunocompromised patients. Ribavirin and pegylated interferon-α are the only available therapies, but both have side effects that are not acceptable for prophylaxis or treatment of mild infections. In addition, these drugs cannot be used for all patient types (e.g. in case of pregnancy, specific organ transplants or co-morbidities) and in resource-poor settings. Hence there is an urgent need for better antiviral treatments that are efficacious and safe, also during pregnancy. In this review, a concise introduction to the virus and disease is provided, followed by a discussion of the available assay systems and potential molecular targets (viral proteins and host factors) for the development of inhibitors of HEV replication. Finally, directions for future research are presented.
Collapse
Affiliation(s)
- Yannick Debing
- Rega Institute for Medical Research, Department of Microbiology and Immunology, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Johan Neyts
- Rega Institute for Medical Research, Department of Microbiology and Immunology, Minderbroedersstraat 10, 3000 Leuven, Belgium.
| |
Collapse
|
|
33
|
Al-Shukri I, Davidson E, Tan A, Smith DB, Wellington L, Johannessen I, Ramalingam S. Rash and arthralgia caused by hepatitis E. Lancet 2013; 382:1856. [PMID: 24290589 DOI: 10.1016/s0140-6736(13)62074-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Intisar Al-Shukri
- Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | | | | | | | | | | | | |
Collapse
|
|
34
|
Smith DB, Vanek J, Wellington L, Johannessen I, Ramalingam S, Simmonds P. Hepatitis E virus mixed infection in immunocompetent patient. Emerg Infect Dis 2013; 19:468-70. [PMID: 23621890 PMCID: PMC3647676 DOI: 10.3201/eid1903.121510] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
We detected 2 hepatitis E virus (HEV) strains in an acutely infected immunocompetent patient. Two populations of genotype 3 virus were observed in the hypervariable regions and open reading frames 2 and 3, indicating multiple infection with hepatitis E virus. Persons with mixed infections may provide the opportunity for virus recombination.
Collapse
Affiliation(s)
- Donald B Smith
- University of Edinburgh, Edinburgh, Scotland, United Kingdom.
| | | | | | | | | | | |
Collapse
|
|
35
|
Ramalingam S, Smith D, Wellington L, Vanek J, Simmonds P, MacGilchrist A, Bathgate A, Simpson K, Johannessen I. Autochthonous hepatitis E in Scotland. J Clin Virol 2013; 58:619-23. [PMID: 24200818 DOI: 10.1016/j.jcv.2013.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 09/27/2013] [Accepted: 10/01/2013] [Indexed: 01/14/2023]
Abstract
BACKGROUND Hepatitis E virus is well recognized cause of acute hepatitis. Traditionally hepatitis E virus (HEV) infections were generally associated with travel to Asia and Africa. Autochthonous hepatitis E is recognized as a major cause acute hepatitis in England and Wales. However, autochthonous hepatitis E has never been documented in Scotland. OBJECTIVES We attempted to determine if autochthonous HEV occurred in Scotland. STUDY DESIGN Samples from 377 individuals in the South-East of Scotland presenting with acute hepatitis were tested over six years. Acute hepatitis E was confirmed by detecting viraemia or documenting seroconversion and ORF-2 region sequenced. Structured interviews were carried out to identify risk factors for infection. RESULTS Sixteen individuals (4.2%) had evidence of past HEV infection. Twelve (3.2%) had acute HEV infection, 10 of whom had viraemia (genotype 1=3; genotype 3=7). Of these seven with genotype 3 infection, three had not travelled outside Scotland within the incubation period, while four had travelled to Spain (n=3) or Turkey (n=1). All three individuals with genotype 1 infection had travelled to the Indian subcontinent. CONCLUSIONS A significant proportion of HEV genotype 3 infections was autochthonous (43%). HEV screening should hence be an integral part of acute hepatitis screening in Scotland, irrespective of the travel history.
Collapse
Affiliation(s)
- Sandeep Ramalingam
- Department of Laboratory Medicine, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh EH16 4SA, United Kingdom.
| | | | | | | | | | | | | | | | | |
Collapse
|
|
36
|
Murrell B, Moola S, Mabona A, Weighill T, Sheward D, Kosakovsky Pond SL, Scheffler K. FUBAR: a fast, unconstrained bayesian approximation for inferring selection. Mol Biol Evol 2013; 30:1196-205. [PMID: 23420840 DOI: 10.1093/molbev/mst030] [Citation(s) in RCA: 912] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Model-based analyses of natural selection often categorize sites into a relatively small number of site classes. Forcing each site to belong to one of these classes places unrealistic constraints on the distribution of selection parameters, which can result in misleading inference due to model misspecification. We present an approximate hierarchical Bayesian method using a Markov chain Monte Carlo (MCMC) routine that ensures robustness against model misspecification by averaging over a large number of predefined site classes. This leaves the distribution of selection parameters essentially unconstrained, and also allows sites experiencing positive and purifying selection to be identified orders of magnitude faster than by existing methods. We demonstrate that popular random effects likelihood methods can produce misleading results when sites assigned to the same site class experience different levels of positive or purifying selection--an unavoidable scenario when using a small number of site classes. Our Fast Unconstrained Bayesian AppRoximation (FUBAR) is unaffected by this problem, while achieving higher power than existing unconstrained (fixed effects likelihood) methods. The speed advantage of FUBAR allows us to analyze larger data sets than other methods: We illustrate this on a large influenza hemagglutinin data set (3,142 sequences). FUBAR is available as a batch file within the latest HyPhy distribution (http://www.hyphy.org), as well as on the Datamonkey web server (http://www.datamonkey.org/).
Collapse
Affiliation(s)
- Ben Murrell
- Department of Mathematical Sciences, Stellenbosch University, Stellenbosch, South Africa
| | | | | | | | | | | | | |
Collapse
|
|
37
|
Abstract
The classification of hepatitis E virus (HEV) variants is currently in transition without agreed definitions for genotypes and subtypes or for deeper taxonomic groupings into species and genera that could incorporate more recently characterized viruses assigned to the Hepeviridae family that infect birds, bats, rodents, and fish. These conflicts arise because of differences in the viruses and genomic regions compared and in the methodology used. We have reexamined published sequences and found that synonymous substitutions were saturated in comparisons between and within virus genotypes. Analysis of complete genome sequences or concatenated ORF1/ORF2 amino acid sequences indicated that HEV variants most closely related to those infecting humans can be consistently divided into six genotypes (types 1 to 4 and two additional genotypes from wild boar). Variants isolated from rabbits, closely related to genotype 3, occupy an intermediate position. No consistent criteria could be defined for the assignment of virus subtypes. Analysis of amino acid sequences from these viruses with the more divergent variants from chickens, bats, and rodents in three conserved subgenomic regions (residues 1 to 452 or 974 to 1534 of ORF1 or residues 105 to 458 of ORF2) provided consistent support for a division into 4 groups, corresponding to HEV variants infecting humans and pigs, those infecting rats and ferrets, those from bats, and those from chickens. This approach may form the basis for a future genetic classification of HEV into four species, with the more divergent HEV-like virus from fish (cutthroat trout virus) representing a second genus.
Collapse
|