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Khan N, Kakakhel S, Malik A, Nigar K, Akhtar S, Khan AA, Khan A. Genetic substructure and host-specific natural selection trend across vaccine-candidate ORF-2 capsid protein of hepatitis-E virus. J Viral Hepat 2024; 31:524-534. [PMID: 38804127 DOI: 10.1111/jvh.13959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 05/03/2024] [Accepted: 05/13/2024] [Indexed: 05/29/2024]
Abstract
Hepatitis E virus is a primary cause of acute hepatitis worldwide. The present study attempts to assess the genetic variability and evolutionary divergence among HEV genotypes. A vaccine promising capsid-protein coding ORF-2 gene sequences of HEV was evaluated using phylogenetics, model-based population genetic methods and principal component analysis. The analyses unveiled nine distinct clusters as subpopulations for six HEV genotypes. HEV-3 genotype samples stratified into four different subgroups, while HEV-4 stratified into three additional subclusters. Rabbit-infectious HEV-3ra samples constitute a distinct cluster. Pairwise analysis identified marked genetic distinction of HEV-4c and HEV-4i subgenotypes compared to other genotypes. Numerous admixed, inter and intragenotype recombinant strains were detected. The MEME method identified several ORF-2 codon sites under positive selection. Some selection signatures lead to amino acid substitutions within ORF-2, resulting in altered physicochemical features. Moreover, a pattern of host-specific adaptive signatures was identified among HEV genotypes. The analyses conclusively depict that recombination and episodic positive selection events have shaped the observed genetic diversity among different HEV genotypes. The significant genetic diversity and stratification of HEV-3 and HEV-4 genotypes into subgroups, as identified in the current study, are noteworthy and may have implications for the efficacy of anti-HEV vaccines.
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Affiliation(s)
- Nasir Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan
| | - Sehrish Kakakhel
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan
| | - Abdul Malik
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Kiran Nigar
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan
| | - Suhail Akhtar
- Department of Biochemistry, A.T. Still University of Health Sciences, Kirksville, Missouri, USA
| | - Azmat Ali Khan
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan
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2
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Wu H, Zhou L, Wang F, Chen Z, Lu Y. Molecular epidemiology and phylogeny of the emerging zoonotic virus Rocahepevirus: A global genetic analysis. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 118:105557. [PMID: 38244748 DOI: 10.1016/j.meegid.2024.105557] [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: 12/22/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 01/22/2024]
Abstract
Human infections with Rocahepevirus ratti genotype C1 (HEV-C1) in Hong Kong of China, Canada, Spain, and France have drawn worldwide concern towards Rocahepevirus. This study conducted a global genetic analysis of Rocahepevirus, aiming to furnish comprehensive molecular insights and promote further research. We retrieved 817 Rocahepevirus sequences from the GenBank database through October 31, 2023, categorizing them according to research, sample collection area and date, genotype, host, and sequence length. Subsequently, we conducted descriptive epidemiological, phylogenetic evolutionary, and protein polymorphism (in length and identity) analyses on these sequences. Rocahepevirus genomes were identified across twenty-eight countries, predominantly in Asia (71.73%, 586/817) and Europe (26.44%, 216/817). The HEV-C1 dominates Rocahepevirus (77.2%, 631/817), while newly discovered Rocahepevirus genotypes (C3/C4/C5 and other unclassified genotypes) were primarily identified in Europe (25/120) and China (91/120). Muridae animals (72.5%, 592/817) serve as the primary hosts for Rocahepevirus, with other hosts encompassing species from the families Soricidae, Hominidae, Mustelidae, and Cricetidae. Additionally, Rocahepevirus genomes (C1 genotype) were identified in sewage samples recently. The phylogenetic evolution of Rocahepevirus exhibits considerable variation. Specifically, HEV-C1 can be classified into at least six genetic groups (G1 to G6), with human HEV-C1 distributed across multiple evolutionary clades. The overall ORF1 and ORF2 amino acid sequence lengths were significantly different (P < 0.001) across Rocahepevirus genotypes. HEV-C1/C2/C3 and HEV-C4/C5 displayed substantial differences in amino acid sequence identity (58.4%-59.6%). The identification of Rocahepevirus genomes has expanded across numerous countries, particularly in European and Asian countries, coinciding with an expanding host range and emergence of new genotypes. The evolutionary path of Rocahepevirus is intricate, where the HEV-C1 dominates globally and internally forms multiple evolutionary groups (G1 to G6), exhibiting diverse genetic variation within human HEV-C1. Significant differences exist in the protein polymorphism (in length and identity) across Rocahepevirus genotypes. Given Rocahepevirus's shift from an animal virus to a zoonotic pathogen, worldwide cooperation in monitoring Rocahepevirus genomes is vital.
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Affiliation(s)
- Han Wu
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety (Fudan University), School of Public Health, Fudan University, Shanghai 200032, China
| | - Lu Zhou
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety (Fudan University), School of Public Health, Fudan University, Shanghai 200032, China
| | - Fengge Wang
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety (Fudan University), School of Public Health, Fudan University, Shanghai 200032, China
| | - Zixiang Chen
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety (Fudan University), School of Public Health, Fudan University, Shanghai 200032, China
| | - Yihan Lu
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety (Fudan University), School of Public Health, Fudan University, Shanghai 200032, China.
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Kinast V, Klöhn M, Nocke MK, Todt D, Steinmann E. Hepatitis E virus species barriers: seeking viral and host determinants. Curr Opin Virol 2022; 56:101274. [PMID: 36283248 DOI: 10.1016/j.coviro.2022.101274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 11/03/2022]
Abstract
The intimate relationship between virus and host cell can result in highly adapted viruses that are restricted to a single host. However, some viruses have the ability to infect multiple host species. Remarkably, hepatitis E viruses (HEV) comprise genotypes that are either 'single-host' or 'multi-host' genotypes, a trait that raises fundamental questions: Why do different genotypes differ in their host range, despite a high degree of genomic similarity? What are the underlying molecular determinants that shape species barriers? Here, we review the current knowledge of viral and host determinants that may affect the evolutionary trajectories of HEV. We also provide a perspective on techniques and methods that address open questions of HEV host range and adaptation.
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Affiliation(s)
- Volker Kinast
- Department of Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany; Department of Medical Microbiology and Virology, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Mara Klöhn
- Department of Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
| | - Maximilian K Nocke
- Department of Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
| | - Daniel Todt
- Department of Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany; European Virus Bioinformatics Center (EVBC), 07743 Jena, Germany.
| | - Eike Steinmann
- Department of Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany; German Centre for Infection Research (DZIF), External Partner Site, Bochum, Germany.
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4
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Two mutations in the ORF1 of genotype 1 hepatitis E virus enhance virus replication and may associate with fulminant hepatic failure. Proc Natl Acad Sci U S A 2022; 119:e2207503119. [PMID: 35969750 PMCID: PMC9407470 DOI: 10.1073/pnas.2207503119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hepatitis E virus (HEV) infection in pregnant women has a high incidence of developing fulminant hepatic failure (FHF) with significant mortality. Multiple amino acid changes in genotype 1 HEV (HEV-1) are reportedly linked to FHF clinical cases, but experimental confirmation of the roles of these changes in FHF is lacking. By utilizing the HEV-1 indicator replicon and infectious clone, we generated 11 HEV-1 single mutants, each with an individual mutation, and investigated the effect of these mutations on HEV replication and infection in human liver cells. We demonstrated that most of the mutations actually impaired HEV-1 replication efficiency compared with the wild type (WT), likely due to altered physicochemical properties and structural conformations. However, two mutations, A317T and V1120I, significantly increased HEV-1 replication. Notably, these two mutations simultaneously occurred in 100% of 21 HEV-1 variants from patients with FHF in Bangladesh. We further created an HEV-1 A317T/V1120I double mutant and found that it greatly enhanced HEV replication, which may explain the rapid viral replication and severe disease. Furthermore, we tested the effect of these FHF-associated mutations on genotype 3 HEV (HEV-3) replication and found that all the mutants had a reduced level of replication ability and infectivity, which is not unexpected due to distinct infection patterns between HEV-1 and HEV-3. Additionally, we demonstrated that these FHF-associated mutations do not appear to alter their sensitivity to ribavirin (RBV), suggesting that ribavirin remains a viable option for antiviral therapy for patients with FHF. The results have important implications for understanding the mechanism of HEV-1-associated FHF.
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Chirohepevirus from Bats: Insights into Hepatitis E Virus Diversity and Evolution. Viruses 2022; 14:v14050905. [PMID: 35632647 PMCID: PMC9146828 DOI: 10.3390/v14050905] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/22/2022] [Accepted: 04/25/2022] [Indexed: 02/06/2023] Open
Abstract
Homologs of the human hepatitis E virus (HEV) have been identified in more than a dozen animal species. Some of them have been evidenced to cross species barriers and infect humans. Zoonotic HEV infections cause chronic liver diseases as well as a broad range of extrahepatic manifestations, which increasingly become significant clinical problems. Bats comprise approximately one-fifth of all named mammal species and are unique in their distinct immune response to viral infection. Most importantly, they are natural reservoirs of several highly pathogenic viruses, which have induced severe human diseases. Since the first discovery of HEV-related viruses in bats in 2012, multiple genetically divergent HEV variants have been reported in a total of 12 bat species over the last decade, which markedly expanded the host range of the HEV family and shed light on the evolutionary origin of human HEV. Meanwhile, bat-borne HEV also raised critical public health concerns about its zoonotic potential. Bat HEV strains resemble genomic features but exhibit considerable heterogeneity. Due to the close evolutionary relationships, bat HEV altogether has been recently assigned to an independent genus, Chirohepevirus. This review focuses on the current state of bat HEV and provides novel insights into HEV genetic diversity and molecular evolution.
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Occurrence of hepatitis E virus (HEV) in Calabrian wild boars. Int J Food Microbiol 2022; 371:109671. [DOI: 10.1016/j.ijfoodmicro.2022.109671] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 03/14/2022] [Accepted: 04/03/2022] [Indexed: 11/24/2022]
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Distribution and Genetic Diversity of Hepatitis E Virus in Wild and Domestic Rabbits in Australia. Pathogens 2021; 10:pathogens10121637. [PMID: 34959591 PMCID: PMC8709427 DOI: 10.3390/pathogens10121637] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 12/27/2022] Open
Abstract
In 2020, Hepatitis E virus (HEV) was detected for the first time in Australian rabbits. To improve our understanding of the genetic diversity and distribution of the virus, 1635 rabbit liver samples from locations across Australia were screened via RT-qPCR for HEV. HEV genomes were amplified and sequenced from 48 positive samples. Furthermore, we tested 380 serum samples from 11 locations across Australia for antibodies against HEV. HEV was detected in rabbits from all states and territories, except the Northern Territory. Seroprevalence varied between locations (from 0% to 22%), demonstrating that HEV is widely distributed in rabbit populations across Australia. Phylogenetic analyses showed that Australian HEV sequences are genetically diverse and that HEV was likely introduced into Australia independently on several occasions. In summary, this study broadens our understanding of the genetic diversity of rabbit HEV globally and shows that the virus is endemic in both domestic and wild rabbit populations in Australia.
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Zorzetto R, Klein RL, Erpen LMS, Klein BD, Giacobbo I, da Silveira RA, Frandoloso R, Kreutz LC. Unusual high prevalence of antibodies to hepatitis E virus in South Brazil. FEMS Microbiol Lett 2021; 368:6312495. [PMID: 34196363 DOI: 10.1093/femsle/fnab076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 06/15/2021] [Indexed: 01/16/2023] Open
Abstract
Hepatitis E virus (HEV) is worldwide distributed and might cause acute or chronic hepatitis mainly in immunocompromised individuals. In previous studies we found a high prevalence of antibodies to HEV within blood donors in south Brazil and also within backyard-raised pigs. Here, we aimed to investigate the prevalence of anti-HEV antibody and HEV RNA within the general population from three major municipalities (Caxias do Sul, Passo Fundo and Santa Maria) in south Brazil. A total of 3000 blood samples were randomly obtained from clinical laboratories at each of the three municipality (n = 1000 each) to determine the presence of anti-HEV antibodies and HEV RNA. Overall, anti-HEV antibodies were detected in 574/1000 (57,4%) samples in Caxias do Sul, 655/1000 (65.5%) samples in Passo Fundo and 554/1000 (55.4%) samples in Santa Maria. The prevalence of HEV-positive samples increased steadily and significantly (P < 0,001) with age and was unusually higher within individual over 40 years. Despite of this, none of the pooled serum samples had detectable levels of HEV RNA. The high anti-HEV antibody prevalence suggests that the virus might be present on the environment and/or foodstuff and poses a permanent threat to immune-compromised individuals.
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Affiliation(s)
- Renata Zorzetto
- Laboratório de Microbiologia e Imunologia Avançada, Faculdade de Agronomia e Medicina Veterinária, Universidade de Passo Fundo, BR 285, Km 292 - Campus I, Bairro São José, Passo Fundo, 99052-900, Brazil
| | - Rafaela Luiza Klein
- Laboratório de Microbiologia e Imunologia Avançada, Faculdade de Agronomia e Medicina Veterinária, Universidade de Passo Fundo, BR 285, Km 292 - Campus I, Bairro São José, Passo Fundo, 99052-900, Brazil
| | - Luana Marina Sheer Erpen
- Laboratório de Microbiologia e Imunologia Avançada, Faculdade de Agronomia e Medicina Veterinária, Universidade de Passo Fundo, BR 285, Km 292 - Campus I, Bairro São José, Passo Fundo, 99052-900, Brazil
| | - Bárbara Diel Klein
- Laboratório de Microbiologia e Imunologia Avançada, Faculdade de Agronomia e Medicina Veterinária, Universidade de Passo Fundo, BR 285, Km 292 - Campus I, Bairro São José, Passo Fundo, 99052-900, Brazil
| | - Igor Giacobbo
- Laboratório de Microbiologia e Imunologia Avançada, Faculdade de Agronomia e Medicina Veterinária, Universidade de Passo Fundo, BR 285, Km 292 - Campus I, Bairro São José, Passo Fundo, 99052-900, Brazil
| | - Rafael Arrua da Silveira
- Scientia Cursos. Rua Carlos Brenner, 220, Bairro Nossa Senhora de Lourdes, 97050-100, Santa Maria, RS, Brazil
| | - Rafael Frandoloso
- Laboratório de Microbiologia e Imunologia Avançada, Faculdade de Agronomia e Medicina Veterinária, Universidade de Passo Fundo, BR 285, Km 292 - Campus I, Bairro São José, Passo Fundo, 99052-900, Brazil
| | - Luiz Carlos Kreutz
- Laboratório de Microbiologia e Imunologia Avançada, Faculdade de Agronomia e Medicina Veterinária, Universidade de Passo Fundo, BR 285, Km 292 - Campus I, Bairro São José, Passo Fundo, 99052-900, Brazil
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9
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Nicolini LAP, Stoney RJ, Della Vecchia A, Grobusch M, Gautret P, Angelo KM, van Genderen PJJ, Bottieau E, Leder K, Asgeirsson H, Leung DT, Connor B, Pandey P, Toscanini F, Gobbi F, Castelli F, Bassetti M, Hamer DH. Travel-related hepatitis E: a two-decade GeoSentinel analysis. J Travel Med 2020; 27:5891692. [PMID: 32789467 PMCID: PMC9494553 DOI: 10.1093/jtm/taaa132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/27/2020] [Accepted: 08/06/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Hepatitis E virus (HEV) is widely distributed worldwide and is endemic in developing countries. Travel-related HEV infection has been reported at national levels, but global data are missing. Moreover, the global availability of HEV diagnostic testing has not been explored so far. The aim of this study is to describe the epidemiology of HEV infections in returning travellers and availability of HEV diagnostic testing in the GeoSentinel surveillance network. METHODS This was a multicentre retrospective cross-sectional study. All confirmed and probable HEV travel-related infections reported in the GeoSentinel Network between 1999 and 2018 were evaluated. GeoSentinel sites were asked to complete a survey in 2018 to assess the availability and accessibility of HEV diagnostic procedures (i.e. serology and molecular tests) throughout the study period. RESULTS Overall, 165 travel-related HEV infections were reported, mainly since 2010 (60%) and in tourists (50%). Travellers were exposed to hepatitis E in 27 countries; most travellers (62%) were exposed to HEV in South Asia. One patient was pregnant at the time of HEV infection and 14 had a concomitant gastrointestinal infection. No deaths were reported. In the 51% of patients with information available, there was no pre-travel consultation. Among 44 GeoSentinel sites that responded to the survey, 73% have access to HEV serology at a local level, while 55% could perform (at a local or central level) molecular diagnostics. CONCLUSION Reported access to HEV diagnostic testing is suboptimal among sites that responded to the survey; this could negatively affect diagnosing HEV. Pre-travel consultations before travel to South Asia and other low-income and high-prevalence areas with a focus on food and water precautions could be helpful in preventing hepatitis E infection. Improved HEV diagnostic capacity should be implemented to prevent and correctly diagnose travel-related HEV infection.
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Affiliation(s)
| | - Rhett J Stoney
- Division of Global Migration and Quarantine, National Center for Emerging and Zoonotic Infectious Diseases, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Andrea Della Vecchia
- Department of Health Sciences, University of Genova, Genova, Italy.,Internal Medicine Unit, Hôpitaux Iris Sud, Bruxelles, Belgium
| | - Martin Grobusch
- Tropical Medicine at the Amsterdam Medical Center, Amsterdam, The Netherlands
| | | | - Kristina M Angelo
- Division of Global Migration and Quarantine, National Center for Emerging and Zoonotic Infectious Diseases, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Emmanuel Bottieau
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, The Netherlands
| | - Karin Leder
- Victorian Infectious Diseases Service, Royal Melbourne Hospital, Melbourne, Australia
| | - Hilmir Asgeirsson
- Clinic of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Daniel T Leung
- International Travel Clinic, University of Utah Hospital and Clinics, Salt Lake City, UT, USA
| | - Bradley Connor
- The New York Center for Travel and Tropical Medicine, New York City, USA
| | - Prativa Pandey
- The CIWEC Clinic Travel Medicine Center, Lainchaur, KTM, Nepal
| | - Federica Toscanini
- Infectious Diseases, Ospedale Policlinico San Martino-IRCCS, Genova, Italy
| | - Federico Gobbi
- Department of Infectious-Tropical Diseases and Microbiology (DITM), IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, Italy
| | - Francesco Castelli
- Clinica di Malattie Infettive e Tropicali, University of Brescia, Brescia, Italy
| | - Matteo Bassetti
- Infectious Diseases, Ospedale Policlinico San Martino-IRCCS, Genova, Italy.,Department of Health Sciences, University of Genova, Genova, Italy
| | - Davidson H Hamer
- Department of Global Health, Boston University School of Public Health, Boston, USA.,Section of Infectious Diseases, Department of Medicine, Boston University School of Medicine, Boston, MA, USA.,National Emerging Infectious Diseases Laboratory, Boston University, Boston, MA, USA
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10
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Chanmanee T, Ajawatanawong P, Louisirirotchanakul S, Chotiyaputta W, Chainuvati S, Wongprompitak P. Phylogenetic analysis of two new complete genomes of the hepatitis E virus (HEV) genotype 3 from Thailand. Mol Biol Rep 2020; 47:8657-8668. [PMID: 33058031 PMCID: PMC7674359 DOI: 10.1007/s11033-020-05908-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 10/08/2020] [Indexed: 02/06/2023]
Abstract
Hepatitis E virus (HEV) is a causative agent of acute viral hepatitis globally. Evolutionary phylogeny classifies the HEV into eight genotypes that correlate with the viral transmission. Only four genotypes have been proven to be responsible for transmission in humans. However, there has been no report on the genomics and genotyping of HEV in Thailand during the past ten years. Here, we identified the genotype distributions of the Thai isolates of HEV and we sequenced two HEV genomes. We screened for 18 Thai isolates of HEV from Siriraj Hospital in Bangkok, from 2014–2016. The HEV genomes were sequenced from the serum and feces of a patient. The results showed that all Thai isolates of HEV were identified as genotype 3 (HEV-3). The ORF2 and genome phylogenies suggested two subgenotypes, called 3.1 and 3.2. The Thai isolates of HEV were frequently found in the subgenotype 3.1. The genome sequences of the two Thai isolates of HEV from the serum and fecal samples of the same patient showed 91% nucleotide similarity with the HEV genotype 3. Comparisons between the HEV genome and the ORF2 phylogenies illustrated that the ORF2 tree can be used to identify HEV genotypes, but it has less phylogenetic power for the HEV evolution. The two new genome sequences of HEV-3 from Thailand could contribute valuable information to the HEV genome study. (226 words)
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Affiliation(s)
- Tipsuda Chanmanee
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Pravech Ajawatanawong
- Division of Bioinformatics and Data Management for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Suda Louisirirotchanakul
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Watcharasak Chotiyaputta
- Division of Gastroenterology, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Siwaporn Chainuvati
- Division of Gastroenterology, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Patimaporn Wongprompitak
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
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11
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Du J, Xia J, Li S, Shen Y, Chen W, Luo Y, Zhao Q, Wen Y, Wu R, Yan Q, Huang X, Cao S, Han X, Cui M, Huang Y. Evolutionary dynamics and transmission patterns of Newcastle disease virus in China through Bayesian phylogeographical analysis. PLoS One 2020; 15:e0239809. [PMID: 32991628 PMCID: PMC7523974 DOI: 10.1371/journal.pone.0239809] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 09/14/2020] [Indexed: 12/17/2022] Open
Abstract
The Chinese poultry industry has experienced outbreaks of Newcastle disease (ND) dating back to the 1920s. However, the epidemic has exhibited a downtrend in recent years. In this study, both observational and genetic data [fusion (F) and haemagglutinin-neuraminidase genes (HN)] were analyzed, and phylogeographic analysis based on prevalent genotypes of Newcastle disease virus (NDV) was conducted for better understanding of the evolution and spatiotemporal dynamics of ND in China. In line with the observed trend of epidemic outbreaks, the effective population size of F and HN genes of circulating NDV is no longer growing since 2000, which is supported by 95% highest posterior diversity (HPD) intervals. Phylogeographic analysis indicated that the two eastern coastal provinces, Shandong and Jiangsu were the most relevant hubs for NDV migration, and the geographical regions with active NDV diffusion seemed to be constrained to southern and eastern China. The live poultry trade may play an important role in viral spread. Interestingly, no migration links from wild birds to poultry received Bayes factor support (BF > 3), while the migration links from poultry to wild birds accounted for 64% in all effective migrations. This may indicate that the sporadic cases of ND in wild bird likely spillover events from poultry. These findings contribute to predictive models of NDV transmission, and potentially help in the prevention of future outbreaks.
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Affiliation(s)
- Jiteng Du
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, People's Republic of China
| | - Jing Xia
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, People's Republic of China
| | - Shuyun Li
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, People's Republic of China
| | - Yuxi Shen
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, People's Republic of China
| | - Wen Chen
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, People's Republic of China
| | - Yuwen Luo
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, People's Republic of China
| | - Qin Zhao
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, People's Republic of China
| | - Yiping Wen
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, People's Republic of China
| | - Rui Wu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, People's Republic of China
| | - Qigui Yan
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, People's Republic of China
| | - Xiaobo Huang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, People's Republic of China
| | - Sanjie Cao
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, People's Republic of China
| | - Xinfeng Han
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, People's Republic of China
| | - Min Cui
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, People's Republic of China
| | - Yong Huang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, People's Republic of China
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12
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De Sabato L, Di Bartolo I, Lapa D, Capobianchi MR, Garbuglia AR. Molecular Characterization of HEV Genotype 3 in Italy at Human/Animal Interface. Front Microbiol 2020; 11:137. [PMID: 32117156 PMCID: PMC7014918 DOI: 10.3389/fmicb.2020.00137] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 01/21/2020] [Indexed: 12/17/2022] Open
Abstract
Hepatitis E virus (HEV) is an emerging public health issue in industrialized countries. In the last decade the number of autochthonous human infections has increased in Europe. Genotype 3 (HEV-3) is typically zoonotic, being foodborne the main route of transmission to humans, and is the most frequently detected in Europe in both humans and animals (mainly pigs and wild boars). In Italy, the first autochthonous human case was reported in 1999; since then, HEV-3 has been widely detected in both humans and animals. Despite the zoonotic characteristic of HEV-3 is well established, the correlation between animal and human strains has been poorly investigated in Italy. In the present study, we compared the subtype distribution of HEV-3 in humans and animals (swine and wild boar) in the period 2000-2018 from Italy. The dataset for this analysis included a total of 96 Italian ORF2 sequences (300 nt long), including both NCBI database-derived (n = 64) and recent sequences (2016-2018, n = 32) obtained in this study. The results show that subtype 3f is the most frequent in humans and pigs, followed by the HEV-3e, HEV-3c and other unassignable HEV-3 strains. Diversely, in wild boar a wider group of HEV-3 subtypes have been detected, including HEV-3a, which has also been detected for the first time in a human patient in Central Italy in 2017, and a wide group of unassignable HEV-3 strains. The phylogenetic analysis including, besides Italian strains, also sequences from other countries retrieved from the NCBI database, indicated that human Italian sequences, in particular those of HEV-3f and HEV-3e, form significant clusters mainly with sequences of animal origin from the same country. Nevertheless, for HEV-3c, rarely detected in Italian pigs, human sequences from Italy are more correlated to human sequences from other European countries. Furthermore, clusters of near-identical human strains identified in a short time interval in Lazio Region (Central Italy) can be recognized in the phylogenetic tree, suggesting that multiple infections originating from a common source have occurred, and confirming the importance of sequencing support to HEV surveillance.
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Affiliation(s)
- Luca De Sabato
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Ilaria Di Bartolo
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Daniele Lapa
- Laboratory of Virology, “L. Spallanzani” National Institute for Infectious Diseases, IRCCS, Rome, Italy
| | - Maria Rosaria Capobianchi
- Laboratory of Virology, “L. Spallanzani” National Institute for Infectious Diseases, IRCCS, Rome, Italy
| | - Anna Rosa Garbuglia
- Laboratory of Virology, “L. Spallanzani” National Institute for Infectious Diseases, IRCCS, Rome, Italy
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13
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Wassenaar TM, Jun S, Robeson M, Ussery DW. Comparative genomics of hepatitis A virus, hepatitis C virus, and hepatitis E virus provides insights into the evolutionary history of Hepatovirus species. Microbiologyopen 2020; 9:e973. [PMID: 31742930 PMCID: PMC7002107 DOI: 10.1002/mbo3.973] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/31/2019] [Accepted: 10/31/2019] [Indexed: 12/17/2022] Open
Abstract
The intraspecies genomic diversity of the single-strand RNA (+) virus species hepatitis A virus (Hepatovirus), hepatitis C virus (Hepacivirus), and hepatitis E virus (Orthohepevirus) was compared. These viral species all can cause liver inflammation (hepatitis), but share no gene similarity. The codon usage of human hepatitis A virus (HAV) is suboptimal for replication in its host, a characteristic it shares with taxonomically related rodent, simian, and bat hepatitis A virus species. We found this codon usage to be strikingly similar to that of Triatoma virus that infects blood-sucking kissing bugs. The codon usage of that virus is well adapted to its insect host. The codon usage of HAV is also similar to other invertebrate viruses of various taxonomic families. An evolutionary ancestor of HAV and related virus species is hypothesized to be an insect virus that underwent a host jump to infect mammals. The similarity between HAV and invertebrate viruses goes beyond codon usage, as they also share amino acid composition characteristics, while not sharing direct sequence homology. In contrast, hepatitis C virus and hepatitis E virus are highly similar in codon usage preference, nucleotide composition, and amino acid composition, and share these characteristics with Human pegivirus A, West Nile virus, and Zika virus. We present evidence that these observations are only partly explained by differences in nucleotide composition of the complete viral codon regions. We consider the combination of nucleotide composition, amino acid composition, and codon usage preference suitable to provide information on possible evolutionary similarities between distant virus species that cannot be investigated by phylogeny.
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Affiliation(s)
| | - Se‐Ran Jun
- Department of Biomedical InformaticsUniversity of Arkansas for Medical SciencesLittle RockARUSA
| | - Michael Robeson
- Department of Biomedical InformaticsUniversity of Arkansas for Medical SciencesLittle RockARUSA
| | - David W. Ussery
- Department of Biomedical InformaticsUniversity of Arkansas for Medical SciencesLittle RockARUSA
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14
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Cagliani R, Forni D, Sironi M. Mode and tempo of human hepatitis virus evolution. Comput Struct Biotechnol J 2019; 17:1384-1395. [PMID: 31768229 PMCID: PMC6872792 DOI: 10.1016/j.csbj.2019.09.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/19/2019] [Accepted: 09/21/2019] [Indexed: 02/07/2023] Open
Abstract
Human viral hepatitis, a major cause of morbidity and mortality worldwide, is caused by highly diverse viruses with different genetic, ecological, and pathogenetic features. Technological advances that allow throughput sequencing of viral genomes, as well as the development of computational tools to analyze such genome data, have largely expanded our knowledge on the host range and evolutionary history of human hepatitis viruses. Thus, with the exclusion of hepatitis D virus, close or distant relatives of these human pathogens were identified in a number of domestic and wild mammals. Also, sequences of human viral strains isolated from different geographic locations and over different time-spans have allowed the application of phylogeographic and molecular dating approaches to large viral phylogenies. In this review, we summarize the most recent insights into our understanding of the evolutionary events and ecological contexts that determined the origin and spread of human hepatitis viruses.
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Affiliation(s)
- Rachele Cagliani
- Bioinformatics, Scientific Institute, IRCCS E. MEDEA, 23842 Bosisio Parini, Lecco, Italy
| | - Diego Forni
- Bioinformatics, Scientific Institute, IRCCS E. MEDEA, 23842 Bosisio Parini, Lecco, Italy
| | - Manuela Sironi
- Bioinformatics, Scientific Institute, IRCCS E. MEDEA, 23842 Bosisio Parini, Lecco, Italy
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15
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Hartard C, Gantzer C, Bronowicki JP, Schvoerer E. Emerging hepatitis E virus compared with hepatitis A virus: A new sanitary challenge. Rev Med Virol 2019; 29:e2078. [PMID: 31456241 DOI: 10.1002/rmv.2078] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 07/19/2019] [Accepted: 07/22/2019] [Indexed: 12/21/2022]
Abstract
Hepatitis A (HAV) and E (HEV) viruses are able to cause liver disease in humans. Among the five classical hepatotropic viruses, they are mainly transmitted via the fecal-oral route. Historically, many similarities have thus been described between them according to their incidence and their pathogenicity, especially in countries with poor sanitary conditions. However, recent advances have provided new insights, and the gap is widening between them. Indeed, while HAV infection incidence tends to decrease in developed countries along with public health improvement, HEV is currently considered as an underdiagnosed emerging pathogen. HEV autochthonous infections are increasingly observed and are mainly associated with zoonotic transmissions. Extra hepatic signs resulting in neurological or renal impairments have also been reported for HEV, as well as a chronic carrier state in immunocompromised patients, arguing in favor of differential pathogenesis between those two viruses. Recent molecular tools have allowed studies of viral genome variability and investigation of links between viral plasticity and clinical evolution. The identification of key functional mutations in viral genomes may improve the knowledge of their clinical impact and is analyzed in depth in the present review.
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Affiliation(s)
- Cédric Hartard
- Laboratoire de Virologie, CHRU de Nancy Brabois, Vandœuvre-lès-Nancy, France.,Laboratoire de Chimie Physique et Microbiologie pour les Matériaux et l'Environnement (LCPME), UMR 7564, Vandoeuvre-lès-Nancy, France.,CNRS, LCPME UMR 7564, Nancy, France.,Faculté des Sciences et Technologies, Institut Jean Barriol, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Christophe Gantzer
- Laboratoire de Chimie Physique et Microbiologie pour les Matériaux et l'Environnement (LCPME), UMR 7564, Vandoeuvre-lès-Nancy, France.,CNRS, LCPME UMR 7564, Nancy, France.,Faculté des Sciences et Technologies, Institut Jean Barriol, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | | | - Evelyne Schvoerer
- Laboratoire de Virologie, CHRU de Nancy Brabois, Vandœuvre-lès-Nancy, France.,Laboratoire de Chimie Physique et Microbiologie pour les Matériaux et l'Environnement (LCPME), UMR 7564, Vandoeuvre-lès-Nancy, France.,CNRS, LCPME UMR 7564, Nancy, France.,Faculté des Sciences et Technologies, Institut Jean Barriol, Université de Lorraine, Vandœuvre-lès-Nancy, France
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16
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Oliveira-Filho EFD, Dos Santos DR, Durães-Carvalho R, da Silva A, de Lima GB, Batista Filho AFB, Pena LJ, Gil LH. Evolutionary study of potentially zoonotic hepatitis E virus genotype 3 from swine in Northeast Brazil. Mem Inst Oswaldo Cruz 2019; 114:e180585. [PMID: 31166480 PMCID: PMC6547807 DOI: 10.1590/0074-02760180585] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 05/10/2019] [Indexed: 12/27/2022] Open
Abstract
Hepatitis E virus (HEV), an emerging virus associated with acute hepatic disease, leads to thousands of deaths worldwide. HEV has already been reported in Brazil; however, there is a lack of epidemiological and molecular information on the genetic variability, taxonomy, and evolution of HEV. It is thus unclear whether hepatitis E is a neglected disease in Brazil or it has low relevance for public health in this country. Here, for the first time, we report the presence of HEV in Northeast Brazil. A total of 119 swine faecal samples were screened for the presence of HEV RNA using real-time polymerase chain reaction (RT-PCR) and further confirmed by conventional RT-PCR; among these, two samples were identified as positive. Molecular evolution analyses based on capsid sequences revealed that the samples had close proximities to HEV sequences belonging to genotype 3 and were genetically related to subtype 3f isolated in humans. Parsimony ancestral states analysis indicated gene flow events from HEV cross-species infection, suggesting an important role of pig hosts in viral spillover. HEV’s ability for zoonotic transmission by inter-species host switching as well as its possible adaptation to new animal species remain important issues for human health.
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Affiliation(s)
- Edmilson Ferreira de Oliveira-Filho
- Fundação Oswaldo Cruz-Fiocruz, Instituto Aggeu Magalhães, Departamento de Virologia, Recife, PE, Brasil.,Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | - Debora Rl Dos Santos
- Universidade Federal Rural do Rio de Janeiro, Instituto de Veterinária, Seropédica, RJ, Brasil
| | - Ricardo Durães-Carvalho
- Fundação Oswaldo Cruz-Fiocruz, Instituto Aggeu Magalhães, Departamento de Virologia, Recife, PE, Brasil
| | - Adalúcia da Silva
- Fundação Oswaldo Cruz-Fiocruz, Instituto Aggeu Magalhães, Departamento de Virologia, Recife, PE, Brasil
| | - Gustavo Barbosa de Lima
- Fundação Oswaldo Cruz-Fiocruz, Instituto Aggeu Magalhães, Departamento de Microbiologia, Recife, PE, Brasil
| | | | - Lindomar J Pena
- Fundação Oswaldo Cruz-Fiocruz, Instituto Aggeu Magalhães, Departamento de Virologia, Recife, PE, Brasil
| | - Laura Hvg Gil
- Fundação Oswaldo Cruz-Fiocruz, Instituto Aggeu Magalhães, Departamento de Virologia, Recife, PE, Brasil
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17
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Primadharsini PP, Nagashima S, Okamoto H. Genetic Variability and Evolution of Hepatitis E Virus. Viruses 2019; 11:E456. [PMID: 31109076 PMCID: PMC6563261 DOI: 10.3390/v11050456] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 05/15/2019] [Accepted: 05/16/2019] [Indexed: 12/16/2022] Open
Abstract
Hepatitis E virus (HEV) is a single-stranded positive-sense RNA virus. HEV can cause both acute and chronic hepatitis, with the latter usually occurring in immunocompromised patients. Modes of transmission range from the classic fecal-oral route or zoonotic route, to relatively recently recognized but increasingly common routes, such as via the transfusion of blood products or organ transplantation. Extrahepatic manifestations, such as neurological, kidney and hematological abnormalities, have been documented in some limited cases, typically in patients with immune suppression. HEV has demonstrated extensive genomic diversity and a variety of HEV strains have been identified worldwide from human populations as well as growing numbers of animal species. The genetic variability and constant evolution of HEV contribute to its physiopathogenesis and adaptation to new hosts. This review describes the recent classification of the Hepeviridae family, global genotype distribution, clinical significance of HEV genotype and genomic variability and evolution of HEV.
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Affiliation(s)
- Putu Prathiwi Primadharsini
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Tochigi 329-0498, Japan.
| | - Shigeo Nagashima
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Tochigi 329-0498, Japan.
| | - Hiroaki Okamoto
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Tochigi 329-0498, Japan.
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18
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Geng Y, Zhao C, Guo T, Xu Y, Wang X, Huang W, Liu H, Wang Y. Detection of Hepatitis E Virus in Raw Pork and Pig Viscera As Food in Hebei Province of China. Foodborne Pathog Dis 2019; 16:325-330. [DOI: 10.1089/fpd.2018.2572] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Yansheng Geng
- Health Science Center, Hebei University, Baoding, China
| | - Chenyan Zhao
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Tingyu Guo
- Health Science Center, Hebei University, Baoding, China
| | - Ying Xu
- Health Science Center, Hebei University, Baoding, China
| | - Xuanpu Wang
- Health Science Center, Hebei University, Baoding, China
| | - Weijin Huang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Huan Liu
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Youchun Wang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, National Institutes for Food and Drug Control, Beijing, China
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19
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Pavesi A. Asymmetric evolution in viral overlapping genes is a source of selective protein adaptation. Virology 2019; 532:39-47. [PMID: 31004987 PMCID: PMC7125799 DOI: 10.1016/j.virol.2019.03.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/25/2019] [Accepted: 03/26/2019] [Indexed: 12/29/2022]
Abstract
Overlapping genes represent an intriguing puzzle, as they encode two proteins whose ability to evolve is constrained by each other. Overlapping genes can undergo “symmetric evolution” (similar selection pressures on the two proteins) or “asymmetric evolution” (significantly different selection pressures on the two proteins). By sequence analysis of 75 pairs of homologous viral overlapping genes, I evaluated their accordance with one or the other model. Analysis of nucleotide and amino acid sequences revealed that half of overlaps undergo asymmetric evolution, as the protein from one frame shows a number of substitutions significantly higher than that of the protein from the other frame. Interestingly, the most variable protein (often known to interact with the host proteins) appeared to be encoded by the de novo frame in all cases examined. These findings suggest that overlapping genes, besides to increase the coding ability of viruses, are also a source of selective protein adaptation. A dataset of 80 pairs of homologous overlapping genes from viruses is examined. Its analysis reveals that half of overlapping genes undergo asymmetric evolution. The most variable gene product is that encoded by the de novo overlapping gene. Overlapping genes evolving asymmetrically are a source of selective protein adaptation.
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Affiliation(s)
- Angelo Pavesi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, I-43124, Parma, Italy.
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20
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Zhu YO, Aw P, Aung MM, Lee HK, Hibberd M, Lee GH. Patterns of mutation within an emerging endemic lineage of HEV-3a. J Viral Hepat 2019; 26:191-198. [PMID: 30315669 DOI: 10.1111/jvh.13015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 09/13/2018] [Indexed: 12/12/2022]
Abstract
The hepatitis E virus can cause chronic infections in immuno-suppressed patients, and cases have been on the rise globally. Viral mutations during such infections are difficult to characterize. We deep-sequenced viral populations from 15 immunocompromised patients with chronic HEV to identify the viral lineage and describe viral mutational hotspots within and across patients. A total of 21 viral RNA samples were collected between 2012 and 2017 from a single hospital in Singapore. Sequences covering a total of 3894 bp of the HEV genome were obtained. Phylogenetic analyses identified all sequences as belonging to the HEV-3a sub-clade and clearly indicate a unique local lineage. Deep sequencing reveals variable viral population complexity during infections. Comparisons of viral samples from the same patients spaced 2-19 months apart revealed rapid nucleotide replacements in the dominant viral sequence in both ribavirin treated and treatment-naive patients. Mutational hotspots were identified within ORF3 and the PCP/HVR domain of ORF1.
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Affiliation(s)
- Yuan O Zhu
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore, Singapore City, Singapore
| | - Pauline Aw
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore, Singapore City, Singapore
| | - Myo Myint Aung
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore City, Singapore
| | - Hong Kai Lee
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Hospital, National University Health System, Singapore City, Singapore
| | - Martin Hibberd
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore, Singapore City, Singapore.,London School of Hygiene and Tropical Medicine, London, UK
| | - Guan Huei Lee
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore City, Singapore
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21
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Kantala T, Maunula L. Hepatitis E virus: zoonotic and foodborne transmission in developed countries. Future Virol 2018. [DOI: 10.2217/fvl-2018-0062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Hepatitis E virus (HEV), together with hepatitis A virus, transmits via the fecal–oral route. The number of domestic hepatitis E cases among Europeans has grown alarmingly during the past 5 years. Surveillance studies suggest that the number of foodborne HEV infections is increasing most rapidly. Zoonotic HEV genotype HEV-3 is prevalent among pigs and wild boars in Europe and many developed countries, whereas zoonotic genotype HEV-4 is more common in pigs in some Asian countries. This review presents the most recent data about possible foodborne transmission of HEV via pigs and other production animals and about the presence of HEV in high-risk foods, such as ready-to-eat meat products. Possible solutions about how to tackle this problem are discussed here.
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Affiliation(s)
- Tuija Kantala
- Department of Food Hygiene & Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, P.O. Box 66, FI-00014, Helsinki, Finland
- Finnish Food Safety Authority Evira, Mustialankatu 3, FI-00790 Helsinki, Finland
| | - Leena Maunula
- Department of Food Hygiene & Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, P.O. Box 66, FI-00014, Helsinki, Finland
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22
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Amorim AR, Mendes GS, Pena GPA, Santos N. Hepatitis E virus infection of slaughtered healthy pigs in Brazil. Zoonoses Public Health 2018; 65:501-504. [PMID: 29441690 DOI: 10.1111/zph.12455] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Indexed: 12/27/2022]
Abstract
Hepatitis E virus (HEV) is an emerging pathogen that can be transmitted through contaminated raw or undercooked meat derived from domestic pigs. HEV infections have been documented among pig herds, pig products and environmental samples raising concern about the spread of the virus. HEV genotypes 3 and 4 are considered zoonotic and have been linked to human cases. HEV was detected in 51 of 335 bile samples (15.2%) from healthy pigs in Minas Gerais, Brazil. Phylogenetic analysis of partial sequences from ORF1 and ORF2 regions yielded discordant results, assigning isolates to subtypes 3c and 3i, respectively, suggesting intragenotypic HEV recombination.
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Affiliation(s)
- A R Amorim
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - G S Mendes
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - G P A Pena
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - N Santos
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
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23
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Origin and dispersal of Hepatitis E virus. Emerg Microbes Infect 2018; 7:11. [PMID: 29410449 PMCID: PMC5837148 DOI: 10.1038/s41426-017-0009-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 11/17/2017] [Accepted: 12/03/2017] [Indexed: 12/21/2022]
Abstract
Hepatitis E virus (HEV, genus Orthohepevirus) is a common cause of hepatitis worldwide. Human-infecting HEV strains (Orthohepevirus A) include human-restricted and enzootic genotypes. Viruses in the Orthohepevirus A species also infect rabbits (HEV-3ra), camels, and swine. Using a selection-informed method, we dated the origin of the Orthohepevirus genus at least 21 million years ago, whereas the Orthohepevirus A species originated in Asia, most likely from a human-infecting ancestor that existed ~4500 to 6800 years ago. In this period, the appearance of large human settlements probably facilitated HEV emergence and spread. The earliest events in Orthohepevirus A evolutionary history involved the separation of the enzootic and human-restricted genotypes, as well as the split of the camel-infecting genotypes, which occurred during the time-frame of camel domestication. The place and timing of HEV-3ra divergence also correspond to the circumstances of rabbit domestication. This study clarifies the origin and historical events underlying HEV dispersal.
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24
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Nan Y, Wu C, Zhao Q, Zhou EM. Zoonotic Hepatitis E Virus: An Ignored Risk for Public Health. Front Microbiol 2017; 8:2396. [PMID: 29255453 PMCID: PMC5723051 DOI: 10.3389/fmicb.2017.02396] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/20/2017] [Indexed: 12/27/2022] Open
Abstract
Hepatitis E virus (HEV) is a quasi-enveloped, single-stranded positive-sense RNA virus. HEV belongs to the family Hepeviridae, a family comprised of highly diverse viruses originating from various species. Since confirmation of HEV's zoonosis, HEV-induced hepatitis has been a public health concern both for developing and developed countries. Meanwhile, the demonstration of a broad host range for zoonotic HEV suggests the existence of a variety of transmission routes that could lead to human infection. Moreover, anti-HEV antibody serosurveillance worldwide demonstrates a higher than expected HEV prevalence rate that conflicts with the rarity and sporadic nature of reported acute hepatitis E cases. In recent years, chronic HEV infection, HEV-related acute hepatic failure, and extrahepatic manifestations caused by HEV infection have been frequently reported. These observations suggest a significant underestimation of the number and complexity of transmission routes previously predicted to cause HEV-related disease, with special emphasis on zoonotic HEV as a public health concern. Significant research has revealed details regarding the virology and infectivity of zoonotic HEV in both humans and animals. In this review, the discovery of HEV zoonosis, recent progress in our understanding of the zoonotic HEV host range, and classification of diverse HEV or HEV-like isolates from various hosts are reviewed in a historic context. Ultimately, this review focuses on current understanding of viral pathogenesis and cross-species transmission of zoonotic HEV. Moreover, host factors and viral determinants influencing HEV host tropism are discussed to provide new insights into HEV transmission and prevalence mechanisms.
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Affiliation(s)
- Yuchen Nan
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Xianyang, China
- Scientific Observing and Experimental Station of Veterinary Pharmacology and Diagnostic Technology, Ministry of Agriculture, Xianyang, China
| | - Chunyan Wu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Xianyang, China
- Scientific Observing and Experimental Station of Veterinary Pharmacology and Diagnostic Technology, Ministry of Agriculture, Xianyang, China
| | - Qin Zhao
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Xianyang, China
- Scientific Observing and Experimental Station of Veterinary Pharmacology and Diagnostic Technology, Ministry of Agriculture, Xianyang, China
| | - En-Min Zhou
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Xianyang, China
- Scientific Observing and Experimental Station of Veterinary Pharmacology and Diagnostic Technology, Ministry of Agriculture, Xianyang, China
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25
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Abstract
Hepatitis E virus (HEV) infection can lead to acute and chronic hepatitis as well as to extrahepatic manifestations such as neurological and renal disease; it is the most common cause of acute viral hepatitis worldwide. Four genotypes are responsible for most infection in humans, of which HEV genotypes 1 and 2 are obligate human pathogens and HEV genotypes 3 and 4 are mostly zoonotic. Until quite recently, HEV was considered to be mainly responsible for epidemics of acute hepatitis in developing regions owing to contamination of drinking water supplies with human faeces. However, HEV is increasingly being recognized as endemic in some developed regions. In this setting, infections occur through zoonotic transmission or contaminated blood products and can cause chronic hepatitis in immunocompromised individuals. HEV infections can be diagnosed by measuring anti-HEV antibodies, HEV RNA or viral capsid antigen in blood or stool. Although an effective HEV vaccine exists, it is only licensed for use in China. Acute hepatitis E is usually self-limiting and does not require specific treatment. Management of immunocompromised individuals involves lowering the dose of immunosuppressive drugs and/or treatment with the antiviral agent ribavirin.
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Hepatitis E Virus Genotypes and Evolution: Emergence of Camel Hepatitis E Variants. Int J Mol Sci 2017; 18:ijms18040869. [PMID: 28425927 PMCID: PMC5412450 DOI: 10.3390/ijms18040869] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 04/11/2017] [Accepted: 04/18/2017] [Indexed: 12/18/2022] Open
Abstract
Hepatitis E virus (HEV) is a major cause of viral hepatitis globally. Zoonotic HEV is an important cause of chronic hepatitis in immunocompromised patients. The rapid identification of novel HEV variants and accumulating sequence information has prompted significant changes in taxonomy of the family Hepeviridae. This family includes two genera: Orthohepevirus, which infects terrestrial vertebrates, and Piscihepevirus, which infects fish. Within Orthohepevirus, there are four species, A–D, with widely differing host range. Orthohepevirus A contains the HEV variants infecting humans and its significance continues to expand with new clinical information. We now recognize eight genotypes within Orthohepevirus A: HEV1 and HEV2, restricted to humans; HEV3, which circulates among humans, swine, rabbits, deer and mongooses; HEV4, which circulates between humans and swine; HEV5 and HEV6, which are found in wild boars; and HEV7 and HEV8, which were recently identified in dromedary and Bactrian camels, respectively. HEV7 is an example of a novel genotype that was found to have significance to human health shortly after discovery. In this review, we summarize recent developments in HEV molecular taxonomy, epidemiology and evolution and describe the discovery of novel camel HEV genotypes as an illustrative example of the changes in this field.
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