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      Update: proposed reference sequences for subtypes of hepatitis E virus (species Orthohepevirus A)

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          Abstract

          In this recommendation, we update our 2016 table of reference sequences of subtypes of hepatitis E virus (HEV; species Orthohepevirus A, family Hepeviridae) for which complete genome sequences are available (Smith et al., 2016). This takes into account subsequent publications describing novel viruses and additional proposals for subtype names; there are now eight genotypes and 36 subtypes. Although it remains difficult to define strict criteria for distinguishing between virus subtypes, and is not within the remit of the International Committee on Taxonomy of Viruses (ICTV), the use of agreed reference sequences will bring clarity and stability to researchers, epidemiologists and clinicians working with HEV.

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          MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

          Sudhir Kumar, Glen Stecher, Koichiro Tamura (2016)
          We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.
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            Proposed reference sequences for hepatitis E virus subtypes

            Donald B. Smith, Peter Simmonds, Jacques Izopet … (2016)
            The nomenclature of hepatitis E virus (HEV) subtypes is inconsistent and makes comparison of different studies problematic. We have provided a table of proposed complete genome reference sequences for each subtype. The criteria for subtype assignment vary between different genotypes and methodologies, and so a conservative pragmatic approach has been favoured. Updates to this table will be posted on the International Committee on Taxonomy of Viruses website (http://talk.ictvonline.org/r.ashx?C). The use of common reference sequences will facilitate communication between researchers and help clarify the epidemiology of this important human pathogen. This subtyping procedure might be adopted for other taxa of the genus Orthohepevirus.
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              Molecular cloning and sequencing of the Mexico isolate of hepatitis E virus (HEV).

              Norman Fry, Miguel A. Tam, Pedro J A Gutiérrez … (1992)
              Hepatitis E virus (HEV) is the major causative agent of hepatitis E or what was formerly known as enterically transmitted non-A, non-B hepatitis. The disease has a worldwide distribution but occurs principally in developing countries in any of three forms: large epidemics, smaller outbreaks, or sporadic infections. Genetic variation of different HEV strains was previously noted and it will be important to determine the extent to which this variation may pose problems in the diagnosis and treatment of HEV infection. To analyze differences at the genetic level between HEV(Mexico; M) and the previously characterized HEV(Burma; B) and HEV(Pakistan; P) isolates, overlapping cDNAs were cloned from samples obtained from an infected human and an experimentally inoculated cynomolgus macaque. These cDNA clones, representing the nearly complete (7185-bp) genome of HEV(M), confirmed an expression strategy for the virus that involves the use of 3 forward open reading frames (ORFs). The HEV(M) strain has an overall 76 and 77% nucleic acid identity with the HEV(B) strain and HEV(P) strain, respectively; however, the degree of sequence variation was not uniform throughout the viral genome. A hypervariable region was identified in ORF1 that exhibited a 58 and 54% nucleic acid sequence and 13% amino acid similarity with the Burma strain and the Pakistan strain, respectively. A large number of the nucleotide differences occurred at the third codon position, with the deduced amino acid sequences similarity of 83, 93, and 87% between HEV(M) and HEV(B) isolates in ORF1, ORF2, and ORF3, respectively, and with 84, 93, and 87% amino acid identities between HEV(M) and HEV(P) isolates in ORF1, ORF2, and ORF3, respectively. The nucleotide sequences derived from the highly conserved regions of HEV genome will be useful in developing polymerase chain reaction-based tests to confirm the viral infection. Knowledge of the extent of the sequence variation encountered with HEV will not only aid in the future development of diagnostic and vaccine reagents but also further our understanding of how HEV strain variation might impact the pathological outcome of infection.
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                Author and article information

                Journal
                Journal ID (nlm-ta): J Gen Virol
                Journal ID (iso-abbrev): J Gen Virol
                Journal ID (hwp): jgv
                Journal ID (publisher-id): jgv
                Title: The Journal of General Virology
                Publisher: Microbiology Society
                ISSN (Print): 0022-1317
                ISSN (Electronic): 1465-2099
                Publication date (Print): July 2020
                Publication date (Electronic): 29 May 2020
                Publication date PMC-release: 29 May 2020
                Volume: 101
                Issue: 7
                Pages: 692-698
                Affiliations
                [ 1​ ] departmentNuffield Department of Medicine , University of Oxford , Oxford, UK
                [ 2​ ] INSERM , UMR1043, Toulouse F-31300, France
                [ 3​ ] The Wellcome Trust/DBT India Alliance , Hyderabad, India
                [ 4​ ] College of Veterinary Medicine, Virginia Polytechnic Institute and State University , Blacksburg, Virginia, USA
                [ 5​ ] departmentDepartment of Infectious Diseases , Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg , 41345 Gothenburg, Sweden
                [ 6​ ] departmentDivision of Virology , Department of Infection and Immunity, Jichi Medical University School of Medicine , Tochigi-ken, Japan
                [ 7​ ] Wageningen Bioveterinary Research, Wageningen University and Research , Lelystad, The Netherlands
                [ 8​ ] departmentDepartment of Medical Microbiology and Immunology , Medical School, University of Pécs , Pécs, Hungary
                [ 9​ ] Centers for Disease Control and Prevention, National Center for HIV/Hepatitis/STD/TB Prevention, Division of Viral Hepatitis , Atlanta, Georgia, USA
                Author notes
                *Correspondence: Donald B. Smith, donald.smith@ 123456ndm.ox.ac.uk

                Other footnote: Purdy, Jameel, Meng, Norder, Okamoto, van der Poel, Reuter and Smith are members of the ICTV Hepeviridae Study Group.

                Author information
                https://orcid.org/0000-0002-2876-5318
                https://orcid.org/0000-0003-2722-2159
                https://orcid.org/0000-0002-7964-4700
                https://orcid.org/0000-0001-5424-9774
                https://orcid.org/0000-0002-2739-1334
                https://orcid.org/0000-0002-7528-3872
                https://orcid.org/0000-0003-0827-0964
                Article
                Publisher ID: 001435
                DOI: 10.1099/jgv.0.001435
                PMC ID: 7660235
                PubMed ID: 32469300
                SO-VID: 1c145895-24f7-45bd-bc7e-d0ef863c424c
                Copyright © © 2020 The Authors
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.

                History
                Date received : 10 March 2020
                Date accepted : 29 April 2020
                Funding
                Funded by: Santé Publique France
                Award Recipient : Jacques Izopet
                Funded by: Wellcome Trust
                Award ID: WT108418AIA
                Award Recipient : Peter Simmonds
                Categories
                Subject: Insight Review
                Subject: Animal
                Subject: Positive-strand RNA Viruses
                Custom metadata
                OpenAccessEmbargo 0

                ScienceOpen disciplines: Microbiology & Virology
                Keywords: hepatitis e virus,hepeviridae,orthohepevirus a
                Data availability:
                ScienceOpen disciplines: Microbiology & Virology
                Keywords: hepatitis e virus, hepeviridae, orthohepevirus a

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