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      Review of Hepatitis E Virus in Rats: Evident Risk of Species Orthohepevirus C to Human Zoonotic Infection and Disease

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          Abstract

          Hepatitis E virus (HEV) (family Hepeviridae) is one of the most common human pathogens, causing acute hepatitis and an increasingly recognized etiological agent in chronic hepatitis and extrahepatic manifestations. Recent studies reported that not only are the classical members of the species Orthohepevirus A (HEV-A) pathogenic to humans but a genetically highly divergent rat origin hepevirus (HEV-C1) in species Orthohepevirus C (HEV-C) is also able to cause zoonotic infection and symptomatic disease (hepatitis) in humans. This review summarizes the current knowledge of hepeviruses in rodents with special focus of rat origin HEV-C1. Cross-species transmission and genetic diversity of HEV-C1 and confirmation of HEV-C1 infections and symptomatic disease in humans re-opened the long-lasting and full of surprises story of HEV in human. This novel knowledge has a consequence to the epidemiology, clinical aspects, laboratory diagnosis, and prevention of HEV infection in humans.

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          MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

          Sudhir Kumar, Glen Stecher, Michael KaWah Li … (2018)
          The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
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            WebLogo: a sequence logo generator.

            Gavin E. Crooks, Gary Hon, John-Marc Chandonia … (2004)
            WebLogo generates sequence logos, graphical representations of the patterns within a multiple sequence alignment. Sequence logos provide a richer and more precise description of sequence similarity than consensus sequences and can rapidly reveal significant features of the alignment otherwise difficult to perceive. Each logo consists of stacks of letters, one stack for each position in the sequence. The overall height of each stack indicates the sequence conservation at that position (measured in bits), whereas the height of symbols within the stack reflects the relative frequency of the corresponding amino or nucleic acid at that position. WebLogo has been enhanced recently with additional features and options, to provide a convenient and highly configurable sequence logo generator. A command line interface and the complete, open WebLogo source code are available for local installation and customization. Copyright 2004 Cold Spring Harbor Laboratory Press
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              ViennaRNA Package 2.0

              Ronny Lorenz, Stephan H Bernhart, Christian Höner zu Siederdissen … (2011)
              Background Secondary structure forms an important intermediate level of description of nucleic acids that encapsulates the dominating part of the folding energy, is often well conserved in evolution, and is routinely used as a basis to explain experimental findings. Based on carefully measured thermodynamic parameters, exact dynamic programming algorithms can be used to compute ground states, base pairing probabilities, as well as thermodynamic properties. Results The ViennaRNA Package has been a widely used compilation of RNA secondary structure related computer programs for nearly two decades. Major changes in the structure of the standard energy model, the Turner 2004 parameters, the pervasive use of multi-core CPUs, and an increasing number of algorithmic variants prompted a major technical overhaul of both the underlying RNAlib and the interactive user programs. New features include an expanded repertoire of tools to assess RNA-RNA interactions and restricted ensembles of structures, additional output information such as centroid structures and maximum expected accuracy structures derived from base pairing probabilities, or z-scores for locally stable secondary structures, and support for input in fasta format. Updates were implemented without compromising the computational efficiency of the core algorithms and ensuring compatibility with earlier versions. Conclusions The ViennaRNA Package 2.0, supporting concurrent computations via OpenMP, can be downloaded from http://www.tbi.univie.ac.at/RNA.
              Article 0 comments Cited 1082 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Viruses
                Journal ID (iso-abbrev): Viruses
                Journal ID (publisher-id): viruses
                Title: Viruses
                Publisher: MDPI
                ISSN (Electronic): 1999-4915
                Publication date (Electronic): 09 October 2020
                Publication date Collection: October 2020
                Volume: 12
                Issue: 10
                Electronic Location Identifier: 1148
                Affiliations
                Department of Medical Microbiology and Immunology, Medical School, University of Pécs, H-7624 Pécs, Hungary; borosakos@ 123456gmail.com (Á.B.); pankovics.peter@ 123456gmail.com (P.P.)
                Author notes
                [* ]Correspondence: reuter.gabor@ 123456gmail.com ; Tel.: +36-72-536252
                Author information
                https://orcid.org/0000-0002-5857-4934
                https://orcid.org/0000-0001-5843-4360
                Article
                Publisher ID: viruses-12-01148
                DOI: 10.3390/v12101148
                PMC ID: 7600399
                PubMed ID: 33050353
                SO-VID: 41d05ef7-6206-4d22-a4c8-90a541a9848c
                Copyright © © 2020 by the authors.
                License:

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                Date received : 13 August 2020
                Date accepted : 07 October 2020
                Categories
                Subject: Review

                ScienceOpen disciplines: Microbiology & Virology
                Keywords: hepatitis e virus,hepevirus,orthohepevirus,rodent,rat,zoonosis,reservoir,cross-species transmission,hepatitis,human
                Data availability:
                ScienceOpen disciplines: Microbiology & Virology
                Keywords: hepatitis e virus, hepevirus, orthohepevirus, rodent, rat, zoonosis, reservoir, cross-species transmission, hepatitis, human

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