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      A novel gyrovirus in a common pheasant ( Phasianus colchicus) with poult enteritis and mortality syndrome

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          Abstract

          A novel gyrovirus was detected in an intestinal specimen of a common pheasant that died due to poult enteritis and mortality syndrome. The genome of the pheasant-associated gyrovirus (PAGyV) is 2353 nucleotides (nt) long and contains putative genes for the VP1, VP2, and VP3 proteins in an arrangement that is typical for gyroviruses. Gyrovirus-specific motifs were identified in both the coding region and the intergenic region of the PAGyV genome. The VP1 of PAGyV shares up to 67.6% pairwise nt sequence identity with reference sequences and forms a distinct branch in the phylogenetic tree. Thus, according to the recently described species demarcation criteria, PAGyV belongs to a novel species in the genus Gyrovirus, family Anelloviridae, for which we propose the name " Gyrovirus phaco 1".

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          MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.

          We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.
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            AliView: a fast and lightweight alignment viewer and editor for large datasets

            Summary: AliView is an alignment viewer and editor designed to meet the requirements of next-generation sequencing era phylogenetic datasets. AliView handles alignments of unlimited size in the formats most commonly used, i.e. FASTA, Phylip, Nexus, Clustal and MSF. The intuitive graphical interface makes it easy to inspect, sort, delete, merge and realign sequences as part of the manual filtering process of large datasets. AliView also works as an easy-to-use alignment editor for small as well as large datasets. Availability and implementation: AliView is released as open-source software under the GNU General Public License, version 3.0 (GPLv3), and is available at GitHub (www.github.com/AliView). The program is cross-platform and extensively tested on Linux, Mac OS X and Windows systems. Downloads and help are available at http://ormbunkar.se/aliview Contact: anders.larsson@ebc.uu.se Supplementary information: Supplementary data are available at Bioinformatics online.
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              RDP4: Detection and analysis of recombination patterns in virus genomes

              RDP4 is the latest version of recombination detection program (RDP), a Windows computer program that implements an extensive array of methods for detecting and visualising recombination in, and stripping evidence of recombination from, virus genome sequence alignments. RDP4 is capable of analysing twice as many sequences (up to 2,500) that are up to three times longer (up to 10 Mb) than those that could be analysed by older versions of the program. RDP4 is therefore also applicable to the analysis of bacterial full-genome sequence datasets. Other novelties in RDP4 include (1) the capacity to differentiate between recombination and genome segment reassortment, (2) the estimation of recombination breakpoint confidence intervals, (3) a variety of ‘recombination aware’ phylogenetic tree construction and comparison tools, (4) new matrix-based visualisation tools for examining both individual recombination events and the overall phylogenetic impacts of multiple recombination events and (5) new tests to detect the influences of gene arrangements, encoded protein structure, nucleic acid secondary structure, nucleotide composition, and nucleotide diversity on recombination breakpoint patterns. The key feature of RDP4 that differentiates it from other recombination detection tools is its flexibility. It can be run either in fully automated mode from the command line interface or with a graphically rich user interface that enables detailed exploration of both individual recombination events and overall recombination patterns.
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                Author and article information

                Contributors
                feher.eniko@vmri.hu
                Journal
                Arch Virol
                Arch Virol
                Archives of Virology
                Springer Vienna (Vienna )
                0304-8608
                1432-8798
                20 March 2022
                20 March 2022
                2022
                : 167
                : 5
                : 1349-1353
                Affiliations
                [1 ]GRID grid.417756.6, Veterinary Medical Research Institute, ; Hungária krt 21, Budapest, 1143 Hungary
                [2 ]GRID grid.432859.1, ISNI 0000 0004 4647 7293, Veterinary Diagnostic Directorate, , National Food Chain Safety Office, ; Tábornok utca 2, Budapest, 1143 Hungary
                [3 ]GRID grid.483037.b, ISNI 0000 0001 2226 5083, University of Veterinary Medicine, ; István utca 2, Budapest, 1078 Hungary
                Author notes

                Handling Editor: Sheela Ramamoorthy.

                Author information
                http://orcid.org/0000-0001-7778-9116
                http://orcid.org/0000-0002-5750-1872
                http://orcid.org/0000-0002-6270-1772
                Article
                5417
                10.1007/s00705-022-05417-7
                9038835
                35306591
                820b6e3a-a564-461d-9b88-3bafe18c7dcf
                © The Author(s) 2022

                Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 30 November 2021
                : 6 February 2022
                Funding
                Funded by: Momentum Program of the Hungarian Academy of Sciences
                Award ID: LP2011-10
                Award Recipient :
                Funded by: National Research, Development and nnovation Office (NKFI-OTKA)
                Award ID: K124655
                Award Recipient :
                Funded by: Veterinary Medical Research Institute
                Categories
                Annotated Sequence Record
                Custom metadata
                © Springer-Verlag GmbH Austria, part of Springer Nature 2022

                Microbiology & Virology
                Microbiology & Virology

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