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      Complete sequence and variability of a new subgroup B nepovirus infecting potato in central Peru

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          Abstract

          The complete bipartite genome (RNA1 and RNA2) of a new nepovirus infecting potato was obtained using small RNA sequencing and assembly complemented by Sanger sequencing. Each RNA encodes a single polyprotein, flanked by 5’ and 3’ untranslate regions (UTR) and followed by a poly (A) tail. The putative polyproteins encoded by RNA1 and RNA2 had sets of motifs which are characteristic of viruses in the genus Nepovirus. Sequence comparisons using the Pro-Pol region and the coat protein, including phylogenetic analysis of these regions, showed closest relationships with nepoviruses. The data obtained support the taxonomical status of this new virus (putative named Potato virus B, PVB) as a member of the genus Nepovirus, subgroup B.

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          The online version of this article (doi:10.1007/s00705-016-3147-6) contains supplementary material, which is available to authorized users.

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          Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: a generic method for diagnosis, discovery and sequencing of viruses.

          Jan F. Kreuze, Ana Julia Pérez, Milton Untiveros … (2009)
          We report the first identification of novel viruses, and sequence of an entire viral genome, by a single step of high-throughput parallel sequencing of small RNAs from diseased, as well as symptomless plants. Contigs were assembled from sequenced total siRNA from plants using small sequence assembly software and could positively identify RNA, ssDNA and dsDNA reverse transcribing viruses and in one case spanned the entire genome. The results present a novel approach which cannot only identify known viral pathogens, occurring at extremely low titers, but also novel viruses, without the necessity of any prior knowledge.
          Article 0 comments Cited 210 times – based on 0 reviews     Review now
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            The relationships of some viruses causing necrotic diseases of the potato

            F. C. BAWDEN, F. Sheffield, F. C. Bawden … (1944)
            Article 0 comments Cited 10 times – based on 0 reviews     Review now
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              Complete genome sequence of a potyvirus infecting yam beans (Pachyrhizus spp.) in Peru.

              E. Romero Adam, Thomas zum Felde, R Tasso … (2012)
              In 2010, yam beans in a field trial in Peru showed viral disease symptoms. Graft-transmission and positive ELISA results using potyvirus-specific antibodies suggested that the symptoms could be the result of a potyviral infection. Small interfering RNA (siRNA) were extracted from one of the samples and sent for high-throughput sequencing. The full genome of a new potyvirus could be assembled from the resulting siRNA sequences, and it was sufficiently different from other sequences to be considered a member of a new species, which we have designated Yam bean mosaic virus (YBMV). Sequence similarity suggests that YBMV has also been detected in yam beans in Indonesia.
              Article 0 comments Cited 8 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Jan Kreuze: 349-6017 , j.kreuze@cgiar.org
                Journal
                Journal ID (nlm-ta): Arch Virol
                Journal ID (iso-abbrev): Arch. Virol
                Title: Archives of Virology
                Publisher: Springer Vienna (Vienna )
                ISSN (Print): 0304-8608
                ISSN (Electronic): 1432-8798
                Publication date (Electronic): 17 November 2016
                Publication date PMC-release: 17 November 2016
                Publication date (Print): 2017
                Volume: 162
                Issue: 3
                Pages: 885-889
                Affiliations
                [1 ]ISNI 0000 0004 0636 5457, GRID grid.435311.1, , International Potato Center (CIP), ; Apartado 1558, Lima 12, Peru
                [2 ]ISNI 0000 0001 2107 4576, GRID grid.10800.39, Facultad de Ciencias Biológicas, Programa de Biología Molecular, , Universidad Nacional Mayor de San Marcos, ; Lima 11, Peru
                [3 ]ISNI 0000 0001 0943 556X, GRID grid.418348.2, , International Center for Tropical Agriculture (CIAT), ; Apartado Aéreo 6713, Cali, Colombia
                Article
                Publisher ID: 3147
                DOI: 10.1007/s00705-016-3147-6
                PMC ID: 5329089
                PubMed ID: 27858290
                SO-VID: cfe1d5a8-ace3-467f-bdff-7825dc12fe71
                Copyright © © The Author(s) 2016
                License:

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

                History
                Date received : 8 August 2016
                Date accepted : 31 October 2016
                Funding
                Funded by: CGIAR research program for roots tubers and bananas
                Categories
                Subject: Annotated Sequence Record
                Custom metadata
                issue-copyright-statement © Springer-Verlag Wien 2017

                ScienceOpen disciplines: Microbiology & Virology
                Data availability:
                ScienceOpen disciplines: Microbiology & Virology

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