EPPO-Q-bank

A database to support plant pest diagnostic activities

Curator Plant Viruses and Viroids database

Dr.ir. René van der Vlugt
Taxonomic expertise and collections
Plant Research International (PRI)
the Netherlands

Curator Plant Viruses and Viroids database

Dr. Annelien Roenhorst
Phytosanitary expertise and collections
National Plant Protection Organization
the Netherlands

Curator Plant Viruses and Viroids database

Dr. Wulf Menzel
Taxonomic expertise and collections
DSMZ
Germany

Curator Plant Viruses and Viroids database

Jerom van Gemert
Phytosanitary expertise and collections
National Plant Protection Organization
the Netherlands

EPPO-Q-bank Plant Viruses and Viroids database 


The free accessible platform to share information on plant viruses and viroids

The goal of the EPPO-Q-bank Plant Viruses and Viroids database is to provide genomic information on (regulated and other important) plant viruses and viroids. A unique feature of EPPO-Q-bank is that it, where possible, also links data to isolates which are physically available. Quality criteria apply to both the database and collection , which are curated by experts in the field.


Outline of the most important features accessed via the different sub-menus

Organisms included

For included organisms a link to Global database provides access to general information. For each organism under ‘Isolates’ information on the availability of isolates, their characteristics, and from where they can be obtained is displayed. Ideally, the information and data on isolates fulfil the minimum requirements as described in the quality criteria. At the moment, however, a too stringent application of these criteria would severely reduce the number of available isolates. Therefore, it was decided to include also isolates that do not fully meet the criteria. This might imply that depending on the intended use, additional characteristics of an isolate/the material obtained, have to be determined.

Methodology

Methodology provides generic protocols for electron microscopy, mechanical inoculation of test plants and serology (DAS-ELISA). Generic and specific molecular tests are included in EPPO Diagnostic Protocols (PM7 series). They can be retrieved from the EPPO Global Database (https://gd.eppo.int/) using the search tool for individual species (see example for Pepino mosaic virus https://gd.eppo.int/taxon/PEPMV0/documents).


Identification(ID)

For nearly all regulated and other important virus and viroid species, a reference sequence from NCBI GenBank is included. In addition, sequence data and other relevant information on available isolates are included; the number of which is still growing. The BLAST option under TAB ‘ID’,  allows identification of regulated and other important viruses and viroids on the basis of direct sequence comparisons. It should be noted, however, that the reference sequences of regulated viruses and viroids currently included, are based on the latest master species list (MSL) of the International Committee on Taxonomy of Viruses of (Currently 2019 V1: https://talk.ictvonline.org/files/master-species-lists/m/msl/9601). In addition to this taxonomic information, ICTV publishes the Virus Metadata Resource (VMR;  https://talk.ictvonline.org/taxonomy/vmr/). This repository provides a list of exemplar viruses for each species recognized by the ICTV and links to their genomic sequence. Still the number of (reference) sequences of common viruses and viroids in EPPO-Q-bank is limited. Therefore, ID based on only Q-bank sequences has its limitations, and extending BLAST searches to NCBI GenBank is recommended.


Obtaining isolates


To obtain one or more isolates from the Q-bank Plant Viruses and Viroids collections, please look at the isolate records for availability and  details or contact one of the curators



Contribution


This database provides information on (regulated) plant viruses and viroids, data on specific isolates and information on where these are available. At the same time, it shows that still for many (regulated) species no isolates are available. As curators we urge virologists worldwide, to share any data and isolates that may be of interest to others. It would be beneficial if isolates and data obtained during research projects and diagnostics could be included in Q-bank, thereby making and keeping them available for future use. If you are willing to share isolates via Q-bank, please contact one of the curators for further information.


General statement on names used in EPPO-Q-bank 

Virus nomenclature is based on the latest release of the official classification by the International Committee on Taxonomy of Viruses (ICTV, 2018 Release, https://talk.ictvonline.org/taxonomy/). The integration of genus within the name of the species is currently not consistently adopted by ICTV working groups and, therefore, in EPPO-Q-Bank species name are without genus names. Names of viruses not included in the official ICTV classification are based on first reports.


More information

The information in this database is compiled by the Q-bank curators based on most current information and to the best of their expert knowledge. If you have remarks, questions or require additional information, please contact us. 

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