All the reviews were carried out by a systematic method, similar to the Cochrane approach, developed during the early stages of the project, and were subjected to an independent quality audit. Disease occurrence and/or pathogen detection information was entered into an Excel data table for that disease in order to facilitate the transfer of the information into a database.
A total of almost 3000 scientific publications and other documents identified by the literature searches, and other means, for the listed diseases were assessed for relevant information and of these 463 were critically reviewed.
A review summary report was prepared for each disease, including causative agent description, available tools for typing (strain identification), descriptive epidemiology including the current worldwide distribution of the host and pathogen (including different strains) and outbreak data in the EU and worldwide. The summary reports for all the listed diseases are presented at Annex B.
The quality audit of the disease reviews was carried out by an independent expert. The reviewers were asked to provide the auditor with between 5 and 10 reviewed documents for each disease/pathogen/. For each source, the entries made in each field of the Excel data entry form were checked independently by the review auditor against the information provided in the relevant publication. The entire record was checked for consistency, and particular attention was paid to how the following fields had been completed: i) classification of report, ii) report type, iii) quality assessment and iv) mortalities. Any omissions or inconsistencies were reported back to the reviewer concerned who then amended their data table accordingly. All the reviews were compared and checked for consistency. The auditors report is presented at Appendix C.
Particular attention was given to the host range and geographical distribution of the various genotypes of VHSV and of the various Bonamia species, addressing doubts about the identification and taxonomy of some, as well as their association with natural outbreaks. Documents containing genotypic information on VHSV were critically reviewed to establish a consensus on the most appropriate typing scheme (the internationally accepted typing scheme) and this scheme was then used to reassess the genotype of the virus isolates entered in the Excel data entry table by the VHS reviewer. In addition, data gaps for VHSV and Bonamia spp. have been identified where further research is needed to address the issues of pathogen definition and strain differentiation. A detailed report of the review is presented at Annex D. For the critical review on the identification of Bonamia species a concise overview was prepared on the characteristics of known Bonamia species (Bonamia exitiosa, Bonamia ostreae, Bonamia roughleyi) and more detailed information collected on the ultrastructure, phylogeny and taxonomy issues of Bonamia species. In addition, three phylogenetic analyses were carried out based on available GenBank sequences to demonstrate the phylogenetic relationship between the Bonamia species. Finally, data gaps for Bonamia spp. were identified where further research is needed to address the issues of pathogen definition and strain differentiation. A detailed report of the review is presented at Annex E.
A database and GIS application was developed to fit the requirements for a geographical representation in a web application of the epidemiological data contained in the Excel spreadsheets completed for each disease. The data tables have been loaded into the GIS database that allows the geographical spread of outbreaks to be displayed as points on a map. The epidemiological data for VHSV and Bonamia spp. provided by the reviewers has been inserted into the database. The diseases occurrence is represented as polygon-based layers based on administrative boundaries at Country/regional/province level and as point-based layers (specific locations) geo-referenced through latitude and longitude data, when geographical coordinates of the point location are available. The occurrences of VHS and Bonamia spp. infections are visualised on the web-GIS application, and the related epidemiological data recorded by the reviewers are accessible through queries.
The application is accessible via the web, and is an interactive tool to navigate into the epidemiological data collected. Using the query tool, the user can retrieve data from the database, and the selected information is shown on the map, reported in summarized form on the left side of the page. The user can also access the table with the complete information related to chosen criteria in tabs over the map. A full description of the database and web-GIS application is provided at Annex G.
This project has created a data resource for EFSA that will inform expert work on each of the diseases in Council Directive 2006/88/EC as amended by Commission Directive 2008/53/EC.
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