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Viruses 2016, 8(11), 302; doi:10.3390/v8110302

The European Classical Swine Fever Virus Database: Blueprint for a Pathogen-Specific Sequence Database with Integrated Sequence Analysis Tools

1
EU and OIE Reference Laboratory for Classical Swine Fever, Institute of Virology, Department of Infectious Diseases, University of Veterinary Medicine, 30559 Hannover, Germany
2
Bernd Zimmermann Software Development, IT Consulting and Support, 31542 Hannover, Germany
These authors contributed equally to this work.
*
Author to whom correspondence should be addressed.
Academic Editor: Andrew Mehle
Received: 23 August 2016 / Revised: 27 October 2016 / Accepted: 1 November 2016 / Published: 7 November 2016
(This article belongs to the Section Animal Viruses)
View Full-Text   |   Download PDF [1412 KB, uploaded 7 November 2016]   |  

Abstract

Molecular epidemiology has become an indispensable tool in the diagnosis of diseases and in tracing the infection routes of pathogens. Due to advances in conventional sequencing and the development of high throughput technologies, the field of sequence determination is in the process of being revolutionized. Platforms for sharing sequence information and providing standardized tools for phylogenetic analyses are becoming increasingly important. The database (DB) of the European Union (EU) and World Organisation for Animal Health (OIE) Reference Laboratory for classical swine fever offers one of the world’s largest semi-public virus-specific sequence collections combined with a module for phylogenetic analysis. The classical swine fever (CSF) DB (CSF-DB) became a valuable tool for supporting diagnosis and epidemiological investigations of this highly contagious disease in pigs with high socio-economic impacts worldwide. The DB has been re-designed and now allows for the storage and analysis of traditionally used, well established genomic regions and of larger genomic regions including complete viral genomes. We present an application example for the analysis of highly similar viral sequences obtained in an endemic disease situation and introduce the new geographic “CSF Maps” tool. The concept of this standardized and easy-to-use DB with an integrated genetic typing module is suited to serve as a blueprint for similar platforms for other human or animal viruses. View Full-Text
Keywords: virus; sequence; database; disease control; classical swine fever virus; sequence; database; disease control; classical swine fever
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MDPI and ACS Style

Postel, A.; Schmeiser, S.; Zimmermann, B.; Becher, P. The European Classical Swine Fever Virus Database: Blueprint for a Pathogen-Specific Sequence Database with Integrated Sequence Analysis Tools. Viruses 2016, 8, 302.

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