A sequence database allowing automated genotyping of Classical swine fever virus isolates

• Published in: Journal of virological methods Vol. 140; no. 1; pp. 95 - 99
• Main Authors: Dreier, Sabrina, Zimmermann, Bernd, Moennig, Volker, Greiser-Wilke, Irene
• Format: Journal Article
• Language: English
• Published: London Elsevier B.V 01-03-2007; Amsterdam Elsevier; New York, NY
• Subjects: Algorithms; Animals; Automation; Base Sequence; Biological and medical sciences; Classical swine fever virus; Classical swine fever virus - classification; Classical swine fever virus - genetics; Classical swine fever virus - isolation & purification; Databases, Genetic; Fundamental and applied biological sciences. Psychology; Genetic typing; Genotype; Internet; Microbiology; Molecular Sequence Data; Phylogeny; Sequence Alignment; Sequence database; Software; Sus scrofa; Techniques used in virology; Virology; Automation; Classical swine fever virus; Sequence database; Genetic typing; Pestivirus; Typing; Microbiology; Genotype; Method; Virology; Virus; Database; Genetics; Isolate; Flaviviridae; Veterinary; Hog cholera virus
• ISSN: 0166-0934; 1879-0984
• DOI: 10.1016/j.jviromet.2006.11.013

Classical swine fever (CSF) is a highly contagious viral disease of pigs. According to the OIE classification of diseases it is classified as a notifiable (previously List A) disease, thus having the potential for causing severe socio-economic problems and affecting severely the international trade of pigs and pig products. Effective control measures are compulsory, and to expose weaknesses a reliable tracing of the spread of the virus is necessary. Genetic typing has proved to be the method of choice. However, genotyping involves the use of multiple software applications, which is laborious and complex. The implementation of a sequence database, which is accessible by the World Wide Web with the option to type automatically new CSF virus isolates once the sequence is available is described. The sequence to be typed is tested for correct orientation and, if necessary, adjusted to the right length. The alignment and the neighbor-joining phylogenetic analysis with a standard set of sequences can then be calculated. The results are displayed as a graph. As an example, the determination is shown of the genetic subgroup of the isolate obtained from the outbreaks registered in Russia, in 2005. After registration (
[e-mail]) the database including the module for genotyping are accessible under
http://viro08.tiho-hannover.de/eg/eurl_virus_db.htm.