title: A nationwide database linking information on the hosts with sequence data of their virus strains: A useful tool for the eradication of bovine viral diarrhea (BVD) in Switzerland.
abstract: Pestiviruses infect a wide variety of animals of the order Artiodactyla, with bovine viral diarrhea virus (BVDV) being an economically important pathogen of livestock globally. BVDV is maintained in the cattle population by infecting fetuses early in gestation and, thus, by generating persistently infected (PI) animals that efficiently transmit the virus throughout their lifetime. In 2008, Switzerland started a national control campaign with the aim to eradicate BVDV from all bovines in the country by searching for and eliminating every PI cattle. Different from previous eradication programs, all animals of the entire population were tested for virus within one year, followed by testing each newborn calf in the subsequent four years. Overall, 3,855,814 animals were tested from 2008 through 2011, 20,553 of which returned an initial BVDV-positive result. We were able to obtain samples from at least 36% of all initially positive tested animals. We sequenced the 5' untranslated region (UTR) of more than 7400 pestiviral strains and compiled the sequence data in a database together with an array of information on the PI animals, among others, the location of the farm in which they were born, their dams, and the locations where the animals had lived. To our knowledge, this is the largest database combining viral sequences with animal data of an endemic viral disease. Using unique identification tags, the different datasets within the database were connected to run diverse molecular epidemiological analyses. The large sets of animal and sequence data made it possible to run analyses in both directions, i.e., starting from a likely epidemiological link, or starting from related sequences. We present the results of three epidemiological investigations in detail and a compilation of 122 individual investigations that show the usefulness of such a database in a country-wide BVD eradication program.
authors.affiliation: Institute of Veterinary Virology, Vetsuisse Faculty University of Bern, Laenggass-Str. 122, PO Box 8466, CH-3001 Bern, Switzerland.
authors.forename: Hanspeter
authors.initials: H
authors.lastname: Stalder
authors.affiliation: Institute of Veterinary Virology, Vetsuisse Faculty University of Bern, Laenggass-Str. 122, PO Box 8466, CH-3001 Bern, Switzerland.
authors.forename: Corinne
authors.initials: C
authors.lastname: Hug
authors.affiliation: Institute of Veterinary Virology, Vetsuisse Faculty University of Bern, Laenggass-Str. 122, PO Box 8466, CH-3001 Bern, Switzerland.
authors.forename: Reto
authors.initials: R
authors.lastname: Zanoni
authors.affiliation: Institute of Veterinary Virology, Vetsuisse Faculty University of Bern, Laenggass-Str. 122, PO Box 8466, CH-3001 Bern, Switzerland.
authors.forename: Hans-Rudolf
authors.initials: HR
authors.lastname: Vogt
authors.affiliation: Institute of Veterinary Virology, Vetsuisse Faculty University of Bern, Laenggass-Str. 122, PO Box 8466, CH-3001 Bern, Switzerland.
authors.forename: Ernst
authors.initials: E
authors.lastname: Peterhans
authors.affiliation: Institute of Veterinary Virology, Vetsuisse Faculty University of Bern, Laenggass-Str. 122, PO Box 8466, CH-3001 Bern, Switzerland. Electronic address: matthias.schweizer@vetsuisse.unibe.ch.
authors.forename: Matthias
authors.initials: M
authors.lastname: Schweizer
authors.affiliation: Institute of Veterinary Virology, Vetsuisse Faculty University of Bern, Laenggass-Str. 122, PO Box 8466, CH-3001 Bern, Switzerland. Electronic address: claudia.bachofen@uzh.ch.
authors.forename: Claudia
authors.initials: C
authors.lastname: Bachofen
mesh_terms: D020121:5' Untranslated Regions; D000818:Animals; D001912:Bovine Virus Diarrhea-Mucosal Disease / Q000175:diagnosis / Q000453:epidemiology* / Q000635:transmission / Q000821:virology; D002417:Cattle; D016358:Contact Tracing / Q000662:veterinary*; D030561:Databases, Nucleic Acid / Q000458:organization & administration*; D003967:Diarrhea / Q000175:diagnosis / Q000453:epidemiology* / Q000821:virology; D001908:Diarrhea Viruses, Bovine Viral / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity; D060740:Disease Eradication / Q000458:organization & administration; D062665:Epidemiological Monitoring / Q000662:veterinary; D005838:Genotype; D058751:Livestock / Q000821:virology; D017720:Molecular Epidemiology; D058889:Molecular Typing; D017422:Sequence Analysis, DNA; D013557:Switzerland / Q000453:epidemiology
chemical_list: D020121:5' Untranslated Regions
keywords: Eradication; Genotype; Molecular epidemiology; Nucleotide sequence database; Pestivirus; Virus transmission