title: A "shotgun" method for tracing the birth locations of sheep from flock tags, applied to scrapie surveillance in Great Britain.
abstract: Movement records are often used to identify animal sample provenance by retracing the movements of individuals. Here we present an alternative method, which uses the same identity tags and movement records as are used to retrace movements, but ignores individual movement paths. The first step uses a simple query to identify the most likely birth holding for every identity tag included in a database recording departures from agricultural holdings. The second step rejects a proportion of the birth holding locations to leave a list of birth holding locations that are relatively reliable. The method was used to trace the birth locations of sheep sampled for scrapie in abattoirs, or on farm as fallen stock. Over 82% of the sheep sampled in the fallen stock survey died at the holding of birth. This lack of movement may be an important constraint on scrapie transmission. These static sheep provided relatively reliable birth locations, which were used to define criteria for selecting reliable traces. The criteria rejected 16.8% of fallen stock traces and 11.9% of abattoir survey traces. Two tests provided estimates that selection reduced error in fallen stock traces from 11.3% to 3.2%, and in abattoir survey traces from 8.1% to 1.8%. This method generated 14,591 accepted traces of fallen stock from samples taken during 2002-2005 and 83,136 accepted traces from abattoir samples. The absence or ambiguity of flock tag records at the time of slaughter prevented the tracing of 16-24% of abattoir samples during 2002-2004, although flock tag records improved in 2005. The use of internal scoring to generate and evaluate results from the database query, and the confirmation of results by comparison with other database fields, are analogous to methods used in web search engines. Such methods may have wide application in tracing samples and in adding value to biological datasets.
authors.affiliation: Veterinary Laboratories Agency-Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK. c.birch@vla.defra.gsi.gov.uk
authors.forename: Colin P D
authors.initials: CP
authors.lastname: Birch
authors.forename: Victor J
authors.initials: VJ
authors.lastname: Del Rio Vilas
authors.forename: Ambrose C
authors.initials: AC
authors.lastname: Chikukwa
mesh_terms: D000003:Abattoirs; D000823:Animal Identification Systems; D000818:Animals; D012372:ROC Curve; D012608:Scrapie / Q000453:epidemiology* / Q000635:transmission; D018571:Sentinel Surveillance / Q000662:veterinary*; D012756:Sheep; D006113:United Kingdom / Q000453:epidemiology