Demographic risk factors for classical and atypical scrapie in Great Britain

Following the bovine spongiform encephalopathy (BSE) crisis, the European Union has introduced policies for eradicating transmissible spongiform encephalopathies (TSEs), including scrapie, from large ruminants. However, recent European Union surveillance has identified a novel prion disease, ‘atypical’ scrapie, substantially different from classical scrapie. It is unknown whether atypical scrapie is naturally transmissible or zoonotic, like BSE. Furthermore, cases have occurred in scrapie-resistant genotypes that are targets for selection in legislated selective breeding programmes. Here, the first epidemiological study of British cases of atypical scrapie is described, focusing on the demographics and trading patterns of farms and using databases of recorded livestock movements. Triplet comparisons found that farms with atypical scrapie stock more sheep than those of the general, non-affected population. They also move larger numbers of animals than control farms, but similar numbers to farms reporting classical scrapie. Whilst there is weak evidence of association through sheep trading of farms reporting classical scrapie, atypical scrapie shows no such evidence, being well-distributed across regions of Great Britain and through the sheep-trading network. Thus, although cases are few in number so far, our study suggests that, should natural transmission of atypical scrapie be occurring at all, it is doing so slowly.

associated with the first such data, but to allow relation of scrapie incidence to earlier movement data, where the trading patterns of the scrapie farms would be presumably unaffected.
Many records were duplicates with identical date, source, destination and batch size. Such duplicates were removed, reducing the number of records to 891 989. This therefore gives a conservative estimate of the numbers of movements, as some duplicates may be real movements. In some records, either the source or the destination CPH code were missing, but these still provide useful data for the other end-point of the movement.
The JAS for 2003 provides geographical locations, premises type and reported stock held for each CPH code. Removing 798 duplicate records from the JAS gave a table containing 509 177 records (covering types of farming enterprise other than just sheep farms).
Movement data and the JAS were cross-referenced and the following summary statistics were obtained for each premises: numbers of movements (on and off separately, and combined), numbers of sheep moved (on, off and combined), mean distance of movements (on, off and combined) and reported stock held. Premises were also classified into one of six large regions, based on the county code of the premises CPH shown in Supplementary Table S2. For the analyses of relative incidence in the abattoir survey, the known natal holding was used where known (assuming preponderance of perinatal transmission; two of the 60 premises). Livestock-trading behaviour is not expected to be altered as a result of atypical scrapie detection in these data. Therefore, we use the longer time frame for atypical scrapie to maximize the numbers of cases available for analysis.
A fourth data source, the 2002 Anonymous Postal Survey on Scrapie (ASS; Sivam et al., 2006), was used to compare incidence of scrapie in different data sources.

Demographic factors
Scrapie farms were paired with both control farms without scrapie notification (198 classical scrapie pairs) and, in the case of atypical scrapie farms, additionally with classical scrapie farms in the same county (76 classical/atypical/control triplets). Matches were made at random within the population of suitable matches, but four criteria determined eligibility of a match.
County. Matches were made to farms in the same county to account for regional variation in farming practices. For 14 atypical scrapie farms, mostly in counties with fewer farms, matching classical scrapie farms were only available in adjoining counties. However, this alone is not indicative of regional differences in the distribution of the two forms of scrapie.
Parish. Matches were made where possible to farms in the same parish, in addition to county.
Movement data. Matches were made preferentially to farms with sheep movement data during 2003, as the JAS also contains data on non-sheep farms and choosing only actively trading farms avoids selecting these as a match. This method may risk introducing a sampling bias, but maximizes the amount of relevant data available for analysis.
Census data. Where no match was available with movement data, matches were made preferentially to farms with sheep recorded on the JAS.
None of the atypical scrapie farms had a history of scrapie since 1998.