Twenty-three replies were returned from 22 countries and the Basque country of Spain. Three replies were excluded from the analysis because of missing information. Data from the following 20 countries or region within a country (hereafter called country) were included in the analysis: (Basque Country (Spain), Belgium, Cyprus, Czech Republic, Denmark, Estonia, Finland, France, Great Britain, Iceland, Ireland, Italy, Lithuania, Northern Ireland, Norway, Portugal, Slovenia, Sweden, Switzerland, The Netherlands).
Bias in the surveillance programmes
Most countries (14/20) considered that animals tested within the healthy slaughter programme were representative of the slaughtered population, the other six considered that some biases could have occurred.
Diagnostic tests used
The number of test results available and the type of diagnostic test used in active surveillance varied between countries. A total of 1,764,056 tests results were reported. Fifteen different diagnostic tests or combinations of tests were represented. Test A was the most common. This was used in 15 countries and represented 50% of the total number of analyses. The second most commonly used was test B, which was used in eight countries and represented 23% of the total number of analyses (Table ).
Tests used in sheep TSE active surveillance between 2001 and 2006.
The large-scale active surveillance programmes started in 2002; although some countries started earlier in healthy slaughter (Ireland, Iceland, Lithuania, Norway) or in fallen stock (Estonia, Iceland, Lithuania, Switzerland) populations, it was decided to limit the analysis to surveillance data from 2002 and onwards.
From 2002 to 2006, 56% of the samples in healthy slaughter and 42% of the samples in fallen stock were examined using test A. The overall use of tests recommended for the detection of AS in active surveillance varied between countries (Figure ) and with time. In 2002, ten countries (Belgium, Estonia, Finland, France, Great Britain, Italy, Lithuania, Norway, Portugal, Sweden) used test A; by 2005 it was used by 15 countries (as above plus Basque Country, Cyprus, Iceland, Northern Ireland, Switzerland). The proportion of samples examined by test A has also increased in countries that used several tests. In 2006, tests A, F and G were used for examination of 73% and 53% of the samples in healthy slaughter and fallen stock, respectively.
Figure 1 Quantity of samples examined by tests A, F and G. In red, five countries processed more than 50,000 tests. In orange, one country processed between 20,000 to 50,000 tests. In yellow, four countries processed 5,000 to 20,000 tests. In pale yellow, five (more ...)
Fourteen countries reported AS cases. It was the only TSE in sheep reported in four countries (Figure ). Five countries detected CS cases only. Most (94%) of the AS cases and 43% of the CS cases were detected by test A (Figure ).
Figure 2 Cases detected in sheep in active surveillance. In red, four countries detected AS only. In strip red and yellow, ten countries detected AS and CS. In yellow, three countries detected CS only. In yellow with black spots, one country detected TSE unclassified (more ...)
Reported AS cases by test. Percentage (number in brackets) of AS cases detected in sheep through active surveillance in 20 EU countries between 2002 and 2006 per test or combination of tests.
Classical scrapie prevalence estimates
The annual national CSPE for each surveillance stream, for which the number of tests exceeds 500, is presented in Figure to Figure (for prevalence estimates for years with less than 500 tests [see Additional file 1
]). Due to higher values of the CSPE in Slovenia and due to lack of separation of AS and CS cases in data from Cyprus the estimates from these countries are reported in separate figures (Figure and ).
Figure 4 Sheep CSPE (‰) in healthy slaughter surveillance. Crude prevalence estimates are represented with their 95% confidence intervals. The dashed line represents the mean CSPE in healthy slaughter for all the countries and all the years. Graph is restricted (more ...)
Sheep TSEs prevalence (‰) in active surveillance in Cyprus. Crude prevalence estimates are presented with their 95% confidence intervals.
Sheep CSPE (‰) in fallen stock surveillance in Slovenia. Crude prevalence estimates are presented with their 95% confidence intervals.
Figure 5 Sheep CSPE (‰) in fallen stock surveillance. Crude prevalence estimates are represented with their 95% confidence intervals. The dashed line represents the mean CSPE in fallen stock for all the countries and all the years. Graph is restricted (more ...)
For each year and country in which at least one CS case was detected, and more than 500 animals were tested, the CSPE in healthy slaughtered animals varied from 0.03‰ [0.0; 0.2] in Switzerland in 2004 to 2.8‰ [0.3;10.1] in Northern Ireland in 2005 (150.9‰ [105.6;206.3] in Cyprus in 2004 for TSE positive). The CSPE in fallen stock varied from 0.2‰ [0.0;1.2] in Norway in 2006 to 22‰ [15.3;29.5] in Slovenia in 2005 (245.6‰ [169.8;335.1] in Cyprus in 2003 for TSE positive). CSPE was null in 48 country-years and 6 countries did not detect any CS case.
Atypical scrapie prevalence estimates
Fourteen countries reported AS cases and it was the only TSE in sheep reported in four countries. The annual national prevalence estimates of AS (ASPE) for each surveillance programme are presented in Figure and Figure .
Figure 8 Sheep ASPE (‰) in healthy slaughter surveillance. Crude prevalence estimates are represented with their 95% confidence intervals. The dashed line represents the mean ASPE in healthy slaughter for all the countries and all the years included in (more ...)
Figure 9 Sheep ASPE (‰), in fallen stock surveillance. Crude prevalence estimates are represented with their 95% confidence intervals. The dashed line represents the mean ASPE in fallen stock for all the countries and all the years included in ASPE calculation. (more ...)
For each year and country in which at least one AS case was detected and more than 500 animals tested, the ASPE in healthy slaughtered animals varied from 0.1‰ [0.0;0.3] in Switzerland in 2004 to 1.4‰ [0.8;2.3] in Great Britain in 2005 and the ASPE in fallen stock varied from 0.3‰ [0.0;1.5] in Norway in 2005 to 2.5‰ [1.0;5.2] in Great Britain in 2003. ASPE was null in 15 country-years and 5 countries did not detect any AS case.
Variability of classical scrapie prevalence estimates
The CS prevalence was significantly higher in fallen stock than in healthy slaughter in seven countries according to logistic regression models (Table ). Six countries had detected CS but without significant difference in the CSPE between streams. Out of these, CS cases had been detected in three (Basque country, Norway, Switzerland) only occasionally. The prevalence in fallen stock was higher than in healthy slaughter in Belgium, although not significantly so (p-value = 0.06) and the prevalence in fallen stock was lower than in healthy slaughter in two countries (Czech Republic, p-value = 0.07 and Northern Ireland p-value = 0.35).
Variability of AS and CS detection with surveillance stream (reference is healthy slaughter) and year of surveillance.
The detection of CS cases also varied with time. In seven countries (Basque country, Belgium, Czech Republic, Iceland, Northern Ireland, Norway, Slovenia), CS cases were not detected in every year, in Switzerland one case was found during the single year of surveillance. There was time-dependent variability of the CS prevalence in five countries, including Cyprus for TSE positives in the healthy slaughter population only, and Ireland in the fallen stock only. The trend was a decrease with time in all countries except Italy and Great-Britain. The results of the Chi-square linear trend test were consistent with the results of the logistic regression model, except for Italy where the trend was significant in healthy slaughter (χ2 = 6.39, df = 1, p-value = 0.01) but not in fallen stock (χ2 = 1.42, df = 1, p-value = 0.23).
Variability of atypical scrapie prevalence estimates
No significant difference between the streams was found in ten countries that detected atypical scrapie (all p-values > 0.1 and OR close to 1). In four countries, the AS prevalence was significantly higher in fallen stock than in healthy slaughter (Table ).
In seven countries (Basque country, Belgium, Finland, Iceland, Northern Ireland, the Netherlands, Sweden) AS cases were not detected in every year. No time-dependent variability of the AS prevalence was found using logistic regression with adjustment on surveillance stream and time, parameterised as a categorical variable. However, there were some discrepant results depending on the parameterisation of the variable time. Significant time dependant effects were found when time was set as a continuous variable or using the Chi-square test for linear trend: significant decreases were found in France in healthy slaughter (χ2 = 4.45, df = 1, p-value = 0.03), in Great Britain in fallen stock (χ2 = 6.84, df = 1, p-value = 0.008), in Norway in fallen stock (χ2 = 3.90, df = 1, p-value = 0.05) and an increase in Portugal in healthy slaughter (χ2 = 11.13, df = 1, p-value = 0.0008).
Comparison of atypical scrapie and classical scrapie prevalence estimates
Differences between the ASPE and the CSPE were found in six countries (Table ). In France and Great Britain, the ASPE was less than the CSPE in fallen stock. For the other countries with a significant difference, the ASPEs were greater than the CSPEs. The countries where no significant difference was found had relatively less samples tested than the other countries. The ORs could be calculated in both surveillance streams for four countries. In these countries, the ORs in the healthy slaughter stream were higher than the ORs in fallen stock. In particular, the probability (as a ratio) of detecting an AS case (rather than a CS one) was three to six times higher among healthy slaughter animals compared to fallen stock.
Comparison of detection of AS and CS in active surveillance in fallen stock and in healthy slaughter. OR is defined as chances to detect AS versus chances to detect CS.
Probability to detect at least one case of AS
If one expects a country ASPE to be similar to the average European ASPE, this prevalence could be estimated by the ratio of the total number of AS cases detected by test A, F or G over the total number of tests A, F or G, which was 0.65‰ for the 20 respondent countries.
The sensitivity of the surveillance programme can be simulated to range from 50% to 100%.
A numerical example (Table ) shows that given the number of samples examined with tests A, F and G in Estonia (4092) and in Lithuania (1933) the probability that no case is detected (given the assumed "design prevalence" of 0.65), even with a perfect sensitivity of the surveillance programme (Se = 100%) is higher than 5% (respectively 7% and 30%).
Probability to detect zero case of AS depending on the sensitivity of the test (in column) and the number of tests (in row) for Estonia and Lithuania.
Comparison of the age of the cases
Data on the age of 1370 cases detected in healthy slaughter, fallen stock and TSE eradication programmes were provided by 15 countries. AS cases were reported in all classes of age over 18 months (Figure ) and they were older than CS cases in healthy slaughter (p-value < 1.10-5) and in fallen stock (p-value < 1.10-5). Also, there was no significant difference between the age of AS cases in healthy slaughter and fallen stock (p-value = 0.14) although CS cases were older in healthy slaughter than in fallen stock (p-value = 0.001).
Age distribution of AS and CS cases according to stream of surveillance (in %).
Description of the genotype of the cases
Eighteen countries provided the PrP genotype of 1258 cases detected in healthy slaughter and fallen stock (Figure ).
Genotype distribution of AS and CS cases. Figure for 414 AS cases and 844 CS cases detected through active surveillance in fallen stock or healthy slaughter.
The distribution of the allele frequencies (Table ) between AS and CS cases was different in healthy slaughter (χ2 = 300.6, df = 4, p-value < 10-5) and fallen stock (χ2 = 384.4, df = 4, p-value < 10-5). In both streams, the frequency of ARR and AHQ carrier was higher in AS cases than in CS cases and the frequency of VRQ carriers was lower in AS cases than in CS cases. The allele frequency in the two surveillance streams was similar for AS (χ2 = 2.547, df = 4, p-value = 0.63). In contrast the allele frequencies differed for CS (χ2 = 45.6, df = 4, p-value < 3.10-9) with more ARR carriers and less ARQ carriers in healthy slaughter compared to fallen stock.
Number and frequency (%) of allele carriers among 1258 AS and CS cases detected between 2002 and 2006 in healthy slaughter and fallen stock in 18 EU countries.