National Scrapie Eradication Program

1. National Scrapie Eradication Program Fiscal Year 2013 Report October 1, 2012 to September 30, 2013 United States Department of Agriculture Animal Plant Health Inspection Service Veterinary Services Surveillance, Preparedness and Response Services Sheep and Goat Health Center Prepared January 31, 2014

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3. Introduction • The National Scrapie Eradication Program focuses on seven primary areas: • Education and prevention • Animal identification and compliance • Surveillance [Regulatory Scrapie Slaughter Surveillance (RSSS) and on-farm] • Tracing and testing positive and exposed animals • Cleanup of infected and source flocks through genetic susceptibility testing and indemnification of susceptible exposed animals • Monitoring of previously infected and exposed flocks • The Scrapie Free Flock Certification Program (SFCP) • Program Update • As of September 30, 2013, the percent of cull sheep found positive at slaughter and adjusted for face color was 0.014 percent (Chart 1). This measure of prevalence has decreased by 90 percent since slaughter surveillance started in FY 2003. • The scrapie program is now in the “tail end” of the eradication process with few animals found positive during slaughter sampling and the annual variation in the number of animals found positive between years falls within the error of the measurement, given the sample size and 95% confidence limits. As a result there is no statistically significant change in the annual detection rate of scrapie between FY 2012 and 2013 in slaughtered animals.

4. Scrapie Surveillance Initiative During the summer of 2013, an outreach program was initiated that focused on producers and accredited veterinarians. The regulatory scrapie slaughter surveillance (RSSS) program misses sheep and goats that are found dead or euthanized on the farm. The outreach effort provided information to producers and accredited veterinarians on collection and submission of samples from dead or euthanized sheep/goats over 18 months of age. More information is available at the APHIS Scrapie Website State Scrapie Sampling Minimums The National Scrapie Eradication Program establishes annual sheep sampling minimums for each state, and tracks the States’ level of compliance with meeting these minimums. These state minimums were implemented in FY 2010 to ensure adequate geographical representation, so that APHIS can find the last remaining cases and document freedom from scrapie. State sampling minimums are established based on the population demographics of mature sheep in each State. Since FY2011, the program has also proposed annual state sampling minimums for goats. Calculation used to derive the sampling minimums is described in the National Scrapie Surveillance Plan. The plan can be viewed and downloaded from the APHIS scrapie website: National Scrapie Surveillance Plan The percentage of the sampling minimum for sheep and for goats that was achieved by each state in FY 2013 is depicted in Figures 1 and1a,respectively; a State’s percentage is based on the total number of sheep and total number of goats sampled through Regulatory Scrapie Slaughter Surveillance (RSSS) and on-farm surveillance. Surveillance

5. Surveillance Regulatory Scrapie Slaughter Surveillance (RSSS) RSSS started April 1, 2003. It is a targeted slaughter surveillance program which is designed to identify infected flocks. Samples have been collected from 397,912 animals since April 1, 2003. There have been 469 NVSL confirmed positive animals (461 classical cases and 8 Nor98-like cases) since the beginning of RSSS. 43,228 samples were collected in FY 2013, 7,563 of which were from goats. Collection site locations and the states that comprise the Eastern and Western Regions are shown in Figure 2. The number of animals collected for FY 2013 by month and by region where collected is shown in Chart 3. A monthly comparison of RSSS collections by fiscal year is displayed in Chart 4. Chart 5depicts RSSS collections by region of collection and by region of eartag origination from FY 2003 through FY 2013. Percent of RSSS samples collected by face color and species from FY 2003 through FY 2013 is plotted in Chart 6. The map in Figure 3shows RSSS sampling by state of collection; Figure 4shows RSSS sampling by state of origination (application). Six black-faced, 1 mottled-faced (greater than 40% black), and 1 white-faced sheep tested positive for scrapie in FY 2013. The distribution of positive cases by state of tag origination (application) is depicted in Figure 5. Chart 7 and Chart 8 show the percent of samples that have tested positive for each face color from FY 2003 through 2013; Chart 1shows the percent of cull sheep found positive at slaughter and adjusted for face color. Positive animals from the same flock and Nor98-like cases are not included in these charts. A retrospective 6 month rolling average of the percent positive, black-faced sheep sampled at RSSS collections sites is shown in Chart 9. Success in tracing RSSS positive animals to flock of origin is shown in Chart 10. Changes in traceability are not statistically significant due to the small numbers of cases.

6. Surveillance • On-Farm Surveillance • Testing of animals in the field has always been part of scrapie surveillance (regulatory field cases and live-animal testing). As the National Scrapie Eradication Program moves closer towards meeting the goal of identifying the last remaining cases of classical scrapie by 2017, finding and testing all sheep and goats meeting targeted sampling criteria is even more important. • 1,363 sheep and 722 goats were tested on-farm for FY 2013. Through trace-forward investigations and flock clean-up plans, three black-faced, one mottled-faced, and three white-faced sheep tested positive in FY 2013. One Nor98-like case was diagnosed in September 2013, but this is not included in the total number of positives. Three clinical suspect goats tested positive. Two were meat-type twin goats residing in the same herd in Maryland. The other was a Nigerian dwarf goat from Arizona confirmed positive in July. The number of animals tested on-farm by month and by species for FY 2013 is shown in Chart 11. • Total Animals Sampled for Scrapie Testing • 45,313 animals were sampled for scrapie testing in FY 2013: • 43,228 RSSS samples and 2,085 on-farm samples [includes regulatory testing (necropsy and live-animal) and on-farm surveillance] (Chart 12); • Of which 37,028 were sheep and 8,285 were goats. • Distribution of sampling by type (RSSS or on-farm) and by species is shown in Chart 13.

7. Positive Cases and Infected/Source Flocks Positive Cases and New Infected/Source Flocks In FY 2013, 18 cases of classical scrapie (eight through RSSS and ten through on-farm surveillance) and 1 Nor98-like case were confirmed by the National Veterinary Services Laboratories (NVSL) (Table 1and Figure 6). As of September 30, 2013, the number of confirmed positive cases in goats since FY 2002 is 34; the most recent case was a Nigerian dwarf goat, confirmed positive in July 2013 (Figure7). Field cases are positive animals that were tested as part of a disease investigation including potentially exposed, exposed and suspect animals, and other animals sampled on-farm. Infected and Source Flocks At the beginning of FY 2013, there were 3 flocks with open infected or source statuses (Table 2 and Figure 8). During the year, 8 new source flocks and 3 new infected flocks were reported (Figure 9) and 8flocks completed a clean-up plan and were released (Figure 10). As of September 30, 2013, 6 scrapie-infected and source flocks had open statuses (Figure 11). The ratio of infected and source flocks released to newly identified infected and source flocks for FY 2013 = 1 : 1.4.New infected and source statuses from FY 1997 to FY 2013 are shown in Chart 2. Indemnity Approximately 396 sheep and goats were indemnified in FY 2013. A breakdown by species and registration status is depicted on Chart 14. The average cost for indemnity and disposal was approximately $186 per animal.

8. Scrapie Flock Certification Program Scrapie Flock Certification Program At the end of the FY, there were 1,049 flocks enrolled in the SFCP—500 complete monitored, 439 certified, 61 export monitored, 13 export certified, and 36 selective monitored (Figure 12). SFCP open statuses by fiscal year from FY 1997 to FY 2013 are depicted in Chart 15. A new revision of the SFCP Standards was published June 20, 2013. The objectives of the revision were to increase surveillance in SFCP flocks and reduce costs associated with flock inspections, while providing a mechanism for flocks to become export certified. The “Complete Monitored” category was eliminated. Flocks with “Complete Monitored” and “Certified” status had the option of converting to the “Export” category or “Select” category by November 18, 2013. The revised SFCP Standards can be viewed at or downloaded from the APHIS scrapie website: SFCP Standards Sheep and Goat Premises in Scrapie Database Compared to NASS 2007 Census Data Figure 13and Figure 14 are maps showing the percent of sheep and goat flocks/herds by state that have been assigned premises/flock identification numbers in the scrapie database. This report is based on information and test results available at the time of report generation. Numbers are subject to change due to later reporting of test results and updates in the database.

9. Percent of RSSS Samples that TestedPositive for Classical ScrapieWeighted by Face ColorFiscal Years 2003 to 2013 (Chart 1) Adjusted to exclude multiple positive animals from the same flock. Does not include Nor98-like scrapie cases found through RSSS (2 in FY 2007, 1 in FY 2008, 4 in FY 2010, and 1 in FY 2011).

10. Infected and Source Flocks New Statuses by YearFiscal Years 1997 to 2013 (Chart 2)

11. Percent of Sampling Minimum Achievedin FY 2013—RSSS and On-farm Surveillance—Sheep WA AK ME MT ND MN OR VT NH WI SD NY ID MA WY CT MI RI CA IA PA NV NJ NE OH IL IN UT DE HI CO MO MD WV KS VA KY NC AZ OK TN NM AR SC AL MS GA TX LA FL (Figure 1)

12. Percent of Sampling Minimum Achievedin FY 2013—RSSS and On-farm Surveillance—Goats* WA AK ME MT ND MN OR VT NH WI SD NY ID MA WY CT MI RI CA IA PA NV NJ NE OH IL IN UT DE HI CO MO MD WV KS VA KY NC AZ OK TN NM AR SC AL MS GA TX LA FL (Figure 1a) * Proposed sampling minimums for goats.

13. RSSS Sample Collections FY 2013177 collection sites in 39 states & sent to 12 laboratories WA AK ME MT ND MN OR VT MA NY NH WI SD RI ID MI WY CT IA PA NV NE NJ West OH IN IL UT DE HI CO VA CA WV MO KS MD KY NC AZ TN OK NM AR SC AL MS GA TX LA East FL States with RSSS collection sites (Figure 2)

14. Slaughter Surveillance Samples Collectedby Month, VS Region Where Collected, and TotalFY 2013 Month (Chart 3)

15. Slaughter Surveillance Samples Collectedby MonthFiscal Years 2009 to 2013 Month (Chart 4)

16. Percent RSSS SamplesFY 2003-2013 By Region of Sample Collection By Region of Eartag Origination (Chart 5)

17. Surveillance Samples Collected at Slaughter FY 2003-2013 (Chart 6) * Other Sheep: hair sheep, and those with gray, red, brown, or unknown face color.

18. Regulatory Scrapie Slaughter SurveillanceNumber of Samples Collected, FY 2013BY STATE OF COLLECTION (Figure 3)

19. Regulatory Scrapie Slaughter SurveillanceNumber of Samples Collected, FY 2013BY STATE OF TAG ORIGINATION (Figure 4)

20. Regulatory Scrapie Slaughter SurveillanceNumber of Positive Samples, FY 2013BY STATE OF TAG ORIGINATION (Figure 5)

21. Percent of RSSS Samples that TestedPositive for Classical Scrapieby Face Color Fiscal Year 2003 – 2013 (Chart 7) Adjusted to exclude multiple positive animals from same flock. Mottled- and white-faced combined. Does not include Nor98-like scrapie cases found through RSSS (2 in FY 2007, 1 in FY 2008, 4 in FY 2010, and 1 in FY 2011).

22. Percent of RSSS Samples that TestedPositive for Classical Scrapie by Face Color during each Fiscal Year (2008 – 2013) (Chart 8)

23. Retrospective 6 Month Rolling Average of Percent Classical Scrapie Positive Black-Faced Cull Sheep Sampled at Slaughter (Chart 9) Includes only sheep with test results reported. Includes multiple positives from same flock.

24. Investigations of RSSS Positive AnimalsFY 2003 – FY 2013 Average % Traceable FY03-FY13 86% (Chart 10) * April – September, 2003

25. On-Farm Surveillance Testingby Month and SpeciesFY 2013 (Chart 11)

26. Number of Animals Sampled for Scrapie Testing by Quarter—FY 2013 (Chart 12)

27. RSSS and On-Farm Surveillance Testingby Species—FY 2013 (Chart 13)

28. Scrapie Confirmed Cases in FY 2013 (Table 1) * Nor98-like case indicated in parentheses and is not counted in the total. ** One RSSS case was traced back to IA but could not be traced to its flock of origin.

29. Scrapie Confirmed Cases in FY 2013 WA AK ME MT ND MN OR VT ID NH WI 1 SD MA NY MI WY RI CT PA IA NV NE NJ 1/2 OH IN 2/4 IL UT DE HI 2 CO 1/1 CA (1) WV MO KS MD - 2 VA KY NC AZ 1 OK TN NM AR 1 SC AL MS GA TX LA FL (Figure 6) Reported by State of ID tag. Collected in FY 2013 and confirmed by EOY reporting date. Field cases include animals removed from infected/source flocks, so State totals often include several animals from the same flock. Nor-98 like scrapie case is indicated in parentheses and is not counted in the total.

30. Scrapie Cases in Goats FY 2002 – FY 2013 WA AK ME MT ND MN 1 OR VT NH WI SD MA NY ID MI WY RI CT IA PA NV 8 NE NJ OH IN IL UT DE HI CO 5 MO WV 1 MD –2 CA KS VA 3 KY 13 NC OK TN NM AZ 1* AR SC AL MS GA TX LA FL (Figure 7) * Most recent positive goat confirmed in July 2013.

31. Scrapie Infected and Source FlocksFY 2013 Overview (Table 2)

32. Scrapie Infected and Source Flocks: Open Statuses as of October 1, 2012 WA AK ME MT ND MN OR VT NH WI SD MA NY ID WY RI MI CA CT IA PA NV NE NJ OH IN IL 1 UT DE HI CO WV MO KS MD VA KY - 1 NC AZ OK 1 TN NM AR SC AL MS GA TX LA FL Open source flocks—3 (Figure 8)

33. New Scrapie Infected and Source FlocksFY 2013 WA AK ME MT ND MN OR 1 VT NH WI SD MA NY ID MI WY RI CT IA 2 NV PA - 1 NE NJ OH 2 IN IL 2 UT DE HI CO MO WV CA KS MD - 1* VA KY NC AZ 1* TN OK 1 NM AR SC AL MS GA TX LA FL New source flocks—8 New infected flock—3 (Figure 9) * Goat herd

34. Released Scrapie Infected and Source Flocks FY 2013 WA AK ME MT ND MN OR VT NH WI SD MA NY ID MI WY RI CT IA NV PA -1 NE NJ OH 2 IN IL 2 UT DE HI CO WV MO CA KS MD - 1 VA KY NC AZ TN OK 2 NM AR SC AL MS GA TX LA FL Flocks released—8 (Figure 10)

35. Scrapie Infected and Source Flocks: Open Statuses as of September 30, 2013 WA AK ME MT ND MN OR 1 VT NH WI SD MA NY ID WY MI RI CT IA 2 NV PA NE NJ OH IN IL 1 UT DE HI CO WV MO CA KS MD VA KY - 1 NC AZ 1 OK TN NM AR SC AL MS GA TX LA FL Open source flocks—5 Open infected flocks—1 (Figure 11)

36. Indemnity Claims FY 2013 Registered and Club Sheep 5% Registered and Club Goats 36% Nonregistered Sheep 59% Nonregistered Goats 0% Total number of animals indemnified: 396 (ER-172, WR-224). Total amount spent: indemnification and disposal $73,568. (ER-$26,784.; WR-$46,784.) . The average cost: $186 per animal. (Chart 14)

37. Scrapie Flock Certification Program: Participating FlocksAs of September 30, 2013 AK 2 WA 26 ME 49 MT 25 ND 2 MN 23 OR 19 VT 34 ID 16 NY 21 WI 43 SD 8 MA-43 MI 19 WY 6 RI-13 CT-19 PA 111 IA 7 NH-23 NV 5 NE 10 NJ-37 OH 19 IN 32 IL 11 UT 29 DE-1 HI 11 WV 18 CO 18 VA 18 MO 12 CA 65 MD-23 KS 10 KY-25 NC-26 TN-9 AZ 1 OK 16 NM 5 AR 10 SC 22 AL 17 MS 15 GA 22 TX 22 LA 11 FL 20 • Total Enrolled Flocks—1,049 • Complete Monitored—500 • Certified—439 • Export Monitored—61 • Export Certified—13 • Selective Monitored—36 (Figure 12)

38. SFCP Open Statusesby Fiscal YearFY 1997 to FY 2013* (Chart 15) * As of September 30, 2013.

39. Percent of Sheep Flocks Reported by NASS (2007 Census Report) Assigned Flock Identification Numbers As of September 30, 2013 WA AK ME MT ND MN OR VT NH WI SD MA NY ID MI WY RI CA CT IA PA NV NE NJ OH IN IL UT DE HI CO WV MO KS MD VA KY NC AZ OK TN NM AR SC AL MS GA TX LA FL (Figure 13)

40. Percent of Goat Herds Reported by NASS (2007 Census Report) Assigned Flock Identification NumbersAs of September 30, 2013 WA AK ME MT ND MN OR VT NH WI SD MA NY ID MI WY RI CA CT IA PA NV NE NJ OH IN IL UT DE HI CO WV MO KS MD VA KY NC AZ TN OK NM AR SC AL MS GA TX LA FL (Figure 14)