National Scrapie Eradication April 2014 Monthly Report

1. National Scrapie Eradication April 2014 Monthly Report National Scrapie Eradication Program Fiscal Year 2018 Report October 1, 2017 to September 30, 2018 U.S. Department of Agriculture Animal and Plant Health Inspection Service Veterinary Services Strategy and Policy Unit Sheep and Goat Health Center Prepared January 31, 2019

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3. Introduction - Program Summary • 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 positive and exposed animals and testing exposed animals • Cleanup of infected and source flocks through genetic susceptibility testing and indemnification of susceptible exposed animals • Monitoring previously infected and exposed flocks • The Scrapie Free Flock Certification Program (SFCP)

4. Introduction - Program Summary Program Summary Performance Measures - For FY 2017 and 2018 the percent of cull black-faced sheep found positive at slaughter was 0 percent (Chart 1) and the percent of cull sheep found positive at slaughter and adjusted for face color* was 0 percent (Chart 2). The retrospective 6-month rolling average of the percent positive, black-faced sheep sampled at RSSS collection sites has been 0 since June 2016. Positive Animals –In August 2018, a Pennsylvania goat sampled at slaughter in July was confirmed positive for classical scrapie. The only other positive goat found through slaughter surveillance was in November 2014. In April 2018, APHIS identified scrapie in a 171 RR sheep from a flock in NC. There was insufficient positive tissue available to rule out non-classical scrapie; no other sheep in the flock have tested positive for scrapie. As of September 30, 2018, the case was still unclassified. One Nor98-like case was reported in October 2017. *White, black and mottled-faced color sheep are weighted based on population; white-faced sheep have the greatest weight. If a white-faced positive sheep is found, this statistic will markedly increase. See notes below for details.

5. Introduction - Program Summary Program Summary Infected and Source Flocks - The RSSS positive goat confirmed in August 2018 was traced to a Pennsylvania herd that has sheep and goats. The herd was designated as a source flock in September (Chart 3). Two other flocks, one in Colorado and one in Texas, have open statuses, but there are no exposed animals on the premises of these flocks. As of September 30, 2018, cleaning and disinfection of these premises had not been completed; cleaning and disinfection must be completed before the infect or source status can be closed. Scrapie in Goats – Two positive goats have been found through RSSS since the beginning of the program in 2003. Samples from the first one were collected in November 2014; samples from the second were collected in July 2018. The most recent positive case brings the total number of NVSL confirmed positive cases in goats to 42. Figure 1shows the number of positive cases by State and by fiscal year of last reported case.

6. Program Summary Scrapie Flock Certification Program (SFCP) – As of September 30, 2018, there were 264flocks participating in the Scrapie Flock Certification Program (SFCP). Statuses of these flocks were 54 export monitored, 47 export certified, and 163 select monitored flocks (Figure 2). SFCP open statuses by fiscal year of Status date* from FY 2007 to FY 2018 are depicted in Chart 4. * Chart 4 represents the cumulative change in SFCP enrollment over time, and includes open and closed statuses/programs, and active and inactive flocks/herds. Previous charts of SFCP participation by year were manually updated and used the enrollment date to determine the year of participation in SFCP. With the change to Tableau charts, the start/status date is used. Many participating flocks were grandfathered into the Export category in 2013 with an earlier status date.

7. Surveillance • Surveillance activities are State-based and are administered as districts by APHIS (Figure 3). For this reason, reporting of surveillance activities is also by District. Surveillance minimums are based on estimated breeding sheep and goat populations in each State. The distribution of sheep and goat populations by District is depicted in Chart 5. The districts are shown as they were in FY 2018. • Components of Scrapie Surveillance • Regulatory Scrapie Slaughter Surveillance (RSSS)started April 1, 2003. It is a targeted slaughter surveillance program which is designed to identify infected flocks. Samples have been collected from 601,726 animals since April 1, 2003. 41,418 RSSS samples were collected in FY 2018, 32,840 from sheep and 8,578 from goats. Collection sites by state are shown in Figure 4.Figure 5 is a hex map, representing the number of animals collected in each State. The number of sheep and goats collected in each Districtis shown in Chart 6. Chart 7 compares RSSS sampling by month for the current year with the monthly average of the previous 4 years.

8. Surveillance • Components of Scrapie Surveillance (continued) • RSSSPositive Cases – Since the beginning of the RSSS program, 485 NVSL confirmed positive animals (472 classical cases, 12 Nor98-like cases, and 1 pending designation) have been found. In FY 2018, 2 sheep and a goat collected through RSSS were confirmed positive. One sheep was positive for Nor98-like scrapie, the other sheep is pending designation as classical or non-classical scrapie, and the goat was positive for classical scrapie. This was the second positive goat found at slaughter; the first was found in November 2014. • On-farm Surveillance includes both regulatory testing of scrapie exposed and potentially exposed sheep and goats and testing sheep and goats on farm for routine surveillance. 1,522 sheep and 714 goats were tested on-farm in FY 2018. None were positive.

9. Surveillance Surveillance Goals The annual target is to test at least 40,000 animals each year for scrapie. 43,654 animals were sampled for scrapie testing in FY 2018, exceeding the goal. Of these, there were 41,418 RSSS samples and 2,236 on-farm samples; 34,362 were from sheep and 9,292 were from goats. Progress towards meeting the national surveillance target is depicted in Chart 8.Distribution of sampling by type (RSSS or on-farm) and by species in FY 2018 is shown in Chart 9. Chart 10 and Table 1 is a breakdown by face-color (sheep) and type (goats) by age. The number of RSSS samples collected by face color and species from FY 2003 through FY 2018 is plotted in Chart 11.

10. Surveillance State 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 and goats in each State. The calculations used to derive the sampling minimums are described in the National Scrapie Surveillance Plan. The State sampling minimums for sheep and goats, and the total number of animals sampled by State of Animal ID, are listed in in the following slides: The percent sampling minimum for sheep and goats achieved by each State in FY 2018 are depicted in Figure 6and Figure 7.

11. Surveillance State Sampling Minimums (Cont.) New surveillance option for meeting state minimums– Historically, several states have had difficulty meeting their annual sampling requirement. In FY 2018, these states were able to increase and, in most cases, meet the sampling minimum by identifying sheep producers or dealers for genotyping of codon 171prior to live-animal testing (rectal biopsy) of the genetically susceptible (QQ) animals. Genotyping is done to reduce the costs associated with live-animals testing. The QQ sheep that were live-animal tested and the genetically less susceptible (QR) and genetically resistant (RR) sheep were credited to the State. Under this option, 689 sheep were genotyped during FY 2018; 145 of these were QQs (21.0%). None of the QQs that were live-animal tested were positive. In all, 535 animals with either a QR or RR genotype were credited to states. These additional samples are included in the Total Number of Sheep Sampled column of Districts Tables (Tables 2 through 7), and in the calculations for the hex maps showing the percent of sampling minimum achieved (Figures 6 and 7). The QR and RRs are not included in any other charts in this report. 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.

12. Percent of RSSS Sheep Samples that Tested Positive for Classical Scrapie - By Face Color FY 2003 – FY 2018* (Chart 1) * Adjusted to exclude multiple positive animals from same flock. Mottled- and white-faced combined. Does not include Nor98-like scrapie cases found through RSSS.

13. Percent of RSSS Sheep Samples that Tested Positive for Classical Scrapie - Weighted by Face ColorFY 2003 – FY 2018* (Chart 2) * Adjusted to exclude multiple positive animals from the same flock. Does not include Nor98-like scrapie cases found through RSSS.

14. Infected and Source Flocks New Statuses by Year – Fiscal Years 1997 to 2018* (Chart 3)

15. Scrapie Cases in GoatsFY 2002 – FY 2018 WA 1 AK ME MT ND MN OR VT NH WI SD MA NY MI 6 ID WY RI CT IA 7 PA – 1* NV NE NJ OH 5 IN IL 1 UT DE HI CO 5* MO WV MD –2 CA 13 KS VA KY NC TN AZ 1 OK NM AR SC GA AL MS TX LA FL (Figure 1) Color code indicates fiscal year of last case by State. 42 NVSL confirmed cases. * RSSS positive goats; samples collected November 2014 and July 2018

16. Scrapie Flock Certification Program: Participating Flocks and Herds* (Figure 2) * As of September 30, 2018

17. SFCP Participating Flocks Based on Status DateFY 2007 to FY 2018* (Chart 4) * As of September 30, 2018. Represents the cumulative change in SFCP enrollment over time, and includes open and closed statuses/programs, and active and inactive flocks/herds. Chart is based on current or last status date; many participating flocks were grandfathered into Export program in 2013 with earlier status date.

18. Surveillance Preparednessand Response Services (SPRS) Districts AK WA ME MT ND MN OR VT NH WI SD NY ID MA WY CT MI RI CA IA PA NE NV NJ OH IL IN DE UT CO WV MO MD KS VA KY NC AZ TN HI OK NM AR SC AL MS GA TX LA VI FL PR (Figure 3)

19. Total Sheep and Goat Populations by District* (Chart 5) * Source: NASS Sheep and Goat, January 31, 2018. ** Includes sheep and goats residing in the Navajo Nation.

20. RSSS Sample Collections – FY 2018178 collection sites in 40 states AK WA ME MT ND MN OR VT WI SD NY ID WY MI RI CA IA PA NE NV NJ OH NH IL IN DE MA UT CO WV MO MD KS CT VA KY NC AZ TN HI OK NM AR SC v AL MS GA TX LA VI v FL PR States with RSSS collection sites (Figure 4)

21. Total RSSS Samples Collected by State – FY 2018 States with no RSSS collections (Figure 5)

22. Total RSSS Samples Collected by District – FY 2018 District (Chart 6)

23. Comparison by Month of RSSS Samples Collected in FY 2018 to Average of FY 2014 – FY 2017 (Chart 7)

24. Cumulative Number of Animals Sampled by MonthFY 2018 (Chart 8)

25. RSSS and On-Farm Surveillance Sampling by Species - FY 2018 41,418Total 2,236 Total (Chart 9)

26. RSSS and On-Farm Surveillance Testingby Species - FY 2018 (Chart 10)

27. RSSS and On-Farm Surveillance Testingby Species - FY 2018 (Table 1) Darker shading represents greater number of animals tested that met targeting criteria.

28. Surveillance Samples Collected at Slaughter FY 2003 – 2018 (Chart 11) Other sheep includes hair sheep, and sheep with gray, red, or unknown face color. Chart includes animals collected for RSSS & CSPS.

29. FY 2018 Sheep and Goat State Sampling Minimums and State Collections - District 1 ME VT NH NY MA CT RI PA NJ DE WV MD VA NC (Table 2)

30. FY 2018 Sheep and Goat State Sampling Minimums and State Collections - District 2 TN SC AL GA FL (Table 3)

31. FY 2018 Sheep and Goat State Sampling Minimums and State Collections - District 3 MN WI MI IA OH IL IN KY (Table 4)

32. FY 2018 Sheep and Goat State Sampling Minimums and State Collections - District 4 OK MO AR MS TX LA (Table 5)

33. FY 2018 Sheep and Goat State Sampling Minimums and State Collections - District 5 MT ND SD ID WY NE KS (Table 6)

34. FY 2018 Sheep and Goat State Sampling Minimums and State Collections - District 6 AK WA OR CA NV UT CO AZ HI NM (Table 7)

35. Percent of Sampling Minimum Achievedin FY 2018—RSSS and On-farm SurveillanceSheep (Figure 6)

36. Percent of Sampling Minimum Achievedin FY 2018—RSSS and On-farm SurveillanceGoats (Figure 7)