National Scrapie Eradication April 2014 Monthly Report

National Scrapie Eradication Program

March 2018 Monthly Report Fiscal Year 2018

U.S. Department of AgricultureAnimal and Plant Health Inspection Service

Veterinary Services

Surveillance, Response and Preparedness Services

Sheep and Goat Health Program

April 20, 2018

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A Note on Navigation

The National Scrapie Eradication Program is transitioning to a new reporting software called Tableau. Tableau is an interactive data visualization tool that allows users to easily select and view data summaries. Since the July 2017 report, some of the graphs in the Monthly Scrapie Report have been from Tableau. Eventually, the public will be able to see and interact with scrapie program reporting data through a web browser linked to Tableau Server. New to the monthly report is the use of hex maps. Hex maps represent each state as a hexagon of equal size, with geographic affinity loosely maintained. These representations allocate equal area, and therefore equal weight, to each state. Filled colors still represent values, but with equal area allocated to each state, encourage focus on the data values rather than states with the most area. States and territories outside the contiguous US are easily represented, also with equal weight.

New Reporting Format

Program SummaryPerformance Measures - At the end of FY 2017 and continuing into FY 2018, the percent of cull black face 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).

Positive Animals - No sheep have tested positive for classical scrapie since April 2016. One Nor98-like case was reported in October 2017. Other than one goat in a herd quarantined since 2005 and depopulated in 2017, no goats have tested positive for scrapie since February 2015. The retrospective 6-month rolling average of the percent positive, black-faced sheep sampled at RSSS collection sites has been 0 since June 2016.

*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.

**Samples collected between October 1, 2017 and March 31, 2018 and confirmed by April 15, 2018.

Introduction - Program Summary

Program SummaryInfected and Source Flocks - No classical scrapie infected or source flocks have been designated since June 2016 (Chart 3). Two flocks, one in Colorado and one in Texas, have open statuses, but there are no exposed animals on the premises of these flocks. Cleaning and disinfection of these premises has to be completed before the infect or source status can be closed.

Scrapie in Goats - Only one positive goat (FY 2015) has been found through RSSS since the start of RSSS in 2003. Since 2002, the total number of positive field cases in goats is 41. Figure 1 shows the number of positive cases by State and by fiscal year of last reported case.

Introduction - Program Summary

Program SummaryScrapie Flock Certification Program (SFCP) – As of March 31, 2018, there were 282 flocks participating in the Scrapie Flock Certification Program (SFCP). Statuses of these flocks were 63 export monitored, 45 export certified, and 174 select monitored flocks (Figure 2). SFCP open statuses by fiscal year of Status date* from FY 1997 to FY 2018 are depicted in Chart 4.

* 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.

SurveillanceSurveillance 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 sheep and goat populations in each State. The distribution of sheep and goat populations by District is depicted in Chart 5.

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 579,277 animals since April 1, 2003. There have been 483 NVSL confirmed positive animals (471 classical cases and 12 Nor98-like cases) since the beginning of RSSS. As of March 31, 2018, 18,969 samples have been collected in FY 2018, 14,937 from sheep and 4,032 from goats. None tested positive for classical scrapie. The number of sheep and goats collected in each District is shown in Chart 6. Figure 4 is a hex map, representing the number of animals collected in each State. Chart 7 compares RSSS sampling by month for the current year with the monthly average of the previous 4 years.

SurveillanceComponents of Scrapie Surveillance (continued)• 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. As of March 31, 2018, 684 sheep and 307 goats have been tested on-farm for FY 2018.

Surveillance MinimumsThe annual target is to test at least 40,000 animals each year for scrapie. As of March 31, 2018, 19,960 animals have been sampled for scrapie testing in FY 2018:

• 18,969 RSSS samples and 991 on-farm samples • Of which 15,621 were sheep and 4,339 were 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 is shown in Chart 9. Chart 10 and Table 1 is a breakdown by face-color (sheep) and type (goats) by age.

SurveillanceState Sampling MinimumsThe 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 6 and Figure 7.

District 1 Table 2 District 3 Table 4 District 5 Table 6

District 2 Table 3 District 4 Table 5 District 5 Table 7

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.

* As of March 31, 2018. Adjusted to exclude multiple positive animals from same flock. Mottled- and white-faced combined. Does not include Nor98-like scrapie cases found through RSSS.

(Chart 1)

M +

W

Bla

ck

0.0%0.1%0.2%0.3%0.4%0.5%0.6%0.7%0.8%0.9%1.0%

% Pos '03

% Pos '04

% Pos '05

% Pos '06

% Pos '07

% Pos '08

% Pos '09

% Pos '10

% Pos '11

% Pos '12

% Pos '13

% Pos '14

% Pos '15

% Pos '16

% Pos '17

% Pos '18

Percent of RSSS Sheep Samples that Tested Positive for Classical Scrapie - By Face Color

FY 2003 – FY 2018*

* As of March 31, 2018. Adjusted to exclude multiple positive animals from the same flock. Does not include Nor98-like scrapie cases found through RSSS.

(Chart 2)

0.00%

0.02%

0.04%

0.06%

0.08%

0.10%

0.12%

0.14%

0.16%

% Pos '03% Pos '04% Pos '05% Pos '06% Pos '07% Pos '08% Pos '09% Pos '10% Pos '11% Pos '12% Pos '13% Pos '14% Pos '15% Pos '16% Pos '17% Pos '18

Percent of RSSS Sheep Samples that Tested Positive for Classical Scrapie - Weighted by Face Color

FY 2003 – FY 2018*

* As of March 31, 2018

(Chart 3)

Infected and Source Flocks New Statuses by Year – Fiscal Years 1997 to 2018*

FY '9

8FY

'00

FY '0

2FY

'04

FY '0

6FY

'08

FY '1

0FY

'12

FY '1

4FY

'16

FY '1

8

0

50

100

150

200

InfectedSource

WY

WV

WI

WA1

VT

VA

UT

TX

TN

SD

SC

RIPA

OR

OK

OH5

NY

NV

NM

NJ

NH

NE

ND

NC

MT

MS

MO

MN

MI6

ME

MD – 2

MA

LA

KYKS

INIL1

ID

IA7

HI

GA

FL

DE

CT

CO5*CA

13AZ1 AR

AK

AL

(Figure 1)

* Only RSSS positive goat, identified in November 2014. 41 total cases. The goat from the long term quarantined herd in CO that tested positive in July 2017 is not included. Color code indicates fiscal year of last case by State.

FY 2015

FY 2014

FY 2013

FY 2011

FY 2010

FY 2009

FY 2008

Prior to FY 2008

Scrapie Cases in GoatsFY 2002 – FY 2018

Scrapie Flock Certification Program: Participating Flocks and Herds*

* As of March 31, 2018(Figure 2)

Program

Export Certified 45

Export Monitored 63

Select 174

Total 282

SFCP Participating Flocks Based on Status DateFY 2007 to FY 2018*

* As of March 31, 2018. Includes enrolled flocks in Puerto Rico. Chart is based on current or last status date; many participating flocks were grandfathered into Export program in 2013 with earlier status date.

(Chart 4)

WY

WV

WI

WA

VT

VI

VA

UT

TX

TN

SD

SC

RI

PR

PA

OR

OK

OH

NY

NV

NM

NJ

NH

NE

ND

NC

MT

MS

MO

MN

MI

ME

MD

MA

LA

KYKS

INIL

ID

IA

HI

GA

FL

DE

CT

CO

CA

AZAR

AK

AL

District One

District Two

District Three

District Four

District Five

District Six (Figure 3)

Surveillance Preparedness and Response Services (SPRS) Districts

Total Sheep and Goat Populations by District*

District 1 District 2 District 3 District 4 District 5 District 6**0

200,000

400,000

600,000

800,000

1,000,000

1,200,000

1,400,000

1,600,000

1,800,000

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

Sheep

Goats

(Chart 6)* As of March 31, 2018

Total RSSS Samples Collected by DistrictFY 2018*

District

* As of March 31, 2018 (Figure 4)

Total RSSS Samples Collected by StateFY 2018*

States with no RSSS collections

* As of March 31, 2018

Comparison by Month of RSSS Samples Collected in FY 2018* to Average of FY 2014 – FY 2017

(Chart 7)

21

Cumulative Number of Animals Sampled by MonthFY 2018*

* As of March 31, 2018. (Chart 8)

(Chart 9)

RSSS & On-Farm Surveillance Sampling by SpeciesFY 2018*

* As of March 31, 2018.

18,969Total 991 Total

* As of March 31, 2018.

RSSS and On-Farm Surveillance Testing by SpeciesFY 2018*

(Chart 10)

* As of March 31, 2018. Darker shading represents greater number of animals tested that met targeting criteria.

(Table 1)

RSSS and On-Farm Surveillance Testing by SpeciesFY 2018*

FY 2018 Sheep and Goat State Sampling Minimums and State Collections - District 1

(Table 2)* As of March 31, 2018. Note that all surveillance samples may not yet have been credited to the State.

WV

VT

VA

RI

PA

NY

NJ

NH

NC

ME

MD

MA

DE

CT

FY 2018 Sheep and Goat State Sampling Minimums and State Collections - District 2

(Table 3)

* As of March 31, 2018. Note that all surveillance samples may not yet have been credited to the State.

TNSC

GA

FL

AL

FY 2018 Sheep and Goat State Sampling Minimums and State Collections - District 3

(Table 4)

* As of March 31, 2018. Note that all surveillance samples may not yet have been credited to the State.

WI

OH

MN

MI

KY

INIL

IA

FY 2018 Sheep and Goat State Sampling Minimums and State Collections - District 4

(Table 5)

* As of March 31, 2018. Note that all surveillance samples may not yet have been credited to the State.

TX

OK

MS

LA

AR

MO

FY 2018 Sheep and Goat State Sampling Minimums and State Collections - District 5

(Table 6)

* As of March 31, 2018. Note that all surveillance samples may not yet have been credited to the State.

WYSD

NE

NDMT

KS

ID

WA

UT

OR

NV

NMHI

CO

CA

AZ

AK

FY 2018 Sheep and Goat State Sampling Minimums and State Collections - District 6

(Table 7)

* As of March 31, 2018. Note that all surveillance samples may not yet have been credited to the State.

* As of March 31, 2018. Percentage of sampling minimum achieved is based on 42% of the annual sampling minimum.

Percent of Sampling Minimum Achieved inFY 2018 - RSSS and On-farm Surveillance

Sheep

(Figure 6)

* As of March 31, 2018. Percentage of sampling minimum achieved is based on 48% of the annual sampling minimum. AK and RI have a sampling minimum of 1 and DE has a sampling minimum of 2.

Percent of Sampling Minimum Achieved inFY 2018 - RSSS and On-farm Surveillance

Goats

(Figure 7)