1. Swine Enteric Coronavirus Diseases
Secreatary’s Advisory Committee on Animal Health
April 2015
Brian J. McCluskey, DVM, MS, PhD, Dip. ACVPM
Chief Epidemiologist
USDA, Animal and Plant Health Inspection Service, Veterinary Services

2. Novel Swine Enteric Coronaviruses
Porcine Epidemic Diarrhea virus (PEDv)
Porcine deltacoronavirus (PDCoV)
Picture from Wikipedia of Corona Virus

3. PEDv History 1969 - Large outbreaks in European swine herds
Diarrhea associated with weaning or feeder pigs
Suckling pigs not always affected
Affecting swine of all ages
Coronavirus-like agent was identified as cause - Porcine Epidemic Diarrhea Virus
– Outbreaks of high morbidity and mortality in China
Distribution:
Asia, Canada, Columbia, Dominican Republic, Europe, United States

4. From: Huang et al., mBio 2013

5. SECD Clinical Signs Clinical signs:
Primary signs are acute watery diarrhea and vomiting
Acute, naïve herd: vomiting, diarrhea, loss of appetite in all pigs. Morbidity approaches 100%
Suckling pigs: diarrhea, dehydration, acidosis.
Mortality between %.
Feeder/Grower pigs: diarrhea, anorexia depression.
Low mortality (1-3%).
Endemic herd: persistent diarrhea in recently weaned pigs.
Severity depends on epidemiological status of the herd
Clinical picture almost indistinguishable from TGE
May not spread quite as quickly as TGE
In some herds suckling pigs not affected (early in PED) – used to call Type 1 and Type 2 PED

6. SECD Differential Diagnosis
Differentials
TGE (coronavirus)
Rotavirus
Other bacterial diarrheal disease
Parasitism

7. SECD Transmission Transmission – fecal/oral route Pig to pig Fomites
Vehicles
Feed
People

8. Epidemiology – Observational Study
Question topic
Type of Variable
Odds Ratio
p value
Interpretation
How many pelleted rations were fed to sows during the last 90 days
Continuous
0.45
0.001
When the number of pelleted rations fed to sows goes up by 1, the odds of being a case goes down 55%.
Origin of sow feed used in the last 90 days
Categorical
2.33
0.002
When sow feed was custom mixed off farm compared to being purchased complete, the odds of being a case goes up 2.3X.
What grain was mixed with in sow feed in the past 90 days.
0.44
When grain was mixed with an amino acid source, salt, calcium, phosphorus and a premix in sow feed compared to only an amino acid source and a base mix, the odds of being a case goes down 56%
How many meal/mash rations were fed to nursery pigs during the last 90 days
1.65
0.05
When the number of meal/ mash rations fed to nursery pigs goes up by 1, the odds of being a case goes up 65%.
How many meal/mash rations were fed to finishers during the last 90 days
1.51
0.004
When the number of meal/ mash rations fed to finishing pigs goes up by 1, the odds of being a case goes up 51%.
Total number of rations fed to finishers during the last 90 days
1.36
0.04
When the total number of rations fed to finishing pigs goes up by 1, the odds of being a case goes up 36%.
What grain was mixed with in finisher feed in the past 90 days.
0.50
<0.001
When grain was mixed with a supplement in finisher feed compared to with an amino acid source and a base mix, the odds of being a case goes down 50%
Contents of premix in the most recent finisher diet
3.50
0.02
When vitamin and trace mineral premix was in the same premix in the most recent finisher diet the odds of being a case goes up 3.5X.

9. Epidemiology – Experimental Study
Cluster, in space and time, of PEDv positive
production sites
Three different companies owned the sites
Hypothesis of airborne spread was tested by air sampling
Distance from known PEDv positive site
Number of PCR positive samples/Number of samples collected
30 ft
0/1
60 ft
3/6
300 ft
0/6
¼ mile
0/5
½ mile
1/5
1 mile
3/13
2 miles
0/4
3 miles
3/7
5 miles
0/8
10 miles
1/3
15 miles

10. Epidemiology – Experimental Study
A hotspot analysis (Getis-Ord Gi*) was
performed to identify statistically
significant geographic clusters of
positive PEDv cases.
A neighborhood search radius of 11.5
miles was selected for this cluster
analysis based on the results of the
Global Moran’s I statistic.
The resulting surface shows geographic
areas with significant clusters of
positive sites in red and areas without
significant clustering of positive sites
in blue.

11. Epidemiology – Experimental Study

12. Epidemiology – System/herd investigations
Investigations are being conducted on operations that are isolated geographically, have no known link to other PEDv positive operations, experienced simultaneous clinical signs in multiple sites within a distinct system or for other epidemiologically significant reasons.
The objectives of these investigation are:
To investigate the potential pathways of introduction of the virus into the system. This objective requires completion of a standardized investigation form and in most cases a personal interview with the person most knowledgeable about the practices and procedures of the operation and a site visit.
To assess the current biosecurity practices on the operation and to determine their role in the initial introduction of virus or in the spread of virus.

13. Investigation Results
Two investigations with feed the most likely introductory pathway (spray dried plasma implicated and feed pellets implicated)
One investigation with pig additions most likely (very small scale producer)
Three investigations with biosecurity breaches most likely (large, highly integrated systems

14. Initial Response Nonregulatory No mandatory reporting
No movement controls
Epidemiological studies to investigate inter-herd transmission
Epidemiological investigations and assessments to discover introductory pathways
Industry and Academia led research efforts to understand viral ecology and disease dynamics

15. National Animal Health Laboratory Network Accession Reporting

17. Federal Order
Impact of disease called for greater Federal and State role
Required reporting allows:
Determination of disease incidence
Improved tracking of disease spread
Rapid detection of new viruses
From: National Hog Farmer, August 2013

21. EMRS LMS SCS MIM COGNOS® Ag Connect® USDA FIREWALL 3rd
Purpose: Query/Report Results
User: VS area offices
COGNOS®
IBM Cognos®
Business Intelligence
EMRS
Emergency Management Response System
Purpose: Response system to collect and manage resources, disease mitigation data
and operations activities
Users: IMTs, AVIC and state animal health officials.
Customer: NCAHEM
Users: VS area offices
Owner: APHIS IT
Purpose: Visualizing data and providing a common operating picture
User: APHIS National Incident Coordinator, NAHLN
Viewers: IMTs; AVICs, SAHO, Industry
Owner: IIAD
LMS
Laboratory Messaging System
Ag Connect®
ERSS, BFES, LCEM, BCOP
Purpose: Messaging
lab results
Users: Field disease diagnosticians
Owner: NVSL / NAHLN
LMS - Centralized repository for laboratory test results
Accepts HL7 electronic results to support any VS program or animal health emergency
Interim Spreadsheet Uploader solution for non-messaging entities
Accessible to surveillance analysts using SQL tools
Integration through web-services with existing VS epidemiological data systems (EMRS 2.0, SCS, VSLS)
Purpose: Collecting surveillance data from 3rd party providers
Users: State and VS animal health officials
SCS
Surveillance Collaboration Services
3rd
Purpose: System for sharing surveillance data
Users: State and Fed animal health officials
Owner: APHIS VS IT
USDA FIREWALL
MIM
Mobile Information Management
Purpose: Collecting surveillance data on a PDA
Users: Field disease diagnosticians
Owner: APHIS VS IT

22. Herd Management Plans
Required for herds meeting the definition of a confirmed positive
Developed with a veterinarian
Include biosecurity measures

24. Funding $26.1 million including: $3.9 million for vaccine development
$2.4 million for laboratory testing
$1.4 million for sequencing
$11 million for biosecurity support

25. Epidemiology Pathways of introduction being examined:
Intentional introduction
Circulating in Feral swine
Clothing/shoes contaminated on trip to China
Human nasal passages
Escape from laboratory or diagnostic sample
Contaminated biological
Antibiotic filler; e.g., rice hulls
Pet food/treats used in swine rations
Vitamin/mineral premixes
Amino acid supplements
Complete feed swine base mixes/premixes
* A major focus of APHIS since the start of 2014 has been on identifying the root cause of SECD virus introduction into the U.S. The pathways listed here either are currently or have been investigated as the source of virus into the U.S. A team of APHIS epidemiologists have been conducting this very detailed work. We intend on writing a preliminary report of the findings in the next few months and once all leads have been followed out to there logical end a final report of the findings will be written. 25

26. Information and Resources
National Pork Board
Website:
American Association of Swine Veterinarians
Website: aasv.org
USDA, APHIS, Veterinary Services
Website: aphis.usda.gov