Swine Enteric Coronavirus Diseases

Brian J. McCluskey, DVM, MS, PhD, Dip. ACVPMChief EpidemiologistUSDA, Animal and Plant Health Inspection Service, Veterinary Services

Secreatary’s Advisory Committee on Animal HealthApril 2015

Novel Swine Enteric Coronaviruses

Porcine Epidemic Diarrhea virus (PEDv)

Porcine deltacoronavirus (PDCoV)

Picture from Wikipedia of Corona Virus

PEDv History

1969 - Large outbreaks in European swine herds Diarrhea associated with weaning or feeder pigs

▪ Suckling pigs not always affected 1976 - Affecting swine of all ages 1978 - Coronavirus-like agent was identified as

cause - Porcine Epidemic Diarrhea Virus 2010-2012 – Outbreaks of high morbidity and

mortality in China Distribution:

Asia, Canada, Columbia, Dominican Republic, Europe, United States

From: Huang et al., mBio 2013

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 50-80+%.

▪ 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

SECD Differential Diagnosis

Differentials TGE (coronavirus) Rotavirus Other bacterial

diarrheal disease Parasitism

SECD Transmission

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

Epidemiology – Observational Study

Question topicType of Variable

Odds Ratio

p value

Interpretation

How many pelleted rations were fed to sows during the last 90 days

Continuous 0.45 0.001When 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 0.002When 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.

Categorical 0.44 0.002

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

Continuous 1.65 0.05When 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

Continuous 1.51 0.004When 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

Continuous 1.36 0.04When 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.

Categorical 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

Categorical 3.50 0.02When 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.

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 0/4

Epidemiology – Experimental Study

A hotspot analysis (Getis-Ord Gi*) wasperformed 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.

Epidemiology – Experimental Study

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.

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

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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

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National Animal Health Laboratory Network Accession Reporting

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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

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Users: VS area offices

Owner: APHIS IT

Ag Connect®

ERSS, BFES, LCEM, BCOP

COGNOS®IBM Cognos®

Business Intelligence

USDA FIREWALL

Purpose: Response system to collect and manage resources, disease mitigation dataand operations activities Users: IMTs, AVIC and state animal health officials.Customer: NCAHEM

Purpose: Visualizing data and providing a common operating pictureUser: APHIS National Incident Coordinator, NAHLN Viewers: IMTs; AVICs, SAHO, IndustryOwner: IIAD

Purpose: Collecting surveillance data on a PDAUsers: Field disease diagnosticians Owner: APHIS VS IT

Purpose: Messaging lab resultsUsers: Field disease diagnosticians Owner: NVSL / NAHLN

Purpose: Query/Report ResultsUser: VS area offices

Purpose: System for sharing surveillance dataUsers: State and Fed animal health officialsOwner: APHIS VS IT

LMSLaboratory Messaging

System

EMRSEmergency Management

Response System

SCSSurveillance

Collaboration Services

MIMMobile Information

Management

Purpose: Collecting surveillance data from 3rd party providersUsers: State and VS animal health officials3rd

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Herd Management Plans

Required for herds meeting the definition of a confirmed positive

Developed with a veterinarian

Include biosecurity measures

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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

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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

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Information and Resources

National Pork Board Website: www.pork.org

American Association of Swine Veterinarians Website: aasv.org

USDA, APHIS, Veterinary Services Website: aphis.usda.gov