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

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 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

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 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.

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

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.

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

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

National Animal Health Laboratory Network Accession Reporting

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

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

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

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

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

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