Swine Health Trends from ISU Vet Diagnostic Lab - Dr. Rodger Main, Iowa State University; Dr. Pablo Pineyro, Iowa State University, from the 2017 Iowa Pork Congress, January 25-26, Des Moines, IA, USA. More presentations at http://www.swinecast.com/2017-iowa-pork-congress

1. Observations, Updates,
and Trends From ISU VDL
Iowa Pork Congress
January 26, 2017
Dr. Rodger Main
Professor and Director
Dr. Pablo Pineyro
Asst. Professor and Diagnostic Pathologist

2. Outline
• Main
– Introduction & General Updates on VDL
– Trends in PEDV and PRRSV at National Level
• Pineyro
– Case based observations and trends
– Swine Disease Topics of Interest
– Senecavirus A

3. ISU-VDL is part of the ISU College of Vet Med

4. ISU-VDL  Who we are Today
• Total ≈ 145 People
– 25 Faculty
– 120 Technical Staff
• Full Service &
Fully Accredited Laboratory
• Veterinary Diagnostic Medicine
– Pathology
– Virology and Molecular Dx
– Bacteriology
– Serology/Immunology
– Toxicology & Nutrition
– Clinical Pharmacology
– Epidemiology
– Information Management Technology

5. Veterinary Diagnostic Laboratory
Iowa State University
Preeminent Food Animal Veterinary Diagnostic Laboratory
Comprehensive Diagnostic Service, Teaching, and Applied Research
– Create = New Knowledge & Capabilities
– Share = Students, Practitioners, & Stakeholders
– Apply = Providing World Class Diagnostic Services
Tripartite Mission – Consistent with Land Grant University

6. Network of Interdependent Relationships to
Improve & Protect Food Animal Agriculture
Food
Animal
Agriculture
Consumer
Genetics
Facilities / Environment
Nutrition
Health
Management
Business / Finance
Practicing
Veterinarian
Veterinary
Diagnostic
Labs
Production
Animal
Medicine
Suppliers
Of Health
Products
Producer
Pathology
Virology
Bacteriology
Serology
Toxicology
Pharmacology
Epidemiology
Parasitology
State and
Federal
Veterinary
Officials &
Agencies
Strategic Alliances → Service, Innovation, & Teaching

7. Serving Food Animal Agriculture
Comprehensive Diagnostic Service, Teaching, and Discovery
(Iowa’s only Full-Service & Fully Accredited Veterinary Diagnostic Laboratory)
Processing > 75,000 cases/year from livestock producers for across US
Applying world-class technology to solve real-world problems

8. ISU VDL Diagnostician receives the case
from the local veterinarian
Select diagnostic tests based on
history and gross lesions
Results coordinated to
arrive at a diagnosis
Bacteriology VirologyToxicology
& Nutrition
Serology
Transmit diagnosis to and assist local veterinarian with intervention
strategies and establishment of best practices
Molecular
Diagnostics
Histopathology Clinical
Pharmacology

9. ≈ 75% Swine, 10% Bovine, 10% Poultry and 5% Everything Else

10. Veterinary Diagnostic Laboratory
Iowa State University
Distribution of ISU VDL’s ≈ 80,000 Cases Accessions Last Year
95% of Diagnostic Services → Food Animal Agriculture

11. Location of Pigs in the US

12. New VDL
Infrastructure
Capital Project
(2017 Session)

13. Capital Project Overview
• New VDL ≈ ↑ Space 60,000 to 83,000 square feet
• Repurposing ≈ 27,500 square feet of current facility repurposed for
College of Veterinary Medicine research and teaching purposes
• $124 M = $100 M (State of IA) + $24M Donor & University

14. VDL 1974 ≈ 10 Faculty & 20 Technical Staff
ISU VDL Facility Infrastructure
Designed in 1973-74 and Populated in 1976
Located within the CVM Building

15. Present Day ≈ 25 Faculty & 120 Technical Staff

16. “Enhance the Quality and Connectivity of VDL Record”
• Consistent
• Complete
• Traceable
• Fit for Digital Era (Incoming & Outgoing)

17. What could VDL improve its role
in support HPAI preparedness / response ?
Early Detection, Rapid Response, &
Effective Communication (Seamless, Timely, Clear)
 Competency of Personnel & VDL Systems
 Quality of Test & Results
 Sensitivity of Assay
 Testing Capacity
 Turn-around Time
 Quality of Information in VDL Record
• Complete, Consistent, Traceable, Fit for Digital Transmission
````

18. Observation at VDL
• Manually Entered Premises Level Identifiers
(Farm Site Information) Are Not Compatible With
Web-Based Data Management Applications
• Need To Transcend VDL Records Into Digital Era

19. Sustained Responses to Large-
Scale Emerging Disease Events:
“Real Life Is Not A Drill”
Preparedness is best defined by the systems used and
practices implemented in-mass on a daily basis.
Fantasy
Island

20. Electronic Submissions
Omission of Submission Fee on Qualifying Web
or Electronic Submissions, Effective, July 1, 2016
Objective = Improve Quality of Veterinary Diagnostic Record & its Fitness for Digital Era

21. Electronic Submission Tool
• Create New Web Submissions
• Create, Manage, Use Submission Templates
– Recurring Test Requests, Instructions, Affiliations, Bill Party
• Pending Web Submissions
• Client Specific = Library of Owner & Sites
• Web or Paper-Based Submissions
• Web-Submissions Editable Until Received @ VDL
All Customizable Functionality in Hands and Control of VDL Client

22. ≈ 10X increase in web submission since Jan 2015
Web = 50% of Swine Submissions in Dec 2016
≈ 100% of Web-Submissions Have
Correct Site Info & PINS

24. Web Submssion ID #

25. Electronic (E) – Forms For Use On Paper-Based Submissions

26. Daily Summary Report
Launched October 2016
Mobile-Friendly Summary of
All Open & Active Cases

27. Hyperlink to
Full Case Report

29. Tool To Forward
Any Individual Case
via E-Mail
Within Client’s
E-mail Browser

31. My Profile & Reporting Preferences
• Access through Client Web Portal
• Enables VDL Clientele to Actively Manage:
– Clinic & Veterinarian’s Contact information
– Reporting Preferences
• Daily Summary Report
– Who, When, & How Often

32. Single point of contact within a clinic can manage the information
& preferences for all the veterinarians associated with their practice.

33. Clinic Preferences
(All Cases From Clinic)
“Vet A Preferences”
(Only Vet A Cases)
“Vet B Preferences”
(Only Vet B Cases)
“Vet C Preferences”
(Only Vet C Cases)
←
←
←
←

34. Continue to Improve VDL Web Reporting Tool

35. Two New Features VDL Web Reporting
* E-mail live link to dynamic case report
* Submit additional test requests

36. Mobile Friendly Version of VDL Client Portal
(Results & Submissions)
Coming
In
2017

37. Swine Diagnostic Data Standardization Project
Rodger Main - ISU VDL
Gary Anderson - KSU VDL
Jane Hennings – SDSU ADRDL
Jerry Torrison & Stephanie Rossow – UMN VDL
Sarah Tomlinson – USDA NAHLN
* Mike Martin – Clemson University
$716,000; 15 month, Infrastructure Development Project
Funded via Swine Health Information Center & USDA
Commenced fully in July 2016
* Dr. Martin is providing the primary technical guidance and support to this project. Mike
is a nationally recognized leader and expert in veterinary diagnostic informatics and HL-7 messaging.

40. 1 Monitoring Health Status of Swine Farms Overtime
(Operation, Production System, Clinic, or Area-Regional Level)
2 Health Status = Qualitative, Quantitative, and/or “Strains” Active

41. Swine Diagnostic Data
Standardization Project
Developing infrastructure to help harness the capabilities the
digital age will have to offer for years to come
Interstate Construction, 1958 Current Day

42. Link to on-line report on AASV Web-Site
VDLs

43. Trends in US PEDV and PDCoV Diagnostic Data
1st US History = Diagnostic test results electronically captured from all VDLs
located throughout the US and integrated into a dynamic web-based reporting tool.

44. US Trends in PEDV PCR Diagnostic Testing Reported to USDA
Case-Level Summary of PEDV PCR Test Results from Across USA

45. US Trends in PEDV PCR Positive Cases
Case-Level Summary of PEDV PCR Test Results from Across USA

46. Enables Visualization of Trends Within Each State

47. Trends in PEDV PCR Positive Cases
in Top 4 Hog Production States

48. Trend in PRRS Outbreaks in US Herds
Swine Health Monitoring Project – University of Minnesota; Dr. Bob Morrision, et al

49. Swine Health Monitoring Project – University of Minnesota; Dr. Bob Morrision, et al
1 Positive Unstable
2 fvi Positive Stable, Ongoing field virus exposure
2 vx Positive Stable, Live virus vaccinated
2. Positive Stable
3. Provisionally Negative
4. PRRSV Elisa Negative

50. Aggregate Data Summary Applications
ISU VDL Historical PRRSV ORF5 Sequencing Data
Trends in the most prevalent field strains of
NA PRRSV RFLP Groupings and EU PRRSV

51. Trends in most prevalent NA PRRSV RFLP Groupings and EU PRRSV
Aggregate Data Summary Applications
ISU VDL Historical PRRSV ORF5 Sequencing Data

52. ISU VDL Historical PRRSV ORF5 Sequencing Data
(Top 4 Hog Production States)
Trends in most prevalent NA PRRSV RFLP Groupings and EU PRRSV (by State)




53. Cluster #1
Cluster # 2
“Survival of the Fittest”

54. Outline
• Main
– Introduction & General Updates on VDL
– Trends in PEDV and PRRSV at National Level
• Pineyro
– Case based observations and trends
– Swine Disease Topics of Interest
• PCV3
• Porcine Pestivirus
• Senecavirus A

55. Cases by system in past 20 months (DX codes)
24 months (2013-15)
System Total %
Respiratory 8032 44%
Enteric 5529 30%
Systemic 3686 20%
Reproductive 378 2%
CNS 285 2%
Arthritis 234 1%
Heart 137 1%
Skin 104 1%
Skeletal 47 0%
Grand Total 18432 100%

56. RESPIRATORY DISEASE
PRRSV
PPIV-1?

57. Swine Respiratory Pathogens
38%
26%
8% 7% 7%
3% 3% 2% 2% 2% 1% 1% 1% 0.16% 0.12% 0.07% 0.01%
0%
10%
20%
30%
40%
50%
PERCENTOFRESPIRATORYACCESSIONS

58. Number of Bronchointerstitial Pneumonia
Caused by PRRSV Diagnosed at ISU-VDL
2
0
1
0
2
0
1
1
2
0
1
2
2
0
1
3
2
0
1
4
2
0
1
5
0
5 0 0
1 0 0 0
1 5 0 0
2 0 0 0
2 5 0 0
NumberofcasesPRRSVNumberofcases/year

59. PRRSV diagnosis

60. PRRS Information
1
6
2 4 2
6
13
17
22
7
15
19
30
9
76
37
45
56 56
101
114
96
81
94
63
68
0
20
40
60
80
100
120
May Jun Jul Aug Sep Oct Nov Dec Jan Feb Mar Apr May
Qtr2 Qtr3 Qtr4 Qtr1 Qtr2
2015 2016
1-3-4
1-7-4
Total cases analyzed 1040
1-3-4 pattern: 144
1-7-4 patter: 896

61. PRRS MLV PCR
PCR - PRRSV BIVI MLV-like
Animal ID Specimen Ct / Result Comment
B, OF, Tube #2 Oral fluid >40 / Negative
Sequencing and Analysis - PRRSV
Animal ID Specimen Target Gene RFLP Comment
B, OF, Tube #2 Oral fluid ORF5 1-3-4 Wild type
Sequence Homology
Reference VirusInglevac ATP Lelystad Prime Pac Inglevac MLV Fostera
Percent Identity 84.6% 62.7% 85.4% 84.8% 85.6%
Nucleotide
ATGTTGGGGAAATGCTTGACCGCGGGTTATTACTCGCAATTGCTTTTTTTGTGGTGTATCGTGC
CATTCTGTCTTGTTGCGCTCGCCAACGCCAACAACGGCAGCAGCTCTCATTTACAGTTGATTTAT
AACCTGACGATATGTGAGCTGAACGGCACAGATTGGCTGAACGATCATTTCAGCTGGGCGGTGGA
GACTTTCGTCATCTTCCCTGCGTTGACCCACATTGTCTCTTATGGCGCCCTCACCACTAGCCATT
TTCTTGACACGGTCGGCCTGATCACTGTGTCCACCGCCGGATATTATCACAAGCGGTATGTATTG
AGCAGCATTTACGCTGTTTGTGCCCTGGCTGCGTTGGTTTGCTTCGCCATTAGGTTGGCGAAAAA
TTGCATGTCCTGGCGCTACTCGTGTACTAGATATACCAATTTTCTCCTGGACACTAAGGGCAAAC
TCTACCGCTGGCGGTCACCCGTCATCATAGAGAAGGGGGGTAAAGTTGATGTTGAGGGCCATTTG
ATTGACCTCAAAAGAGTTGTGCTTGATGGTTCCGCGGCAACTCCTGTAACCAAAGTTTCAGCGGA
ACAATGGGGTCGTCCTTAG
PCR Applied Biosystems - PRRSV
Animal ID Specimen US Ct / Result EU Ct / Result Comment
B, OF, Tube #2 Oral fluid 25.3 / Positive >=37 / Negative
PCR has primers to MLV vaccine virus
Positive indicates vaccine virus
Note:
Can’t rule out wild-type infection in
addition to vaccine virus
Slide courtesy of Dr. Darin Madson

62. PRRS Sequencing
• Can there be more than 1 PRRS isolate within a clinical sample?
• When you sequence the PCR product, which isolate do you get?
• Is the most predominate (highest titered sample) sequenced?
• Is that virus the issue?
• PRRS sequencing primers are close to MLV vaccine virus;
preferential will sequence this virus even if there are other
present
– If near somewhat equal quantities
• May need to use Next Generation Sequencing
(NGS) to determine
Slide courtesy of Dr. Darin Madson

63. New respiratory disease diagnosed
that ISU has been involved
Asymptomatic pigs reported
ISU-VDL offers PCR
PCR is based on K-State information
“We screened 300 random samples,
including nasal swabs, lung tissue or oral
fluids, and found that 6% tested positive
for the parainfluenza virus,” Hause says.
“We were also able show that the virus
replicates in the upper respiratory tract.
We then developed a serology assay to
look for antibodies to see how common
it is for pigs to have been exposed to
this, and about 50-60% of the samples
were positive. This suggests the virus did
not just arrive here or that it is in just
one area of the country.”
~ Dr. Hause

64. Palinsky et al, 2016

65. Prevalence of Porcine Parainfluenza Virus Type 1 (PPIV-1) in U.S. Swine Herds
Gauger P, Harmon K, Lin XK, Park J, Pineyro P, Welch M, Zhang JQ
33%
40%
42%
27%
0%
5%
10%
15%
20%
25%
30%
35%
40%
45%
0
50
100
150
200
250
300
350
400
IA NC IL MO IN OH NE OK VA MI MN WI AR KS PA AR TN CO SD GA KY ND
PercentPositive(%)
SpecimenCount(n)
Negatives Positives Percent Positive of Total Tested Percent Positive by State (n>100)
Iowa State University Animal Industry Report - 2017
PPIV-1 qRT-PCR Positive specimens by state

66. 98
228
311
72
36
96
85
10
37%
42%
27%
14%
0%
5%
10%
15%
20%
25%
30%
35%
40%
45%
0
50
100
150
200
250
300
350
Suckling (0-3 weeks) Nursery (3-8 weeks) Grow/Finish (8-26 weeks) Adults (>26 weeks)
PercentPositive
SpecimenCount
# tested # positive % positive
PPIV-1 Sample breakdown by age reported
Prevalence of Porcine Parainfluenza Virus Type 1 (PPIV-1) in U.S. Swine Herds
Gauger P, Harmon K, Lin XK, Park J, Pineyro P, Welch M, Zhang JQ

67. ENTERIC DISEASE
Salmonellosis

68. 22%
15%
14%
11%
8%
7%
6%
4%
3% 3% 2% 2% 1% 1% 1%
Agents of pig diarrhea: > 6 weeks of age (ISU-VDL)
Slide courtesy of Dr. Darin Madson

69. Nursery Enteric (last 3 years)
0
200
400
600
800
1000
1200
1400
Slide courtesy of Dr. Darin Madson

70. Grow-Finish Enteric (last 3 years)
0
100
200
300
400
500
600
Slide courtesy of Dr. Darin Madson

71. ISU-VDL total #of Salmonella isolates/year ISU-VDL
1354
1656
1468
2570 2628
2244
1580
1428
2084 2038
3044
1924
0
500
1000
1500
2000
2500
3000
3500
2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014
Year
Antibiotic sensitivity was performed on all Salmonella isolates used to build this chart
#ofIsolates
Slide courtesy of Dr. Darin Madson

72. Sick Pig Salmonella sp isolations
Slide courtesy of Dr. Darin Madson

73. Total cases of Salmonella cholerasuis septicemia diagnosed
201
155
93
133
63
49
35
26
21
12 14 13
0
50
100
150
200
250
2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014
#ofIsolates
Slide courtesy of Dr. Darin Madson

74. Salmonella - antibiotic resistance over the years
This information is from a on-going project and contain preliminary data.
Slide courtesy of Dr. Darin Madson

75. SYSTEMIC DISEASE
PCV3?
Porcine Pestivirus
SVA

76. A novel porcine circovirus associated with porcine dermatitis
and nephropathy syndrome and reproductive failure (PCV3)

77. A novel porcine circovirus associated with porcine dermatitis
and nephropathy syndrome and reproductive failure (PCV3)

78. A novel porcine circovirus associated with porcine dermatitis
and nephropathy syndrome and reproductive failure (PCV3)

79. Slide courtesy of Dr. Darin Madson
Congenital tremor (Pestivirus)

80. Background  congenital tremors
• Myoclonia congenital (CT)
• Repeated contractions of skeletal muscle present at/shortly
after birth that go away when piglets are sleeping
• First described ~ 90 years ago
• “Dancing pigs” in 1922
• Globally reported
• Sporadic disease
Slide courtesy of Dr. Darin Madson

81. Slide courtesy of Dr. Darin Madson

82. Background  congenital tremors
AI AII AIII AIV AV
Cause CSF
Unknown
virus
Genetic: sex-
linked
Genetic:
autosomal
Trichlorfon
% litters
affected
High High Low Low High
Mortality
Medium to
high
Low High High High
Slide courtesy of Dr. Darin Madson

83. Slide courtesy of Dr. Darin Madson

84. Pestivirus Identification
NS3 Npro
Slide courtesy of Dr. Darin Madson

85. Slide courtesy of Dr. Darin Madson

87. Sow Inoculation Study
Slide courtesy of Dr. Darin Madson

88. Porcine congenital tumors - Testing Options
• RT-qPCR available ISU-VDL
• Serum
• Central nervous system tissue
• Heart
• Lymph node

89. Idiopathic vesicular disease and neonatal mortality
associated (Seneca Virus A)

90. Introduction- Clinical Signs & Lesions
• Vesicular lesions of the snout and feet of sows, lameness
• No additional lesions found on necropsy
Canning et al. 2016.

91. Senecavirus A in neonatal pigs
Slide courtesy of Dr. Chris Rademacher
• Piglets- death of weakness, lethargy, diarrhea, hyperemia

92. Senecavirus A diagnosis

94. 0
2
4
6
8
10
12
14
#SVAPCRPositiveCases
Date by Week
Senecavirus A PCR Positive Cases by Farm Type
Sow Growing Pig Unknown/Other
Slide courtesy of Jordan Kraft

95. What is the serological prevalence in U.S.
herds?

96. S o w s
2 8 .9 5 % P o s itive
7 1 .0 5 % N e g a tive
T o ta l= 1 9 8 6
P ig le ts
1 4 .2 3 % P o s itive
8 5 .7 7 % N e g a tive
T o ta l= 3 9 7 1
Total Prevalence
Seroprevalence results
Between Farm Prevalence
Sows
80.00% Positive
20.00% Negative
Total=75
Piglets
61.81% Positive
38.19% Negative
Total=144

97. http://www.drodd.com/images13/blank-us-map28.png
0/0
0/0
0/0
0/0
0/0
0/0
62/155
40%
0/29
0%
0/0
0/0
0/0
0/0 0/0
1/29
3%
28/55
51%
3/25
12%
30/50
60%
0/29
0%
16/60
27% 13/101
13%
23/184
12%
0/0
0/0
0/0
16/145
11%
157/391
40%
4/31
13%
57/125
45%
0/0
0/0
0/0 0/0 0/0
0/0
0/0
34/293
12%
0/30
0%
0/0
51/252
20%
0/0
0/0
0/0
0/0
0/0
0/0
Seroprevalence in adult pigs by state. Positive/total (percentage)

98. Seroprevalence in grower and fattener pigs by state.
Positive/total (percentage)
http://www.drodd.com/images13/blank-us-map28.png
0/0
0/0
0/0
0/0
0/0
0/30
0%
0/0
0/0
0/0
0/0
27/109
0/0 0/0
0/30
0%
0/0
24/379
6%
54/225
24%
22/85
26%
8/88
9%
4/72
6%
118/675
17%
20/104
19%
0/0
0/0
2/77
3%
41/695
6%
59/282
21%
14/457
3%
0/0
0/0
0/0 0/0 0/0
0/0
0/0
12/197
6%
54/406
13%
0/0
0/0
0/0
0/0
0/0
0/0
0/0
0/60
0%

99. • Increment in cases of Idiopathic Vesicular Disease
associate with the presence of SV-A in show and
finisher pigs
• Increment in cases of PWM associated with Idiopathic
Vesicular Disease in sow and associate with the
presence of SV-A
• We identified a new SV-A contemporary strain
genetically different from the historical SV-A US strain
• We determine the serological prevalence of SVA in sow
herds and finisher farms
Summary

100. • Viral mutation origin
• Host-pathogen interaction
• Predisposing factors
• Clinical, serological and viral prevalence
• Viral persistence in the environment
• Viral inactivation
Questions to be answered

101. Questions?
Thank you for your attention

103. Observations, Updates, and Trends
From ISU VDL
Thank You
&
Questions
Dr. Rodger Main
Professor and Director
Dr. Pablo Pineyro
Asst. Professor and Diagnostic Pathologist