Drs. Jeff Zimmerman & Rodger Main - Evolution of Biosurveillance

Evolution of Biosurveillance

Rodger Main and Jeff ZimmermanIowa State University

Ames, Iowa

Why talk about surveillance?

2009 pH1N1 … "swine flu"

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Surveillance = data based on testing.

Serum Feces Tonsil0%

20%

40%

60%

80%

100%

18%36%

55%9%

18%

27%

Percentage of positive sows

Clinically affetcted Clinically normal

Sows: % Senecavirus A rRT-PCR-positive 11 sows with SVA lesions 11 clinically normal sows

Clinically affected Clinically normal

Serum Feces Tonsil

Courtesy of Dr. Pablo Piñeyro

Serum Feces Tonsil0%

20%

40%

60%

80%

100%

33% 33% 33%

18%36% 27%

Percentage of positive piglets

Clinically affetcted Clinically normal

Courtesy of Dr. Pablo Piñeyro

Piglets: % Senecavirus A rRT-PCR-positive

Clinically affected Clinically normal

Serum Feces Tonsil

How to make surveillance work? (fast, accurate, affordable, practical)

How to make it work?

• Federal-State-Industry partnership– Long-recognized fact.

• GAO-15-664T (July 8, 2015)– Resources that constitute a national biosurveillance capability are

largely owned by nonfederal entities.– Strengthen and leverage nonfederal partners … to build and maintain

national biosurveillance capability.

How to make surveillance work? (fast, accurate, affordable, practical)

… in a Fed-State-Industry partnership … ?

"Start where you are, with what you have."George Washington Carver

VDL 1 VDL 2 VDL 3 VDL 4

Centralized Database

"Start where you are, with what you have." GWC

Anticipate the need for testing capacity …UMN (FY 2012) 1,374,925 tests runSDSU (FY 2013) 400,292 tests runISU (2013) 1,128,455 tests run

VETS VISIT FARMS → Dx SAMPLES SENT TO VDL → Dx RESULTS SENT TO VETS

Shared Database

VDL 1 VDL 2 VDL 3 VDL 4

VETS VISIT FARMS → Dx SAMPLES SENT TO VDL → Dx RESULTS SENT TO VETS

VDL 1 VDL 2 VDL 3 VDL 4

Shared Database

Coordinated Emergency Response

VETS VISIT FARMS → Dx SAMPLES SENT TO VDL → Dx RESULTS SENT TO VETS

"Start where you are, with what you have."

• On the farm … – Vets know the producers, the pigs, the farms. – Vets know how to collect and deliver samples to

the VDLs quickly.• The VDLs …

– Know how to receive, process, and test massive numbers of specimens.

– Know how to manage huge databases & deliver results quickly.

We have an unprecedented opportunity to create an effective surveillance system.

Things to think about, bumps in the road, hurdles, etc. etc.

• So who will collect the samples?– Federally-accredited, swine specialist vets (AASV) and others under their

supervision– "mission of the National Veterinary Accreditation Program is to ensure the health

of the … animal population and to protect the public health and well-being."`

Collecting samples in the U.S. classical swine fever eradication program ~1970

What sample will they collect?

• The specimen "most fit for purpose"– Screening? For detection = oral fluids– Confirmation/follow-up? Individual pig samples – Pre-movement? Individual animal samples

ISU - VDL - oral fluid tests:• 2010 - 10,231

• 2011 - 32,591

• 2012 - 60,034

• 2013 - 94,101 • 2014 - 146,831

• 2015 - ~175,000 TOTAL 518,788

Our vets & producers know oral fluids.

Continual test assessment & improvement

Oral fluids … sensitive screening sample for antibody- and nucleic acid-based assays

PRRSV Prevalence

Pigs(+/total)

ONE Oral Fluid SAMPLE probability of detection

Sample size to match OF probability of detection

4% 1/25 15% Bleed 4 pigs12% 3/25 45% Bleed 5 pigs20% 5/25 75% Bleed 7 pigs36% 9/25 95% Bleed 8 pigs

Olsen et al. 2013. Probability of detecting PRRSV infection using pen-based swine oral fluid specimens as a function of within-pen prevalence. J Vet Diagn Invest 25:328-335

What tests will we run?

• For FADs, options very limited. PCRs on selected samples e.g., CSFV - tonsil, tonsil scrapings, nasal swabs.

• Repertoire of tests & samples must be expanded. • Fed-State-Industry partnership USDA retains

ownership of tests and test results

What tests will we run?

• Commercial kits. (Fed-State-Industry)• High through-put.• Robust technology.• Reproducible/repeatable.• Accurate. Dx specific.

CONTINUAL TEST ASSESSMENT/IMPROVEMENTPigs inoculated with ALD strain CSFV.Dr. Y Panyasing, Chulalongkorn University

VDL 1 VDL 2 VDL 3 VDL 4

Centralized Database We have an unprecedented opportunity to create an effective surveillance system

VETS VISIT FARMS → Dx SAMPLES SENT TO VDL → Dx RESULTS SENT TO VETS

Evolution of Biosurveillance

Rodger Main and Jeff ZimmermanIowa State University

Ames, Iowa

HPAI Spring 2015

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300ISU VDL AIV PCR Cases by Week

H5 Positive Cases

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ISU VDL AIV H5 Positive Cases by Week

Diagnostic Case Submissions ≠ Number of Infected Premises {10 week HPAI Outbreak in IA}

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0100200300400500600700800900

1000110012001300

ISU VDL AIV PCR Tests by Week H5 Positive Tests

Negative Tests

{4 months sustained response at VDL}

Summary HPAI Infected Premises• 35 Commercial Turkey Farms• 22 Commercial Table Egg Layer Farms• 13 Commercial Table Egg Pullet Farms• 1 Commercial Breeder Flock• 5 Backyard Producers• 1 Commercial Mail Order Breeder Operation

• Total = 77 HPAI Infected Premises

Data courtesy of:Dr. David Schmitt, State VeterinarianIowa Department of Agriculture and Land Stewardship

2015 Iowa Affected Poultry

Data courtesy of:Dr. David Schmitt, State VeterinarianIowa Department of Agriculture and Land Stewardship

Core Elements of FAD Preparedness at VDL(Remained same as identified during PEDV)

• Competent Personnel & Robust VDL Systems• Validated Assays• High-Throughput Testing Platforms• User Friendly & Effective Sample Types• PINs on VDL Records• Automated Electronic Messaging of Results

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 High-Throughput & Sensitive Assays User Friendly & Effective Sample Types Testing Capacity Turn-around Time Quality of Information in VDL Record

• Complete, Consistent, Traceable, Fit for Digital Transmission

AIV Diagnostic Record Information Flow

Submitter(Producer)

VDL Receiving / Case Entry

State & FederalPrimary Points of Contact

VDL LIMSLab Information

Management System

USDALab Messaging Service

State & Federal OperationsEMERS

Emergency Management Emergency Response System

Human Readable Digital Code

5 W’s = Who, What, When, Where, and Why

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

Manual Transcription of PINs Doesn’t Work!• O80DS6G, 1O8SG60, B0GD6O1, 0OD71G5, O71G6D0,

5S0D61O, O80DS6G, 1O8SG60, B0GD6O1, 0OD71G5, O71G6D0, 5S0D61O, O80DS6G, 1O8SG60, B0GD6O1, 0OD71G5, O71G6D0, 5S0D61O, O80DS6G, 1O8SG60, B0GD6O1, 0OD71G5, O71G6D0, 5S0D61O, O80DS6G, 1O8SG60, B0GD6O1, 0OD71G5, O71G6D0, 5S0D61O,006DO17, D176S501, 001SD6S, O80DS6G, 1O8SG60, B0GD6O1, 0OD71G5, O71G6D0, 5S0D61O, O80DS6G, 1O8SG60, B0GD6O1, 0OD71G5, O71G6D0, 5S0D61O, O71G6D0, 5S0D61O, O80DS6G

1 Day, 1 VDL, (Submitter and Case Entry Staff)≈ 350 Cases or 700 Transcriptions of PINs / Day

Our Conclusion or “Litmus Test”

Can You “Scan It” or “Click On It” ?

If Yes = It Works (Repeatable, Connected, Automation)

If No = It Doesn’t Work (Inconsistent, Manual Data Transfer)

Diagnostic Record Information Flow

SubmitterVDL Receiving /

Case Entry

Human Readable Digital Code

• Premises Level Data On VDL Submission Form Case Entry• Completeness• Consistency• Traceability• Connectivity

Katie WoodardClient Outreach/Education

Less More

X

Front-end of Diagnostic Process

ISU VDL IT Team

Sustained Responses to Large-Scale Emerging Disease Events: “Real Life Is Not A Drill”

Baseline Stakeholder Expectations of VDL’s

• Competent VDL Personnel & Infrastructure• Quality Assays & Test Results• Turn-Around-Time (Same Day/Next Day)• Electronic Distribution of Results• Cost Effective Service• Protect & Sustain Continuity Their Business (All consistent with the mission of the NAHLN)

Serving Food Animal Agriculture Comprehensive Diagnostic Service, Teaching, and Discovery

(Iowa’s only Full-Service & Fully Accredited Veterinary Diagnostic Laboratory)

Processing > 70,000 cases/year from livestock producers for across USApplying world-class technology to solve real-world problems

Network of Interdependent Relationships to Improve & Protect Food Animal Agriculture

Food

AnimalAgriculture Consumer

GeneticsFacilities / Environment

Nutrition

HealthManagement

Business / Finance

Practicing Veterinarian

VeterinaryDiagnostic

Labs

Production AnimalMedicine

SuppliersOf Health Products

Producer

Pathology Virology

Bacteriology Serology

ToxicologyPharmacolog

yEpidemiology Parasitology

State and Federal VeterinaryOfficials & Agencies Strategic Alliances → Service, Innovation, & Teaching

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

Highly Collaborative Journey

Southeast IA North AmericaMB-MO (Princeton)

Pilot Project Participants

Information Mgt Technology

Peer VDLs

B. Martinez, Z. WhedbeeA. Perez (UMN)

R Main, B. Crim, K. Mueller, K Woodard, J Bjustrom-KraftIT Team

D. Polson, E Lowe, E Mondaca

$

(HIMS) (HIMS) (NAHLN) (Data Standards)

Objective• Link VDL submissions, corresponding

test results, attending veterinarian insight, and an interpreted health status of farm sites to a highly capable spatiotemporal disease management tool for use in area-regional, veterinary clinic, or production system swine health monitoring and control initiatives.

Desired Outcome

• Provide User-Friendly System for Monitoring Health Status of Swine Herds Overtime– Individual Farm or Operation– Production System– Veterinary Practice – Area-Regional Project

Working on Both Ends & Everywhere in Between

# 1

# 2

# 6

# 3

# 5

# 4

Front End

• Transcend Quality of VDL Records into Digital Era

“Electronic transfer of premises level identifiers (PINs) on VDL submission form”

VDL’s Efforts to Improve Quality of VDL Record(Completeness, Consistency, Traceability, Connectivity)

• Provide clients two options to transcend quality of VDL records in to digital era.

1. Web-Submissions2. Premises Specific Bar-Code Labels

Both options:* Result in electronic transfer of the full complement or premises or site level identifiers.

Middle

• Diagnostic Data Standards (PRRS, PEDV, PDCoV, M hyo, SIV)• Rules Based Algorithms For Assigning Status / Classification • Web-Based Database Application (SAHDD)

• House Participant Premises Level Data (Pre-Populated)• Receive and Interpret (VDL Cases Results & Attending Vet)• Assign Status & Classification• Archive Data• Push to 3rd Party Database Application (BioPortal) for Analysis & Reporting

B Crim

K Mueller

J Bjustrom-Kraft

Back End

• Web-Based Database Application (Disease BioPortal)• Spatiotemporal and Bionformatic Analysis and Reporting• Update Structure, Design, & Capabilities of Database• Create Reporting Functionality Applicable to Swine Health Monitoring

• Health Status & Classification of Herds Over Time• Sequencing Analysis ( Monitor Various Strains / Variants)

B Martinez Z Whedbee

D Polson E Lowe

E Mondaca

Synergistic Collaborations

Where We Are Today• Ensure VDL Record “Fit” for Digital Era

ISU VDL Web-Portal (last updated, 11/04/2015)– Web-Submissions (Electronic)– Site-Specific Bar-Codes (Paper)

• SAHDD (Secure Animal Health Diagnostic Database)– Receives Input (VDL Case Results & Veterinarian Input)– Interprets Case Results– Assigns Health Status to Case and Site (By Pathogen)– Assigns Health Classification to Site (By Pathogen)– Archives & Push to Disease BioPortal

• Disease Bioportal – Data Analysis & Summary

• Advanced Spatiotemporal & Bioinformatic Analysis Capabilities – User Group Defined Dashboards – Site Specific and/or Aggregate Data Capabilities

All Components Web-Based, Permissioned Access

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

Next Steps• Transition Development Service in 2016

– Initially offering & operating service as a “Bureau”• Deliver a “Viewable Product”

– Client Specific Dashboards (Disease BioPortal)– View Only Access to SAHDD

SAHDDAccount Manager

Vet Clinic“ABC”

Genetic Company

“XYZ”

ARC Project“SE IA”

Production System“DEF” Disease BioPortal

Client Specific Dashboards

SAHDDClient SpecificPremises Level

History

Permission Users(Clients)

View Only

Summary – Evolution of Biosurveillance

• Risks, Gaps & Opportunities for Improvement• Systems of Surveillance Need to Evolve

– Federal, State, & Industry Partnerships

• Address the Obvious & Put into Routine Practice – Assays, High-Throughput Platforms, Traceability, & IT– Continuity of Business Programs

• Emergency Preparedness ?? → Routine Practices• Progress on New Tools For Private Sector Applications

* Early Stages - Dawn of New Age for Animal Health Information Management

Evolution of Biosurveillance

Rodger Main and Jeff ZimmermanIowa State University

Ames, Iowa

Thank You ! Questions ?