2016 National Institute of Animal Agriculture Swine Health Update
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The document provides an overview and update on swine health surveillance programs conducted by the USDA Animal and Plant Health Inspection Service Veterinary Services. It discusses various swine disease surveillance streams including for pseudorabies virus, swine brucellosis, and the Swine Health Protection Act. It also summarizes fiscal year 2015 testing data and regional reports for different swine influenza virus subtypes and comprehensive integrated surveillance activities for various foreign animal diseases.
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2016 National Institute of Animal Agriculture Swine Health Update
- 1. National Institute of Animal Agriculture Kansas City, 2016 Swine Health Update Presented by Troy Bigelow John Schiltz Troy Bigelow John Korslund Ellen Kasari Swine Health Staff U.S. Department of Agriculture Animal and Plant Health Inspection Service Veterinary Services April, 2016 Veterinary Services
- 2. Overview • Programs – PRV – SB – SHPA • CIS Activities – SECD – Influenza – CSF – ASF/FMD – PRV/SB • Other Swine Activities – Seneca Valley Virus – NLRAD/Emerging Diseases 2
- 3. Comprehensive Surveillance • What is Comprehensive Integrated Surveillance (CIS)? – CIS is a standardized data collection and information management approach that facilitates designed sample targeting in response to multiple and evolving swine health information needs. • October, 2013 -USAHA resolution update of Comprehensive Integrated Surveillance in Swine (CISS) activities on implementing surveillance through appropriate surveillance streams and results. 3
- 4. CIS Principles • Comprehensive Integrated Surveillance (CIS) is an approach to animal disease surveillance that focuses on or allows: – cost-efficiency – targeted surveillance in appropriate streams. – contains an ongoing evaluation and improvement process that allows VS to increase or decrease surveillance for new and emerging diseases as well as existing endemic diseases, – flexibility to expand or contract surveillance streams based on current surveillance needs. 4
- 5. Programs- CISS • PRV – 2003 Program Standards still apply – Surveillance for PRV is very important for rapid detection and demonstration of freedom • Diagnostic Lab (NAHLN) submissions are KEY component (Practitioner submitted samples) • High Risk swine identification/testing for PRV – Testing on farms – Markets – Garbage Feeders, • Provide information on Feral swine to producers – Feral swine remain a risk for PRV-approx. 15-20% positive (varies on year) 5
- 6. Programs-CISS • PRV – Demonstration of Freedom • Sow Boar Testing – Annual reports still rely on 5% of State’s breeding population » Testing at KY laboratory » Movement testing, high risk testing and other testing can count towards the 5% » Analyzing this stream for reduction opportunities. – Findings FY15 • High Risk testing identified 1 transitional herd in TX in 2015-Depopulated 6
- 7. Programs-CISS • PRV – Market Swine surveillance • Tested 7,228 animals in 2015 – Represents 7 states with IA being 75% • Stream targets healthy animals • 5 plants one day a week • Not effective for rapid detection • Does not Impact CISS • VS plans to cease activity and will re-establish as when need emerges 7
- 8. • PRV FY15 testing data 8 Surveillance Stream Fiscal Year 2015 Diagnostic Laboratory Serologic Submissions 27679 swine from 3002 herds Cull Sow-Boars at Slaughter 210643 Market Swine at Slaughter 7228 Feral Swine 3063 Swine Cases Highly Suspicious for PRV 0 Total 248613
- 9. Programs-CISS • Swine Brucellosis – SB UM & R still applies • Collecting on 5% of State’s breeding population – Testing at KY laboratory – Movement testing, high risk testing and other testing can count towards the 5% – Feral swine remain a reservoir – Future plans include: • Analyzing SB surveillance activities and needs. 9
- 10. • Swine Brucellosis Testing FY15 – Cull sow/boar- 210,643 – Feral- 3,051 • Continue to identify non-negatives needing trackback – two transitional herds identified in FY15 SB 10
- 11. Programs • Swine Health Protection Act (9CFR 166) – Inspections • Work with States to determine primary enforcement/inspection activities (who is doing the work) 11
- 12. FY15 SHPA Activities • 27,754 Searches for Non-licensed feeders • 44 non-licensed feeders identified • 10,369 licensed premises • 531 licenses issued • 4891 inspections of licensed premises • 642 temperature checks 12
- 13. Surveillance • CSF – Collection of high risk samples is necessary from designated states – Collection of tonsils/tonsil swabs from high risk swine – Garbage Feeder swine • When doing investigations: – If swine have symptoms of CSF, test per FAD guidelines – If there is a dead pig present, sample for CSF by taking tonsil and tissues and submit for surveillance – Swabs for PCR testing are also important – Remember CSF, ASF, FMD can all be spread by undercooked garbage 13
- 14. • CSF Data 14
- 15. SECD • Federal Order was revised Jan 4, 2016 • Revision-eliminated biosecurity payments • Eliminated payments for herd plan • Purpose- try to get funding to last longer – DRO verification continues and is necessary for reporting – Reporting will remain important to track disease trends – Data entered in EMRS 15
- 16. SECD – Program funding for testing is expected to be exhausted this spring – Discussions continue on how program will work after funding lapse – Diagnostic funding to last through April 2016. After April, producers are responsible for testing fees – Reporting responsibilities will continue until decisions on programs future are determined 16
- 17. SECD 17 0 10 20 30 40 50 60 70 80 90 NumberofPremises Week Received DUAL INFECTION PDCoV PEDV 0 100 200 300 400 500 600 700 800 900 1000 NumberofAccessions Week Received PEDV Accessions Tested PEDV Positive Accessions 0 100 200 300 400 500 600 700 800 900 1000 NumberofAccessions Week Received PDCOV Accessions Tested PDCOV Positive Accessions
- 18. Influenza A virus in Swine (IAV-S) 18 DATA DISCLAIMER • Surveillance is voluntary, passive, and for the most part anonymous • No measure of disease prevalence by – time – location – subtype • State-level data summaries are not disclosed externally beyond internal state stakeholders
- 19. 0 200 400 600 800 1000 1200 Accessions Positive Accessions Subtyped Accessions VI Positive Accessions 19 IAV-S Data FY10-16 YTD : Program totals since 2010 Samples Tested 103,163 Accessions 28,759 Positive Accessions 10,329 VI Positives 3,449 Subtyped Accessions 6,619
- 20. 0 0.12 0.12 0.12 34.58 0 0.35 0 0.12 0 0 0 0 0 0 0 0 0.12 1.41 0 0 0 0 0 0 0 0 0 0.23 10.55 0.12 0 0 0 0 0 0 0 0 1.52 0.23 22.16 0.7 0.82 0 2.11 0.12 17.35 4.69 0.12 0.23 2.11 H1.alpha H1.beta H1.delta1 H1.delta2 H1.gamma H1.pandemic H3.Human_H3 H3.IV H3.IV−A H3.IV−B H3.IV−C H3.IV−D H3.IV−E N1.Classical N1.Pandemic N2.1998 N2.2002 NA type HAtype 0 10 20 30 percent Percentage of HA and NA combinations − Oct 2014 to Sept 2015 20 National breakdown FY 2015 :
- 21. 21 0 10 20 30 Oct−14 Nov−14 Dec−14 Jan−15 Feb−15 Mar−15 Apr−15 May−15 Jun−15 Jul−15 Aug−15 Sep−15 NumberofSwineIsolates Human_H3 IV IV−A IV−B IV−C IV−D IV−E H3 phylo−cluster by month
- 23. Region1 Region2 Region3 Region4 Region5 0 50 100 150 14Q1 14Q2 14Q3 14Q4 15Q1 15Q2 15Q3 15Q4 14Q1 14Q2 14Q3 14Q4 15Q1 15Q2 15Q3 15Q4 14Q1 14Q2 14Q3 14Q4 15Q1 15Q2 15Q3 15Q4 14Q1 14Q2 14Q3 14Q4 15Q1 15Q2 15Q3 15Q4 14Q1 14Q2 14Q3 14Q4 15Q1 15Q2 15Q3 15Q4 Numberofswineisolates H1N1 H1N2 H3N1 H3N2 mixed Virus Type by Region 23
- 24. • Posted to website – http://www.aphis.usda.gov/animal-health/swine- health-surveillance 24 Regional reports:
- 25. 25 FY 2015 Region Samples Access Matrix PCR Positive Access VI Positive Access Subtyped Access H1N1 H1N2 H3N2 H3N1 Mixed 1 2,285 860 338 172 275 105 82 80 7 2 14,893 4,717 1,593 469 1,009 298 317 332 3 55 3 3,152 485 181 72 140 29 78 32 1 4 5,547 1,612 737 92 364 108 90 131 1 33 5 124 82 16 3 12 9 3 UNK 1,479 548 207 32 131 59 26 35 10 FY15 Totals 27,480 8,304 3,072 840 1,931 608 593 613 4 106 Percent 36.99 27.34 62.86 19.79 19.30 19.95 0.13 3.45 Regional Breakdown FY 2015 Data :
- 26. • Virus isolate forwarded to NVSL for confirmation and sequencing • Originated from the traceable side of the Influenza A Virus in swine (IAV-S) surveillance program. • Samples collected 12/16/ 2015 and submitted to a NAHLN lab for Influenza testing / surveillance – Unusual subtype identified through the established algorithm: • Matrix PCR (+) = influenza A virus identified • Subtyping PCRs (-) = not an H1 or H3 virus = unusual finding • VI – isolate acquired • three gene sequence…. suspicious for H4 and N6, all avian genes 26 Interesting Finding-H4N6
- 27. • 1200 sow, farrow to wean herd in Missouri – 5 Gilts: “sick” /aborted; other pigs coughing – Tested PRRS negative • Confirmation at NVSL by whole genomic sequencing – H4N6 and composed of avian genes; NOT HPAI or LPAI. – H4N6 common subtype in wild bird influenza (#3) – Sequence deposited in GenBank. • Follow-up- additional samples collected from herd – ~ 65 serum / nasal swabs submitted to the NAHLN lab for testing – Evidence is lacking the virus is persisting. 27 Interesting Finding-H4N6
- 28. • Internal Review: program assessment looked at achieved results / stakeholder input / analyze changes needed for transition into CIS • Results: – Strong stakeholder support for the program – Met or partially met 8 of the 9 goals/objectives – Relevant to continue some level of program support – 4 main areas for continuation / enhancement • Build on existing stakeholder networks • Enhance communication and transparency • Focus on resource efficiency • Improve data management 28 Program assessment / review:
- 29. • External review: looked at technical and scientific merit of the program / make recommendations for future program efficiencies • Results: – Applauded the non-regulatory approach for an endemic disease that has swine industry support and engagement – Twenty-six (26) recommendations made for either the program as it currently exists or a revised program due to budget limitations – Nine priorities for action identified 29 Program assessment / review:
- 30. 30 Program assessment / review: Summaries of assessments posted to website – http://www.aphis.usda.gov/animal-health/swine-health- surveillance
- 31. Influenza A virus in Swine (IAV-S) 31 • Current Influenza funding is projected to last through FY 2016. Funding beyond FY2016 is uncertain. • Working to identifying budgetary resources within programs funds to continue surveillance activities into the future • Collaboration meetings with industry are being planned to re-assess program goals and future activities
- 32. Surveillance • ASF/FMD Pilot – Pilot in FY14-15 – Samples submitted to various NAHLN labs – Sample numbers hampered by HPAI deployments – Pilot was successful in identifying issues • DATA, DATA, DATA, issues were identified and are being addressed. – Full implementation on hold until issues identified are addressed – Passive surveillance is effective in demonstrating freedom for trade. 32
- 33. Other • Senecavirus A (SVA) – Formally referred to as Seneca Valley Virus – LOOKS Like FMD, ACTS Like FMD – Cannot be differentiated from FMD without laboratory testing – USDA role is to rule out FMD – Many FAD investigations, especially in the Midwest – Still seeing, although lower number 33
- 35. 35
- 36. Bilateral necrosis and ulceration with sloughing of hoof wall 36
- 37. Other • Senecavirus A (SVA) – Guidance document issued in October 2015 • Remains in effect until replaced • A revised version is in finalization process. – Clarifies – Streamlines – Expected to be released soon. 37
- 38. SVA – Guidance Document Overview • Treat as FAD investigation following current procedures • Report all vesicular lesion cases!! • If SVA is confirmed in the area- Submit samples at lower priority (no need to send air plane if SVA) • Remember to send duplicate samples to NAHLN and FADDL • Testing priority can always be elevated depending on results of NAHLN Lab • We are not paying for SVA testing in NAHLN labs ---- our concern is FMD 38
- 39. National List of Reportable Animal Diseases (NLRAD) What is it? • A single uniform, science- and policy- based, nationally supported standardized list of animal diseases/agents What will it do? • Provide the basis for consistent reporting with uniform case findings and reporting criteria • Facilitate commerce and meeting international reporting obligations • Support export certifications • Contribute to the assessment, response and reporting of listed zoonotic and endemic animal diseases • Facilitate response to an emerging disease or issue in the United States
- 40. National List of Reportable Animal Diseases (NLRAD) • VS, in collaboration with SAHO, laboratories, and industry, continues to move forward with NLRAD • Concept papers are being drafted by working groups: – Laboratory implementation – Confidentiality – Reporting and data management – Roll-out and communication – Updates to the NLRAD – Development of an implementation plan • Implementation Plan to be released for public review before USAHA 2016 Annual Meeting 40
- 41. Emerging Diseases Framework - Internal working group working on implementation plan. Draft will be shared with stakeholders for input. - Generic approach that addresses all commodities - Collaboration with Swine Health Information Center (SHIC), NPB and others on epidemiological investigations for SVA - VS representatives sitting on SHIC working groups 41
- 42. Questions?
Editor's Notes
- Thanks for the opportunity to provide a swine health center update Probably getting tired of sitting and right before lunch – I will try to get through this and get you an early start JK – back from DHS detail
- Areas we will cover today
- WS provides surveillance of feral swine
- 5% surveillance level being reconsidered – international acceptance and confidence of detection District 4 high risk states: Arkansas, Missouri, Texas, and Oklahoma Still do some meat juice testing of market hogs
- Send the completed form to swine health team member Trying to associate epi info with the testing info
- We will provide notices when NAHLN labs are ready for SB testing And, when we make the transition from the sharepoint site to EMRS for investigations and closure of PRV and SB non-negatives
- Provides slaughter data for your state You can access your state data for completing annual reports for state certification
- OK has garbage feeders.
- Feral swine in AR, LA, MO, MS, OK, and TX (4th quarter report) TX is high risk state – back yard and waste feeding Blood samples from high risk waste feeding states: AR, CA, HI, NM, NC, OK and TX
- CCC Funding for diagnostic purposes will expire this spring, based on current projections Even when Dx funding ceases, still mandatory reporting and we will still be providing situational updates DRO activities will continue – production type, age class, number of animals. Now that there is no further monetary incentive to maintain an infected status – may see more negative status requests. No coop agreements this year.
- Epi curve would seem to indicate that the worst of this winter is over, but it lags behind due to unverified cases and time lags.
- About 6-10 cases last year of human variant influenza
- Added trend lines to Accessions (in purple), Positive accessions (in green) and VI positives (in blue) Notice that while we have a strong upward trend in accessions (Purple) , but we do not see that same elevation in our positive accessions (Green), - so we are seeing lots of negative accessions………….. and our virus isolate trend line- we hardly see any elevation at all. (Blue) Keep in mind, one of the goals of surveillance is obtain virus isolates… isolates allow: Sequencing and phylogenetic analysis of those sequences (work done in collaboration with ARS) Antigenic work to determine vaccine effectiveness (ARS, Researchers, biologics companies) Make viruses available updates to vaccines and diagnostic reagents As a result, we want to reassess some aspects about the program…to determine what can be done to make this program more efficient.
- Point out this is National Data - This is a heat map of the FY 2015 hemagglutinin (HA), and neuraminidase (NA) genes with published sequences in GenBank from 856 isolates from the surveillance program that were characterized by phylogenetic analysis through collaboration with ARS-NADC (Dr. Amy Vincent’s lab); HA clade breakdown is on the Y axis The H1 subtype viruses were classified as alpha, beta, gamma, delta1, delta2, or pandemic H1N1 2009 (H1N1pdm09) phylogenetic clusters based on a previously published nomenclature system The H3 subtype viruses were classified as Cluster IV, Cluster IV-A, Cluster IV-B, Cluster IV-C, Cluster IV-D, Cluster IV-E, Cluster IV-F, or Human-like H3 NA clades are on the X axis – they are broken down into N1 Classical, N1 Pandemic, N2 (1998 lineage) and N2 (2002 lineage) On the right hand side you can see a color gradation that represents the % of samples – darker the color, higher the % of an HA / NA combination that was found.. The dominant viruses detected in FY15 were: gamma H1N1, (34.58%) Darkest blue- point it out delta1 H1N2, (22.16%) Cluster IV-A H3N2, and delta2 H1N2 All viruses characterized in FY15 contained the pandemic-lineage M gene. The emerging human-like H3N2 continued to be detected with slightly increased frequency.
- Lets take a little closer look at the human like H3’s (gray). This is something USDA is watching. The Human-like H3 is the result of a human insertion into swine subtypes. The human –like H3 was discovered by ARS in January 2014 in an H3N1 sample. In collaboration with a NAHLN lab, some retrospective samples were looked at , and subsequently added to the USDA surveillance data. What they found was several H3N2 samples from 2012 with the Human like H3 . Those early detections were limited to 2 - 3 states, but detections have been slowly expanding in geographic location… Now found in about 7 states.
- In FY 2015, USDA began issuing stakeholder reports with regional information to try to provide more useful information to stakeholders. The Regions were designated in collaboration with Industry and AASV representatives and align closely to USDA Districts. The Numbers above regional designations are the NASS 2012 numbers for swine populations in those regions.
- This is a two year moving window of the subtype break down by region; it covers FY2014 through FY 2015. A couple of things to point out: You can see most submissions come from Region 2 and Region 1… this is consistent with NASS swine populations; Regions 3, 4, and 5 are also relatively consistent with NASS relative population size, but we are really hoping to see more submissions from Regions 3 – 5, and especially from Region 5- which is largely under-represented. the decreases seen in the last quarter for FY 2015 are due to a time lag for posting of sequences to Genbank… as these become available, the number will increase in these reports. This particular graph does not show the clade breakdown for each region like the last slide, however heat maps for each region are generated and included in Stakeholder reports. – those stakeholder reports are posted on the web fro easy access – NEXT SLIDE
- Feedback on these reports is very helpful and will be used to assist USDA in making these reports more useful for States and Stakeholders.
- This is a regional breakdown of the FY 2015 IAV-S data: Things of note are: Only 37% of the accessions are influenza positive (36.99), - this just reemphasizes what we showed in the first graph with national data… we are seeing LARGE numbers of negative submissions. While we can get general subtype information from the subtyping PCRs in the testing algorithm, we only get a virus isolate for sequencing from about 27% of the positive accessions. (so from the 37% of positive accession, only 27% of those can we get an virus to sequence) Its from those sequences (all posted in Genbank) that we get the clade breakdowns and – hopefully in the future- antigenic information that would allow comparison to vaccine effectiveness.
- In December 2015, an unusual finding was flagged early in the IAV-S surveillance algorithm by one of the NAHLN labs. They contacted NVSL to let them know about the finding and that they were sending in this sample for confirmation…. The sample- a traceable accession – had been submitted and tested Matrix PCR positive- the Matrix PCR is a screening PCR that can tell us whether or not sample is influenza A virus or not; So we knew the sample was IAV positive; However, when the lab moved to the subtyping PCRs (which identify H1 or H3, and N1 or N2) - they were all negative. This red flagged an unusual finding - - and one of the purposes of the USDA surveillance is to identify these unusual findings so that it can be looked at to determine if this may be a concern for swine producers…. The NAHLN lab was able to grow an isolate from one of the samples submitted, and they proceeded to sequence the HA, NA and M genes. Their results were suspicious for H4N6, but unclear; They were confident all the genes were avian genes. The sample was submitted to NVSL for confirmation and seqeuncing
- Because the sample was traceable, we could investigate to some degree further. Good news is the virus does not appear to persist in the herd; unlikely that further spread (not well adapted). The NAHLN lab is working with the practitioner to further investigate – question of whether those animals came into the farm already exposed.
- In 2015 the USDA IAV-S surveillance program underwent a program assessment and review. Actually it was divided into two parts: The first was an internal assessment performed by APHIS Policy and Program Development , Program Assessment and Accountability office. A Program Assessment is a determination, through objective measurement and systematic analysis, of the manner and extent to which Federal programs achieve intended objectives. The PAA group is independent, objective, and unbiased. Reside in the Policy and Program Development (PPD) division, and produce assessment reports free of influence, and provide perspective and commentary used to strengthen and improve APHIS programs. A PAA team looked at whether the IAV-S surveillance program had achieved the goals and objectives it had set out to meet, seeking stakeholder input from a wide variety of stakeholders, and provided an overall assessment of the program. .
- The external review was provided by Dr. Ian Gardner, an internationally respected epidemiologist.
- The summaries of the two program assessments are posted to the USDA web site The web address is the same address where the IAV-S reports are posted. Point out The address is placed on this slide again in case it was missed when we talked about the location of the surveillance reports.
- So- what does the future hold for IAV-S surveillance? At current spending levels, we are projecting the funding for IAV-S surveillance will last through FY 2016. Funding beyond FY2016 is uncertain, however as CEAH works towards implementing CIS, they are identifying efficiencies in other disease surveillance activities that may conserve resources that could then be applied to IAV-S surveillance. We are planning to hold a collaborative meeting with stakeholders to reassess the influenza surveillance goals and to modify the surveillance activities based on assessment findings and recommendations, and resources.
- No longer sampling
- Big concern centers around complacency
- Slaughter lesions – number have been reported at slaughter Conducting traceback on these animals – does time in transit, lairage, etc. (stressors) affect lesion development and clinical signs SVA peaked in summer/fall then fell off Still seeing cases