1. 1. Growing diversity of H3N2 influenza A virus in swine: Impact on control in swine and at the human animal interface. Amy L. Vincent, DVM PhD Research Veterinary Medical Officer National Animal Disease Center USDA-ARSUSDA-NADC Team USDA-NVSL USDA-NAHLN Laboratories USDA-NSU US Swine Producers and Veterinarians
2. 2. USDA IAV Surveillance in Swine Implemented in 2009 Samples began being submitted in November 39 participating NAHLN labs Approved diagnostic assays Matrix FluA screening PCR HA and NA subtyping PCR Virus Isolation Isolates sent to NVSL repository Sequencing priority on HA, NA and M genes Sequences deposited to GenBank public database Passive Surveillance Primary source of samples are from diagnostic samples from clinically affected pigs, voluntary and anonymous Small number of samples sent directly to NVSL associated with zoonotic events as identified by Public Health: H3N2v 2
3. 3. Systematic approaches to monitor IAV in swine Genetic AnalysisSequencing Antigenic AnalysisSwine Studies Regional/national efforts USDA, CEIRS, ESNIP, etc. International networks CEIRS, ESNIP, OFFLU
4. 4. U.S. swine IAV surveillance results What does the USDA data tell us ? Trends in HA and NA dynamics Subtypes: H1N1, H1N2, and H3N2 Phyloclusters: defined using genetic distance of the HA H1s with alpha, beta, gamma, pdm09, and delta (human seasonal origin) H3s with historical Clusters I, II and III, along with a rapidly expanding contemporary Cluster IV Evidence of reassortment Matrix Lineage: Classical swine origin or pandemic matrix gene as an indicator of reassortment and virus evolution. Viruses for further research (NADC and others) Viruses for vaccine development
5. 5. H3 & H1 Phyloclusters in 2009-2013 200 180Number of Swine Isolates160 140 H3N2120no data H1N1 pdm100H1N2 delta2 H1N2 delta180H1N1 gamma H1N1 beta60H1N1 alpha 40 20 0 09Q410Q110Q210Q310Q411Q1 11Q2 11Q3 11Q412Q112Q212Q312Q413Q113Q213Q3 Year by quarter
6. 6. Phylogenetic relationships of H3 swine IAVPhylogenetic clade Cluster I Cluster II Cluster III Cluster IV6 clusters evolving forward into 2013HA associated with H3N2v0.02Between clade amino acid identity ~94%: within clade amino acid identity ~98% Tavis Anderson, IRV accepted
7. 7. 200 180 160 140 120 100 80 60 40 20 0 09Q4 10Q1 10Q2 10Q3 10Q4 11Q1 11Q2 11Q3 11Q4 12Q1 12Q2 12Q3 12Q4 13Q1 13Q2 13Q3Number of Swine isolatesMatrix lineage 2009-2012No dataYear by quarter North AmericanPandemic pdm09 Matrix gene currently ~75%0.02Tavis Anderson, IRV accepted
8. 8. Reassortment generates new viruses
9. 9. Reassortment patterns of H3N2 virus in U.S. swineGenotypes associated with H3N2v(Kitikoon et al., 2013, J Gen Virol)
10. 10. Are the H3 genetic clusters impacting cross-reactivity? H3 antibodies had inconsistent cross-reactivity among sub-clusters and with vaccines DF TX/2011IA/2011IA/2011IL/2011IN/2011IN/2012NY/2011IN/2011PA/2010IVI&IVI Vaccine 3CVaccine 2A IL/2009MN/2009(IV)IA/2007(I)IV MN/2006TX/1998Virus (cluster) TX/1998 MN/2006 IA/2007 MN/2009 IL/2009 PA/2010 IN/2011 NY/2011 IN/2012 IL/2012 MI/2012 MN/2012 MN/2012 MN/2012 IA/2012 IN/2011 IL/2011 IA/2011 IA/2011 IA/2012 IA/2011 TX/2011 IL/2012 IA/2012 NE/2012IVaccine 1SeraHomologous < 4-fold reduction = 4-8-fold reduction > 8-fold reduction(A)(B) (C) (D)(F)Pravina Kitikoon, IRV accepted
11. 11. Cause or Consequence? What is driving the observed increase in diversity? Reassortment? Pig movement? Ineffective vaccines? Unknown factors? With all this antigenic diversity, how well are control measures working on a national level? Can we develop a system for more efficient updates of commercial vaccines? What are the implications for human health?
12. 12. Human Infections with variant IAV - USA Case Count: Detected U.S. Infections with Variant Influenza Viruses by State since December 2005 Reporting State Hawaii Illinois Indiana Iowa Kansas Maine Maryland Michigan Minnesota Missouri Ohio Pennsylvania South Dakota Texas Utah West Virginia WisconsinTotalH3N2v 1 5 154 5 1 2 12 8 8 108 16Total H1N1vH1N2v20111 2 33H3N2v 2012 1 4 138 12013* 1 1422 2 212 6 51 43107 11211 1 1 5 212 23471453661 3 201230918339*2013 human cases recently report associated with county fair swine exposure http://www.cdc.gov/flu/swineflu/variant-cases-us.htm
13. 13. H3N2v, 2011-13 >339 cases in humans primarily associated with children at swine barns at agricultural fairs in summers of 2011, 2012 and again in 2013 All genotype 1 H3N2 Nearly all HA cluster type A Nearly all NA 2002 lineage Low serologic cross-reactivity in children and teenage population Many questions regarding recommendations to fair officials, exhibitors, and exhibited stock How to screen stock before entering exhibit Recommendations on vaccines for kids and pigs Animal movement practices at fairs/venues Multi-disciplinary team drafted guidance documents early 2013
14. 14. Epi-Curve for Confirmed H3N2v Cases State of IsolationJuly - Sept 28, 2012 (N=306)MN (n=4)40MD (n=12) 35PA (n=11)30WI (n=20)25MI (n=5)WV (n=3)20IL (n=4) 15 OH (n=106) 10IN (n=138) HI (n=1)5 0 7/97/167/237/308/68/138/208/279/3Illness Onset Date (Includes illness onset dates imputed from specimen collection dates and report dates)http://www.cdc.gov/vaccines/acip/meetings/downloads/slides-oct-2012/02-influenza-Finelli.pdf9/10
15. 15. Proportion of Persons with Hemagglutination Inhibition Antibody Titer >40 to Influenza A (H3N2)v Virus by Year of Birth NORWAYCANADAUSA9080 Proportion70 6050 40 30 20 10 02011 2001 1991 1981 1971 1961 1951 1941 1931 1921 1911 Slide courtesy of Dr. Nancy Cox, CDC Skowronski DM. et al. JID. 2012 August 12; CDC, Unpublished data, 2012; Waalen et al., Euro Surveill 17:pii=20170, 2012
16. 16. Future Challenges and Gaps for Swine Exhibits Swine IAVs in a period of frequent reassortment and HA evolution. Continued monitoring and timely dissemination of information required. Currently available vaccines for swine do not prevent nasal shedding, some performed better than others. There is no uniform system to select swine IAV for vaccine updates. Mass vaccinating has been shown to dramatically decrease viral shedding. Mixed immune populations comingled together will continue to be difficult to manage. A sensitive and specific pen-side test is not available and clinical signs are not sufficient for identifying shedding pigs at points of concentration. Pig movement and mixing is difficult to track with fair and show pigs. There is variability among exhibition venues and markets for animal movement and show requirements. Guidelines & recommendations for swine IAV implemented in a number of states for the 2013 Fair season. Partnerships between animal health, human health, and the swine industry are critical to minimize the impact of these events.
17. 17. Acknowledgments NADC Michelle Harland Gwen Nordholm Daniela Rajao Alessandra Dias Matt Sandbulte Brian Campbell Kelly Lager Crystal Loving Mark Kehrli Jason Huegel Jason Crabtree Tyler Standley Darrell Bayles Pravina Kitikoon Tavis Anderson Phil Gauger Jamie Henningson Alessio Lorusso Doug Braucher Janice Zanella Eraldo Zanella Sabrina Swenson John Korslund Marie Gramer Nicola Lewis Daniel Perez Martha Nelson Richard Webby James Roth Ruben Donis Hana Golding Surender KhuranaU.S. Producers and Swine VetsFunding: USDA-ARS USDA-APHIS National Pork Board CDCMany thanks to USDA NCAH Visual Services