UPDATE ON AVIAN INFLUENZA

MIA KIM TORCHET TI, DVM MS PHD S E C T I O N H E A D - AV I A N , D I A G N O S T I C V I R O L O G Y L A B O R AT O R Y U . S . D E PA R T M E N T O F A G R I C U LT U R E A N I M A L A N D P L A N T H E A LT H I N S P E C T I O N S E R V I C E VETERINARY SERVICES N AT I O N A L V E T E R I N A R Y S E R V I C E S L A B O R AT O R I E S OC TOBER 2016

The disease = Avian Influenza (AI) The agent = influenza A virus (IAV) Influenza A viruses with high pathogenicity (HPAI) and H5 and H7 subtypes with low pathogenicity (H5/H7 LPAI) are reportable worldwide.

Waterfowl are natural hosts for H1-H16 influenza A of avian origin, but not usually HPAI. Influenza A viruses tend to circulate within flyways seasonally and wax/wane and in multiyear cycles. The only HPAI currently recognized to circulate in natural reservoir hosts emerged in domestic poultry in Asia (goose Guangdong [GsGD] lineage H5N1) 2

Avian Influenza Ecology

Exposure Adaptation

LP incl. H5/H7

GsGD H5 reasst

Re-adaptation of GsGD H5N1 HPAI

H5N8/H5N2/H5N1

LP incl. H5/H7

Potential for HA Mutation H5/H7

HPAI (H5/H7) Mammals

Over 200 avian species are susceptible hosts ADAPTED AND COURTESY OF USDA ARS SOUTHEAST POULTRY RESEARCH LAB (SEPRL)

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IAV can rapidly EVOLVE • Antigenic Drift • Antigenic Shift

• Pathotype: determined in CHICKENS • Potential for H5/H7 to mutate from LPAI to HPAI – Addition of basic amino acids (AA) most common, H5 or H7 – Accumulation of basic AA – Insertion of random sequence (H7) – Viruses with different cleavage sites may often circulate simultaneously

LP

HP

Courtesy C. Lee, OSU

• Host Adaptation

e.g. Gs/GD lineage H5N2

ADAPTED FROM E. SPACKMAN AND M. PANTIN-JACKWOOD SEPRL

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OIE HPAI 2005-2016 Sept

Triangles = Wild bird H5 HPAI GsGD

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Network cheat sheet

• Oldest viruses are centrally located • Orientation of branch for visual only • Length of branch is meaningful - indicates number of

nucleotide substitutions from index case • Longer branches originating from the spine suggestive of point source or independent introduction • Shorter branches radiating from cluster suggestive of secondary or lateral spread

Recall:

• All viruses are highly similar and all >99% identical to index (oldest) detections • More wild bird viruses are available from the Pacific Flyway as compared to Midwest for analysis

Network analysis H5Nx 5-genes

Europe 2014

Canada & US 2014-15

S.Korea/Japan 2014-15

TMRCA HA gene • • • •

icA H5 Jun 2013 EA H5N8 Oct 2014 EA/AM H5N2 Nov2014 EA/AM H5N1/N8 Dec 2014

China 2008-14 Courtesy Lee DH, USDA ARS SEPRL For more information refer to Highly pathogenic avian influenza viruses and generation of novel reassortants, United States, 2014–2015. Emerg Infect Dis. 2016 Jul [6Oct16]. http://dx.doi.org/10.3201/eid2 207.160048

China 2005 (oldest) H5 GsGD 2.3.4

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H5N2 Midwest First Detections

8-gene network: 17 detections spanning 5 states and 16 counties from 27 February to 20 April 2015; long branches suggest largely point source introductions with limited evidence of lateral spread

13 1 4 6 1 1 3 2

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9

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12,16, 15 1 1 70 7 51

Network analysis with DH Lee USDA/ARS/SEPRL Mapping with USDA/CEAH Refer to H5 September 2015 Epi and Virus Report

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Aug 2016 AK EA/AM H5N2 2.3.4.4

Jun 2016 Russia EA H5N8 2.3.4.4

HPAI 2016

https://www.gov.uk/government/uploads/system/uploads/attachment_data/file/534405/poa-avian-flu-russia.pdf

Phylogeny of other US H5/H7s

Use of sequencing both for rapid determination of LPAI/HPAI and lineage as well as virus characterization Ongoing internal and external collaboration on bioinformatics

HA H5s 2015-2016

2015 LBM NJ H5N1 LPAI Long horizontal branch – N1s 2016 TKY MO H5N1 LPAI not similar

LBM/BYD COMM WILD

2013 LBM PA H5N2

2016 LBM Northeast H5N2 LPAI

Different from H5N2 2.3.4.4

2006-07 LBM NY H5N2 2008 CKN NJ H5N2 2010 TKY BC H5N2 2006 DCK PA H5N2 2002 DCK ME H5N2 Wild bird 2015-16 2014 QUA CA H5N8

Different from H5N8 2.3.4.4

2001-02 LBM NY H5N2,N8 2004 LBM TX H5N2 2000 LBM NY/NJ H5N2 1993 CKN NJ / EMU TX H5N2 1994-95 CKN MX H5N2 2000-05 CKN MX H5N2 1968 TKY WI H5N9

1983-84 CKN PA/VA H5N2 HPAI

2014-15 EA H5 HPAI 2.3.4.4 1961 TRN SO. AFRICA H5N3

HA H7s 2015-2016 2015 BYD PA H7N7 LPAI Wild bird 2015-16

Different from H5N8 2.3.4.4 2016 TKY IN H7N8 HPAI/LPAI 2014 CKN DE H7N7

LBM/BYD COMM WILD

2012-14 CKN MX H7N3

2011 GSE NE H7N9

2015 TKY CA H7N3 LPAI 2010 DCK NJ H7N3

2001 DCK PA H7N3

2004 CKN BC H7N3

1995 TKY UT H7N3 1997, 2002 CKN PA H7N2

1998 GSE NY H7N2

1998 QUA PA H7N2 2001-03 PLT NJ, MA, NY H7N2

2001-02 NY, NC, VA PLT H7N2 1998 GSE NY H7N2

1971 TKY OR H7N3

Team Avian, Diagnostic Virology Mia Kim Torchetti, DVM MS PhD U.S. Department of Agriculture Animal and Plant Health Inspection Service Veterinary Services 515-337-7551 [email protected]

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