UPDATE ON AVIAN INFLUENZA

M I A K I M TO R C H E T T I , D V M M S P H D

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 LO G Y L A B O R ATO R YU. S . D E PA R T M E N T O F A G R I C U LT U R EA 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 EV E T E R I N A R Y S E R V I C E SN 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 ATO R I E S

O C TO B E R 2 0 1 6

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)

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ADAPTED AND COURTESY OF USDA ARS SOUTHEAST POULTRY RESEARCH LAB (SEPRL) 3

Avian Influenza Ecology

Re-adaptation ofGsGD H5N1 HPAI

Mammals

LP incl. H5/H7

H5N8/H5N2/H5N1

GsGD H5reasst

HPAI (H5/H7)Potential for HA Mutation H5/H7

ExposureAdaptation

LP incl. H5/H7

Over 200 avian species are susceptible hosts

IAV can rapidly EVOLVE

ADAPTED FROM E. SPACKMAN AND M. PANTIN-JACKWOOD SEPRL 4

• Antigenic Drift

• Antigenic Shift

• Host Adaptation

e.g. Gs/GD lineage H5N2

• 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 Courtesy C. Lee, OSU

LP HP

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

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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

Network analysis H5Nx 5-genes

Europe 2014 Canada & US 2014-15

China 2005 (oldest)

H5 GsGD 2.3.4

TMRCA HA gene

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

S.Korea/Japan 2014-15

China 2008-14

13

11

8

12,16, 15 1

710

914

1

4

6

753

2

8-gene network: 17 detections spanning 5 states and 16 counties from27 February to 20 April 2015; long branches suggest largely point source introductions with limited evidence of lateral spread

Refer to H5 September 2015 Epi and Virus Report 9

H5N2 Midwest First Detections

Network analysis with DH Lee USDA/ARS/SEPRLMapping with USDA/CEAH

HPAI 2016

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

Aug 2016 AKEA/AM H5N2 2.3.4.4 Jun 2016 Russia

EA H5N8 2.3.4.4

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

2014-15 EA H5 HPAI 2.3.4.4

1961 TRN SO. AFRICA H5N31983-84 CKN PA/VA H5N2 HPAI

LBM/BYDCOMMWILD

2000-05 CKN MX H5N2

1968 TKY WI H5N9

1994-95 CKN MX H5N21993 CKN NJ / EMU TX H5N22000 LBM NY/NJ H5N2

2004 LBM TX H5N22001-02 LBM NY H5N2,N8

2014 QUA CA H5N8

Wild bird 2015-16

2002 DCK ME H5N2 2006 DCK PA H5N2 2010 TKY BC H5N2

2008 CKN NJ H5N2

2006-07 LBM NY H5N2

2016 LBM Northeast H5N2 LPAI2013 LBM PA H5N2

2016 TKY MO H5N1 LPAI

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

Different from H5N8 2.3.4.4

Different from H5N2 2.3.4.4

2015 BYD PA H7N7 LPAI

LBM/BYDCOMMWILD

2016 TKY IN H7N8 HPAI/LPAI

Wild bird 2015-16

2014 CKN DE H7N7

2011 GSE NE H7N9 2012-14 CKN MX H7N3

2010 DCK NJ H7N3

2004 CKN BC H7N32001 DCK PA H7N3

1995 TKY UT H7N3

1998 QUA PA H7N21997, 2002 CKN PA H7N2

1998 GSE NY H7N2

1998 GSE NY H7N22001-03 PLT NJ, MA, NY H7N2

2001-02 NY, NC, VA PLT H7N2

1971 TKY OR H7N3

HA H7s 2015-2016

Different from H5N8 2.3.4.4

2015 TKY CA H7N3 LPAI

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Team Avian, Diagnostic Virology

Mia Kim Torchetti, DVM MS PhD

U.S. Department of AgricultureAnimal and Plant Health Inspection ServiceVeterinary Services515-337-7551Nvsl.dvl.avian@aphis.usda.gov