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Veterinary Services Animal and Plant Health Inspection Service

U.S. Department of Agriculture

NVSL UPDATE FOR AVIAN

INFLUENZA & NEWCASTLE

DISEASE

Mia Kim Torchetti, DVM MS PhD

Committee on Poultry and Other Avian SpeciesVeterinary ServicesUSDA, APHISNational Veterinary Services LaboratoriesDiagnostic Virology Laboratory - AvianNVSL.DVL.AVIAN@usda.govPh. 515-337-7551

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Veterinary Services Animal and Plant Health Inspection Service

U.S. Department of Agriculture

Newsflash! New Media Tubes• BHI without antibiotics is available in 3ml

blue cap-plastic tube for up to 5 OP or CL swabs from avian species

• BHI with antibiotics is available in 5.5ml white cap-plastic tube for up to 11 OP swabs from gallinaceous poultry or environmental samples

Order form https://www.aphis.usda.gov/library/forms/pdf/NVSLKitRequestForm.pdf

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3 ml BHI - no abx

5.5 ml BHI + abx

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Veterinary Services Animal and Plant Health Inspection Service

U.S. Department of Agriculture

FY2019 US Samples Submitted (>8300)

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43%

1%

3%4%

16%

33%

COMM

DIAG

EXPORT

FAD

IMPORT

LBM-BYD

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Veterinary Services Animal and Plant Health Inspection Service

U.S. Department of Agriculture

2018-19 H5 and H7 Events

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All of North American wild bird origin

Date State Production typeInitial

sample SubtypeSep-18* CA commercial turkeys Sera H7N3 LPAIOct-18 MN commercial turkeys Swab H5N2 LPAIMar-19 PA, CT LBM ducks Swab H7N3 LPAIApr-19 CA commercial ducks Swab H5N2 LPAI

Jun-19 CAnon-commercial backyard ducks

Swab H7N3 LPAI

* reported in previous year

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Veterinary Services Animal and Plant Health Inspection Service

U.S. Department of Agriculture

2018 MN H5N2 LPAI Independent introductions by county

• Phylogenetic analysis suggests independent introduction by county followed by secondary spread within county.

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Wild bird data courtesy of National Center for Foreign Animal Diseases, Winnipeg, Canada

Virus from County 1

Virus from County 2

PB2 96% 95%PB1 94% 95%PA 99% 89%HA 99% 99%NP 99% 93%NA 99% 99%MP 99% 97%

NS (MALL) 99% 78%

NS(NOPI) 79% 99%

Analysis of common genes for viruses from Kandiyohi (green), Stearns (purple), and Canadian wild birds (blue)

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Veterinary Services Animal and Plant Health Inspection Service

U.S. Department of Agriculture

2018 MN H5N2 LPAI Phylogenetic analysis across all 8 genes

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Kandiyohi (green) & Stearns (purple) counties

NA stalk deletion was acquired

Wild bird data courtesy of National Center for Foreign Animal Diseases, Winnipeg, Canada

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Veterinary Services Animal and Plant Health Inspection Service

U.S. Department of Agriculture

2018 September AM H7N3 LPAIEarly September - slight increase in mortality with respiratory signs in turkeysDay 1: CAHFS reported AI antibody and presumptive H7Day 3: North American wild bird H7N3 LPAI confirmedDay 18: second flock detected with H7N3

• Two additional flocks identified through incident area surveillance (one backyard)

Day 40: fifth and final flock confirmed

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Veterinary Services Animal and Plant Health Inspection Service

U.S. Department of Agriculture

• Highlights need for virus monitoring during controlled marketing

Virus Changes Associated with Poultry Adaptation

Neuraminidase stalk deletion

Samples collected NA gene Last detectionearly September mixedearly September noneearly September nonemid September deletionmid September none n/amid September deletion 10/30/2018early October deletion 11/05/2018

n/a

n/a

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Veterinary Services Animal and Plant Health Inspection Service

U.S. Department of Agriculture

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←2018 MN turkeys H5N2 LPAI

←2019 CA ducks H5N2 LPAI

←2014 CA quail H5N8 LPAI

←2015 NJ LBM H5N1 LPAI

←2017 WI turkeys H5N2 LPAI

←2016 MO turkeys H5N1 LPAI

←2016 Northeast (NE) LBM H5N2 LPAI

2010 Canada turkeys LPAI

←Early to mid-2000s (NE) LBM H5N2 LPAI

←2014-15 US EA/AM H5 HPAI

H5 HA PhylogenyFY2019 in blue

Wild birdCommercial

LBM/Upland game/BackyardHPAI

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Veterinary Services Animal and Plant Health Inspection Service

U.S. Department of Agriculture

H7 HA PhylogenyFY2019 in blue

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←2018 MO, TX H7N1 LPAI (independent introductions)

←2017 TN, AL, KY, GA H7N9 LPAI (+TN HPAI)

←2016 IN turkeys H7N8 LPAI (+HPAI)2018 CA turkeys H7N3 LPAI2019 CA ducks H7N3 LPAI

2015 PA LBM H7N7 LPAI

2014 NJ pheasant H7N3 LPAI2014 DE LBM H7N7 LPAI2019 PA, CT LBM H7N3 LPAI

←2010 NJ LBM H7N3 LPAI←Late 90’s to mid-2000 NE LBM H7N2 LPAI

Wild birdCommercial

LBM/Upland game/BackyardHPAI

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Veterinary Services Animal and Plant Health Inspection Service

U.S. Department of Agriculture

AM H7N3 LPAI NA Deletion in Backyard Ducks

HA NA** PB2 PB1 PA NP MP NS99.0 99.8 99.7 99.6 99.7 99.7 99.4 98.899.0 99.8 99.6 99.6 99.8 99.7 99.6 98.799.0 99.8 99.7 99.6 99.8 99.6 99.6 98.899.0 99.8 99.7 99.6 99.7 99.7 99.7 98.799.0 99.8 99.6 99.6 99.7 99.7 99.7 98.798.9 99.8 99.6 99.6 99.7 99.7 99.7 98.7

**comparison to virus with deletion (both present at site)

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Veterinary Services Animal and Plant Health Inspection Service

U.S. Department of Agriculture

Wild Bird Viruses in LBM/Upland game/ Backyard birds

• H1N1 PA duck• H2N8 OR duck• H3N8 (equine lineage) PA

Muscovy duck• H4N6 TN duck • H6N1 PA, NJ duck• H6N8 PA duck

• H10N1 WY quail• H10N7 FL chicken• H11N9 TX chicken

OTHER INFLUENZA A:• Swine lineage H1 MO, MN,

NC (also H3)• H1N1pdm from UT mink

farm, and black bear from zoo in LA

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Veterinary Services Animal and Plant Health Inspection Service

U.S. Department of Agriculture

Live Bird Market H2N2

0

20

40

60

80

100

120

140

160

CT NJ NY PA

2018

domestic waterfowl environment

other bird poultry (gall)

0

20

40

60

80

100

120

140

160

CT NJ NY

2019

domestic waterfowl environment

other bird poultry (gall)

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Veterinary Services Animal and Plant Health Inspection Service

U.S. Department of Agriculture

LBM H2N2 HA Phylogeny• Branches colored by

year:• 2019• 2018• 2017• Older in black

• Tip labels colored by state• No evidence of

reassortment

• NA stalk deletion observed in 2 states along with amino acid substitutions at the cleavage site

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Veterinary Services Animal and Plant Health Inspection Service

U.S. Department of Agriculture

California vND Incident 2018

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Veterinary Services Animal and Plant Health Inspection Service

U.S. Department of Agriculture

APMV-1 (aka Avian Avulavirus 1)

Pigeon/dove (PPMV-1), cormorant, and

classical vaccineviruses are distinct

from the CA vNDviruses

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Veterinary Services Animal and Plant Health Inspection Service

U.S. Department of Agriculture

Genetic Analysis CA2018• Analysis of the CA2018 viruses isolates

supports a single, recent introduction followed by secondary spread

• No change in the amino acid profile of the cleavage site has been observed for sequenced viruses (PGGRRQKR/FVGAII)

• The ICPI ranges between 1.6-1.8 (n=11)• Chickens remain predominantly affected,

other species identified include quail, peafowl (peacock) and turkey, as well as duck, goose, parakeet, and pigeon

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Dimitrov KM, et al. Virology, 2019 Vol 531:203-218. https://doi.org/10.1016/j.virol.2019.03.010

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Veterinary Services Animal and Plant Health Inspection Service

U.S. Department of Agriculture

Tracking Sustained Virus Changes

Early divergence into two main groups is defined by the presence of a sustained single nucleotide polymorphism in the fusion gene compared to a closely related reference sequence (GenBank: KF767466.1)

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Veterinary Services Animal and Plant Health Inspection Service

U.S. Department of Agriculture

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Special Thanks to:• CAHFS, MPTL• USDA ARS SEPRL and CEAH• SAHOs, NPIP and NAHLN Labs• Team Avian, Diagnostic Virology Lab

Remember to send duplicate samples to

your NAHLN lab and to NVSL in parallel for the

fastest confirmation!