Influenza A Virus - Swine Surveillance – Canada

Yohannes Berhane

National Centre for Foreign Animal Disease

Winnipeg, Manitoba, Canada

OFFLU swine influenza virus meeting27 – 28 February 2019OIE Headquarters, Paris, France

Total Pigs on Farm by Province for 2017

NFLD0%

PEI0%

NS0%

NB0%

QUE31%

ONT25%

MB25%

SASK7%

AB11%

BC1%

• Monitor novel swine influenza viruses in Canadain pigs

• Contributors:

▪ Animal Health Laboratory (AHL), Guelph, Ontario▪ Manitoba Agriculture, Food and Rural Initiatives

(MAFRI), Winnipeg, Manitoba▪ Veterinary Diagnostics and Epidemiological

surveillance complex (MAPAQ) and Bio-Vet, Saint-Hyacinthe, Quebec

Passive surveillance of swine influenza

H1N1/N2

Province H1N1/N2 pH1 1A.2 () 1A.1 () 1B.2.2 (1))

Ontario 132 24 56 52 1

Quebec 17 - 17 - -

Manitoba 32 2 - 30 -

Total 182 26 73 82 1

Passive surveillance of swine influenzaH1N1/N2

H3N2

Province H3N2 IV IVBII Human like

swine

Ontario 61 22 39 -

Quebec 26 25 1

Manitoba 25 7 18 -

Total 112 29 82 1

Passive surveillance of swine influenzaH3N2

1A3.3.2H1N1pdm09

1A.3.3.3 (-H1)1A.3.2 (-2-H1)

1A.2 (-H1)

1A.1 (-H1)

1B.2.2.2 (-1b)

1B.2.1 (-2)1B.2.2.1 (-1a)

Phylogenetic tree analysis of H1 subtype swine influenza viruses circulating in Canadian swine populations

using the Bayesian Markov Chain Monte Carlo(BMCMC)

1A3.3.2

H1N1pdm09

Canadian strains

US strains

1A.2 (-H1)

1A.1 (-H1N1/N2)

Canada only

US & Canada

1B.2.2 (1-H1N1/N2)

-1b

-1a

IV-A

IV-E

IV-B

IV-CIV-D

IV

IV-F

III

III

Phylogenetic tree analysis of H3 subtype swine influenza viruses circulating in Canadian swine

populationsusing the Bayesian Markov Chain Monte Carlo

(BMCMC)

IV-B ON, QC

MB

IV

ON

MB

Cluster II

Influenza A swine (1A.2/Beta) viruses in poultry

- Breeder turkeys were diagnosed with more than 80% drop in egg production- PB2, NP & Matrix – pandemic; PB1, PA & NS – TRIG; N1 classical swine and HA

1A.2/Beta

WIN-AH-2017-FAV-0023 Identity similarity Top matches at GenBank

PB2 2258/2280 (99.0) KU204713 A/swine/Indiana/A01260983/2015 (H3N2)

PB1 2290/2339 (97.9) JN706698 A/turkey/Ontario/FAV-10/2011 (H3N2)

PA 2171/2229 (97.4) JN706699 A/turkey/Ontario/FAV-10/2011 (H3N2)

HA 1642/1701 (96.5) KF986921 A/swine/Illinois/A01291953/2013 (H1N1)

NP 1536/1569 (97.9) JN706701 A/turkey/Ontario/FAV-10/2011 (H3N2)

NA-1 1372/1419 (97.3) KC333154 A/swine/Pennsylvania/A01432180/2012 (H1N1)

Matrix 1018/1027 (99.1) JN683632 A/turkey/Ontario/FAV-9/2011 (H3N2)

NS 871/891(97.8) JN706704 A/turkey/Ontario/FAV-10/2011

Pandemic H1N1 (Mexico 09) viruses in poultry

- 56 week old breeder turkeys were diagnosed with drop in egg production- All 8 gene segments belong to pandemic H1N1 of human origin implying

reverse zoonosis

WIN-AH-2017-FAV-0023 Identity similarity Top matches at GenBank

PB2 2278/2280 (99.9) A/Nebraska/11/2018(H1N1)

PB1 2270/2274 (99.8) A/Nebraska/11/2018(H1N1)

PA 2147/2151 (99.8) A/Nebraska/11/2018(H1N1)

HA 1700/1701(99.9) A/Nebraska/11/2018(H1N1)

NP 1493/1497 (99.7) A/Nebraska/11/2018(H1N1)

NA-1 1409/1410 (99.9) A/Nebraska/11/2018(H1N1)

Matrix 981/982(99.9) A/Nebraska/11/2018(H1N1)

NS 843/844 (99.9) A/Nebraska/11/2018(H1N1)

Acknowledgements

MAFRI - Dr. Neil Pople

AHL - Dr Davor Ojkic

LEAQ – Dr. FairbrotherJulie-Hélène

BIOVET – Dr Andre Broes

NCFAD- Wanhong Xu- Brad Pickering- Matt Suderman- Tamiko Hisanaga- Genomics group

USDA-ARS- Dr Amy Vincent- Dr Tavis Anderson