Influenza virus prevalence and

risk factors in weaning-age pigs

Leman Swine Conference

Tuesday, September 17 2013

Matt Allerson, DVM, PhD

University of Minnesota

College of Veterinary Medicine

Influenza A Virus

• Orthomyxoviridae family– Type

•A, B, and C

– Subtype• HA and NA

• H1N1, H1N2, H3N2

– Clusters• H1 = α, β, γ, δ, and pandemic

• H3 = I, II, III, and IV

Image: www.cdc.gov

Influenza A Virus

• Cause of disease in many animal species

– Pigs Humans Avian

• pH1N1

• vH3N2

• Pigs

– Respiratory disease

– Transmission between species

– Economic impact

Influenza A Virus

• Economic impact

– $3.23 difference from baseline in loss per head

placed (Dykhuis Haden et al., 2012)

– $10.41 difference from baseline in loss per head

placed due to SIV/PRRSV combination (Dykhuis

Haden et al., 2012)

Influenza A virus

• Seroprevalence– 20-47% (Hinshaw et al., 1978)

– 51% (Chambers et al., 1991)

– 27% H1, 8% H3 (Olsen et al., 2000)

– 83% in sow herds in Ontario (Poljak et al., 2008)

– Over 90% in sow herds in Belgium, Germany, and Spain (Van Reeth et al., 2008)

• Active surveillance (Corzo et al., 2013)

– 91% of growing pig sites tested influenza virus positive at least once

Background

Influenza A virus

IncidenceDuration

“What should we do about flu?”

• M. Torremorell, 2011 Leman conference

– Not ignore influenza

– Take a “PRRS-like” approach

• How much is it costing us

• Address flu at the top of the production system with a

focus on producing negative pigs at weaning

• Understand where the viruses come from

Sow farms

Day

of sampling

Sampling

event

Sows Gilts Pigs 3-10

days of age

Pigs 11-26

days of age

0 1 0/60 0/59 1/60 6/60

27 2 0/60 0/60 0/60 4/58

56 3 NT NT NT 0/58

Overall 0/120 0/119 1/120 10/176

Sow farms

Subpopulation Median

Sows 0.17

Gilts 0.23

Pigs 3-10 days of age 0.15

Pigs 11-26 days of age 0.26

Median ELISA S/N ratios

Vaccination estimates

Source Year Breeding Growing

USDA:APHIS 2000 56% 20%

USDA:APHIS 2006 70% 15-20%

Beaudoin et al. 2007-09 71% 8%

Objectives

• Assess the prevalence and temporal patterns of influenza virus infection in weaning age pigs

• Characterize viruses obtained within selected sow farms

• Evaluate the association between sow herd attributes (including influenza vaccination) and the prevalence of influenza virus positive weaning-age pigs

Methods

• 52 sow farms

– Farrow to wean sow herds

– History of influenza virus infection at the sow

herd within the previous year

– Replacement gilts introduced to the sow herd

from a source outside of the sow herd premises

• 8 production systems

• 6 different states

Methods

• 30 weaning age pigs sampled monthly

– Nasal swabs

– 3 to 6 sampling events

• RRT-PCR• Virus isolation

• Subtyped and HA sequencing

• HA gene sequences compared within farm

Sow farms

Sampling

Events

Pools(pools of 3 swabs)

n=52

n=252

n=2,520

44% +

26% +

15% +

Results

Pool results

Sampling event Sampling event

Farm 1 2 3 4 5 6 Farm 1 2 3 4 5 6 1 H1 H1 H1 27

2 28

3 29 H1 H1

4 30 H1 H1 H1 H1

5 H3 31

6 32 H3

7 33

8 34 H1

9 H3 H3 H3 35 H3 H3 H3 H3 H3 H3

10 36 H3 H3 H3/H1 H3 H3 H3

11 H1 H1 H1 37 H1 H1 H1 H1 H1 H1

12 38 H1 H1

13 H1 H1 39

14 40 H3 H3

15 41

16 H3 H3 42

17 43

18 44 H1 H1 H1 H1

19 H1 H1 H1 45 H3

20 46

21 47 H3 H3 H3

22 48

23 49

24 50 H1 H1

25 H1 H1 51 H1 H1

26 52 H1 H1 H1

ResultsFarm

ID

Count of HA

gene sequences

compared

Subtype Lowest % identity

between all

sequences

1 3 H1 99.8

9 3 H3 99.7

11 2 H1 99.8

13 2 H1 99.4

19 3 H1 99.5

25 2 H1 99.8

30 2 H1 99.9

35 6 H3 98.8

36 6 H3 98.8

37 6 H1 99.4

38 2 H1 99.9

40 2 H3 100

44 4 H1 99.8

47 2 H3 99.8

50 2 H1 99.7

51 2 H1 99.9

52 3 H1 99.8

• HA gene sequences

similar across (+)

sampling events

within farm

• 3 sow herds tested

(+) for 6 consecutive

sampling events over

durations of 156, 165,

and 165 days

• Different viruses

across farms

Results

• 88% of sow herds that tested IAV negative at the first sampling event continued to test negative throughout the study period

• 84% of sow herds that tested influenza virus positive at the first sampling event tested positive for at least one additional sampling event

• 3 sow herds tested positive for 6 consecutive sampling events over durations of 156, 165, and 165 days

Discussion

• Weaning age pig as a target for influenza virus testing and surveillance

• Maintenance within herds and transport to distant sites

• Sampling event results repeatable over study period

• HA gene sequences were also similar over positive sampling events within herds

• Sow herds an important population for influenza virus epidemiology and diversity

Dissemination

• Regional movement

• Transport of influenza virus via weaning age

pigs

Spatial dynamics (Nelson et al., 2011)

• Spatial dissemination of human origin H1

viruses (δ cluster) in North America

• Dissemination follows swine movement

Example – influenza positive 3 months

3,000 head sow farm

Weaning 1,200 pigs per week

15,000 pigs

10 different sites?

Still to come……

• Association of influenza virus weaning age

pig status:

– Vaccination

– Filtration

– Gilt introductions

– Pig density

– Etc.

Limitations

• Farm selection

• Not able to assess seasonality

• HA sequence comparison only

Acknowledgements

• Funding and support

– Merck Animal Health

– Newport Laboratories

– Novartis Animal Health

– Zoetis

• Producers and veterinarians

Thank you!

Questions?