Swine influenza virus prevalence and risk factors in weaning-age pigs - Matt Allerson, University of Minnesota, College of Veterinary Medicine, from the 2013 Allen D. Leman Swine Conference, September 14-17, 2013, St. Paul, Minnesota, USA. More presentations at http://www.swinecast.com/2013-leman-swine-conference-material

1. 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

2. 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

3. Influenza A Virus
• Cause of disease in many animal species
– Pigs
Humans
Avian
• pH1N1
• vH3N2
• Pigs
– Respiratory disease
– Transmission between species
– Economic impact

4. 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)

5. 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

6. Background
Influenza A virus
Duration
Incidence

7. “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

8. Sow farms
Day
of sampling
Sampling Sows
event
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
0/120
0/119
1/120
10/176
Overall

9. Sow farms
Median ELISA S/N ratios
Subpopulation
Median
Sows
0.17
Gilts
0.23
Pigs 3-10 days of age 0.15
Pigs 11-26 days of age 0.26

10. Vaccination estimates
Source
Year
USDA:APHIS
2000
56%
20%
USDA:APHIS
2006
70%
15-20%
71%
8%
Beaudoin et al. 2007-09
Breeding Growing

11. 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

12. 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

13. 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

14. Results
Sow farms
n=52
44% +
Sampling
Events
n=252
26% +
Pools
n=2,520
15% +
(pools of 3 swabs)

15. Pool results

16. Sampling event
Farm
1
2
3
1
H1
H1
4
Sampling event
5
H1
6
Farm
1
2
3
4
5
H1
H1
H1
6
H1
27
2
28
3
29
4
30
5
H3
H1
H1
31
6
32
7
33
8
34
H1
35
H3
H3
H3
H3
H3
H3
36
H3
H3
H3/H1
H3
H3
H3
37
H1
H1
H1
H1
H1
H1
38
H1
H1
H3
H3
H1
H1
H1
H3
H3
H3
9
H3
H3
H3
10
11
H1
H1
H1
12
13
H1
H1
H3
39
14
40
15
41
16
H3
H3
42
17
43
18
44
H1
45
H3
19
H1
H1
H1
20
46
21
47
22
48
23
49
24
50
H1
H1
51
H1
H1
52
H1
H1
25
26
H1
H1
H1

17. Results
Farm
ID
1
9
11
13
19
25
30
35
36
37
38
40
44
47
50
51
52
Count of HA
gene sequences
compared
Subtype
Lowest % identity
between all
sequences
3
3
2
2
3
2
2
6
6
6
2
2
4
2
2
2
3
H1
H3
H1
H1
H1
H1
H1
H3
H3
H1
H1
H3
H1
H3
H1
H1
H1
99.8
99.7
99.8
99.4
99.5
99.8
99.9
98.8
98.8
99.4
99.9
100
99.8
99.8
99.7
99.9
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

18. 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

19. 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

20. Dissemination
• Regional movement
• Transport of influenza virus via weaning age
pigs

21. Spatial dynamics (Nelson et al., 2011)
• Spatial dissemination of human origin H1
viruses (δ cluster) in North America
• Dissemination follows swine movement

22. Example – influenza positive 3 months
3,000 head sow farm
Weaning 1,200 pigs per week
15,000 pigs
10 different sites?

23. Still to come……
• Association of influenza virus weaning age
pig status:
– Vaccination
– Filtration
– Gilt introductions
– Pig density
– Etc.

24. Limitations
• Farm selection
• Not able to assess seasonality
• HA sequence comparison only

25. Acknowledgements
• Funding and support
– Merck Animal Health
– Newport Laboratories
– Novartis Animal Health
– Zoetis
• Producers and veterinarians

26. Thank you!
Questions?