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?