Spatial epidemiology of avian influenza in Asia and intensifying poultry production systems
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Transcript of Spatial epidemiology of avian influenza in Asia and intensifying poultry production systems
M. Gilbert
Université Libre de Bruxelles
Livestock Systems and Environment (LSE) Seminar
ILRI, Nairobi, 23 January 2014
Spatial epidemiology of avian influenza in Asia and intensifying
poultry production systems
Spatial epidemiology of avian
influenza in Asia and intensifying
poultry production systems
M. Gilbert
Biological control and spatial ecology,
Université Libre de Bruxelles
http://lubies.ulb.ac.be/Spatepi.html
HPAI H5N1 (FAO Empres-I): 2004-2012
A moving target #1: distribution in Thailand
1 Jan 2004 – 1 Jul 2004 1 Jul 2004 – 1 Jul 2005 1 Jul 2005 – end 2008
A moving target #2: distribution in Indonesia
2004 - 2008
2009
2010
2011
2006
A moving target #3: distribution in India &
Bangladesh
2007-2011 2012
Outbreaks
A moving target #3: distribution in China
Human cases
Positive markets
How to deal with those different situations ?
Pattern of spread
• Absence can be suitable
Pattern of surveillance and control
• What is an absence ?
Analysis
• Break down by country / epidemic phase
Comparative analysis
• Gain a general understanding from multiple studies
Focus on a limited set of factors
• What animal is infected
• Pattern of excretion (quantity, duration)
• Contacts with other hosts
Hosts
• How host are moved;
• How fomites are moved;
• Surveillance, prevention, control
Anthropogenic
• How and where the virus persists outside the host
• How and where poultry are raised
Environment
Time line
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EMP
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sia)
THA
IDN
CHN
IND
BGD
VNM
2004 First steps: firefighting in Thailand
HPAI H5N1 & ducks in Thailand
Farm chicken
Native chicken HPAI H5N1
Gilbert et al. (2006) EID 12(2):227-234
HPAI H5N1 & ducks in Thailand
Farm ducks
Free grazing ducks
HPAI H5N1
Gilbert et al. (2006) EID 12(2):227-234
Free-grazing ducks can be mapped using
remotely sensed indicators
Gilbert et al. (2007) Ag., Eco. Env. 119:409-415
Thailand and Vietnam model
• Cropping intensity, domestick duck density, human population density, chicken density (VNM) as main risk factors
• In Thailand: Paul et al. (2010); Tiensin et al. (2009)
• In Vietnam: Pfeiffer et al. (2007)
Spatial model: building and validation 0.0 0.2 0.4 0.6 0.8 1.0
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0.4
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1 - Specificity
Se
nsitiv
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AUC = 0.66 +/- 0.00844
Thailand: Wave I
0.0 0.2 0.4 0.6 0.8 1.0
0.0
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1 - Specificity
Se
nsitiv
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AUC = 0.74 +/- 0.0139
Thailand: Wave III
0.0 0.2 0.4 0.6 0.8 1.0
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1 - Specificity
Se
nsitiv
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AUC = 0.66 +/- 0.0081
Vietnam: Wave I
0.0 0.2 0.4 0.6 0.8 1.00
.00
.40
.81 - Specificity
Se
nsitiv
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AUC = 0.742 +/- 0.0142
Vietnam: Wave II
0.0 0.2 0.4 0.6 0.8 1.0
0.0
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1 - Specificity
Se
nsitiv
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AUC = 0.612 +/- 0.0213
Vietnam: Wave III
0.0 0.2 0.4 0.6 0.8 1.0
0.0
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1 - Specificity
Se
nsitiv
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AUC = 0.63 +/- 0.0249
North Vietnam: Wave III
0.0 0.2 0.4 0.6 0.8 1.0
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Se
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Thailand
Wave IWave IIWave III
0.0 0.2 0.4 0.6 0.8 1.0
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Vietnam
Wave IWave IIWave III
Gilbert et al. (2008) PNAS 105: 4769-4774
Spatial model: predictions
Gilbert et al. (2008) PNAS 105: 4769-4774
Predictions in Indonesia
Loth et al. (2011) Prev. Vet. Medecine. Doi:10.1016/j.prevetmed.2011.06.006
Predictions in South Asia
Gilbert et al. (2010) Ecohealth 7(4):448-58
Outbreak density profile in Thailand Thailand
Ou
tbre
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sity
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Gilbert et al. (2010) Ecohealth 7(4):448-58
Outbreak density profile in Thailand vs.
Vietnam
ThailandO
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THA Vietnam
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VNM
Outbreak density profiles
ThailandO
utb
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sity
0.0
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Vietnam
Ou
tbre
ak D
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sity
0.0
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India
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Bangladesh
Ou
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0.0
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Gilbert et al. (2010) Ecohealth 7(4):448-58
Production structure in Thailand
Van Boeckel et al. (2012) Ag., Eco. Env. 10.1016/j.agee.2011.12.019
Disagregating poultry data
Van Boeckel et al. (2012) Ag., Eco. Env. 10.1016/j.agee.2011.12.019
BRT model in Thailand
Van Boeckel et al. PLOS ONE 7(11): e49528.
doi:10.1371/journal.pone.0049528
Different duck systems
Delineate areas where HPAI
can persist
Free-grazing,
local movements
e.g. Bangladesh,
India, Indonesia,
Nigeria
Free-grazing
intensive
movements
e.g. Central plain of
Thailand, Vietnam
deltas
Farmed
e.g. North-
eastern
Thailand
Review paper on HPAI H5N1 risk factors
Review paper on HPAI H5N1 risk factors
• Factors have been studied at various scale: farm to country level;
• Factors were very different from one study to another: real difficulty in comparing studies outcomes;
• Overall, some factors showed consistent association with the risk of HPAI H5N1 presence across countries and scales:
• Domestick duck density;
• Anthropogenic (Human pop. density, distance to roads, markets)
• Indicators of water presence
• The effect of chicken density is variable, most likely due to differences in production systems
Review of HPAI H5N1 risk factors
• Factors have been overlooked:
• Socio-economic;
• Trade and market networks;
• Wild bird distribution and movement;
Duck distribution
Intensification of duck production in China
First
report of
H5N1
China: 75% of ducks
• Outbreaks (mainly in chicken farms)
• H5N1 positives from markets
Martin et al. (2011) Plos Pathogens 7(3): e1001308
BRT model
• Outbreaks
• Chicken and human
pop. density;
• More emphasis on the
intensive productions
areas
• Market surveillance
• Hpop, duck density, and
% water.
• Duck/rice ecosystem in
the south
Martin et al. (2011) Plos Pathogens 7(3): e1001308
• Poyang lake: main lake for migratory
watefowls
• Poyang lake: wild geese farms
• Poyang lake: main lake for migratory
watefowls
Poyang lake populations
0.5 million wild birds (75 species);
3 millions « farmed » wild birds;
Surrounded by 10 counties with
26 million ducks and geese in farms;
21 million domestic chicken in farms;
6 million people;
Temporal patterns in Poyang lake
Cappelle et al. (in revision)
Spatial patterns in Poyang lake
Cappelle et al. (in revision)
Live-bird market networks
Martin et al. (2011)
Intensified poultry production rapidly, duck
population that outweights all other coutries
In regions with extensive interface with the wild
avifauna
Connectivity between regions is facilitated by
long-distance trade between live-bird markets
Relevance to H7N9 ?
China
A quick virtual tour in Huzhou
Detailed investigation for all 12 confirmed H7N9 cases
in Huzhou, Zhejiang province
(http://www.eurosurveillance.org/ViewArticle.aspx?Art
icleId=20481).
Linked to markets with:
Chickens infection rate of samples = 36 / 129 = 27%
Pigeon infection rate of samples = 2 / 6 = 33%
A quick virtual tour in Huzhou
A quick virtual tour in Huzhou
A quick virtual tour in Huzhou
A quick virtual tour in Huzhou
H7N9 in China: geographic space
H7N9 in China: var space
•Human population
•Duck population
•Chicken population
•% of land occupied
by water
•% of land occupied
by rice paddy fields
•Accessibilit y(travel
time to major cities)
•Live-bird market
density
BRT profiles
H7N9 risk maps
Combined risk
Live bird markets
• Important and widespread in China, Vietnam, Bangladesh, Indonesia, Cambodia
• Can allow disease spread and persistence through the meta-population of live-bird markets
• Social Network Analysis combined with mathematical modelling shows potential for targetting markets where intervention would be most beneficial (Fournie et al. 2012, 2013)
• The current missing elements to understand AI (H5N1/H7N9) persistence and spread ?
Intensification of duck production in China
First
report of
H5N1
Global trends
0
500,000,000
1,000,000,000
1,500,000,000
2,000,000,000
2,500,000,000
19
61
19
65
19
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19
77
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81
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89
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93
19
97
20
01
20
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09
Heads
Cattle & Buffaloes Sheep and Goats
Chicken (/10) Pork
Where are we going ?
• On-going intensification in China, extensive wild bird
interface, high LBM density
• India / Bangladesh: intensification, duck population,
extensive interface with wild birds, live bird markets
• Is large-scale farming with high biosafety the only way to
intensify production safely ?
• Can subsistance and commercial poultry farming co-
exist ?
Back to Thailand
One of the highest density of domestick
ducks;
Extensive irrigated land;
Large commercial sector;
Smallholders & native chickens;
High human population density;
Few or no live-bird markets
Conclusion
• Key role of ducks => differ according to production
systems
• Intensification of duck production in contact with WB
genetic pool of viruses
• Spread to other poultry and human exposure facilitated
by LBM networks
• Try not having both
Thank you Acknowledgments:
J. Cappelle, L. Hogerwerf, L. Loth, V. Martin, S.
Newman, M. Paul, D. Pfeiffer, D. Prosser, T. Robinson,
J. Slingenbergh, K. Stevens, W. Thapongtharm, T. Van
Boeckel, R. Wallace, W. Wint, X. Xiao
,