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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N1

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sia)

THA

IDN

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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

0.0

0.4

0.8

1 - Specificity

Se

nsitiv

ity

AUC = 0.66 +/- 0.00844

Thailand: Wave I

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 = 0.74 +/- 0.0139

Thailand: Wave III

0.0 0.2 0.4 0.6 0.8 1.0

0.0

0.4

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1 - Specificity

Se

nsitiv

ity

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

ity

AUC = 0.742 +/- 0.0142

Vietnam: Wave II

0.0 0.2 0.4 0.6 0.8 1.0

0.0

0.4

0.8

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Se

nsitiv

ity

AUC = 0.612 +/- 0.0213

Vietnam: Wave III

0.0 0.2 0.4 0.6 0.8 1.0

0.0

0.4

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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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nsitiv

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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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nsitiv

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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

ak D

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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

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VNM

Outbreak density profiles

ThailandO

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sity

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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

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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

,