Global mapping of highly pathogenic avian influenza H5N1 and H5Nx clade 2.3.4.4 viruses with spatial cross-validation

Université Libre de Bruxelles, Belgium
International Livestock Research Institute, Kenya
Swiss Institute of Bioinformatics, Switzerland
University of Oklahoma, United States
Food and Agriculture Organization of the United Nations, Italy
Regional Office for Asia and the Pacific, Thailand
Food and Agriculture Organization of the United Nations, Vietnam

Nov 25, 2016

https://doi.org/10.7554/eLife.19571

Open access
Copyright information

Abstract
Data availability
Article and author information
Metrics

Abstract

Global disease suitability models are essential tools to inform surveillance systems and enable early detection. We present the first global suitability model of highly pathogenic avian influenza (HPAI) H5N1 and demonstrate that reliable predictions can be obtained at global scale. Best predictions are obtained using spatial predictor variables describing host distributions, rather than land use or eco-climatic spatial predictor variables, with a strong association with domestic duck and extensively raised chicken densities. Our results also support a more systematic use of spatial cross-validation in large-scale disease suitability modelling compared to standard random cross-validation that can lead to unreliable measure of extrapolation accuracy. A global suitability model of the H5 clade 2.3.4.4 viruses, a group of viruses that recently spread extensively in Asia and the US, shows in comparison a lower spatial extrapolation capacity than the HPAI H5N1 models, with a stronger association with intensively raised chicken densities and anthropogenic factors.

Data availability

The following previously published data sets were used

1. Tuanmu and Jetz
(2014) A global 1-km consensus land-cover product for biodiversity and ecosystem modelling
Public.

http://www.earthenv.org/landcover
1. Robinson
2. T.P.
3. Wint
4. G.R.W.
5. Conchedda
6. G.
7. Van Boeckel
8. T.P.
9. Ercoli
10. V.
11. Palamara
12. E.
13. Cinardi
14. G.
15. D'Aietti
16. L.
17. Hay
18. S.I.
19. Gilbert
20. M.
(2014) Mapping the Global Distribution of Livestock
Public.

http://www.livestock.geo-wiki.org/home-2/
1. Gilbert
2. M.
3. Conchedda
4. G.
5. Van Boeckel
6. T.P.
7. Cinardi
8. G.
9. Linard
10. C.
11. Nicolas
12. G.
13. Thanapongtharm
14. W.
15. D'Aietti
16. L.
17. Wint
18. W.
19. Newman
20. S.H.
21. Robinson
22. T.P.
(2015) Income Disparities and the Global Distribution of Intensively Farmed Chicken and Pigs
Public.

http://www.livestock.geo-wiki.org/home-2/
1. Linard
2. C.
3. Gilbert
4. M.
5. Snow
6. R.W.
7. Noor
8. A.M.
9. Tatem
10. A.J.
(2012) Population Distribution, Settlement Patterns and Accessibility across Africa in 2010
Public.

http://www.worldpop.org.uk
1. Gaughan
2. A.E.
3. Stevens
4. F.R.
5. Linard
6. C.
7. Jia
8. P.
9. Tatem
10. A.J.
(2013) High Resolution Population Distribution Maps for Southeast Asia in 2010 and 2015
Public.

http://www.worldpop.org.uk
1. Sorichetta
2. A.
3. Hornby
4. G.M.
5. Stevens
6. F.R.
7. Gaughan
8. A.E.
9. Linard
10. C.
11. Tatem
12. A.J.
(2015) High-resolution gridded population datasets for Latin America and the Caribbean in 2010, 2015, and 2020
Public.

http://www.worldpop.org.uk
1. CIESIN
(2016) Population Count Grid, v3: Gridded Population of the World (GPW), v3
Public.

http://sedac.ciesin.columbia.edu/entri
1. Scharlemann
2. J.P.W.
3. Benz
4. D.
5. Hay
6. S.I.
7. Purse
8. B.V.
9. Tatem
10. A.J.
11. Wint
12. G.R.W.
13. Rogers
14. D.J.
(2008) Global Data for Ecology and Epidemiology: A Novel Algorithm for Temporal Fourier Processing MODIS Data
Public upon request.

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001408
1. FAO
(2016) EMPRES-i - Global Animal Disease Information System
Public.

http://empres-i.fao.org/
1. Claes
2. F.
3. Kuznetsov
4. D.
5. Liechti
6. R.
7. Von Dobschuetz
8. S.
9. Dinh Truong
10. B.
11. Gleizes
12. A.
13. Conversa
14. D.
15. Colonna
16. A.
17. Demaio
18. E.
19. Ramazzotto
20. S.
21. Larfaoui
22. F.
23. Pinto
24. J.
25. Le Mercier
26. P.
27. Xenarios
28. I.
29. Dauphin
30. G.
(2014) The EMPRES-i genetic module: a novel tool linking epidemiological outbreak information and genetic characteristics of influenza viruses
Public.

http://openflu.vital-it.ch/
1. OIE
(2016) World Animal Health Information System
Public.

http://www.oie.int/wahis_2/public/wahid.php/Diseaseinformation/diseasehome

Article and author information

Author details

Madhur S Dhingra

Spatial Epidemiology Lab, Université Libre de Bruxelles, Brussels, Belgium

Competing interests
The authors declare that no competing interests exist.
Jean Artois

Spatial Epidemiology Lab, Université Libre de Bruxelles, Brussels, Belgium

Competing interests
The authors declare that no competing interests exist.
Timothy P Robinson

Livestock Systems and Environment, International Livestock Research Institute, Nairobi, Kenya

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-4266-963X
Catherine Linard

Spatial Epidemiology Lab, Université Libre de Bruxelles, Brussels, Belgium

Competing interests
The authors declare that no competing interests exist.
Celia Chaiban

Spatial Epidemiology Lab, Université Libre de Bruxelles, Brussels, Belgium

Competing interests
The authors declare that no competing interests exist.
Ioannis Xenarios

Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics, Lausanne, Switzerland

Competing interests
The authors declare that no competing interests exist.
Robin Engler

Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics, Lausanne, Switzerland

Competing interests
The authors declare that no competing interests exist.
Robin Liechti

Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics, Lausanne, Switzerland

Competing interests
The authors declare that no competing interests exist.
Dimitry Kuznetsov

Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics, Lausanne, Switzerland

Competing interests
The authors declare that no competing interests exist.
Xiangming Xiao

Department of Microbiology and Plant Biology, University of Oklahoma, Norman, United States

Competing interests
The authors declare that no competing interests exist.
Sophie Von Dobschuetz

Animal Production and Health Division, Food and Agriculture Organization of the United Nations, Rome, Italy

Competing interests
The authors declare that no competing interests exist.
Filip Claes

Emergency Center for Transboundary Animal Diseases, Regional Office for Asia and the Pacific, Bangkok, Thailand

Competing interests
The authors declare that no competing interests exist.
Scott H Newman

Emergency Center for Transboundary Animal Diseases, Food and Agriculture Organization of the United Nations, Hanoi, Vietnam

For correspondence
scott.newman@fao.org

Competing interests
The authors declare that no competing interests exist.
Gwenaëlle Dauphin

Animal Production and Health Division, Food and Agriculture Organization of the United Nations, Rome, Italy

For correspondence
Gwenaelle.Dauphin@fao.org

Competing interests
The authors declare that no competing interests exist.
Marius Gilbert

Spatial Epidemiology Lab, Université Libre de Bruxelles, Brussels, Belgium

For correspondence
marius.gilbert@gmail.com

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-3708-3359

Funding

National Institutes of Health (1R01AI101028-02A1)

Madhur S Dhingra
Jean Artois
Xiangming Xiao
Marius Gilbert

United States Agency for International Development (Emerging Pandemic Threats program)

Scott H Newman

Biotechnology and Biological Sciences Research Council (BB/L019019/1)

Timothy P Robinson

Fonds De La Recherche Scientifique - FNRS (PDR T.0073.13)

Catherine Linard
Marius Gilbert

Medical Research Council (ESEI UrbanZoo (G1100783/1))

Timothy P Robinson

CGIAR (Research Programs on Agriculture for Nutrition and Health (A4NH) and Livestock)

Timothy P Robinson

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.