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Epidemiology and Infection
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SEASONALITY DYNAMICS OF AVIAN INFLUENZA OCCURRENCES IN CENTRAL
AND WEST AFRICA
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T. L. Fuller1,*, M. F. Ducatez2,3, K. Y. Njabo1, E. Couacy-Hymann4, T. Chasar1, G. L. Aplogan5,
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S. Lao1, F. Awoume6, A. Téhou7, Q. Langeois2,3, S. Krauss8, T. B. Smith1,9
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California, Los Angeles USA
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Hôtes Agents Pathogènes, Toulouse, France
Center for Tropical Research, Institute of the Environment and Sustainability, University of
Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1225, Interaction
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Toulouse, Toulouse, France
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Central Laboratory for Animal Diseases (LANADA), Bingerville, Côte d’Ivoire
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Laboratoire de Diagnostic Vétérinaire et de Sérosurveillance (LADISERO), Parakou, Benin
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Laboratoire Vétérinaire de Lomé, Lomé, Togo
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Centre National de Gestion de Réserve de Faune (CENAGREF), Cotonou, Benin
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Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis,
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Tennessee, USA
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*To whom correspondence and requests for reprints should be addressed: Email:
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fullertl@ucla.edu. Mailing address: 619 Charles E. Young Drive East, La Kretz Hall Suite 300,
Université de Toulouse, Institut National Polytechnique, École Nationale Vétérinaire de
Department of Ecology and Evolutionary Biology, University of California, Los Angeles USA
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Institute of the Environment and Sustainability, University of California, Los Angeles 90049
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USA
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SUPPLEMENTARY MATERIAL
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Table S1. Variables used to predict AIV in Central African birds.
Variable
Source
Reference(s)
Avian family and migratory status http://avibase.bsceoc.org/avibase.jsp?lang=EN
(1)
Rainy season timing:
one rainy season (July-Sep) vs.
two (May & Sep-Oct)
http://trmm.gsfc.nasa.gov/
(2, 3)
Relative humidity (%)
http://www.cru.uea.ac.uk/cru/data/hrg/tmc/
(4)
Poultry density
http://www.fao.org/ag/againfo/resources/en/
glw/glw_dens.html
(5)
Habitat type
https://lpdaac.usgs.gov/products/modis_prod (6)
ucts_table/mcd12q1
Ground-based rainfall data to
validate satellite estimates
http://www.statisticscameroon.org/news.php?id=170
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6
2
(3, 7)
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Table S2. Cycle threshold (CT) cutoffs considered evidence of the influenza A virus based
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on a search of the Web of Science database. In the studies cited below, samples with CT-
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values below the cutoff were classified as influenza positive.
Host species
Cutoff Reference
Human
38
(8)
Wild birds
35
(9)
Human
27
(10)
Human
40
(11)
Human
28.6
(12)
Human
40
(13)
Human
39
(14)
Environmental
30
(15)
Median
37
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5
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Table S3. Akaike weights for models that included avian family, rainy season timing, and
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percent migratory birds per site as predictors of AIV positives in Central African birds.
AIC
Delta
Akaike
AIC
weight
1307.91
0.00
0.87
AIV Positive = Rainy season timing + Avian family
1312.34
4.43
0.10
AIV Positive = Rainy season timing
1322.77
14.86
0.00
AIV Positive = Avian family
1316.48
8.57
0.01
AIV Positive = Avian family + Percent migrants
1316.07
8.16
0.01
AIV Positive = Percent migrants
1327.29
19.38
0.00
AIV Positive = Rainy season timing + Percent migrants
1317.80
9.89
0.01
Model
AIV Positive = Rainy season timing + Avian family +
Percent migrants
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Table S4. Avian family, rainy season timing, and percent migratory birds per site are
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equally important predictors of the rate of RT-PCR positives in Central African birds. The
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weight of each variable was defined as the sum of the weights of all models that included the
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variable (Table S3). Since the all three variables had similar weights, no variable had much
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greater influence on the rate of AIV positives than the other variables.
Effect
Akaike weight
Avian family
Categorical variable: the analysis included
37 families
Rainy season timing
Categorical variable: one rainy season
(July-Sep) vs. two (May & Sep-Oct)
Percent migratory birds per site
Range: 0-44.83%
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5
0.347
0.34
0.312
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Figure S1. Sampling locations in Central Africa with two annual rainy seasons. We
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calculated mean monthly rainfall during the year when the site was sampled using precipitation
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radar from the Tropical Rainfall Measuring Mission (TRMM). These sites exhibited a bimodal
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distribution of precipitation with spring and fall rainy seasons, typically occurring in May and
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September-October, respectively. The dashed vertical line in each panel indicates the median
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sampling date.
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Figure S2. Sampling locations in Central Africa with peak rainfall occurring from July to September. As in Fig. S1, rainfall
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estimates were obtained from TRMM and the vertical line represents sampling date.
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(2)
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(3)
République du Cameroun. Annuaire Statistique du Cameroun. Yaoundé, Cameroon:
Institut National de la Statistique, 2012.
(4)
New M, Lister D, Hulme M, Makin I. A high-resolution data set of surface climate over
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Franceschini G, Robinson TP, Morteo K, Dentale D, Wint W, Otte J. The Global
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(6)
Friedl MA, Sulla-Menashe D, Tan B, et al. MODIS Collection 5 global land cover:
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(7)
Grieser J. New_LocClim: Local Climate Estimator. United Nations Food & Agriculture
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(8)
Hernes SS, Quarsten H, Hamre R, Hagen E, Bjorvatn B, Bakke PS. A comparison of
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(9)
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rapid influenza antigen test: Reappraisal with experience from the 2009 H1N1 pandemic. J
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(13) DeByle C, Bulkow L, Miernyk K, et al. Comparison of nasopharyngeal flocked swabs
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