Supplementary file

Table S1. Data used in the study

Data Description Sources

Epidemiological dataHuman leptospirosis case in Upper Yangtze River Basin (UYRB) and Pearl River Basin (PRB)

Notification data (2005-2016) containing information on age, gender, code of county, county’s coordinates, case classification (suspected, probable, confirmed).

China Center for Disease Control and Prevention

Environmental variablesPrecipitation Gridded precipitation data (1-km x 1-km). Values were sampled at

county-level using ArcGIS software.WorldClim (https://www.worldclim.org/)

Land surface temperature (LST)

Raster data with 1-km spatial resolution. Monthly LST for each county for period of 2005-2016 is sampled using ArcGIS software. Values were sampled at county-level using ArcGIS software.

MODIS Terra, MODIS11A2 8-day, 1 km spatial resolution (https://modis.gsfc.nasa.gov/data/dataprod/mod11.php)

Normalized difference vegetation index (NDVI)

Monthly NDVI value for each county for period of 2005-2016 were sampled using ArcGIS software. The NDVI value ranges from -1 to 1.

MODIS Terra 13Q1 v006 Vegetation Indices 16-Day L3 Global, 250 meter spatial resolution (https://lpdaac.usgs.gov/products/mod13q1v006/)

Normalized difference water Index (NDWI)

Monthly NDWI value for each county for period of 2005-2016 were sampled using ArcGIS software. NDWI calculated by using formula (RNIR-RSWIR) / (RNIR + RSWIR). The value of the index ranges from -1 to 1.

MODIS Terra MOD09A1.V6 8-day, 500 m spatial resolution (https://modis.gsfc.nasa.gov/data/dataprod/mod09.php)

Elevation GTOPO30 Digital elevation model (DEM), 1-km (30-arc seconds) spatial resolution. Values are sample at county-level using ArcGIS software

https://www.usgs.gov/centers/eros/science/usgs-eros-archive-digital-elevation-global-30-arc-second-elevation-gtopo30?qt-science_center_objects=0#qt-science_center_objects

Slope Slope was calculated from the SRTM-DEM elevation data by using ArcGIS toolbox. The mean slope values for each county were

sampled.Land cover Land cover types for 2005 and 2015. Reclassified into 6 categories:

Cultivated land (1), Forested land (2), Grassland (3), Waterbodies (4), Artificial surfaces (5), and Bare land

Data Center for Resources and Environmental Sciences, Chinese Academy of Sciences (RESDC) (http://www.resdc.cn/)

Hydrological features Yangtze River Basin and Pearl River Basin boundaries and streams HYDRO1k - USGShttps://gcmd.nasa.gov/records/GCMD_HYDRO1k.html;

World Bank. Major River Basins of the Worldhttps://datacatalog.worldbank.org/dataset/major-river-basins-world

Gassert, F., T. Luo, T. Shiao, and M. Luck. 2013. “Yangtze River Basin Study.” Working Paper. Washington, DC: World Resources Institute.https://www.wri.org/resources/data-sets/yangtze-river-basin-study

Livestock density (Pig and Cattle density)

Gridded pigs and cattle density with year of reference is 2010. Cell resolution 0.00833 (1-km x 1-km). Values are sample at county-level using ArcGIS software.

FAO-GeoNetwork model of livestock density (GLW 2.01) (http://www.fao.org/geonetwork/srv/en/main.home)

Urban/rural Raster data for urban or rural classification with a 5x5 km resolution. A 5x5 km resolution rural/urban surface derived from the Global Rural-Urban Mapping Project (GRUMP), (http://sedac.ciesin.columbia.edu/data/set/grump-v1-urban-extents ).

Socioeconomic variablesPopulation Annual population data by county (2005-2015) for incidence

estimation. For spatial modelling, raster (gridded) population data (in people per hectare) of 2010 and 2015 for China at the resolution of 100 m were used.

China National Bureau of Statistics (http://www.stats.gov.cn/english/)WorldPop database (https://www.worldpop.org/project/categories?id=3).

Population density Gridded (raster) population density map with 1-km spatial resolution based on UN WPP-Adjusted Population Density, v4.10 (2010, 2015)

Socioeconomic data and application centers (SEDAC) – Center for International Health Science Information Network (CIESIN) ( http://sedac.ciesin.columbia.edu/data/set/gpw-v4- population-density-adjusted-to-2015-unwpp-country-

totals-rev10/data-download ) Farmland/crop production

Raster data for crop production 2010 (in kg per ha) with 1-km spatial resolution. Values were sampled at county-level using ArcGIS software.

Resource and Environmental Science Data Center of the Chinese Academy of Sciences (http://www.resdc.cn)

Gross Domestic Product (GDP)

Raster map of 2010 Gross Domestic Product (GDP) of China with 1-km resolution. Values are sampled at county-level using ArcGIS software.

Global change research data publishing and repository (http://www.geodoi.ac.cn/weben/doi.aspx?Id=125)

Table S2. Quarterly leptospirosis notifications in Upper Yangtze River Basin (UYRB) and Pearl River Basin (PRB) for period 2005-2010 and 2011-2016

Region Characteristics 2005-2010 2011-2016

Q1 Q2 Q3 Q4 Total Q1 Q2 Q3 Q4 TotalUYRB Sex Female 0 12 695 64 771 2 9 186 28 225

Male 3 44 1510 166 1723 2 20 411 65 498Age group

Under 19 years

0 7 399 34 440 0 1 44 2 47

19 years 3 49 1806 196 2054 4 28 553 91 676Occup Non-farmer 0 13 380 36 429 3 5 67 9 84

Farmer 3 43 1825 194 2065 1 24 530 84 639Total 3 56 2205 230 2494 4 29 597 93 723

PRB gender Female 18 58 150 52 278 10 39 62 31 142Male 46 140 355 98 639 29 68 206 111 414

Age group

Under 19 years

6 30 109 18 163 0 13 39 6 58

19 years 58 168 396 132 754 39 94 229 136 498Occup Non-farmer 37 83 168 54 342 21 46 100 51 218

Farmer 27 115 337 96 575 18 61 168 91 338Total 64 198 505 150 917 39 107 268 142 556

Abbreviations: URYB, Upper Yangtze River Basin; PRB, Pearl River Basin; Q, quarter.

Table S3. Spearman’s correlation coefficient between covariates, Upper Yangtze River Basin (UYRB)

Prec NDVI NDWI LST Elev Slope Landcov Cattle Pig Urban Crop Pop GDPPrecipitation 1

NDVI 0.06 1NDWI 0.26 -0.62 1LST -0.48 0.04 -0.65 1Elevation -0.28 0.51 -0.65 0.29 1Slope -0.22 0.47 -0.43 0.11 0.88 1Land cover -0.02 0.32 -0.38 0.09 0.71 0.62 1Cattle density -0.23 0.10 0.17 -0.28 -0.10 -0.07 -0.13 1Pig density 0.12 -0.42 0.46 -0.22 -0.77 -0.81 -0.66 0.20 1Urban/Rural 0.03 0.41 -0.12 0.03 0.04 0.03 -0.26 0.04 0.06 1Crop production 0.11 -0.60 0.39 0.12 -0.70 -0.75 -0.63 -0.31 0.65 0.06 1Population density 0.005 -0.57 0.28 -0.07 -0.22 -0.21 0.10 0.009 0.12 -0.82 0.11 1GDP 0.05 -0.58 0.24 -0.0004 -0.19 -0.19 0.10 -0.12 0.06 -0.73 0.16 0.73 1

Table S4. Spearman’s correlation coefficient between covariates, Pearl River Basin

Prec NDVI NDWI LST Elev Slope Landcov Cattle Pig Urban Crop Pop GDPPrecipitation 1NDVI -0.28 1NDWI 0.15 -0.28 1LST 0.14 0.22 0.08 1Elevation -0.67 0.40 -0.20 -0.17 1Slope -0.23 0.53 -0.15 -0.09 0.66 1Land cover 0.02 -0.23 0.05 0.04 -0.004 -0.06 1Cattle density -0.43 0.35 -0.20 -0.05 0.42 0.30 -0.09 1Pig density -0.06 0.008 0.03 0.05 -0.17 -0.17 0.06 0.27 1Urban/Rural 0.36 -0.64 0.22 0.05 -0.47 -0.54 0.51 -0.41 -0.03 1Crop production -0.10 -0.04 -0.01 0.07 -0.31 -0.47 -0.45 0.04 0.19 -0.11 1Population density 0.18 -0.47 0.17 0.05 -0.30 -0.36 -0.16 -0.16 -0.002 0.72 -0.16 1GDP 0.36 -0.69 0.22 0.06 -0.49 -0.59 0.44 -0.41 0.004 0.94 -0.08 0.63 1Abbreviations: Prec, precipitation; NDVI, normalized difference vegetation index; MNDWI, modified normalized difference water index; LST, land surface temperature; Elev, elevation; Landcov, land cover; Pop, population density; GDP, gross domestic product

Table S5. Results of non-spatial multivariable analysis between environmental, socioeconomic factors and leptospirosis count, Upper Yangtze River Basin (UYRB)

Coefficient 95% CI P-valueLower Upper

EnvironmentPrecipitation -0.00007 -0.0001 -0.00003 <0.001LST -0.065 -0.070 -0.06 <0.001NDVI -9.31 -9.60 -9.03 <0.001NDWI -7.04 -7.24 -6.83 <0.001Cattle density 0.012 0.0125 0.0128 <0.001Pig density 0.0036 0.003 0.004 <0.001Land cover -0.416 -0.431 -0.400 <0.001Elevation -0.0004 -0.0003 -0.0003 <0.001SocioeconomicCrop production -0.0002 -0.00022 -0.00021 <0.001GDP -0.001 -0.0002 -0.00021 <0.001Urban -4.801 -5.170 -4.432 <0.001

Quarter1 Ref2 -0.567 -0.697 -0.436 <0.0013 0.380 0.254 0.505 <0.0014 0.326 0.200 0.451 <0.001

Year2005-2010 Ref2011-2016 -0.035 -0.042 -0.028 <0.001

Constant 14.64 14.21 15.07 <0.001

Table S6. Results of non-spatial multivariable analysis between environmental, socioeconomic factors and leptospirosis count, Pearl River Basin (PRB)

Coefficient 95% CI P-valueLower Upper

EnvironmentPrecipitation 0.0003 0.0002 0.0004 <0.001LST -0.051 -0.056 0.047 <0.001NDVI 2.911 2.759 3.064 <0.001NDWI 0.442 0.377 0.507 <0.001Cattle density -0.027 -0.028 -0.026 <0.001Pig density 0.002 0.002 0.003 <0.001Land cover -0.037 -0.039 -0.035 <0.001Elevation 0.001 0.0011 0.0013 <0.001SocioeconomicGDP 0.00003 0.0002 0.0004 <0.001

Quarter1 Ref2 0.066 -0.002 0.135 0.0593 0.140 0.063 0.216 <0.0014 -0.593 -0.650 -0.536 <0.001

Year2005-2010 Ref2011-2016 0.195 0.169 0.220 <0.001

Constant 2.863 2.676 3.050 <0.001

2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 20160

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Figure S1. Temporal variation of incidence of leptospirosis in UYRB, by quarter, 2005-2016.

2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 20160

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Figure S2. Temporal variation of incidence of leptospirosis in PRB, by quarter, 2005-2016

Figure S3. Maps of standard deviation of predicted incidence of human leptospirosis (top), spatially-structured random effect (center), and probability of non-zero case of leptospirosis (bottom) in Upper Yangtze River Basin (UYRB)

Figure S4. Maps of standard deviation of predicted incidence of human leptospirosis (top), spatially-structured random effect (center), and probability of non-zero case of leptospirosis (bottom) in Pearl River Basin (PRB)