Introduction
Hantaviruses are rodent-borne viruses belonging to the family Bunyaviridae, and can cause two kinds of human diseases, i.e., hemorrhagic fever with renal syndrome (HFRS) in Europe and Asia and hantavirus pulmonary syndrome (HPS) in the Western Hemisphere.1 Each hantavirus species is predominately associated with a distinct or a few related rodents as its primary natural reservoirs. Humans usually acquire hantavirus infection by contact or inhalation of aerosols and secretions from infected rodent hosts. In China, Hantaan virus (HTNV) and Seoul virus (SEOV), the recognized causative agents of HFRS, are respectively associated with Apodemus agrarius and Rattus norvegicus.2
Hemorrhagic fever with renal syndrome is a significant public health problem in mainland China. The number of incident cases accounts for 90% of the total reported cases in the world.2 Shandong Province is one of the most severe endemic areas in mainland China. Although integrated control measures including vaccination have been carried out for years, the disease incidence has not substantively decreased and new foci continuously emerged.
The incidence and geographic distribution of HFRS are known to be mainly determined by the population density, infection rate, and distribution of rodent hosts, which are usually influenced by the natural habitat structure including the availability of cover and burrow space, etc.3–8 Environmental changes in habitat could lead to an increase in virus transmission risk from infected rodents to humans.4–9 Studies on HPS indicated that the emergence of hantavirus was associated with weather and climatic events like El Niño Southern Oscillation.3,10,11 The prevalence of HFRS in China was determined by various environmental factors such as elevation, precipitation, temperature, vegetation, and soil types.12–14 Our previous study revealed that precipitation, humidity, and temperature was associated with the seasonal variation of HFRS incidence in Shandong Province.15 In this study, we used the surveillance data of the province to identify the risk factors and affected areas of hantavirus infections in rodent hosts based on the ecologic niche modeling (ENM) approach.
Materials and Methods
Collection of surveillance data.
Shandong Province is located on the eastern edge of the North China Plain (N34°22′52″–N38°15′02″, E114°19′53″–E122°43′), the downstream of the Yellow River. Surveillance on hantavirus infections in rodent hosts were carried out in four administrative regions including Jiaonan City, Zhangqiu City, Qingzhou City, and Jvnan County (Figure 1), according to the protocol made by Chinese Centers for Disease Control and Prevention. Briefly, several sites were selected for the surveys in spring and late autumn to early winter, when there were epidemic peaks of HFRS in the province. A total of 100–150 traps per patch with peanuts as bait were placed for two to three consecutive nights.16 Universal precautions were strictly followed including wearing protective clothing, footwear, surgical masks, and gloves. After identification of species and sex, blood samples were collected and lung tissues were removed from the captured rodents and stored in liquid nitrogen until tested. The rodent carcasses were disinfected and buried deeply in the field. For unidentified rodent species in the field, the craniums were brought to the laboratory for further identification.
Map of Shandong Province, P. R. China. The gray shades indicate the study areas where field surveillance on hantavirus infection in rodents was carried out from 2005 to 2008.
Citation: The American Society of Tropical Medicine and Hygiene 84, 3; 10.4269/ajtmh.2011.10-0314
Map of Shandong Province, P. R. China. The gray shades indicate the study areas where field surveillance on hantavirus infection in rodents was carried out from 2005 to 2008.
Citation: The American Society of Tropical Medicine and Hygiene 84, 3; 10.4269/ajtmh.2011.10-0314
Map of Shandong Province, P. R. China. The gray shades indicate the study areas where field surveillance on hantavirus infection in rodents was carried out from 2005 to 2008.
Citation: The American Society of Tropical Medicine and Hygiene 84, 3; 10.4269/ajtmh.2011.10-0314
Lung tissues were examined for hantavirus antigens at the Center for Disease Control and Prevention of Shandong Province using indirect immunofluorescent assay (IFA) previously described by Lee and others.17 In addition, data on reported HFRS cases were retrieved from the Shandong Notifiable Disease Surveillance System.
Collection and management of environmental data.
Data on eco-geographical variables (EGV) possibly contributing to transmission of hantavirus in rodent hosts were collected (Table 1).13,18–20 The data of each variable were converted to the study's geographic projection (Krasovsky_1940_Albers) and clipped to the study area. Elevation value was derived from a shuttle radar topography mission database with a spatial resolution of 1 km (http://srtm.csi.cgiar.org). Slope and aspect values were calculated from elevation using tools in ARCGIS 9.1 (Environmental Sciences Research Institute, Redlands, CA). Data on precipitation, relative humidity (RH), and temperature were obtained from China Meteorological Data Sharing Service System (http://cdc.cma.gov.cn). Land cover data were derived from the Global Land Cover Facility (GLCF) Data Products and Satellite Imagery (http://gcma.nasa.gov). Normalized difference vegetation index (NDVI) was generated from “Free Vegetation Products” (http://free.vgt.vito.be) in digital number value, and annual maximum values were calculated. Land surface temperature during daytime (LSTD) and land surface temperature during nighttime (LSTN) were derived from MODIS Land Products (http://modis-land.gsfc.nasa.gov) and processed using Environment for Visualizing Images software (version 4.3) (Research Systems Inc., Boulder, CO).
Eco-geographical variables (EGVs) for model building and percent contribution*
| Variable | Data source | Type | Contribution (%) |
|---|---|---|---|
| Temperature | China Meteorological Data Sharing Service System (http://cdc.cma.gov.cn) | Continuous | 8.5 |
| RH | China Meteorological Data Sharing Service System (http://cdc.cma.gov.cn) | Continuous | 9.4 |
| Precipitation | China Meteorological Data Sharing Service System (http://cdc.cma.gov.cn) | Continuous | ** |
| Land cover | The Global Land Cover Facility (GLCF) Data Products and Satellite Imagery (http://gcma.nasa.gov) | Categorical | 31.2 |
| NDVI | Free Vegetation Products (http://free.vgt.vito.be) | Continuous | 13.3 |
| LSTD | MODIS Land Products (http://modis-land.gsfc.nasa.gov) | Continuous | ** |
| LSTN | MODIS Land Products (http://modis-land.gsfc.nasa.gov) | Continuous | 11.1 |
| Elevation | SRTM digital elevation data provided by CGIAR (http://www.srtm.csi.cgiar.org) | Continuous | 26.5 |
| Slope | Degree of slope (maximum rate of change in elevation from each pixel to its neighbors) derived from the SRTM digital elevation data | Continuous | ** |
| Aspect | Derived from DEM | Categorical | ** |
RH = relative humidity; NDVI = normalized difference vegetation index; LSTD = land surface temperature during daytime; LSTN = land surface temperature during nighttime.
The variable was excluded from the final model.
Ecological niche models.
The ENMs were developed to understand environmental variation associated with the distribution of infected rodent reservoirs.21 A recent introduced presence-only distribution modeling technique—the Maximum Entropy approach, was applied in various domains and achieved high predictive accuracy,22–28 and showed the best predictive power across all sample sizes.3,25,29–31 Detailed descriptions of the Maximum Entropy program (MAXENT, version 3.3.1) can be found in References 25 and 32. There were 33 sample sites positive for hantavirus infection in rodents from the study areas during 2005–2008, and 10,000 background points (2,500 for each year) are sampled by a spatially random method. The importance of EGVs contributing to the distribution of hantavirus infection was determined by three analyses. In the jackknife analysis of the average gain with training and test data, models were respectively created with each individual variable, all the remaining variables and all variables in turn. Next, corresponding results were compared. Second, the average values of area under the curve (AUC) of 10 iterations were compared. Third, the average percentage contribution of each variable was evaluated. In each iteration of the training algorithm, the increase or decrease in regularized gain was added or subtracted with the input of the corresponding variable, giving a heuristic estimate of variable contribution for the model.25
The final model predictors were selected using a stepwise fashion, as saturated models are likely to be oversized, over-fitted, or redundant.33,34 To determine variable significance, several models using the same occurrence data but different variable sets were examined. These included models with single predictors alone, as well as leaving out individual predictors from suites of variables. The loss in modeling performance for individual models were compared with the model generated using all predictors. The algorithm converges to the optimum probable distribution, and the gain is interpreted as representing how much better the distribution fits the sample points than a uniform distribution.25,29,32
Model evaluation.
To validate the accuracy and power of the model and to evaluate the predicted effects, we divided the rodent data into two parts. The data from 2005 to 2008 were used to construct the model, and the data in 2009 were applied to validate the prediction. The model was also validated by overlaying reported human case localities from 2004 to 2007 onto each prediction map.
The model prediction was cross-validated using a 25% subset of randomly selected data points and with 75% of the points for training. The data for evaluation were merged with 10,000 randomly selected background points and were entered into a receiver operating characteristic (ROC) plot analysis to derive AUC.24,25,35 Ten random partitions rather than a single one were made to allow for assessing the average results of the algorithms and statistical testing of differences in performance.25 The 10 replicates multivariate Maximum Entropy models were run with linear, quadratic, and hinge features, and tested with ROC plots. Model accuracy using AUC was characterized as 0.50–0.60 = insufficient; 0.60–0.70 = poor; 0.70–0.80 = average; 0.80–0.90 = good; 0.90–1 = excellent.36,37
Results
A total of 3,729 rodents of 8 species (except for 2 unidentified) were captured out of 415,890 traps at 57 trapping sites (Supplemental Appendix: Table A1). Fifty-three rodents from 33 sites were positive for hantavirus by IFA including 37 R. norvegicus, 11 Mus musculus, 4 Rattus rattus, and 1 A. agrarius (Supplemental Appendix: Tables A2 and A3).
Preliminary modeling and analyses indicated that stepwise elimination of precipitation, aspect, slope, and LSTD improved the model either because their inclusion generated a negative test gain or the AUC value was higher when the variables were removed.38 The remaining 6 EGVs were associated with the presence of infected rodents, and their percent contribution was listed in Table 1. The relative importance of each variable to the presence of infected rodents was evaluated by jackknife plots of training gain, test gain, and AUC (Figure 2). Elevation and land cover provided reasonably good fits to the training data, indicating they contained the most useful information that was not already contained in the other variables. Although RH provided only a little gain (Figure 2A), omitting it decreased the training gain considerably (see the lighter blue bars), implying it was necessary for estimating the distribution of the rodents. The response curves indicated nonlinear associations between the probability of infected rodents and variation of each EGV (Figure 3). Two types of lands, i.e., “Rainfed croplands” (code 14) and “Mosaic Vegetation/Croplands” (code 30) were highly associated with the presence of hantavirus-infected rodent hosts (Figure 3A). The probability of infected rodents increased with elevation, peaked at about 180 m, and decreased subsequently (Figure 3B). The response curves of NDVI, LSTN, and temperature show similar patterns (Figure 3C, D, and F), in which the risk for presence of infected rodent hosts was initially increased, peaked at a certain value, and declined thereafter. The risk for presence of infected rodents was highest when RH was around 55%, dropped to the lowest at 66%, increased to the second peak at 71%, and declined again (Figure 3E).
Jackknife analysis results of training gain, test gain, and area under the curve (AUC). The blue, light blue, and red bar represents results of the model created with each individual variable, all the remaining variables and all variables.
Citation: The American Society of Tropical Medicine and Hygiene 84, 3; 10.4269/ajtmh.2011.10-0314
Jackknife analysis results of training gain, test gain, and area under the curve (AUC). The blue, light blue, and red bar represents results of the model created with each individual variable, all the remaining variables and all variables.
Citation: The American Society of Tropical Medicine and Hygiene 84, 3; 10.4269/ajtmh.2011.10-0314
Jackknife analysis results of training gain, test gain, and area under the curve (AUC). The blue, light blue, and red bar represents results of the model created with each individual variable, all the remaining variables and all variables.
Citation: The American Society of Tropical Medicine and Hygiene 84, 3; 10.4269/ajtmh.2011.10-0314
Response curves for the variables related to presence of hantavirus-infected rodents. Red lines are mean values for the 10 Maxent runs and blue bars represent ± 1 SD.
Citation: The American Society of Tropical Medicine and Hygiene 84, 3; 10.4269/ajtmh.2011.10-0314
Response curves for the variables related to presence of hantavirus-infected rodents. Red lines are mean values for the 10 Maxent runs and blue bars represent ± 1 SD.
Citation: The American Society of Tropical Medicine and Hygiene 84, 3; 10.4269/ajtmh.2011.10-0314
Response curves for the variables related to presence of hantavirus-infected rodents. Red lines are mean values for the 10 Maxent runs and blue bars represent ± 1 SD.
Citation: The American Society of Tropical Medicine and Hygiene 84, 3; 10.4269/ajtmh.2011.10-0314
The average ROC for 10 replicate runs of the model was 0.864 with a standard deviation of 0.074, indicating the model performance was good. On the basis of the model, a map predicting the risk of hantavirus-infected rodent hosts was constructed. To validate the model, 19 records of hantavirus-infected rodents at the field surveillance sites in 2009 were overlaid on the risk map. All points fell on the moderate and high risk areas and 13 points on the high risk area (Figure 4). The model was further validated for veracity by overlaying the locality of each human case in a different year onto the risk maps (Figure 5). The percentages of HFRS cases in predicted low, moderate, and high risk areas are listed in Table 2. For example, 41.9% cases in 2004 occurred in the predicted high risk areas, the area proportion of which was 24.3% of the province. In contrast, 29.4% cases were reported in low risk areas that accounted for 48.2% terrain. The results were similar in other years (Table 2). Thresholds were determined using “maximum training sensitivity plus specificity logistic threshold” and “balance training omission, predicted area and threshold value logistic threshold” for classification.39–41 With the 10 partitions, the result gave average values for the cut points of 0.380 and 0.149, respectively.
The predicted risk map of hantavirus-infected rodents for 2009 overlaid with real infected hosts' localities from surveillance data.
Citation: The American Society of Tropical Medicine and Hygiene 84, 3; 10.4269/ajtmh.2011.10-0314
The predicted risk map of hantavirus-infected rodents for 2009 overlaid with real infected hosts' localities from surveillance data.
Citation: The American Society of Tropical Medicine and Hygiene 84, 3; 10.4269/ajtmh.2011.10-0314
The predicted risk map of hantavirus-infected rodents for 2009 overlaid with real infected hosts' localities from surveillance data.
Citation: The American Society of Tropical Medicine and Hygiene 84, 3; 10.4269/ajtmh.2011.10-0314
Comparison of the four predicted hantavirus risk maps from 2004 to 2007 by Maximum Entropy model and validation of the predicted risk maps by overlaying and comparing them with the human hemorrhagic fever with renal syndrome (HFRS) cases localities.
Citation: The American Society of Tropical Medicine and Hygiene 84, 3; 10.4269/ajtmh.2011.10-0314
Comparison of the four predicted hantavirus risk maps from 2004 to 2007 by Maximum Entropy model and validation of the predicted risk maps by overlaying and comparing them with the human hemorrhagic fever with renal syndrome (HFRS) cases localities.
Citation: The American Society of Tropical Medicine and Hygiene 84, 3; 10.4269/ajtmh.2011.10-0314
Comparison of the four predicted hantavirus risk maps from 2004 to 2007 by Maximum Entropy model and validation of the predicted risk maps by overlaying and comparing them with the human hemorrhagic fever with renal syndrome (HFRS) cases localities.
Citation: The American Society of Tropical Medicine and Hygiene 84, 3; 10.4269/ajtmh.2011.10-0314
Percentages of the human cases in low, moderate, and high predicted risk areas in 2004–2007
| Year | Cases % (area %) | ||
|---|---|---|---|
| Low (< 0.149) | Moderate (0.149–0.380) | High (> 0.380) | |
| 2004 | 29.4% (48.2%) | 28.7% (27.6%) | 41.9% (24.3%) |
| 2005 | 33.7% (57.0%) | 33.8% (27.2%) | 32.4% (15.8%) |
| 2006 | 28.7% (40.8%) | 24.7% (31.1%) | 46.6% (28.0%) |
| 2007 | 31.8% (46.1%) | 28.6% (28.6%) | 39.6% (25.3%) |
Values in parentheses following the “Low, Moderate, High” are the risk probability and values in parentheses following the case percentage are the geographic extent of the respective areas.
Discussion
Hemorrhagic fever with renal syndrome has been recognized as a serious public health problem in Shandong Province since the first human case was recognized in 1962. In this study, we combined an eco-epidemiologic approach with GIS and remote sensing techniques to increase our understanding of the habitat of hantavirus-infected rodent hosts, and anticipate the natural foci of the disease in the province. The ENM offers a valuable approach to predict risk of an infectious disease, whenever the “absence” data are unavailable.
To predict the potential distribution of hantavirus-infected hosts within Shandong Province, we used field surveillance data from 2005 to 2008, and validated the model with the data of 2009. In addition, the predicted risk maps were consistent with the locations where human cases occurred from 2004 to 2007. On the basis of the prediction map of 2009 (Figure 4), the high risk area for hantavirus-infected hosts is clustered predominantly in the central and southern regions of the province. On the basis of the EGV's examined, land cover, elevation, NDVI, and LSTN were most strongly associated with distribution of hantavirus-infected rodents. Land cover usually influences the virus occurrence in hosts by affecting the contact rate between infected and susceptible rodents. Here, the suitable habitat for rodents is rain-fed croplands and mosaics of vegetation/croplands. Although a certain land cover type is often associated with the presence of hantavirus-infected rodents, it was not always the largest contributor.42 The NDVI correlated with the amount and productivity of vegetation and crops, which are the food source for rodents, and also significantly affected the presence of infected rodents. The LSTN rather than LSTD was also associated with the presence of infected rodents. Because R. norvegicus and M. musculus are commonly nocturnal, the nighttime land surface temperature may directly influence their activities. The nonlinearities in the effects of nighttime temperatures (Figure 3) imply that it's unlikely for hantavirus to be transmitted among rodent hosts at a too high or too low temperature.
The HTNV and SEOV, the two major causative agents of HFRS in mainland China, are respectively associated with distinct rodent species. In future studies, HTNV- and SEOV-related HFRS cases should be differentiated to explore the difference in the association between presence of hantavirus-infected rodents and related environmental factors; because each rodent species has its own ecological tolerances.13 Further research based on the two hantavirus types may generate different prediction maps that provide clues to changes in the epidemic area.
Because using niche models to predict disease distributions in temporal and/or spatial domains can lead to variance of the output from each run of the model, we attempted to dampen this variability by averaging the model outputs based on 10 random replicates data sets. In fact, several studies have showed that different modeling approaches may yield substantially different predictions.22,42 Thus, future work could be using a suite of different modeling approaches for prediction.
ACKNOWLEDGMENTS:
We thank Feng-min Hui at College of Global Change and Earth System Science, Beijing Normal University for his assistance in processing the remote sensing data. We also thank Sake J. de Vlas at Department of Public Health of Erasmus Medical Center (MC), University Medical Center Rotterdam for his comments on the manuscript.
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