2Postgraduate Program in Tropical Medicine, University of Brasilia, Distrito Federal, Brazil
3Institute of Tropical Pathology and Public Health, Federal University of Goias, Goiania, Brazil
Keywords: Ecological Niche Modeling; Ecoepidemiology; Hantavirus; Rodent-borne disease; Maxent
HPS is an emerging disease which has thus far been the most prevalent form in the Americas [3]. In Brazil, the first occurrence of HPS was reported in 1993 in the city of Juquitiba, in the state of Sao Paulo [4]. Since then, knowledge of the disease has been growing parallel to its range in Brazil; the presence of the disease has been established in all regions of the country [5,6]. HPS is a notifiable disease for the Brazilian Ministry of Health and its importance for public health is due to the high case-fatality rates (~ 40%) and limited knowledge about its epidemiology [1,2]. The main risk factors for illness are the exercise of agricultural activities, domestic activities associated with exposure to rodents and houses near forest remnants where wild rodents occur [2].
Necromys lasiurus (Lund 1840) is reservoirs of hantavirus in Brazil. Is an omnivorous and terrestrial species which feeds mainly on seeds [6]. Is widely distributed within the Brazilian Cerrado and Caatinga biomes, areas where human land use and modification of the natural environment are widespread. Most HPS cases in Brazil occurred in areas with the presence of this rodent. Can be found in many habitats, but prefer open and dry areas, being absent or infrequent in moist forest environments [6]. A number of studies have indicated that regional distributions of host and pathogens are associated with climatic and environmental factors [6-10].
Changes in the landscape of the Cerrado have largely been caused by the newly permitted use of land for grazing beef cattle and, more recently, for large-scale agriculture (the soybean in particular). Current estimates indicate that, every year, approximately 3 million hectares of natural habitat are lost from an original area of 2.045 million square kilometers [11]. These patterns of land use have been identified as key drivers of habitat loss, and it is essential to consider such factors when conducting predictive modeling of the distribution of zoonotic reservoir species [12]. However, there are currently few modeling studies that have explicitly emphasized changes in land use and their impacts on habitat and emerging diseases [13]. Given these factors, the current study sought to analyze the potential geographical distribution of N. lasiurus while trying to understand how land use and occupation influence the predictive distribution models of this hantavirus reservoir species in the Brazilian Cerrado.
Distributional data was collected and converted into geographic coordinates (latitude / longitude) in Decimal Degrees format (DD) using the WGS-84 datum surface. Occurrence points for N. lasiurus were separated into two sets: one for trial runs (75% of the points were for testing out the model) and one for testing (25% of the points to assess the model). This data was grouped together, and duplicate or unreliable records were removed.
Type |
Spatial resolution |
Temporal resolution |
Fonte |
|
Topography |
Elevation |
90 m |
2000 |
*INPE |
Bio1 |
Average annual temperature |
1 km |
1950-2000 |
INPE |
Bio2 |
Diurnal variation average temperature |
1 km |
1950-2000 |
INPE |
Bio3 |
Isotherm |
1 km |
1950-2000 |
INPE |
Bio 12 |
Annual rainfall |
1 km |
1950-2000 |
INPE |
Bio 14 |
Driest month precipitation |
1 km |
1950-2000 |
INPE |
Percentage of herbaceous cover |
Vegetation |
500 m |
2001 |
**ORNL |
Land use |
Use and land cover |
1: 5.000.000 |
2008 |
***FAO |
*National Institute for Space Research– INPE - Brazil
**United Nations Food and Agricultue Organization– FAO - Italy
*** Oak Ridge National Laboratory– USA
The layer land use has a spatial resolution of 5 arc minutes or 0.083333 decimal degrees with scale of 1: 5.000.000 with Datum WGS-84. Land use classes present in the modeling are: urban, bare, water, cropland, grassland, rangeland and forestry land.
The Maxent software was used because it is considered the most appropriate when a data set is comprised of only occurrence data [21]. When Maxent is used to model species distribution, it estimates the probability of species occurrence and the distribution of probability of maximum entropy. The results are subject to a set of constraints that represent the incompleteness of the information on the target distribution. This process is known as the principle of maximum entropy [20].
The principle of maximum entropy is expressed as a finite set X (which will later be interpreted as a set of pixels in the study area). Individual elements are referred to as X points. The distribution π assigns a non-negative probability π (x) for each point x, and the sum of these probabilities is 1. Approximation to π is also a probability distribution, which is denoted with π. The entropy of π is defined as (Figure 1):
An area of 1 would represent the “perfect” model; an area of 0.5 indicates that the model was selected at random. From a practical point of view, a validation test can adopt the following AUC values as indicators of model quality: excellent (0.90 - 1.0); good (0.80 - 0.90); average (0.70 - 0.80); poor (0.60 - 0.70); or very poor (0.50 - 0.60) [22].
To identify which variables had the greatest influence on the distribution of the rodent species, a jackknife test was run in Maxent [20]. This test measures the predictive effects of each variable in the model, and, in doing so, determines the quality of the models produced only with the variables being tested; the models themselves are omitted.
Figure 2 shows areas with high suitability, beginning northeast of Roraima State where savanna-type vegetation exists. The map also shows suitability in the region surrounding the city of Novo Airão in the state of Amazonas. There are additional suitable areas for the species to the west, at the mouth of the Tapajós River near the city of Santarém in Pará State, and north of the city of Obidos, Pará. These locations also possess open grassy vegetation with shrubs and small trees. There are additional areas of very suitable habitat in southwestern Rondônia State and in central Mato Grosso State, specifically on the Parecis Plateau and on the outskirts of the city of Cuiaba.
In Northeastern Brazil, there is a strong potential for occupancy at higher altitudes areas, including the mountains of Ibiapaba and Baturité and the Cariri Plateau on the border between the states of Ceará, Pernambuco, and Paraiba, as well as in certain areas of Rio Grande do Norte State, mainly in the regions of Seridó and Borborema. In addition, areas favorable to the species were found near the São Francisco River and in the highland Cerrado regions in the states of Goiás, Minas Gerais and São Paulo.
The model also infers a strong likelihood of the species being present in the Mantiqueira Mountains and the Serra do Mar mountain range in Southeastern and Southern Brazil, as well as in areas originally covered by the Atlantic Forest in the coastal states of Parana, Santa Catarina, and Rio Grande do Sul.
There is also significant potential for N. lasiurus occupancy in northwestern São Paulo State, where the Cerrado biome has been substantially modified by sugarcane plantations. There is also potential for distribution in the coastal regions of the states of Espirito Santo, Rio de Janeiro, Santa Catarina, and Rio Grande do Sul, where there is a mixed vegetation complex that includes areas of Atlantic Forest, mangroves, and salt marsh vegetation.
Another area highlighted and indicated by ENM as having a very strong probability of N. lasiurus occurrence (Figures 2 and 3) was the northwestern region of Roraima State, which is best known for its unique Lavrado ecosystem: a savanna area characterized by open vegetation covering very poor white sand soil. Large variations in altitude and rainfall result in a mosaic of vegetation types, including hills covered by extensive grasslands, narrow gallery forests, and rocky areas dominated by cactus [23]. Given this combination of floral characteristics and edaphic and pedological features, this unique ecosystem is very similar to the savanna of the Cerrado biome.
Table 1 shows the statistical results of the Maxent algorithm, including the Minimum Training Presence (MPT) threshold values, which represent the cut-off points chosen to examine areas with good environmental suitability for N. lasiurus. The table also presents the results of the inclusion and exclusion of the land use variable in the habitat quality modeling process.
The performance evaluation, which used the Area Under the Curve (AUC) for the occurrence points used to perform a trial with the data, found that the values derived from the ROC curves indicated that modeling with and without the variable land use both exhibited both a good performance (Table 2). Table 3 shows estimates of the contributions of the variables used in each model. These estimates were calculated using the jackknife technique on the points used in predictive analysis for N. lasiurus distribution.
The jackknife test revealed that percentage of herbaceous cover accounted for 38.9% of modeling variation, while the land use variable accounted for 37.9% (Table 3). Both had the same weight in the model. When the model was created without the land use variable, the jackknife result for the percentage of herbaceous cover layer increased to over 60%. Additionally, applying the jackknife technique and omitting the percentage of herbaceous cover variable was found to cause a loss of gain in both models.
When the land use variable was included, a decrease in predictive pixels was observed. It can be inferred that this decrease in predictive modeling pixels occurred as a result of environmental changes caused by human activity, such as farming and urban expansion into abandoned agricultural regions or even into regions which still harbor native forest (Table 2). This finding differed from when this variable was excluded, in which case an increase in predictive pixels was observed.
Variable |
Cut limit value |
Predicted Area fraction |
Omission rate |
AUC |
Present |
0.075 |
0.504 |
0.1 |
0.93 |
Absent |
0.049 |
0.678 |
0.033 |
0.92 |
Environmental data |
Contribution of modeling with Land use (%) |
Contribution of modeling without Land Use (%) |
Elevation |
8.9 |
15.4 |
Isotherm |
0.3 |
1.3 |
Percentage of herbaceous cover |
40.5 |
63.6 |
Annual rainfall |
3.5 |
6.8 |
Driest month precipitation |
5 |
1.3 |
Average annual temperature |
2.2 |
10.9 |
Use and land cover |
38.6 |
* |
Diurnal variation average temperature |
4 |
3.8 |
The distribution of N. lasiurus throughout Brazil that was predicted by the two models is compatible with the distribution modeled by Oliveira, et al. [6]. These authors also found areas of potential distribution in South- Central Brazil and in regions further north and northeast. Their results suggest that there is also the potential for hantavirus transmission in other parts of the country.
These conclusions are consistent with those reported by Lima, et al. who found hantavirus antibodies in asymptomatic patients from Ceará State, even though there were no records of the disease there at the time [26]. The authors also mention the capture of N. lasiurus with the same seroreactive in the Ibiapaba Mountains, located in the same state. This site is highlighted in both cartograms as a predictive area for the rodent (Figures 2 and 3).
In the dry season, the seeds of the grass genus Brachiaria are important sources of both energy and water for this species, such that the presence of N. lasiurus has been linked to that of this plant. Studies of hantavirus infection in humans living in the Brazilian Cerrado have found that most cases occurred in houses close to Brachiaria fields, a result which suggests a strong association between N. lasiurus and this type of vegetation this open areas [27].
The potential coastal distribution of N. lasiurus demonstrates that the possibility of the rodent’s occurrence is due to the presence of Brachiaria spp. and other exotic grasses grown to establish pastures in the region, which provide shelter and food for open-area rodents in these formerly forested areas.
The use of the land use variable in the models shows that anthropogenic layers used in models of potential distribution place significant weight on model outcome. It is clear that the use of this variable is key in understanding the current distribution of the species investigated herein, since environmental changes represented by the land use variable are responsible for recent changes in floral and faunal biodiversity.
The results of the current study indicate that the ecological model of the potential distribution of wild animals involved in infectious disease transmission cycles provide supplemental information for studies on disease transmission. Together, these studies can generate information on hotspots that may eventually be the center of future epidemics.
It is important to recognize that there are challenges to obtaining appropriate data for environmental and anthropic variables to perform these predictive studies. The scale of the information used must be compatible with the species distribution. Therefore, it is necessary to monitor the Receiver Operating Characteristic (ROC) curves in order to avoid potential overestimation of the distribution of the species under study. This step is vital because, if overestimation occurs, it can cause a series of uncertainties and may invalidate the entire model.
We also emphasize the importance of knowing the extent to which these rodents participate in the epidemiological cycle of this disease. The models created herein indicate a strong potential of N. lasiurus occurrence in the Northern and Northeastern regions of Brazil. These areas are poorly explored and lack ecoepidemiological studies to know what species of rodents occur and the prevalence of infection in rodents [28].
It is also important to exercise caution when interpreting the results. More eco-physiological studies on N. lasiurus are needed to develop an accurate understanding of which of the potential range areas this rodent actually inhabits. Furthermore, a species movement analysis focusing on the dispersibility of the species would provide information on which locations are accessible to it. It is need expand our knowledge on enzootic cycles of the hantavirus strains present in Brazil. To do so, more eco-epidemiological and spatial analyses are needed. They will provide information that will aid in the understanding the complexity of hantavirus and ultimately, in the development of local epidemiological surveillance systems.
This study showed that the variables land use and vegetation cover were found to significantly influence potential N. lasiurus distribution. These variables should be considered when predicting the occurrence of this medically important rodent.
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