Introduction

Multiple lines of evidence suggest that ecological and anthropogenic factors play important roles in elevating incidence of diseases around the world [1]. Landscape composition (e.g., relative abundance of landscape units) and configuration (e.g., spatial arrangement of landscape units) may affect disease incidence by altering interactions, abundance, and movements of hosts, vectors, and people, although the effects of these landscape variables on disease dynamics are understood only for a handful of well-studied cases [2]. For instance, in the Amazon Basin and East Africa, deforestation increases standing water and sunlight, and enhances breeding success of some mosquito species, which can increase risk of malaria transmission [3]. Habitat fragmentation and decreasing habitat patch size increase the risk of Lyme disease transmission in North America [4; 5] and Hantavirus Cardiopulmonary Syndrome (HPS) transmission risk in Panamá [6].

HPS ranks among the major emerging diseases of the last century, and is expected to remain a public health threat into the future [7]. It was first recognized in May 1993 in the Four Corners region of the US [8], and a few months later, in the city of Juquitiba, in the state of São Paulo, Brazil [9]. Rodents in the family Cricetidae are the primary hosts of HPS in Brazil [10; 11], a virus (family Bunyaviridae) that causes two syndromes in humans: HPS in the Americas, and hemorrhagic fever with renal syndrome (HFRS) in Eurasia and Africa [11]. Transmission to humans occurs via inhalation of aerosolized virus particles derived from the urine, saliva, and feces of infected rodents [12; 13]. HPS is associated with high lethality rates (35% in the US; 41% in Brazil; 38% in Canada) [14; 9; 15].

Currently, most studies support the hypothesis that forest loss, forest fragmentation, and anthropogenic landscape change, as consequences of natural habitats conversion to agricultural areas increases prevalence of Hantavirus in reservoir species [16; 6; 17; 18]. This effect occurs because these species are generally habitat generalists [19; 20] that can tolerate and adapt to ecological changes [21], being favored in disturbed environments [6; 17] and becoming abundant in altered landscapes [19; 6; 22; 23]. In addition, greater population densities of these reservoir species increase intraspecific encounters and consequent Hantavirus transmission [20; 16].

Climate can also influence host rodent population abundance and Hantavirus transmission dynamics. Several studies in North America have uncovered positive associations between precipitation, population size of rodent hosts, and Hantavirus prevalence [24; 10; 25]. High precipitation increases vegetation growth, boosting rodent densities and enhancing probability of human-rodent encounters and consequent Hantavirus transmission [26; 27]. Temperature may also affect reproduction and survival rates of small rodents, as well as the time that the virus remains infectious in the environment [28]; these effects influence transmission risk, although their direction is not entirely clear [29].

Additionally, several socio-economic variables can also influence disease transmission. HPS epidemiology is complex, involves many factors, and the distribution and abundance of the reservoir species does not necessarily imply transmission of the disease. Agricultural practices (such as mechanization, use of personal protective equipment and adequate infrastructure to handle and stock production), public sanitation, types of preventive measures used, education, behavior, and economic conditions also influence HPS transmission [30].

The relationship between landscape, climate, and social factors associated with Hantavirus transmission remains unexamined, particularly in Latin America. Evaluating the relative contributions of these factors to Hantavirus transmission can enable predictions of future outbreaks, and can be critical to design effective surveillance, control, and mitigation programs. Here, we rely on a Bayesian model to fill this research gap for the state of São Paulo, Brazil: we quantify associations between HPS incidence and the size of risk populations (e.g., number of rural men older than 14 years) and potential drivers including landscape structure (e.g., percentage of landscape units and fragmentation of native habitats), climate (e.g. temperature, precipitation), and social factors (Human Development Index, HDI dismembered, poverty and Gini Index). We make the following predictions:

1. HPS incidence will be greater in municipalities with a lower proportion of native habitat cover, a large proportion of agriculture and habitat edge areas, and with a large number of fragments, because HPS reservoir species are habitat generalist which increase in abundance in edge habitats and in agricultural landscapes;
2. HPS incidence will be greater at higher precipitation, once it affects rodent population dynamics, increasing their abundance;
3. HPS incidence will be greater in municipalities with lower human development index (HDI), and with a large number of population at risk, since economic and social conditions can also affect HPS transmission, and the bigger the number of people in contact with infected rodents the greater is the chance of HPS transmission. We then use the results to identify high-risk areas for HPS incidence across the state of São Paulo.

Materials and Methods

Study Area

We focused analyses in São Paulo, Brazil, including both the cerrado and Atlantic forest biomes (Fig 1), in southeastern Brazil, with an area of ~248,210 km², and a population of ~42 million (21.5% of Brazil’s population); [31]. At present, only 13% of the state of São Paulo is still covered by remnants of its original biomes (cerrado and Atlantic forest), with the remaining area being covered by agriculture, especially a mixture of sugarcane plantations [32], pasture [33], and urban landscapes. Cerrado covered originally 33% of the state [34], but now almost 81% of its area is converted to anthropic uses [34]. It comprises a mosaic of vegetation types ranging from savanna with sparse shrubs and small trees to almost-closed woodland [35]. The region sees rainy summers and dry winters, with annual precipitation of 1390 mm [35]. The Atlantic forest originally covered ~69% of the state [36]. Only 13.9% of the original vegetation remains, and is now highly fragmented [36]. These areas are characterized by hot and rainy summer, without a defined dry season [37]; annual precipitation ranges 1000–2200 mm [38].

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Fig 1. Hantavirus incidence between 1993 and 2012 across the 645 municipalities of the state of Sao Paulo, and cerrado (in orange) and Atlantic forest (in green) delimitation in the state.

https://doi.org/10.1371/journal.pone.0163459.g001

Results

During 1993–2012, 207 HPS cases were reported for the state, with increasing numbers in the last 10 years (Fig 2). Of the total, 57 cases were reported from the cerrado region (161 municipalities; 0.35 cases per municipality) whereas 150 (484 municipalities; 0.30 cases per municipality) in the Atlantic forest region. The largest number of HPS cases are concentrated in the northeastern region, followed by the western region, although there are cases statewide (Fig 1). Increases in HPS incidence were particularly marked in the 2000s, raising was 250% if compared to the number of cases in the 1990s. Only in 2005 we can observe a decrease in the number of reported cases especially for cerrado region, but after this period it augment further, reaching a peak of 28 cases only in 2010 (Fig 2).

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Fig 2. Reported HPS cases between 1993 and 2012 in the cerrado and Atlantic forest regions of the state of São Paulo.

https://doi.org/10.1371/journal.pone.0163459.g002

The majority of the factors considered in our model exhibited significant trends over the study period. Proportion of native vegetation cover increased between 2000 and 2010 for both cerrado (8.10 to 11.38%) and Atlantic forest (12.16 to 16.20%) municipalities, despite concomittant increases in proportion of sugarcane cultivated in these regions over the same period (Table 1). The average number of native vegetation patches also increased in both cerrado (208 to 557) and Atlantic forest (149 to 413) regions (Table 1). HDI and the size of the population at risk (e.g., males > 14 yrs old) also increased over the years for which data were available in both regions (Table 2); annual mean temperature and annual precipitation did not show any significant trend (S7 Table).

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Table 1. Average and range values of percent of sugarcane cultivated, percent of native vegetation cover, and number of patches for the municipalities of cerrado and Atlantic forest regions, for the years 2000 and 2010.

https://doi.org/10.1371/journal.pone.0163459.t001

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Table 2. Average and range values of HDI (Human Development Index) and Population at risk (rural men older than fourteen years) for the municipalities of cerrado and Atlantic forest regions, for the years that the data is available.

https://doi.org/10.1371/journal.pone.0163459.t002

Overall, our statistical models fit well to the data (cerrado: R² = 0.19; Bayesian p-value = 0.49; Atlantic forest: R² = 0.23; Bayesian p-value = 0.50), and showed significant effects of landscape, climate, and social variables on Hantavirus infection risk, as is described below in detail.

In cerrado, probability of Hantavirus infection risk was significant and positively related to HDI and to proportion of municipality occupied by sugarcane plantation (Fig 3). Number of patches and annual mean temperature also showed a positive relationships, but they were not significant, with greater risk of HPS infection in more fragmented habitats and in years with higher annual mean temperatures (Fig 3).

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Fig 3. Parameter estimates with mean (black dot) and credible intervals (2.5–97.5%) of predictors of HPS risk for cerrado and Atlantic forest region.

Habitat cover = percentage of native vegetation cover; N° Patches = number of native vegetation fragments; Precipitation = total annual precipitation; Temperature = mean annual temperature; Pop at Risk = population at risk, i.e. rural men aged over 14 years; HDI = Human Development Index; Sugarcane = percentage of municipality occupied by sugar cane plantations.

https://doi.org/10.1371/journal.pone.0163459.g003

For Atlantic forest, population at risk, HDI, and proportion of sugarcane were all significantly positively associated with Hantavirus infection risk (Fig 3). Annual mean temperature and number of patches had marginally significant positive relationships to Hantavirus infection, with a higher chance of Hantavirus infection in municipalities with higher temperatures and more fragmented forests.

Using results from the statistical models, we mapped HPS risk across the state. Overall, 6% of the state was classified as medium (5–10%) or high (> 10%) risk category for HPS infection, and 94% was indicated as low risk (<5%) category (Fig 4A). All municipalities with a medium to high risk of Hantavirus infection are shown with black outlines in the risk map and represent municipalities where preventive measures should be allocated.

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Fig 4.

Map of Hantavirus infection probability (%) (A) mean (B) and coefficient of variation (B) among years across the state of São Paulo. Black dots depict number of reported cases between 1993 and 2012. Municipalities with no symbol means no reported cases of HPS. Black outlines indicate municipalities with medium to high risk (> 5%) of Hantavirus infection and where preventive effort should be allocated.

https://doi.org/10.1371/journal.pone.0163459.g004

Not surprisingly, municipalities with highest mean risk were those that already had many HPS cases (Fig 4A). Municipalities in the northeastern region have particularly high mean risk (up to 46%), followed by some municipalities of the east, close to the Serra do Mar (in Atlantic forest region) and in the west of the state, with a mean risk up to 21%. The municipalities of São Carlos, Ribeirão Preto, Pontal, Sertãozinho and Araraquara, located in the northeast of the state (Fig 4A), are the ones that present a very large mean risk for Hantavirus infection (> 20%). The coefficient of variation of Hantavirus infection risk across years (Fig 4B) is smaller in the eastern part of the state, where habitat cover is relatively high (S1A Fig). Based on our model, a large number of municipalities that have not registered HPS infection have HPS risk of up to 2.5% (Fig 4A). At the same time, some municipalities that had HPS cases have a small risk of Hantavirus infection (8% of the state). Maps with the minimum and maximum risk are shown in S2 Fig.

Discussion

This study is the first to link landscape structure, climate, and social variables to Hantavirus infection risk in the Neotropics. Our model identified >6% of the state of São Paulo as presenting medium-to-high risk of Hantavirus transmission (39 municipalities). This disease that has so far killed at least 99 people (47.8% lethality rate) in the state, and 637 people in Brazil, since 1993 [9]. A key finding of our study is that the extent of sugarcane plantations was the most important predictor of Hantavirus infection, and this relationship held in both the cerrado and the Atlantic forest. Increases in HPS incidence were noted in the 2000s, when high oil prices led to substantial expansion of sugarcane cultivation in the state [64].

Sugarcane plantations support greater abundances of rodents than other ecosystems, whether natural or agricultural [16; 43; 65]. Brazil is the largest producer (~ 490 x 10⁶ tons/year in 2011–2012) and exporter of sugarcane in the world [66], with most of this production (~76%) in São Paulo [67]. Yields in these plantations can reach 120 tons/year/ha [68], serving as a readily available source of food and cover for rodents [46]. Moreover, in recent years sugarcane cultivation has become increasingly mechanized, as a result of legislation limiting burning prior to harvest (Law n°. 11.241, 19 September, 2002). These shifts in predominant harvest mode may have reduced rodent mortality (large numbers previously were killed by burning), increasing population sizes, and consequently augmenting Hantavirus infection risk [41; 65; 47]. Sugarcane cultivation is projected to increase still further in coming decades [69], with implications for HPS risk across São Paulo and neighboring states in southern and central Brazil.

Surprisingly, high HDI was associated with increased HPS incidences in both regions. This result was unexpected because a number of studies have found no relationship between Hantavirus infection and socio-economic status [40; 41]; others studies have found poor sanitary and living conditions to be positively associated with incidence [13; 70]. For São Paulo, however, the positive association between HDI and HPS risk may reflect better socioeconomic conditions in municipalities where sugarcane is dominant economically: sugarcane municipalities have, on average, stronger social welfare indicators [71; 72], with this sector contributing to the concentration of income [71], even outperforming the greater São Paulo Metropolitan Region [71].

HPS studies elsewhere have found that most individuals affected by HPS participate in agricultural or forestry activities [30; 40; 41; 42; 72]. This connection exists because HPS transmission requires contact between humans and aerosolized excreta of infected rodents, which is most likely in this demographic group. This pattern was clear for the Atlantic forest, which showed a positive relationship between population at risk (number of males older than 14 years old) and HPS incidence; however, this relationship did not hold for the cerrado. Another study in the cerrado [73] also failed to uncover an association between Hantavirus infection and the size of rural populations. One possible reason for absence of such association may be that cerrado municipalities have a longer history of sugarcane cultivation and more land proportionally cultivated for sugarcane than Atlantic forest municipalities (S1B Fig); this crop also brings large numbers of temporary workers from other states who do not end up in the official population statistics [74], which may have reduced the strength of any association between the size of the population at risk and HPS incidence. Another possibility is that some Atlantic forest municipalities have taken longer to achieve large-scale mechanization (e.g., in 2007, regions such as Pindamonhangaba and Guaratinguetá still had 0% mechanization; [75]), leading to greater transmission probabilities for workers in this biome. Workers in unmechanized plantations may have greater probability of contact with rodent excreta, as unmechanized plantations use workers in all steps of the production process, whereas in mechanized systems they work only in some steps of the process [75].

In Atlantic forest, our model showed marginal positive associations of fragmentation with Hantavirus incidence, supporting studies elsewhere [6; 17; 76], whereas in cerrado this association was not significant. The same result was found for proportion of habitat cover. In tropical regions HPS risk is expected to be higher in areas with a small proportion of habitat cover [6; 17], which contrasts with our results for Atlantic forest. For cerrado, the proportion of habitat cover had no association with HPS risk. We hypothesize that this may reflect the fact that most of municipalities within Atlantic forest have a small amount of habitat cover (~8.6%), and are composed of second-growth forests in early to medium stages of succession [77]. Both hantavirus reservoir rodent species in São Paulo (N. lasiurus and O. nigripes) are habitat generalists [43; 78]. While O. nigripes is known to survive in small and isolated forest remnants [23; 79], and prefers early successional stages inside the forest [78; 79; 80], becoming more abundant in these landscapes, N. lasiurus seems to prefer less dense and open areas [43; 81], occurring in disturbed and open habitats [78].

High annual mean temperature was marginally associated with greater HPS risk in the Atlantic forest. For cerrado, this association was not significant. This result supports findings elsewhere [26; 82; 83; 84]. Temperature can affect vegetation growth [29] and the survival rate of rodents [85], with mild temperatures (10–25°C) being most favorable for rodent breeding [86]. Additionally, reservoir rodents normally exhibit a peak in hantavirus infection during warmer months [87; 88; 89; 90], probably because high temperature leads to greater aerosolization of the virus and higher rates of inhalation by both humans and rodents [12; 13]. At present there are no data available on the effects of temperature on HPS virus survival, but laboratory experiments found that Puumala viruses (aetiological agent of Hantavirus infection in Western Europe) can remain infectious for longer (i.e.12 to 15 days) at room temperature (23°C; 73°F) [91], losing their viability if kept at 37°C [91]. The average temperature for São Paulo municipalities, from 1993 to 2012 was 22.9° C, with maximum temperature of 27° C, while the highest HPS infection risks were found between 22.5°C and 25°C, intermediate conditions for São Paulo state. This temperature range would be ideal for virus survival in nature, if JUQV and ARAV virus conditions are the same as for the Puumala virus. Studies conducted over shorter spatial scales than the work presented here would be necessary to link climatic factors to HPS incidence.

There was no effect of precipitation on Hantavirus risk, even in the cerrado, which has a marked dry season [92]. The association between precipitation and Hantavirus infection is still controversial, with no association in some studies [83; 93], negative effects in others [85], while in others increased rainfall in fall to spring have resulted in higher HPS transmission [26; 27], and in rodent outbreaks [24]. These studies, however, were performed in arid and semi-arid regions (85–100 mm precipitation per year) [24; 94], which show an increase in both rodent richness and abundance in response to high precipitation [24; 94]. Since our study was performed in a tropical region where annual mean precipitation is considerably high, the effects of this climatic variable on rodent resources and population dynamics may not be important.

According to our risk map, a large number of municipalities that had no reported cases nevertheless have some HPS risk (0.9–4.9%). Although this risk may seem small, the combination of lack of effective prevention and treatment options (with high lethality makes HPS a serious public health risk. Additionally, as rare events (~1% of events) and undiagnosed asymptomatic infections that are typically not reported to official statistics [70], these numbers may be underestimated. This situation is of special concern in view of the high variation of infection risk in several municipalities that had no HPS infections reported. Due to its high lethality, an infection risk up to 5% should be considered as a medium risk, and municipalities with risk higher than this value or with very high coefficient of variation should be included in preventive measures programs. Northeastern municipalities showed the highest risk across the state (up to 46%), probably because sugarcane cultivation is intense in that region: it is essential to implement awareness campaigns and reinforce diagnostic protocols to detect HPS infections in these municipalities, especially in sugarcane properties. Simple, low cost measures such as use of personal protective equipment in any environment where wild rodent excreta is frequently present, rodent control and proper clean-up of their excrement in human dwellings, seal homes against the entry of rodents, and apply other rodent-proofing techniques, may go a long way toward reducing HPS incidence and human mortality.

Supporting Information

Acknowledgments

This study was developed within the “Interface project,” supported by the São Paulo research foundation FAPESP (n. 2013/23457-6). PP was funded by the Brazilian Ministry of Education (CAPES) doctoral studentship during 2012–2013, and by FAPESP grant 2013/12515-5. JP and RP were funded by the National Council for Scientific and Technological Development (CNPQ, 307934/2011-0 and 308205/2014-6, respectively). LRT was funded by Coordenação de Aperfeiçoamento de Pessoal de Ensino Superior (CAPES) Foundation (project 068/2013). We would like to thank all the researchers that provided insights that greatly improved previous versions, especially Naomi Schwartz, Benedicte Bachelot, Andrew Quebbeman, Mariana Vidal, Natalia Aristizábal, and Patricia Ruggiero, for comments on drafts of the manuscript. We also would like to give a special thanks to Town Peterson and an anonymous reviewer for insights and comments on manuscript, which greatly improved this article.