Distributional ecology of Andes hantavirus: a macroecological approach

Modeling potential risk areas of Orthohantavirus transmission in Northwestern Argentina using an ecological niche approach

BACKGROUND

Hantavirus Pulmonary Syndrome (HPS) is a rodent-borne zoonosis in the Americas, with up to 50% mortality rates. In Argentina, the Northwestern endemic area presents half of the annually notified HPS cases in the country, transmitted by at least three rodent species recognized as reservoirs of Orthohantavirus. The potential distribution of reservoir species based on ecological niche models (ENM) can be a useful tool to establish risk areas for zoonotic diseases. Our main aim was to generate an Orthohantavirus risk transmission map based on ENM of the reservoir species in northwest Argentina (NWA), to compare this map with the distribution of HPS cases; and to explore the possible effect of climatic and environmental variables on the spatial variation of the infection risk.

METHODS

Using the reservoir geographic occurrence data, climatic/environmental variables, and the maximum entropy method, we created models of potential geographic distribution for each reservoir in NWA. We explored the overlap of the HPS cases with the reservoir-based risk map and a deforestation map. Then, we calculated the human population at risk using a census radius layer and a comparison of the environmental variables' latitudinal variation with the distribution of HPS risk.

RESULTS

We obtained a single best model for each reservoir. The temperature, rainfall, and vegetation cover contributed the most to the models. In total, 945 HPS cases were recorded, of which 97,85% were in the highest risk areas. We estimated that 18% of the NWA population was at risk and 78% of the cases occurred less than 10 km from deforestation. The highest niche overlap was between Calomys fecundus and Oligoryzomys chacoensis.

CONCLUSIONS

This study identifies potential risk areas for HPS transmission based on climatic and environmental factors that determine the distribution of the reservoirs and Orthohantavirus transmission in NWA. This can be used by public health authorities as a tool to generate preventive and control measures for HPS in NWA.

Revealing the complexity of vampire bat rabies "spillover transmission"

BACKGROUND

The term virus 'spillover' embodies a highly complex phenomenon and is often used to refer to viral transmission from a primary reservoir host to a new, naïve yet susceptible and permissive host species. Spillover transmission can result in a virus becoming pathogenic, causing disease and death to the new host if successful infection and transmission takes place.

MAIN TEXT

The scientific literature across diverse disciplines has used the terms virus spillover, spillover transmission, cross-species transmission, and host shift almost indistinctly to imply the complex process of establishment of a virus from an original host (source/donor) to a naïve host (recipient), which have close or distant taxonomic or evolutionary ties. Spillover transmission may result in unsuccessful onward transmission, if the virus dies off before propagation. Alternatively, successful viral establishment in the new host can occur if subsequent secondary transmission among individuals of the same novel species and among other sympatric susceptible species occurred. As such, virus spillover transmission is a common yet highly complex phenomenon that encompasses multiple subtle stages that can be deconstructed to be studied separately to better understand the drivers of disease emergence. Rabies virus (RABV) is a well-documented viral pathogen which still inflicts heavy impact on humans, companion animals, wildlife, and livestock throughout Latin America due substantial spatial temporal and ecological-natural and expansional-overlap with several virus reservoir hosts. Thereby, the rabies disease system represents a robust avenue through which the drivers and uncertainties surrounding spillover transmission can be unravel at its different subtle stages to better understand how they may be affected by coarse, medium, and fine scale variables.

CONCLUSIONS

The continued study of viral spillover transmission necessitates the elucidation of its complexities to better assess the cross-scale impacts of ecological forces linked to the propensity of spillover success. Improving capacities to reconstruct and predict spillover transmission would prevent public health impacts on those most at risk populations across the globe.

West Nile virus in Spain: Forecasting the geographical distribution of risky areas with an ecological niche modelling approach

West Nile virus (WNV), a well-known emerging vector-borne arbovirus with a zoonotic life cycle, represents a threat to both public and animal health. Transmitted by ornithophilic mosquitoes, its transmission is difficult to predict and even more difficult to prevent. The massive and unprecedented number of human cases and equid outbreaks in Spain during 2020 interpellates for new approaches. For the first time, we present an integrate analysis from a niche perspective to provide an insight to the situation of West Nile disease (WND) in Spain. Our modelling approach benefits from the combined use of global occurrence records of outbreaks of WND in equids and of its two alleged main vectors in Spain, Culex pipiens and Cx. perexiguus. Maps of the climatic suitability for the presence of the two vectors species and for the circulation of WNV are provided. The main outcome of our study is a map delineating the areas under certain climatic risk of transmission. Our analyses indicate that the climatic risk of transmission of WND is medium in areas nearby the south Atlantic coastal area of the Cadiz Gulf and the Mediterranean coast, and high in southwestern Spain. The higher risk of transmission in the basins of the rivers Guadiana and Guadalquivir cannot be attributed exclusively to the local abundance of Cx. pipiens, but could be ascribed to the presence and abundance of Cx. perexiguus. Furthermore, this integrated analysis suggests that the WNV presents an ecological niche of its own, not fully overlapping the ones of its hosts or vector, and thus requiring particular environmental conditions to succeed in its infection cycle.

Modeling the Potential Distribution of the Malaria Vector Anopheles (Ano.) pseudopunctipennis Theobald (Diptera: Culicidae) in Arid Regions of Northern Chile

The extreme north of Chile presents a subtropical climate permissive of the establishment of potential disease vectors. Anopheles (Ano.) pseudopunctipennis is distributed from the south of the United States to the north of Argentina and Chile, and is one of the main vectors of malaria in Latin America. Malaria was eradicated from Chile in 1945. Nevertheless, the vector persists in river ravines of the Arica and Tarapacá regions. The principal effect of climate change in the north of Chile is temperature increase. Precipitation prediction is not accurate for this region because records were erratic during the last century. The objective of this study was to estimate the current and the projected distribution pattern of this species in Chile, given the potential impact due to climate change. We compiled distributional data for An. (Ano.) pseudopunctipennis and constructed species distribution models to predict the spatial distribution of this species using the MaxEnt algorithm with current and RCP 4.5 and 8.5 scenarios, using environmental and topographic layers. Our models estimated that the current expected range of An. (Ano.) pseudopunctipennis extends continuously from Arica to the north of Antofagasta region. Furthermore, the RCP 4.5 and 8.5 projected scenarios suggested that the range of distribution of An. (Ano.) pseudopunctipennis may increase in longitude, latitude, and altitude limits, enhancing the local extension area by 38 and 101%, respectively, and local presence probability (>0.7), from the northern limit in Arica y Parinacota region (18°S) to the northern Antofagasta region (23°S). This study contributes to geographic and ecologic knowledge about this species in Chile, as it represents the first local study of An. (Ano.) pseudopunctipennis. The information generated in this study can be used to inform decision making regarding vector control and surveillance programs of Latin America. These kinds of studies are very relevant to generate human, animal, and environmental health knowledge contributing to the "One Health" concept.

Sarcoptic mange: An emerging panzootic in wildlife

Sarcoptic mange, a skin infestation caused by the mite Sarcoptes scabiei, is an emerging disease for some species of wildlife, potentially jeopardizing their welfare and conservation. Sarcoptes scabiei has a near-global distribution facilitated by its forms of transmission and use of a large diversity of host species (many of those with broad geographic distribution). In this review, we synthesize the current knowledge concerning the geographic and host taxonomic distribution of mange in wildlife, the epidemiological connections between species, and the potential threat of sarcoptic mange for wildlife conservation. Recent sarcoptic mange outbreaks in wildlife appear to demonstrate ongoing geographic spread, increase in the number of hosts and increased virulence. Sarcoptic mange has been reported in at least 12 orders, 39 families and 148 species of domestic and wild mammals, making it one of the most generalist ectoparasites of mammals. Taxonomically, the orders with most species found infested so far include Perissodactyla (67% species from the entire order), Artiodactyla (47%), and Diprotodontia (67% from this order). This suggests that new species from these mammal orders are likely to suffer cross-species transmission and be reported positive to sarcoptic mange as surveillance improves. We propose a new agenda for the study of sarcoptic mange in wildlife, including the study of the global phylogeography of S. scabiei, linkages between ecological host traits and sarcoptic mange susceptibility, immunology of individuals and species, development of control strategies in wildlife outbreaks and the effects of global environmental change in the sarcoptic mange system. The ongoing transmission globally and sustained spread among areas and wildlife species make sarcoptic mange an emerging panzootic in wildlife. A better understanding of sarcoptic mange could illuminate the aspects of ecological and evolutionary drivers in cross-species transmission for many emerging diseases.

Hantavirus pulmonary syndrome outbreaks associated with climate variability in Northwestern Argentina, 1997-2017

Background

Rodent-borne hantaviruses (genus Orthohantavirus) are the etiologic agents causing two human diseases: hemorrhagic fever with renal syndrome (HFRS) in Euroasia; and hantavirus pulmonary syndrome (HPS) in North and South America. In South America fatality rates of HPS can reach up to 35%–50%. The transmission of pathogenic hantaviruses to humans occurs mainly via inhalation of aerosolized excreta from infected rodents. Thus, the epidemiology of HPS is necessarily linked to the ecology of their rodent hosts and the contact with a human, which in turn may be influenced by climatic variability. Here we examined the relationship between climatic variables and hantavirus transmission aim to develop an early warning system of potential hantavirus outbreaks based on ecologically relevant climatic factors.

Methodology and main findings

We compiled reported HPS cases in northwestern Argentina during the 1997–2017 period and divided our data into biannual, quarterly, and bimestrial time periods to allow annual and shorter time delays to be observed. To evaluate the relationship of hantavirus transmission with mean temperature and precipitation we used dynamic regression analysis. We found a significant association between HPS incidence and lagged rainfall and temperature with a delay of 2 to 6 months. For the biannual and quarterly models, hantavirus transmission was positively associated with lagged rainfall and temperature; whereas the bimestrial models indicate a direct relationship with the rainfall but inverse for temperature in the second lagged period.

Conclusions/Significance

This work demonstrates that climate variability plays a significant role in the transmission of hantavirus in northwestern Argentina. The model developed in this study provides a basis for the forecast of potential HPS outbreaks based on climatic parameters. Our findings are valuable for the development of public health policies and prevention strategies to mitigate possible outbreaks. Nonetheless, a surveillance program on rodent population dynamics would lead to a more accurate forecast of HPS outbreaks.

Hantavirus pulmonary syndrome (HPS) is a Pan-American emerging disease with a high mortality rate caused by a rodent-borne virus. In Argentina, almost half of the HPS infections occur in the northwestern endemic region. Most of the reported cases (75%) developed severe respiratory insufficiency, of which 30% required mechanical ventilation and 15% with a fatal outcome. In this study area, nearly half of the population is below the poverty line, particularly in rural areas, where most infections occur. Since there are no vaccines currently available nor specific therapeutic treatments, prevention of hantavirus infection involves mainly environmental management practices and educational campaigns. Our results provide a framework for the planning and implementation of early public health prevention campaigns based on the significant relationship between hantavirus outbreaks and delayed climatic variables.

Biodefense Implications of New-World Hantaviruses

Hantaviruses, part of the Bunyaviridae family, are a genus of negative-sense, single-stranded RNA viruses that cause two major diseases: New-World Hantavirus Cardiopulmonary Syndrome and Old-World Hemorrhagic Fever with Renal Syndrome. Hantaviruses generally are found worldwide with each disease corresponding to their respective hemispheres. New-World Hantaviruses spread by specific rodent-host reservoirs and are categorized as emerging viruses that pose a threat to global health and security due to their high mortality rate and ease of transmission. Incidentally, reports of Hantavirus categorization as a bioweapon are often contradicted as both US National Institute of Allergy and Infectious Diseases and the Centers for Disease Control and Prevention refer to them as Category A and C bioagents respectively, each retaining qualitative levels of importance and severity. Concerns of Hantavirus being engineered into a novel bioagent has been thwarted by Hantaviruses being difficult to culture, isolate, and purify limiting its ability to be weaponized. However, the natural properties of Hantaviruses pose a threat that can be exploited by conventional and unconventional forces. This review seeks to clarify the categorization of Hantaviruses as a bioweapon, whilst defining the practicality of employing New-World Hantaviruses and their effect on armies, infrastructure, and civilian targets.

Influence of climate change on the predicted distributions of the genus Tympanoctomys (Rodentia, Hystricomorpha, Octodontidae), and their conservation implications

Viscacha rats (genus Tympanoctomys Yepes, 1942) are ecologically, physiologically, and behaviorally unusual octodontid rodents endemic to the Monte and Patagonian desert biomes of Argentina. The geographic ranges of the different species of Tympanoctomys have been described in general terms but have not been associated with spatial and climate data. Within species, populations are patchily distributed and genetically distinct. We investigated the predicted distribution of Tympanoctomys and the influence of climate fluctuations on their geographic range in historical, current, and future, scenarios. Our objectives were to characterize the environmental niche of the genus, propose a paleoclimatic context for the oldest fossils, characterize the environmental niches for T. barrerae and T. kirchnerorum, and forecast potential future distributions for these taxa. Ecological niche models were constructed using occurrence records from 1941 to the present wherein we identified several precipitation and temperature variables as important predictors of the geographic distributions of the genus, and the species T. barrerae and T. kirchnerorum. Based on our models’ results, we hypothesize that the distribution of Tympanoctomys has contracted from historical to modern times. At the species level, T. kirchnerorum likely experienced the most dramatic change, suffering a large contraction of its historical distribution resulting in its limited present distribution. Given these findings, projected future climate fluctuations and global warming are expected to affect the distributions and persistence of these species.

Integrating data mining and transmission theory in the ecology of infectious diseases

Our understanding of ecological processes is built on patterns inferred from data. Applying modern analytical tools such as machine learning to increasingly high dimensional data offers the potential to expand our perspectives on these processes, shedding new light on complex ecological phenomena such as pathogen transmission in wild populations. Here, we propose a novel approach that combines data mining with theoretical models of disease dynamics. Using rodents as an example, we incorporate statistical differences in the life history features of zoonotic reservoir hosts into pathogen transmission models, enabling us to bound the range of dynamical phenomena associated with hosts, based on their traits. We then test for associations between equilibrium prevalence, a key epidemiological metric and data on human outbreaks of rodent-borne zoonoses, identifying matches between empirical evidence and theoretical predictions of transmission dynamics. We show how this framework can be generalized to other systems through a rubric of disease models and parameters that can be derived from empirical data. By linking life history components directly to their effects on disease dynamics, our mining-modelling approach integrates machine learning and theoretical models to explore mechanisms in the macroecology of pathogen transmission and their consequences for spillover infection to humans.

Mapping suitability for rice production in inland valley landscapes in Benin and Togo using environmental niche modeling

Inland valleys (IVs) in Africa are important landscapes for rice cultivation and are targeted by national governments to attain self-sufficiency. Yet, there is limited information on the spatial distribution of IVs suitability at the national scale. In the present study, we developed an ensemble model approach to characterize the IVs suitability for rainfed lowland rice using 4 machine learning algorithms based on environmental niche modeling (ENM) with presence-only data and background sample, namely Boosted Regression Tree (BRT), Generalized Linear Model (GLM), Maximum Entropy (MAXNT) and Random Forest (RF). We used a set of predictors that were grouped under climatic variables, agricultural water productivity and soil water content, soil chemical properties, soil physical properties, vegetation cover, and socio-economic variables. The Area Under the Curves (AUC) evaluation metrics for both training and testing were respectively 0.999 and 0.873 for BRT, 0.866 and 0.816 for GLM, 0.948 and 0.861 for MAXENT and 0.911 and 0.878 for RF. Results showed that proximity of inland valleys to roads and urban centers, elevation, soil water holding capacity, bulk density, vegetation index, gross biomass water productivity, precipitation of the wettest quarter, isothermality, annual precipitation, and total phosphorus among others were major predictors of IVs suitability for rainfed lowland rice. Suitable IVs areas were estimated at 155,000-225,000 Ha in Togo and 351,000-406,000 Ha in Benin. We estimated that 53.8% of the suitable IVs area is needed in Togo to attain self-sufficiency in rice while 60.1% of the suitable IVs area is needed in Benin to attain self-sufficiency in rice. These results demonstrated the effectiveness of an ensemble environmental niche modeling approach that combines the strengths of several models.

Spatiotemporal Dynamics of Hantavirus Cardiopulmonary Syndrome Transmission Risk in Brazil

BACKGROUND

Hantavirus disease in humans is rare but frequently lethal in the Neotropics. Several abundant and widely distributed Sigmodontinae rodents are the primary hosts of Orthohantavirus and, in combination with other factors, these rodents can shape hantavirus disease. Here, we assessed the influence of host diversity, climate, social vulnerability and land use change on the risk of hantavirus disease in Brazil over 24 years.

METHODS

Landscape variables (native forest, forestry, sugarcane, maize and pasture), climate (temperature and precipitation), and host biodiversity (derived through niche models) were used in spatiotemporal models, using the 5570 Brazilian municipalities as units of analysis.

RESULTS

Amounts of native forest and sugarcane, combined with temperature, were the most important factors influencing the increase of disease risk. Population at risk (rural workers) and rodent host diversity also had a positive effect on disease risk.

CONCLUSIONS

Land use change-especially the conversion of native areas to sugarcane fields-can have a significant impact on hantavirus disease risk, likely by promoting the interaction between the people and the infected rodents. Our results demonstrate the importance of understanding the interactions between landscape change, rodent diversity, and hantavirus disease incidence, and suggest that land use policy should consider disease risk. Meanwhile, our risk map can be used to help allocate preventive measures to avoid disease.

Climatic constraints and the distribution of Patagonian mice

We generated potential distribution models for 14 sigmodontine rodent species that inhabit the Andean–Patagonian forest region and adjacent areas, and retrieved the main climatic variables responsible for these models. Our main objective was to compare these climatic variables and the distribution patterns generated for each species, and explore the effects of the physical environment in shaping the composition of rodent communities in the area. We retrieved a total of 1,215 records of species presence from 580 sites. Maxent was used to generate potential distribution models for the 14 rodent species studied. We used a total of 20 variables obtained from the WorldClim database, including elevation and 19 bioclimatic variables, in addition to normalized difference vegetation index (NDVI) and enhanced vegetation index (EVI). Our results showed a clear discrimination between two groups of rodents, one concentrated in the western part of our study area, with more humid climate and a rugged mountainous and discontinuous habitat, and another inhabiting the eastern, drier part of our study area, which appears to be more uniform in habitat characteristics. These groups showed a mosaic of phylogenetically non-related species from different tribes, that probably arrived or expanded into Patagonia during the last millennia. The overlap of all models showed the forest-steppe ecotone east of Nahuel Huapi Lake and south to −43° latitude as the area with the highest species richness (8–11 species). All species showed a high correspondence with temperature and precipitation that define patterns at a landscape scale, with little to very little information contained in the typical vegetation variables that would define local conditions.

En este trabajo generamos modelos de distribución potencial para cada especie de roedor sigmodontino que habita la región de los bosques andino-patagónicos y áreas adyacentes, identificando las principales variables climáticas que influyen en dichas distribuciones. Nuestro principal objetivo fue comparar las variables climáticas y los patrones de distribución generados para cada especie, y explorar los efectos del entorno físico en la composición de los ensambles de especies. Recopilamos un total de 1215 registros de presencia de especies de 580 sitios. Se utilizó MaxEnt para generar los modelos de distribución potencial de las 14 especies de roedores estudiadas, con 20 variables obtenidas de la base de datos WorldClim, incluida la elevación, 19 variables bioclimáticas, además del NDVI y EVI. Nuestros resultados muestran una clara discriminación entre dos grupos de roedores, uno concentrado en el área occidental, con un clima más húmedo y montañoso, y otro que habita en el área más seca del este. Curiosamente, estos grupos muestran un mosaico de especies, filogenéticamente no relacionadas y de diferentes tribus, que probablemente llegaron o se expandieron en la Patagonia durante los últimos milenios. La superposición de todos los modelos muestra el ecotono bosque-estepa, al este del lago Nahuel Huapi y hacia el sur hasta los -43°, como la zona más rica en especies (8 a 11 especies). Todas las especies muestran una alta correspondencia con las variables ambientales (temperatura y precipitación) que definen patrones a escala del paisaje, con muy poca información contenida en las variables típicas de la vegetación que definirían las condiciones locales.

A 19 Year Analysis of Small Mammals Associated with Human Hantavirus Cases in Chile

Small mammals present in areas where hantavirus cardiopulmonary syndrome (HCPS) cases had occurred in central and southern Chile were captured and analyzed to evaluate the abundance of rodents and seroprevalence rates of antibodies to Andes orthohantavirus (ANDV). Sampling areas ranged from the Coquimbo to Aysén regions (30–45° S approx.) regions. Ninety-two sites in peridomestic and countryside areas were evaluated in 19 years of sampling. An antibody against ANDV was detected by strip immunoassay in 58 of 1847 specimens captured using Sherman traps. Of the eleven species of rodents sampled, Abrothrix olivacea, Oligoryzomys longicaudatus and Abrothrix hirta were the most frequently trapped. O. longicaudatus had the highest seropositivity rate, and by logistic regression analysis, O. longicaudatus of at least 60 g had 80% or higher probability to be seropositive. Sex, age and wounds were significantly related to seropositivity only for O. longicaudatus. Across administrative regions, the highest seropositivity was found in the El Maule region (34.8–36.2° S), and the highest number of HCPS cases was registered in the Aysén region. Our results highlight the importance of long term and geographically extended studies, particularly for highly fluctuating pathogens and their reservoirs, to understand the implications of the dynamics and transmission of zoonotic diseases in human populations.

The ecological dynamics of hantavirus diseases: From environmental variability to disease prevention largely based on data from China

Hantaviruses can cause hantavirus pulmonary syndrome (HPS) in the Americas and hemorrhagic fever with renal syndrome (HFRS) in Eurasia. In recent decades, repeated outbreaks of hantavirus disease have led to public concern and have created a global public health burden. Hantavirus spillover from natural hosts into human populations could be considered an ecological process, in which environmental forces, behavioral determinants of exposure, and dynamics at the human–animal interface affect human susceptibility and the epidemiology of the disease. In this review, we summarize the progress made in understanding hantavirus epidemiology and rodent reservoir population biology. We mainly focus on three species of rodent hosts with longitudinal studies of sufficient scale: the striped field mouse (Apodemus agrarius, the main reservoir host for Hantaan virus [HTNV], which causes HFRS) in Asia, the deer mouse (Peromyscus maniculatus, the main reservoir host for Sin Nombre virus [SNV], which causes HPS) in North America, and the bank vole (Myodes glareolus, the main reservoir host for Puumala virus [PUUV], which causes HFRS) in Europe. Moreover, we discuss the influence of ecological factors on human hantavirus disease outbreaks and provide an overview of research perspectives.