A habitat-based model for the spread of hantavirus between reservoir and spillover species

Forecasting Outbreaks of Hantaviral Disease: Future Directions in Geospatial Modeling

Hantaviral diseases have been recognized as 'place diseases' from their earliest identification and, epidemiologically, are tied to single host species with transmission occurring from infectious hosts to humans. As such, human populations are most at risk when they are in physical proximity to suitable habitats for reservoir populations, when numbers of infectious hosts are greatest. Because of the lags between improving habitat conditions and increasing infectious host abundance and spillover to humans, it should be possible to anticipate (forecast) where and when outbreaks will most likely occur. Most mammalian hosts are associated with specific habitat requirements, so identifying these habitats and the ecological drivers that impact population growth and the dispersal of viral hosts should be markers of the increased risk for disease outbreaks. These regions could be targeted for public health and medical education. This paper outlines the rationale for forecasting zoonotic outbreaks, and the information that needs to be clarified at various levels of biological organization to make the forecasting of orthohantaviruses successful. Major challenges reflect the transdisciplinary nature of forecasting zoonoses, with needs to better understand the implications of the data collected, how collections are designed, and how chosen methods impact the interpretation of results.

Rabies virus in white-nosed coatis (Nasua narica) in Mexico: what do we know so far?

Rabies is a neglected disease that affects all mammals. To determine the appropriate sanitary measures, the schedule of preventive medicine campaigns requires the proper identification of the variants of the virus circulating in the outbreaks, the species involved, and the interspecific and intraspecific virus movements. Urban rabies has been eradicated in developed countries and is being eradicated in some developing countries. In Europe and North America, oral vaccination programs for wildlife have been successful, whereas in Latin America, Asia, and Africa, rabies remains a public health problem due to the habitation of a wide variety of wild animal species that can act as rabies virus reservoirs in their environment. After obtaining recognition from the WHO/PAHO as the first country to eliminate human rabies transmitted by dogs, Mexico faces a new challenge: the control of rabies transmitted by wildlife to humans and domestic animals. In recent years, rabies outbreaks in the white-nosed coati (Nasua narica) have been detected, and it is suspected that the species plays a significant role in maintaining the wild cycle of rabies in the southeast of Mexico. In this study, we discussed cases of rabies in white-nosed coatis that were diagnosed at InDRE (in English: Institute of Epidemiological Diagnosis and Reference; in Spanish: Instituto de Diagnostico y Referencia Epidemiologicos) from 1993 to 2022. This study aimed to determine whether white-nosed coatis might be an emergent rabies reservoir in the country. A total of 13 samples were registered in the database from the Rabies laboratories of Estado de Mexico (n = 1), Jalisco (n = 1), Quintana Roo (n = 5), Sonora (n = 1), and Yucatan (n = 5). Samples from 1993 to 2002 from Estado de Mexico, Jalisco, and Sonora were not characterized because we no longer had any samples available. Nine samples were antigenically and genetically characterized. To date, coatis have not been considered important vectors of the rabies virus. The results from our research indicate that the surveillance of the rabies virus in coatis should be relevant to prevent human cases transmitted by this species.

Rabies Virus Variants Detected from Cougar (Puma concolor) in Mexico 2000–2021

In 2019, the World Health Organization (WHO) and the Pan-American Health Organization (PAHO) recognized Mexico as a country free of human rabies transmitted by dogs. Nevertheless, the sylvatic cycle remains as a public health concern in the country. Although cougars (Puma concolor) are not reservoirs of any rabies virus variant (RVV), these felines could act as vectors at the top of the food chain, and their relationships with other organisms must be considered important for the regulatory effect on their prey’s populations. In this study, genetic and antigenic characterization was performed on all cougar rabies cases diagnosed at the Rabies Laboratory Network of the Ministry of Health (RLNMH) in Mexico from 2000 to 2021. Samples from other species, a skunk, a horse (Equus caballus) (attacked by a cougar), and a gray fox (Urocyon cineroargenteus), were included as reference. Rabies cases in cougars were restricted to two Northern states of Mexico (Sonora and Chihuahua). Five out of six samples of cougars were RVV7 (Arizona gray fox RVV) and one from Sonora was RVV1. Interestingly, there is no evidence of RVV1 in dogs in the Northern states since the 1990s but skunk species now harbor this RVV1 in this region of the country.

Occurrence of mesocarnivores in montane sky islands: How spatial and temporal overlap informs rabies management in a regional hotspot

Interspecific interactions among mesocarnivores can influence community dynamics and resource partitioning. Insights into these interactions can enhance understanding of local ecological processes that have impacts on pathogen transmission, such as the rabies lyssavirus. Host species ecology can provide an important baseline for disease management strategies especially in biologically diverse ecosystems and heterogeneous landscapes. We used a mesocarnivore guild native to the southwestern United States, a regional rabies hotspot, that are prone to rabies outbreaks as our study system. Gray foxes (Urocyon cinereoargenteus), striped skunks (Mephitis mephitis), bobcats (Lynx rufus), and coyotes (Canis latrans) share large portions of their geographic ranges and can compete for resources, occupy similar niches, and influence population dynamics of each other. We deployed 80 cameras across two mountain ranges in Arizona, stratified by vegetation type. We used two-stage modeling to gain insight into species occurrence and co-occurrence patterns. There was strong evidence for the effects of elevation, season, and temperature impacting detection probability of all four species, with understory height and canopy cover also influencing gray foxes and skunks. For all four mesocarnivores, a second stage multi-species co-occurrence model better explained patterns of detection than the single-species occurrence model. These four species are influencing the space use of each other and are likely competing for resources seasonally. We did not observe spatial partitioning between these competitors, likely due to an abundance of cover and food resources in the biologically diverse system we studied. From our results we can draw inferences on community dynamics to inform rabies management in a regional hotspot. Understanding environmental factors in disease hotspots can provide useful information to develop more reliable early-warning systems for viral outbreaks. We recommend that disease management focus on delivering oral vaccine baits onto the landscape when natural food resources are less abundant, specifically during the two drier seasons in Arizona (pre-monsoon spring and autumn) to maximize intake by all mesocarnivores.

Impact of Predator Exclusion and Habitat on Seroprevalence of New World Orthohantavirus Harbored by Two Sympatric Rodents within the Interior Atlantic Forest

Understanding how perturbations to trophic interactions influence virus-host dynamics is essential in the face of ongoing biodiversity loss and the continued emergence of RNA viruses and their associated zoonoses. Herein, we investigated the role of predator exclusion on rodent communities and the seroprevalence of hantaviruses within the Reserva Natural del Bosque Mbaracayú (RNBM), which is a protected area of the Interior Atlantic Forest (IAF). In the IAF, two sympatric rodent reservoirs, Akodon montensis and Oligoryzomys nigripes, harbor Jaborá and Juquitiba hantavirus (JABV, JUQV), respectively. In this study, we employed two complementary methods for predator exclusion: comprehensive fencing and trapping/removal. The goal of exclusion was to preclude the influence of predation on small mammals on the sampling grids and thereby potentially reduce rodent mortality. Following baseline sampling on three grid pairs with different habitats, we closed the grids and began predator removal. By sampling three habitat types, we controlled for habitat-specific effects, which is important for hantavirus-reservoir dynamics in neotropical ecosystems. Our six-month predator exclusion experiment revealed that the exclusion of terrestrial mammalian predators had little influence on the rodent community or the population dynamics of A. montensis and O. nigripes. Instead, fluctuations in species diversity and species abundances were influenced by sampling session and forest degradation. These results suggest that seasonality and landscape composition play dominant roles in the prevalence of hantaviruses in rodent reservoirs in the IAF ecosystem.

Probability of a zoonotic spillover with seasonal variation

Zoonotic infectious diseases are spread from animals to humans. It is estimated that over 60% of human infectious diseases are zoonotic and 75% of them are emerging zoonoses. The majority of emerging zoonotic infectious diseases are caused by viruses including avian influenza, rabies, Ebola, coronaviruses and hantaviruses. Spillover of infection from animals to humans depends on a complex transmission pathway, which is influenced by epidemiological and environmental processes. In this investigation, the focus is on direct transmission between animals and humans and the effects of seasonal variations on the transmission and recovery rates. Fluctuations in transmission and recovery, besides being influenced by physiological processes and behaviors of pathogen and host, are driven by seasonal variations in temperature, humidity or rainfall. A new time-nonhomogeneous stochastic process is formulated for infectious disease spread from animals to humans when transmission and recovery rates are time-periodic. A branching process approximation is applied near the disease-free state to predict the probability of the first spillover event from animals to humans. This probability is a periodic function of the time when infection is introduced into the animal population. It is shown that the highest risk of a spillover depends on a combination of animal to human transmission, animal to animal transmission and animal recovery. The results are applied to a stochastic model for avian influenza with spillover from domestic poultry to humans.

Bioaccumulation of Pathogen Exposure in Top Predators

Predator-prey interactions present heightened opportunities for pathogen spillover, as predators are at risk of exposure to infectious agents harbored by prey. Epizootics with high morbidity and mortality have been recorded following prey-to-predator spillover events, which have had significant conservation implications for sensitive species. Using felids as a detailed case study, we have documented both virulent and clinically silent infections in apex predators following transfer of microbes from prey. We draw on these examples and others to examine the mechanisms that determine frequency and outcome of predator exposure to prey-based pathogens. We propose that predator-prey dynamics should be more thoroughly considered in empirical research and disease dynamic modeling approaches in order to reveal answers to outstanding questions relating to pathogen bioaccumulation.

A lateral flow biosensor based on gold nanoparticles detects four hemorrhagic fever viruses

The pathogen of viral hemorrhagic fever (VHF), which is harmful to human health, is a hemorrhagic fever virus. Clinicians have long needed convenient and sensitive point-of-care rapid diagnostic tests (RDTs) for hemorrhagic fever viruses. Commonly used methods for pathogen detection rely on conventional culture-based tests, antibody-based assays and polymerase chain reaction (PCR)-based techniques. However, these methods are costly, laborious and time-consuming. Herein, we present a simple and sensitive biosensor for the rapid detection of hemorrhagic fever viruses. For this assay, we develop lateral flow biosensors (LFBs) based on magnetic beads and nicking enzyme-assisted isothermal strand-displacement amplification (SDA) for the detection of hemorrhagic fever viruses. The detection limit of this assay is 10 fM.

Sympatry and habitat associations of sigmodontine rodents in a neotropical forest-savanna interface

Small mammal communities in the Neotropics are composed largely of sigmodontine rodents. However, many questions regarding these communities remain unanswered, especially those pertaining to fine-scale sympatry and habitat selection. To address this, we examined sigmodontine community structure and vegetation in the western margin of the Upper Paraná Atlantic Forest and the southwestern-most extent of the Cerrado (CE) (an extensive South American savanna ecoregion) of Paraguay. Vegetation classifications were derived from satellite imagery combined with maps based on extensive ground-based surveys. The three most abundant species (Akodon montensis, Hylaeamys megacephalus, and Oligoryzomys nigripes) were found most often in microsympatry with conspecifics, and were negatively associated with other species. Akodon montensis was associated with high forest (HF), and H. megacephalus with bamboo understory (BU), whereas O. nigripes did not exhibit a habitat preference. The first two species' distributions within the landscape were found to be driven primarily by habitat selection, and O. nigripes by a behavioral response (avoidance) to the presence of the other two species. Moreover, habitat influences whether or not a particular species associates with, or avoids, conspecifics or other species.

Habitat, species richness and hantaviruses of sigmodontine rodents within the Interior Atlantic Forest, Paraguay

Four of the nine sigmodontine tribes have species that serve as reservoirs of rodent-borne hantaviruses (RBO-HV), few have been studied in any depth. Several viruses have been associated with human cases of hantavirus pulmonary syndrome often through peridomestic exposure. Jabora (JABV) and Juquitiba (JUQV), harbored by Akodon montensis and Oligoryzomys nigripes, respectively, are endemic and sympatric in the Reserva Natural de Bosque Mbaracayú (RNBM), Paraguay, a protected area of the Interior Atlantic Forest. Rodent communities were surveyed along a 30 km stretch of the RNBM in eight vegetation classifications (Low, High, Bamboo, Riparian and Liana Forests, Bamboo Understory, Cerrado, and Meadow/Grasslands). We collected 417 rodents from which 11 species were identified; Akodon montensis was the predominant species (72%; 95%CI: 64.7%-76.3%), followed by Hylaeamys megacephalus (15% (11.2%-18.2%)) and Oligoryzomys nigripes (9% (6.6%-12.4%)). We examined the statistical associations among habitat (vegetation class) type, rodent species diversity, population structure (age, sex, and weight), and prevalence of RBO-HV antibody and/or viral RNA (Ab/RNA) or characteristic Leishmania tail lesions. Ab/RNA positive rodents were not observed in Cerrado and Low Forest. A. montensis had an overall Ab/RNA prevalence of 7.7% (4.9%-11.3%) and O. nigripes had an overall prevalence of 8.6% (1.8%-23.1%). For A. montensis, the odds of being Ab/RNA positive in High Forest was 3.73 times of the other habitats combined. There was no significant difference among age classes in the proportion of Ab/RNA positive rodents overall (p = 0.66), however, all 11 RNA-positive individuals were adult. Sex and habitat had independent prognostic value for hantaviral Ab/RNA in the study population; age, presence of tail scar/lesion (19% of the rodents) and weight did not. Adjusting for habitat, female rodents had less risk of becoming infected. Importantly, these data suggest habitat preferences of two sympatric rodent reservoirs for two endemic hantaviruses and the importance of including habitat in models of species diversity and habitat fragmentation.

Hantavirus in new geographic regions, Sweden

In Sweden, human cases of Puumala hantavirus (PUUV) infections are reported from the northern endemic regions. We found hantavirus-specific antibodies in yellow-necked mice (Apodemus flavicollis) trapped in human dwellings in the surroundings of the cities of Uppsala and Stockholm, which are situated far south from the traditional endemic areas of PUUV. Because the yellow-necked mouse is the most common rodent in human dwellings, hantaviruses in this rodent species may be important for the public health.

Stochastic SIS metapopulation models for the spread of disease among species in a fragmented landscape

Two stochastic models are derived for a susceptible–infectious–susceptible epidemic spreading through a metapopulation: a continuous time Markov chain (CTMC) model and an Itô stochastic differential equation (SDE) model. The stochastic models are numerically compared. Close agreement suggests that computationally intense CTMC simulations can be approximated by simpler SDE simulations. Differential equations for the moments of the SDE probability distribution are also derived, the steady states are solved numerically using a moment closure technique, and these results are compared to simulations. The moment closure technique only coarsely approximates simulation results. The effect of model parameters on stability of the disease-free equilibrium is also numerically investigated.

Life-long shedding of Puumala hantavirus in wild bank voles (Myodes glareolus)

The knowledge of viral shedding patterns and viraemia in the reservoir host species is a key factor in assessing the human risk of zoonotic viruses. The shedding of hantaviruses (family Bunyaviridae) by their host rodents has widely been studied experimentally, but rarely in natural settings. Here we present the dynamics of Puumala hantavirus (PUUV) shedding and viraemia in naturally infected wild bank voles (Myodes glareolus). In a monthly capture-mark-recapture study, we analysed 18 bank voles for the presence and relative quantity of PUUV RNA in the excreta and blood from 2 months before up to 8 months after seroconversion. The proportion of animals shedding PUUV RNA in saliva, urine and faeces peaked during the first month after seroconversion, but continued throughout the study period with only a slight decline. The quantity of shed PUUV in reverse transcription quantitative PCR (RT-qPCR) positive excreta was constant over time. In blood, PUUV RNA was present for up to 7 months but both the probability of viraemia and the virus load declined with time. Our findings contradict the current view of a decline in virus shedding after the acute phase and a short viraemic period in hantavirus infection - an assumption widely adopted in current epidemiological models. We suggest the life-long shedding as a means of hantaviruses to survive over host population bottlenecks, and to disperse in fragmented habitats where local host and/or virus populations face temporary extinctions. Our results indicate that the kinetics of pathogens in wild hosts may differ considerably from those observed in laboratory settings.

Hantavirus reservoirs: current status with an emphasis on data from Brazil

Since the recognition of hantavirus as the agent responsible for haemorrhagic fever in Eurasia in the 1970s and, 20 years later, the descovery of hantavirus pulmonary syndrome in the Americas, the genus Hantavirus has been continually described throughout the World in a variety of wild animals. The diversity of wild animals infected with hantaviruses has only recently come into focus as a result of expanded wildlife studies. The known reservoirs are more than 80, belonging to 51 species of rodents, 7 bats (order Chiroptera) and 20 shrews and moles (order Soricomorpha). More than 80genetically related viruses have been classified within Hantavirus genus; 25 recognized as human pathogens responsible for a large spectrum of diseases in the Old and New World. In Brazil, where the diversity of mammals and especially rodents is considered one of the largest in the world, 9 hantavirus genotypes have been identified in 12 rodent species belonging to the genus Akodon, Calomys, Holochilus, Oligoryzomys, Oxymycterus, Necromys and Rattus. Considering the increasing number of animals that have been implicated as reservoirs of different hantaviruses, the understanding of this diversity is important for evaluating the risk of distinct hantavirus species as human pathogens.

Characterization of Juquitiba virus in Oligoryzomys fornesi from Brazilian Cerrado

The Juquitiba virus, an agent of Hantavirus Cardiopulmonary Syndrome, is one of the most widely distributed hantavirus found in South America. It has been detected in Oligoryzomys nigripes, Akodon montensis, Oxymycterus judex, Akodon paranaensis in Brazil and in O. nigripes, Oryzomys sp. and Oligoryzomys fornesi rodents in Argentine, Paraguay and Uruguay. Here, we report the genomic characterization of the complete S segment from the Juquitiba strain, isolated from the lung tissues of O. fornesi, the presumed rodent reservoir of Anajatuba virus in Brazilian Amazon, captured in the Cerrado Biome, Brazil.

Mathematical Modeling of Viral Zoonoses in Wildlife

Zoonoses are a worldwide public health concern, accounting for approximately 75% of human infectious diseases. In addition, zoonoses adversely affect agricultural production and wildlife. We review some mathematical models developed for the study of viral zoonoses in wildlife and identify areas where further modeling efforts are needed.

Hantaviruses in the americas and their role as emerging pathogens

The continued emergence and re-emergence of pathogens represent an ongoing, sometimes major, threat to populations. Hantaviruses (family Bunyaviridae) and their associated human diseases were considered to be confined to Eurasia, but the occurrence of an outbreak in 1993–94 in the southwestern United States led to a great increase in their study among virologists worldwide. Well over 40 hantaviral genotypes have been described, the large majority since 1993, and nearly half of them pathogenic for humans. Hantaviruses cause persistent infections in their reservoir hosts, and in the Americas, human disease is manifest as a cardiopulmonary compromise, hantavirus cardiopulmonary syndrome (HCPS), with case-fatality ratios, for the most common viral serotypes, between 30% and 40%. Habitat disturbance and larger-scale ecological disturbances, perhaps including climate change, are among the factors that may have increased the human caseload of HCPS between 1993 and the present. We consider here the features that influence the structure of host population dynamics that may lead to viral outbreaks, as well as the macromolecular determinants of hantaviruses that have been regarded as having potential contribution to pathogenicity.

A global perspective on hantavirus ecology, epidemiology, and disease

Hantaviruses are enzootic viruses that maintain persistent infections in their rodent hosts without apparent disease symptoms. The spillover of these viruses to humans can lead to one of two serious illnesses, hantavirus pulmonary syndrome and hemorrhagic fever with renal syndrome. In recent years, there has been an improved understanding of the epidemiology, pathogenesis, and natural history of these viruses following an increase in the number of outbreaks in the Americas. In this review, current concepts regarding the ecology of and disease associated with these serious human pathogens are presented. Priorities for future research suggest an integration of the ecology and evolution of these and other host-virus ecosystems through modeling and hypothesis-driven research with the risk of emergence, host switching/spillover, and disease transmission to humans.