Temporal and Spatial Analysis of Sin Nombre Virus Quasispecies in Naturally Infected Rodents

Sin Nombre virus (SNV) is thought to establish a persistent infection in its natural reservoir, the deer mouse (Peromyscus maniculatus), despite a strong host immune response. SNV-specific neutralizing antibodies were routinely detected in deer mice which maintained virus RNA in the blood and lungs. To determine whether viral diversity played a role in SNV persistence and immune escape in deer mice, we measured the prevalence of virus quasispecies in infected rodents over time in a natural setting. Mark-recapture studies provided serial blood samples from naturally infected deer mice, which were sequentially analyzed for SNV diversity. Viral RNA was detected over a period of months in these rodents in the presence of circulating antibodies specific for SNV. Nucleotide and amino acid substitutions were observed in viral clones from all time points analyzed, including changes in the immunodominant domain of glycoprotein 1 and the 3' small segment noncoding region of the genome. Viral RNA was also detected in seven different organs of sacrificed deer mice. Analysis of organ-specific viral clones revealed major disparities in the level of viral diversity between organs, specifically between the spleen (high diversity) and the lung and liver (low diversity). These results demonstrate the ability of SNV to mutate and generate quasispecies in vivo, which may have implications for viral persistence and possible escape from the host immune system.     

Sin Nombre virus infection of deer mice in Montana: characteristics of newly infected mice, incidence, and temporal pattern of infection

Sin Nombre virus (SNV), hosted by the deer mouse (Peromyscus maniculatus), is the principal cause of hantavirus pulmonary syndrome (HPS) in North America. To improve our understanding of factors that contribute to the occurrence of HPS, we conducted an extensive field study of the characteristics of newly infected (as determined by recent acquisition of antibody) deer mice and the temporal pattern of antibody acquisition (seroconversion) from 1994 through 2004 in Montana, USA. We sampled 6,584 individual deer mice, of which 2,747 were captured over multiple trapping periods. Among these 2,747 deer mice, we detected 171 instances of seroconversion. There was no relationship between seroconversion and the acquisition of scars. However, recently infected Montana deer mice were more likely to be older, more likely to be males, and more likely to be in breeding condition. In addition, recently infected male deer mice gained less weight over the 1-mo period following seroconversion than did those that did not acquire antibody, suggesting that SNV infection may have negatively impacted the health of infected rodents. Incidence was highly variable among years, and timing of infections was primarily associated with the breeding season (generally early spring through late fall).     

Using MODIS satellite imagery to predict hantavirus risk

Aims Sin Nombre virus (SNV), a strain of hantavirus, causes hantavirus pulmonary syndrome (HPS) in humans, a deadly disease with high mortality rate (> 50%). The primary virus host is the deer mouse, and greater abundance of deer mice has been shown to increase the human risk of HPS. Our aim is to identify and compare vegetation indices and associated time lags for predicting hantavirus risk using remotely sensed imagery. Location Utah, USA. Methods A 5‐year time‐series of moderate‐resolution imaging spectroradiometer (MODIS) satellite imagery and corresponding field data was utilized to compare various vegetation indices that measure productivity with the goal of indirectly estimating mouse abundance and SNV prevalence. Relationships between the vegetation indices and deer mouse density, SNV prevalence and the number of infected deer mice at various time lags were examined to assess which indices and associated time lags might be valuable in predicting SNV outbreaks. Results The results reveal varying levels of positive correlation between the vegetation indices and deer mouse density as well as the number of infected deer mice. Among the vegetation indices, the normalized difference vegetation index (NDVI) and the enhanced vegetation index (EVI) produced the highest correlations with deer mouse density and the number of infected deer mice using a time lag of 1.0 to 1.3 years for May and June imagery. Main conclusions This study demonstrates the potential for using MODIS time‐series satellite imagery in estimating deer mouse abundance and predicting hantavirus risk. The 1‐year time lag provides a great opportunity to apply satellite imagery to predict upcoming SNV outbreaks, allowing preventive strategies to be adopted. Analysis of different predictive indices and lags could also be valuable in identifying the time windows for data collection for practical uses in monitoring rodent abundance and subsequent disease risk to humans.     

Epizootiology of Sin Nombre and El Moro Canyon hantaviruses, southeastern Colorado, 1995-2000

Sin Nombre virus (SNV) is an etiologic agent of hantavirus pulmonary syndrome. To better understand the natural history of this virus we studied population dynamics and temporal pattern of infection of its rodent hosts in southeastern Colorado (USA) from 1995 to 2000. We present evidence for the presence of two hantaviruses, SNV in deer mice (Peromyscus maniculatus) and El Moro Canyon virus in western harvest mice (Reithrodontomys megalotis), at our study sites. Sin Nombre virus appeared only sporadically in deer mouse populations; overall prevalence of antibody to SNV was 2.6%. El Moro Canyon virus was enzootic: seroconversions occurred throughout the year; antibody prevalence (11.9% overall) showed a delayed-density-dependent pattern, peaking as relative abundance of mice was declining. Males of both host species were more frequently infected than were females. An apparently lower mean survivorship (persistence at the trapping site) for SNV antibody-positive deer mice could indicate a detrimental effect of SNV on its host, but might also be explained by the fact that antibody-positive mice were older when first captured.     

How Host Population Dynamics Translate into Time-Lagged Prevalence: An Investigation of Sin Nombre Virus in Deer Mice

Human cases of hantavirus pulmonary syndrome caused by Sin Nombre virus are the endpoint of complex ecological cascade from weather conditions, population dynamics of deer mice, to prevalence of SNV in deer mice. Using population trajectories from the literature and mathematical modeling, we analyze the time lag between deer mouse population peaks and peaks in SNV antibody prevalence in deer mice. Because the virus is not transmitted vertically, rapid population growth can lead initially to reduced prevalence, but the resulting higher population size may later increase contact rates and generate increased prevalence. Incorporating these factors, the predicted time lag ranges from 0 to 18 months, and takes on larger values when host population size varies with a longer period or higher amplitude, when mean prevalence is low and when transmission is frequency-dependent. Population size variation due to variation in birth rates rather than death rates also increases the lag. Predicting future human outbreaks of hantavirus pulmonary syndrome may require taking these effects into account.     

Deer mouse movements in peridomestic and sylvan settings in relation to Sin Nombre virus antibody prevalence

Prevalence of antibody to Sin Nombre virus (SNV) has been found to be nearly twice as high in deer mice (Peromyscus maniculatus) in peridomestic settings as in sylvan settings in two studies in Montana and one in New Mexico. We investigated whether this difference may be related to a difference in deer mouse movements in the two settings. We used radiotelemetry to determine home range size and length of movement for 22 sylvan (1991-1992) and 40 peridomestic deer mice (1995-1999). We also determined the percentage of locations inside versus outside of buildings for peridomestic mice. Though variable, average home range size for female deer mice was significantly smaller for peridomestic deer mice than for sylvan deer mice. The smaller home range in peridomestic settings may concentrate shed SNV, and protection from solar ultraviolet radiation inside buildings may increase environmental persistence of SNV. Both these factors could lead to increased SNV exposure of deer mice within peridomestic populations and result in higher antibody prevalence. Peridomestic deer mice moved between buildings and outside areas, which is evidence that SNV can be transmitted between peridomestic and sylvan populations.     

Transmission Ecology of Sin Nombre Hantavirus in Naturally Infected North American Deermouse Populations in Outdoor Enclosures

Sin Nombre hantavirus (SNV), hosted by the North American deermouse (Peromyscus maniculatus), causes hantavirus pulmonary syndrome (HPS) in North America. Most transmission studies in the host were conducted under artificial conditions, or extrapolated information from mark-recapture data. Previous studies using experimentally infected deermice were unable to demonstrate SNV transmission. We explored SNV transmission in outdoor enclosures using naturally infected deermice. Deermice acquiring SNV in enclosures had detectable viral RNA in blood throughout the acute phase of infection and acquired significantly more new wounds (indicating aggressive encounters) than uninfected deermice. Naturally-infected wild deermice had a highly variable antibody response to infection, and levels of viral RNA sustained in blood varied as much as 100-fold, even in individuals infected with identical strains of virus. Deermice that infected other susceptible individuals tended to have a higher viral RNA load than those that did not infect other deermice. Our study is a first step in exploring the transmission ecology of SNV infection in deermice and provides new knowledge about the factors contributing to the increase of the prevalence of a zoonotic pathogen in its reservoir host and to changes in the risk of HPS to human populations. The techniques pioneered in this study have implications for a wide range of zoonotic disease studies.     

Sin Nombre Virus and Rodent Species Diversity: A Test of the Dilution and Amplification Hypotheses

Background

Species diversity is proposed to greatly impact the prevalence of pathogens. Two predominant hypotheses, the “Dilution Effect” and the “Amplification Effect”, predict divergent outcomes with respect to the impact of species diversity. The Dilution Effect predicts that pathogen prevalence will be negatively correlated with increased species diversity, while the Amplification Effect predicts that pathogen prevalence will be positively correlated with diversity. For many host-pathogen systems, the relationship between diversity and pathogen prevalence has not be empirically examined.

Methodology/Principal Findings

We tested the Dilution and Amplification Effect hypotheses by examining the prevalence of Sin Nombre virus (SNV) with respect to diversity of the nocturnal rodent community. SNV is directly transmitted primarily between deer mice (Peromyscus maniculatus). Using mark-recapture sampling in the Spring and Fall of 2003–2005, we measured SNV prevalence in deer mice at 16 landscape level sites (3.1 hectares each) that varied in rodent species diversity. We explored several mechanisms by which species diversity may affect SNV prevalence, including reduced host density, reduced host persistence, the presence of secondary reservoirs and community composition. We found a negative relationship between species diversity and SNV prevalence in deer mice, thereby supporting the Dilution Effect hypothesis. Deer mouse density and persistence were lower at sites with greater species diversity; however, only deer mouse persistence was positively correlated with SNV prevalence. Pinyon mice (P. truei) may serve as dilution agents, having a negative effect on prevalence, while kangaroo rats (Dipodomys ordii), may have a positive effect on the prevalence of SNV, perhaps through effects on deer mouse behavior.

Conclusions/Significance

While previous studies on host-pathogen systems have found patterns of diversity consistent with either the Dilution or Amplification Effects, the mechanisms by which species diversity influences prevalence have not been investigated. Our study indicates that changes in host persistence, coupled with interspecific interactions, are important mechanisms through which diversity may influence patterns of pathogens. Our results reveal the complexity of rodent community interactions with respect to SNV dynamics.     

Delayed density-dependent prevalence of Sin Nombre virus infection in deer mice (Peromyscus maniculatus) in central and western Montana

Understanding how transmission of zoonoses takes place within reservoir populations, such as Sin Nombre virus (SNV) among deer mice (Peromyscus maniculatus), is important in determining the risk of exposure to other hosts, including humans. In this study, we examined the relationship between deer mouse populations and the prevalence of antibodies to SNV, a system where the effect of host population abundance on transmission is debated. We examined the relationship between abundance of deer mice in late summer-early autumn and SNV antibody prevalence the following spring-early summer (termed delayed density-dependent [DDD] prevalence of infection) at both regional and local scales, using 12 live-trapping grids for 11-14 yr, across central and western Montana. When all trapping grids were combined (regional scale), there was a significant DDD relationship for individual months and when months within seasons were averaged. However, within individual grids (local scale), evidence of DDD prevalence of infection was observed consistently at only one location. These findings suggest that, although there is evidence of DDD prevalence of infection at regional scales, it is not always apparent at local scales, possibly because the regional pattern of DDD infection prevalence is driven by differences in abundance and prevalence among sites, rather than in autumn-spring delays. Transmission of SNV may be more complex than the original hypothesis of autumn-spring delayed density dependence suggests. This complexity is also supported by recent modeling studies. Empirical investigations are needed to determine the duration and determinants of time-lagged abundance and antibody prevalence. Our study suggests predicting local, human exposure risk to SNV in spring, based on deer mouse abundance in autumn, is unlikely to be a reliable public health tool, particularly at local scales.     

Experimental parasite community perturbation reveals associations between Sin Nombre virus and gastrointestinal nematodes in a rodent reservoir host

Individuals are often co-infected with several parasite species, yet measuring within-host interactions remains difficult in the wild. Consequently, the impacts of such interactions on host fitness and epidemiology are often unknown. We used anthelmintic drugs to experimentally reduce nematode infection and measured the effects on both nematodes and the important zoonosis Sin Nombre virus (SNV) in its primary reservoir (Peromyscus spp.). Treatment significantly reduced nematode infection, but increased SNV seroprevalence. Furthermore, mice that were co-infected with both nematodes and SNV were in better condition and survived up to four times longer than uninfected or singly infected mice. These results highlight the importance of investigating multiple parasites for understanding interindividual variation and epidemiological dynamics in reservoir populations with zoonotic transmission potential.     

A temporal dilution effect: hantavirus infection in deer mice and the intermittent presence of voles in Montana

The effect of intermittently occurring, non-reservoir host species on pathogen transmission and prevalence in a reservoir population is poorly understood. We investigated whether voles, Microtus spp., which occur intermittently, influenced estimated standing antibody prevalence (ESAP) to Sin Nombre hantavirus (SNV, Bunyaviridae: Hantavirus) among deer mice, Peromyscus maniculatus, whose populations are persistent. We used 14 years of data from central Montana to investigate whether ESAP among deer mice was related to vole presence or abundance while controlling for the relationship between deer mouse abundance and ESAP. We found a reduction in deer mouse ESAP associated with the presence of voles, independent of vole abundance. A number of studies have documented that geographic locations which support a higher host diversity can be associated with reductions in pathogen prevalence by a hypothesized dilution effect. We suggest a dilution effect may also occur in a temporal dimension at sites where host richness fluctuates. Preservation of host diversity and optimization of environmental conditions which promote occurrence of ephemeral species, such as voles, may result in a decreased ESAP to hantaviruses among reservoir hosts. Our results may extend to other zoonotic infectious diseases.     

Long-term dynamics of Sin Nombre viral RNA and antibody in deer mice in Montana

Infections with hantaviruses in the natural host rodent may result in persistent, asymptomatic infections involving shedding of virus into the environment. Laboratory studies have partially characterized the acute and persistent infection by Sin Nombre virus (SNV) in its natural host, the deer mouse (Peromyscus maniculatus). However, these studies have posed questions that may best be addressed using longitudinal studies involving sequential sampling of individual wild-caught, naturally infected mice. Using enzyme immunoassay and polymerase chain reaction (PCR) analysis of monthly blood samples, we followed the infection status of deer mice in a mark-recapture study in Montana for 2 yr. Only six of 907 samples without IgG antibody to SNV contained detectable SNV RNA, suggesting that there is a very brief period of viremia before the host develops detectable antibody. The simultaneous presence of both antibody and viral RNA in blood was detected in consecutive monthly samples for as long as 3 mo. However, chronic infection was typified by alternating characteristics of PCR positivity and PCR negativity. Two possible interpretations of these results are that 1) viral RNA may be consistently present in the blood of chronically infected deer mouse, but that viral RNA is near the limits of PCR detectability or 2) SNV RNA sporadically appears in blood as a consequence of unknown physiological events. The occurrence of seasonal patterns in the proportion of samples that contains antibody and that also contained SNV RNA demonstrated a temporal association between recent infection (antibody acquisition) and presence of viral RNA in blood.     

Habitat variation influences movement rates and population structure of an intertidal fish

Deer mice (Peromyscus maniculatus) are the primary reservoir for Sin Nombre virus (SNV), a North American hantavirus that causes disease with high mortality in humans. Recent studies have proposed that habitat disturbance affects prevalence of SNV in deer mice; however, the outcomes proposed in these studies are in opposition to each other. Our objectives were to test these divergent hypotheses by: (1) measuring SNV infection in deer mice within a patchwork of disturbance; and (2) evaluating the relationships between SNV prevalence, population density and demography as possible mechanisms. In 2003 and 2004, we sampled 1,297 deer mice from 17 sites with varying levels of disturbance in the Great Basin Desert. Across sites and years, SNV prevalence varied from 0.0 to 38.9%. We found a negative relationship between SNV prevalence and disturbance. Although we found no direct relationship between SNV prevalence and deer mouse density, we found that density was highest on sites with the lowest levels of disturbance. The number of deer mice that survived across seasons (e.g., trans-seasonal survivors) differed across levels of disturbance and was greatest on our least disturbed study sites moderate on sites with intermediate levels of disturbance and zero on highly disturbed sites. On low-disturbance sites, a greater proportion of trans-seasonal survivors were SNV seropositive (28.80%) compared to the intermediate-disturbance sites (16.67). Collectively, our results indicate that habitat disturbance plays a predictive role in SNV prevalence, with highly disturbed sites having reduced long-term survival of deer mice, including survival of infected individuals.     

Analyses of gene flow among populations of deer mice (Peromyscus maniculatus) at sites near hantavirus pulmonary syndrome case-patient residences

Gene flow and potential for Sin Nombre virus (SNV) trafficking of the deer mouse (Peromyscus maniculatus) was studied in Delta and Mesa counties of western Colorado (USA). The study areas included Grand Mesa and surrounding grazing and agricultural areas. This area has several natural potential barriers to rodent gene flow, including rivers, cliffs, and mountains. Ten study sites were utilized in a spatially nested design ranging from 0.65-81 km apart; four of these sites were at or near human hantavirus pulmonary syndrome (HPS) case-patient residences. One HPS case occurred on the north side of Grand Mesa in 1993; the other three (two confirmed, one presumptive) occurred on the south side of Grand Mesa between 1999-2000. Blood and tissue samples were collected from each of 221 deer mice captured from 1999-2000. Blood samples were tested for IgG antibody to SNV. At least one deer mouse had antibody to SNV at nine of 10 sites. Genomic DNA was isolated from tissue samples and alleles at six microsatellite loci were amplified by polymerase chain reaction (PCR). Polymorphisms were resolved on denaturing polyacrylamide gels and visualized by silver staining. Traditional population genetic analyses of this study indicated moderate population subdivision among the populations surveyed, slight evidence of isolation by distance, and that the Gunnison River system may hinder gene flow in this area. Application of assignment tests indicated that approximately 73-85% of mice were assigned to their population of capture. Many of the misclassifications occurred among sites less than 1 km apart; however, some long-distance misclassifications were noted. Additionally, some misclassifications were noted among study sites on different sides of the Gunnison River system, indicating that the riparian corridor of this system may facilitate some gene flow. Overall, these data indicate that SNV trafficking is more likely at the local level, but some long-distance trafficking may be possible, especially where select habitat variables favor long-distance movements.     

Changes in sin nombre virus antibody prevalence in deer mice across seasons: the interaction between habitat, sex, and infection in deer mice

We examined the impact of season and habitat on Sin Nombre virus (SNV) seroprevalence in deer mice (Peromyscus maniculatus) in Utah's Great Basin Desert from May 2002 through summer 2003. Low mouse captures in 2002 limited analysis for that year. In two seasons during 2003, mouse density and sagebrush cover were positively linked (spring: r = 0.8, P = 0.01; summer: r = 0.8, P = 0.04). In the spring, seroprevalence was negatively correlated with density (r = -0.9, P< 0.01); male and female antibody prevalence did not differ; and scarring was unrelated to antibody status. In the summer, density and antibody prevalence were unrelated; male seroprevalence was higher (chi(2) = 3.6, P = 0.05); and seropositive mice had more scars (t = 2.5, P = 0.02). We speculate nesting behavior could maintain SNV over the winter, whereas summer territoriality could be responsible for transmission.     

Testing Mechanisms of the Dilution Effect: Deer Mice Encounter Rates, Sin Nombre Virus Prevalence and Species Diversity

Species diversity has been shown to decrease prevalence of disease in a variety of host–pathogen systems, in a phenomenon termed the Dilution Effect. Several mechanisms have been proposed by which diversity may decrease prevalence, though few have been tested in natural host-pathogen systems. We investigated the mechanisms by which diversity influenced the prevalence of Sin Nombre virus (SNV), a directly transmitted virus in deer mice (Peromyscus maniculatus). We monitored both intra and interspecific encounters of deer mice using foraging arenas at five sites in the Great Basin Desert with disparate levels of species diversity to examine two potential mechanisms which may contribute to the dilution of SNV prevalence: (1) reduced frequency of encounters between deer mice, or (2) reduced duration of contacts between deer mice. We also investigated the relationship between deer mouse density and these mechanisms, as density is often predicted to influence both inter and intraspecific encounters. Results of our study indicate that frequency of intraspecific interactions between deer mice was reduced with increased diversity. Species diversity did not impact average duration of encounters. Density was correlated with absolute, but not relative rates of encounters between deer mice, suggesting that encounters may be influenced by factors other than density. Our study indicates that species diversity influences the dynamics of SNV by reducing encounters between deer mice in a trade-off between intra and interspecific interactions.     

Experimental Andes Virus Infection in Deer Mice: Characteristics of Infection and Clearance in a Heterologous Rodent Host

New World hantaviruses can cause hantavirus cardiopulmonary syndrome with high mortality in humans. Distinct virus species are hosted by specific rodent reservoirs, which also serve as the vectors. Although regional spillover has been documented, it is unknown whether rodent reservoirs are competent for infection by hantaviruses that are geographically separated, and known to have related, but distinct rodent reservoir hosts. We show that Andes virus (ANDV) of South America, carried by the long tailed pygmy rice rat (Oligoryzomys longicaudatus), infects and replicates in vitro and in vivo in the deer mouse (Peromyscus maniculatus), the reservoir host of Sin Nombre virus (SNV), found in North America. In experimentally infected deer mice, viral RNA was detected in the blood, lung, heart and spleen, but virus was cleared by 56 days post inoculation (dpi). All of the inoculated deer mice mounted a humoral immune response by 14 dpi, and produced measurable amounts of neutralizing antibodies by 21 dpi. An up-regulation of Ccl3, Ccl4, Ccl5, and Tgfb, a strong CD4⁺ T-cell response, and down-regulation of Il17, Il21 and Il23 occurred during infection. Infection was transient with an absence of clinical signs or histopathological changes. This is the first evidence that ANDV asymptomatically infects, and is immunogenic in deer mice, a non-natural host species of ANDV. Comparing the immune response in this model to that of the immune response in the natural hosts upon infection with their co-adapted hantaviruses may help clarify the mechanisms governing persistent infection in the natural hosts of hantaviruses.     

The role of heterogeneity in the persistence and prevalence of Sin Nombre virus in deer mice

Many diseases persist at a relatively low prevalence, seemingly close to extinction. For a chronic disease in a homogeneous population, reducing the transmission rate by a fraction proportional to the prevalence would be sufficient to eradicate the disease. This study examines how higher prevalence of the Sin Nombre virus in male deer mice (Peromyscus maniculatus) might contribute to disease persistence. Analyzing data from over 2,000 individual mice captured in 19 sites over 4 years, we found prevalences of 18.5% in males and 8.8% in females. By examining recaptures, we determined that males are more likely to contract the infection because of higher susceptibility or higher encounter rates. Comparing across 86 sampling periods, we found a higher proportion of males when population densities were low. A capture-recapture analysis indicates that males live longer than females. A mathematical model based on the measured parameters and population size trajectories suggests that the combined heterogeneity in encounters, susceptibility, and mortality may buffer the disease from extinction by concentrating disease in the subgroup most likely to transmit the disease. This buffering effect is not significantly stronger in a fluctuating population, indicating that these forms of heterogeneity might not be the key for disease persistence through host population bottlenecks.