Genome-wide support for incipient Tula hantavirus species within a single rodent host lineage

Evolutionary divergence of viruses is most commonly driven by co-divergence with their hosts or through isolation of transmission after host shifts. It remains mostly unknown, however, whether divergent phylogenetic clades within named virus species represent functionally equivalent byproducts of high evolutionary rates or rather incipient virus species. Here, we test these alternatives with genomic data from two widespread phylogenetic clades in Tula orthohantavirus (TULV) within a single evolutionary lineage of their natural rodent host, the common vole Microtus arvalis. We examined voles from forty-two locations in the contact region between clades for TULV infection by reverse transcription (RT)-PCR. Sequencing yielded twenty-three TULV Central North and twenty-one TULV Central South genomes, which differed by 14.9-18.5 per cent at the nucleotide and 2.2-3.7 per cent at the amino acid (AA) level without evidence of recombination or reassortment between clades. Geographic cline analyses demonstrated an abrupt (<1 km wide) transition between the parapatric TULV clades in continuous landscape. This transition was located within the Central mitochondrial lineage of M. arvalis, and genomic single nucleotide polymorphisms showed gradual mixing of host populations across it. Genomic differentiation of hosts was much weaker across the TULV Central North to South transition than across the nearby hybrid zone between two evolutionary lineages in the host. We suggest that these parapatric TULV clades represent functionally distinct, incipient species, which are likely differently affected by genetic polymorphisms in the host. This highlights the potential of natural viral contact zones as systems for investigating the genetic and evolutionary factors enabling or restricting the transmission of RNA viruses.

Exploring the influence of density-dependence and weather on the spatial and temporal variation in common vole (Microtus arvalis) abundance in Castilla y León, NW Spain

BACKGROUND

The common vole has invaded the agroecosystems of northwestern Spain, where outbreaks cause important crop damage and management costs. Little is yet known about the factors causing or modulating vole fluctuations. Here, we used 11 years of vole abundance monitoring data in 40 sites to study density-dependence and weather influence on vole dynamics. Our objective was to identify the population dynamics structure and determine whether there is direct or delayed density-dependence. An evaluation of climatic variables followed, to determine whether they influenced vole population peaks.

RESULTS

First- and second-order outbreak dynamics were detected at 7 and 33 study sites, respectively, together with second-order variability in periodicity (2-3 to 4-5-year cycles). Vole population growth was explained by previous year abundance (mainly numbers in summer and spring) at 21 of the sites (52.5%), by weather variables at 11 sites (27.5%; precipitation or temperature in six and five sites, respectively), and by a combination of previous abundance and weather variables in eight sites (20%).

CONCLUSIONS

We detected variability in vole spatiotemporal abundance dynamics, which differs in cyclicity and period. We also found regional variation in the relative importance of previous abundances and weather as factors modulating vole fluctuations. Most vole populations were cyclical, with variable periodicity across the region. Our study is a first step towards the development of predictive modeling, by disclosing relevant factors that might trigger vole outbreaks. It improves decision-making processes within integrated management dealing with mitigation of the agricultural impacts caused by voles. © 2023 Society of Chemical Industry.

Seasonal Adaptation: Geographic Photoperiod-Temperature Patterns Explain Genetic Variation in the Common Vole Tsh Receptor

The vertebrate photoperiodic neuroendocrine system uses the photoperiod as a proxy to time the annual rhythms in reproduction. The thyrotropin receptor (TSHR) is a key protein in the mammalian seasonal reproduction pathway. Its abundance and function can tune sensitivity to the photoperiod. To investigate seasonal adaptation in mammals, the hinge region and the first part of the transmembrane domain of the Tshr gene were sequenced for 278 common vole (Microtus arvalis) specimens from 15 localities in Western Europe and 28 localities in Eastern Europe. Forty-nine single nucleotide polymorphisms (SNPs; twenty-two intronic and twenty-seven exonic) were found, with a weak or lack of correlation with pairwise geographical distance, latitude, longitude, and altitude. By applying a temperature threshold to the local photoperiod-temperature ellipsoid, we obtained a predicted critical photoperiod (pCPP) as a proxy for the spring onset of local primary food production (grass). The obtained pCPP explains the distribution of the genetic variation in Tshr in Western Europe through highly significant correlations with five intronic and seven exonic SNPs. The relationship between pCPP and SNPs was lacking in Eastern Europe. Thus, Tshr, which plays a pivotal role in the sensitivity of the mammalian photoperiodic neuroendocrine system, was targeted by natural selection in Western European vole populations, resulting in the optimized timing of seasonal reproduction.

FREQUENT LEPTOSPIRA SPP. DETECTION BUT ABSENCE OF TULA ORTHOHANTAVIRUS IN MICROTUS SPP. VOLES, NORTHWESTERN SPAIN

The common vole (Microtus arvalis) is a major agricultural pest in Europe and is a reservoir for several zoonotic agents, such as Leptospira spp. and Tula orthohantavirus (TULV). However, little is known about the occurrence of those pathogens in voles from Spain, where the species has largely expanded its distribution range in the past decades, causing agricultural pests and zoonotic diseases. For a molecular survey, 580 common voles and six Lusitanian pine voles (Microtus lusitanicus) were collected in 26 localities from four provinces of northwestern Spain. We assessed the presence of Leptospira spp. DNA in kidney tissue by PCR targeting the lipL32 gene, detecting a prevalence of 7.9% (95% confidence interval, 5.9-10.4) for common voles and of 33.3% (95% confidence interval, 4.3-77.7) for Lusitanian pine voles. We identified Leptospira kirschneri in 24 animals and Leptospira borgpetersenii in two animals, using secY gene-specific PCR. We analyzed environmental and demographic factors (such as age class, weight, and sex) and population dynamics data for their potential effect on the Leptospira spp. prevalence in those voles. The Leptospira spp. DNA detection rate in common voles increased significantly with maximum air temperature, vole weight, and amount of accumulated rainfall during the 90 d before capture and within the peak phase of the population cycle. We assessed the presence of TULV in lung tissue of 389 voles by reverse-transcription PCR, with no positive results. The absence of TULV might be explained by the evolutionary isolation of the common vole in Spain. The detection of two Leptospira genomospecies underlines the necessity for further typing efforts to understand the epidemiology of leptospiral infection in the common vole and the potential risk for human health in Spain.

Spatial and Temporal Dynamics and Molecular Evolution of Tula orthohantavirus in German Vole Populations

Tula orthohantavirus (TULV) is a rodent-borne hantavirus with broad geographical distribution in Europe. Its major reservoir is the common vole (Microtus arvalis), but TULV has also been detected in closely related vole species. Given the large distributional range and high amplitude population dynamics of common voles, this host-pathogen complex presents an ideal system to study the complex mechanisms of pathogen transmission in a wild rodent reservoir. We investigated the dynamics of TULV prevalence and the subsequent potential effects on the molecular evolution of TULV in common voles of the Central evolutionary lineage. Rodents were trapped for three years in four regions of Germany and samples were analyzed for the presence of TULV-reactive antibodies and TULV RNA with subsequent sequence determination. The results show that individual (sex) and population-level factors (abundance) of hosts were significant predictors of local TULV dynamics. At the large geographic scale, different phylogenetic TULV clades and an overall isolation-by-distance pattern in virus sequences were detected, while at the small scale (<4 km) this depended on the study area. In combination with an overall delayed density dependence, our results highlight that frequent, localized bottleneck events for the common vole and TULV do occur and can be offset by local recolonization dynamics.

Hantavirus-Leptospira coinfections in small mammals from central Germany

European orthohantaviruses (Puumala orthohantavirus (PUUV); Dobrava-Belgrade orthohantavirus (DOBV), genotype Kurkino; Tula orthohantavirus (TULV)), and Leptospira spp. are small mammal-associated zoonotic pathogens that cause diseases with potentially similar symptoms in humans. We investigated the frequency of Leptospira spp. and hantavirus single and double infections in small mammals from 22 sites in Thuringia, central Germany, during 2017. TULV infections were detected at 18 of 22 sites (mean prevalence 13.8%, 93/674). PUUV infections were detected at four of 22 sites (mean prevalence 1.5%, 7/471), and respective PUUV sequences formed a novel phylogenetic clade, but DOBV infections were not detected at all. Leptospira infections were detected at 21 of 22 sites with the highest overall prevalence in field voles (Microtus agrestis) with 54.5% (6/11) and common voles (Microtus arvalis) with 30.3% (205/676). Leptospira–hantavirus coinfections were found in 6.6% (44/671) of common voles but only in two of 395 bank voles. TULV and Leptospira coinfection probability in common voles was driven by individual (age) and population-level factors. Coinfections seemed to be particularly associated with sites where Leptospira spp. prevalence exceeded 35%. Future investigations should evaluate public health consequences of this strong spatial clustering of coinfections.

Patchy Occurrence of Cowpox Virus in Voles from Germany

Cowpox virus (CPXV), genus Orthopoxvirus, family Poxviridae, is a zoonotic pathogen in Eurasian wild rodents. High seroprevalences have been reported previously for vole and murine species in Europe. In contrast, viral DNA was only rarely detected, and very few reservoir-derived CPXV isolates exist. In this study, CPXV DNA and CPXV-reactive antibodies were monitored in wild small mammals for 5 years in four German federal states. Screening of liver tissues of 3966 animals by CPXV real-time PCR (qPCR) revealed five voles of two species positive for CPXV DNA. Two positive bank voles (Myodes glareolus) and two positive common voles (Microtus arvalis) originated from two plots in Baden-Wuerttemberg. One positive bank vole originated from Mecklenburg-Western Pomerania. None of the small mammals from Thuringia and North Rhine-Westphalia was positive in the qPCR. CPXV antigen-based indirect immunofluorescence assays of 654 highly diluted chest cavity fluid samples detected two bank voles and two common voles from the same sites in Baden-Wuerttemberg to be highly seroreactive. Five animals were CPXV DNA positive, and four other animals were orthopoxvirus seropositive. Our study indicates both a very low prevalence and a patchy occurrence of CPXV in common and bank voles and absence in other rodent and shrew species in Germany. The multiple detection of infected voles at one site in Baden-Wuerttemberg and continued detection in a region of Mecklenburg-Western Pomerania classify these regions as potential endemic foci.

Rodent Host Abundance and Climate Variability as Predictors of Tickborne Disease Risk 1 Year in Advance

Using long-term data on incidences of Lyme disease and tickborne encephalitis, we showed that the dynamics of both diseases in central Europe are predictable from rodent host densities and climate indices. Our approach offers a simple and effective tool to predict a tickborne disease risk 1 year in advance.

Concentration of Mercury in the Livers of Small Terrestrial Rodents from Rural Areas in Poland

Small terrestrial mammals could be used as accumulative biomonitors of different environmental contaminants, but the knowledge of the level of Hg in their bodies is scant. The aim of our research was to verify the factors influencing Hg bioaccumulation and to analyze the concentration of total mercury (Hg) in the livers of four species of wild terrestrial rodents from different rural areas of Poland: the yellow-necked mouse (Apodemus flavicollis), striped field mouse (Apodemus agrarius), common vole (Microtus arvalis), and bank vole (Myodes glareolus). The concentration of total Hg was analyzed in liver tissue by atomic absorption spectrometry using a direct mercury analyzer. The concentration of Hg found in the livers of rodents ranged from <1 to 36.4 µg/kg of wet weight, differed between study sites, species, and sexes, and was related to body weight. We addressed feeding habits as potential causes of differences in liver Hg concentration among species.

Detection of Francisella tularensis in three vole species in Central Europe

Francisella tularensis is a zoonotic, gram-negative bacterium that causes tularemia in humans. Depending on its subspecies and the route of transmission, mild to lethal courses have been reported. F. tularensis subsp. holarctica is the only subspecies found in Europe and affects a plenitude of vertebrates including lagomorphs and rodents. Population outbreaks of certain rodent species are likely to be involved in the transmission of this pathogen. This molecular survey aims to evaluate the presence of F. tularensis in small mammals from three Central European countries. Using a real-time polymerase chain reaction, F. tularensis DNA was detected in common voles (Microtus arvalis) from Switzerland and in field voles (Microtus agrestis) and a bank vole (Myodes glareolus) from Germany, but not in any other small mammal species. All common voles from the Czech Republic were negative for F. tularensis DNA. The prevalence in the three vole species varied between 1.3% and 3.0%. In conclusion, Francisella tularensis DNA was detected in three vole species in two of three countries investigated. The observed low prevalence raises questions on the role of voles for the transmission of Francisella tularensis in Central Europe.

Influence of no-tillage versus tillage system on common vole (Microtus arvalis) population density

BACKGROUND

While the 'no-tillage' management system generally improves soil properties and helps to control arthropod pests, it may also intensify crop infestation by the common vole (Microtus arvalis Pallas). In this study, we evaluated the impact of soil management (no-tillage or tillage), crop and previous crop (winter wheat or winter rape), and season (spring or autumn) on common vole density using data from the Common Vole Monitoring Programme undertaken by the Plant Protection Service of the Czech Republic between 2000 and 2009.

RESULTS

Models predicted low mean values of vole infestation across management types, crops, and seasons. The untilled fields hosted significantly more voles than the tilled fields in spring but not in autumn. More common voles were found in winter rape than in winter wheat during both seasons.

CONCLUSION

Recent studies suggest that no-tillage management is more profitable than tillage management as a result of its positive impact on soil properties and pest control. During periods of high vole infestation, however, tillage may constitute an alternative strategy for reducing yield losses. © 2017 Society of Chemical Industry.

The complete mitochondrial genome of the common vole, Microtus arvalis (Rodentia: Arvicolinae)

The common vole, Microtus arvalis belongs to the genus Microtus in the subfamily Arvicolinae. In this study, the complete mitochondrial genome of M. arvalis was recovered using shotgun sequencing and an iterative mapping approach using three related species. Phylogenetic analyses using the sequence of 21 arvicoline species place the common vole as a sister species to the East European vole (Microtus levis), but as opposed to previous results we find no support for the recognition of the genus Neodon within the subfamily Arvicolinae, as this is, as well as the genus Lasiopodomys, found within the Microtus genus.

The interplay between seasonality and density: consequences for female breeding decisions in a small cyclic herbivore

BACKGROUND

Cyclic rodent population dynamics are subjected to both intrinsic regulatory processes such as density-dependence and extrinsic environmental forcing. Among extrinsic factors, seasonal environmental variation is understood to facilitate cycles. In rodents, these processes have been studied mostly independently and their relative importance for population dynamics is poorly known.

RESULTS

We performed a detailed analysis of common vole (Microtus arvalis) reproduction in a cyclic population using a spatially extensive data set over 17 years in central-western France. Environmental seasonality was the main source of explained variation in common vole reproduction. Additionally, inter-annual variation in the environment explained a smaller part of the variance in reproduction in spring and summer than in winter, whereas the effect of density was only found in autumn and winter. In particular, we detected a strong impact of plant productivity on fecundity during the breeding season, with low vegetation productivity being able to bring vole reproduction nearly to a halt. In contrast, vole reproduction during autumn and winter was mainly shaped by intrinsic factors, with only the longer and heavier females being able to reproduce. The effect of population density on reproduction was negative, mediated by direct negative effects on the proportion of breeders in autumn and winter during outbreak years and by a delayed negative effect on litter size the following year.

CONCLUSIONS

During the main breeding season, variability of female vole reproduction is predominantly shaped by food resources, suggesting that only highly productive environment may induce vole outbreaks. During fall and winter, variability of female vole reproduction is mainly controlled by intrinsic factors, with high population density suppressing reproduction. This suggests, in this cyclic population, that negative direct density dependence on reproduction could explain winter declines after outbreaks.