Individual-based modeling of white-tailed deer (Odocoileus virginianus) movements and epizootiology

White-tailed deer (Odocoileus virginianus) are important game mammals and potential reservoirs of diseases of domestic livestock, so diseases of deer are of great concern to wildlife managers. In many situations, models can be useful for integrating existing data, understanding disease transmission patterns, and predicting effects on host populations. Individual-based modeling (IBM) has become more commonplace in ecology as a tool to link individual behavior to population dynamics and community interactions, especially for gauging the effects of management actions. Spatially explicit IBMs are especially useful when ecological processes, such as disease transmission, are affected by the spatial composition of the environment. I developed a spatially explicit IBM, DeerLandscapeDisease (DLD), to simulate direct and indirect disease transmission in white-tailed deer. Using data from GPS-collared deer in southern Illinois, I developed methods to identify habitats and times of high contact probability. I parameterized movement models, for use in DLD, using field data from GPS-collared deer in both southern and east-central Illinois. I then used DLD to simulate deer movements and epizootiology in two different landscapes: a predominantly agricultural landscape with fragmented forest patches in east-central Illinois and a landscape dominated by forest in southern Illinois. Behavioral and demographic parameters that could not be estimated from the field data were estimated using published literature of deer ecology. I assumed that bioavailability of infectious pathogens deposited in the environment decreased exponentially. Transmission probabilities were estimated by fitting to published trends in infection prevalence, assuming that infection probability during an encounter was equal for all age classes, so infection prevalence varied with sex- and age-specific behavior. DLD simulations of chronic wasting disease epizootiology demonstrated significant effects of landscape structure, social behavior, and mode of transmission on prevalence, emphasizing the importance of spatial, temporal and behavioral heterogeneity in disease modeling. These results demonstrate the utility of IBMs in incorporating spatio-temporal variables as well as animal behavior when predicting and modeling disease spread

The annual, temporal and spatial pattern of Setaria tundra outbreaks in Finnish reindeer : a mechanistic transmission model approach

BackgroundIn northern Finland (Lapland), reindeer are reared as semi-domesticated animals. The region has a short summer season of 2-3 months, yet reindeer are infected with the mosquito-borne filarioid parasite Setaria tundra. The infection causes peritonitis and perihepatitis, which cause significant economic losses due to reduced body weight of infected animals. The objective of this study was to: (i) describe the spatial and temporal pattern of outbreaks in three different areas across Finnish Lapland; and (ii) construct a temperature-driven mechanistic transmission model to quantify the potential role of temperature on intensity of S. tundra transmission in reindeer.MethodsWe developed a temperature-driven transmission model able to predict the number of S. tundra potentially transmitted from an infectious reindeer. We applied the model to the years 2004-2015, and compared the predictions to the proportion of reindeer whose livers were condemned due to S. tundra infection at the time of slaughter.ResultsThe mean proportion of liver condemnation increased in reindeer slaughtered in late autumn/winter compared to earlier dates. The outbreaks were geographically clustered each year but there were no fixed foci where outbreaks occurred. Larger outbreaks were recorded in the southern regions of reindeer-herding areas compared to the central or northern parts of Lapland. Our model showed that temperatures never allowed for transmission of more than a single generation of S. tundra each season. In southern (Kuusamo) and central (Sodankyla) Lapland, our model predicted an increasing trend from 1979 to 2015 for both the duration of the effective transmission period of S. tundra (P <0.001) and for the potential number of L3 S. tundra larvae being transmitted from an infectious reindeer (P <0.001).ConclusionsThe effective transmission period for S. tundra in reindeer is very short in Lapland, but it increased over the period studied. Only one generation of S. tundra can be transmitted in one season among reindeer in Lapland. Increasing temperatures may facilitate a range expansion and increasing duration of effective transmission period for S. tundra.Peer reviewe

Social Affiliation and Contact Patterns Among White-tailed Deer in Disparate Landscapes: Implications for Disease Transmission

In social species, individuals contact members of the same group much more often than those of other groups, particularly for contacts that could directly transmit disease agents. This disparity in contact rates violates the assumptions of simple disease models, hinders disease spread between groups, and could decouple disease transmission from population density. Social behavior of white-tailed deer has important implications for the long-term dynamics and impact of diseases such as bovine tuberculosis and chronic wasting disease (CWD), so expanding our understanding of their social system is important. White-tailed deer form matrilineal groups, which inhabit stable home ranges that overlap somewhat with others—a pattern intermediate between mass-action and strict territoriality. To quantify how group membership affects their contact rates and document the spectrum of social affiliation, we analyzed location data from global positioning system (GPS) collars on female and juvenile white-tailed deer in 2 study areas: near Carbondale in forest-dominated southern Illinois (2002–2006) and near Lake Shelbyville in agriculture-dominated central Illinois (2006–2009). For each deer dyad (i.e., 2 individual deer with sufficient overlapping GPS data), we measured space-use overlap, correlation of movements, direct contact rate (simultaneous GPS locations \u3c 10 m apart), and indirect contact rate (GPS locations \u3c 10 m apart when offset by 1 or 3 days). Direct contact rates were substantially higher for within-group dyads than between-group dyads, but group membership had little apparent effect on indirect contact rates. The group membership effect on direct contact rates was strongest in winter and weakest in summer, with no apparent difference between study areas. Social affiliations were not dichotomous, with some deer dyads showing loose but positive affiliation. Even for obvious within-group dyads, their strength of affiliation fluctuated between years, seasons, and even days. Our findings highlight the poor fit between deer behavior and simple models of disease transmission and, combined with previous infection data, suggest that direct contact is the primary driver of CWD transmission among free living female and juvenile white-tailed deer

Potential drivers of human tick-borne encephalitis in the orebro region of Sweden, 2010-2021

Incidence of tick-borne encephalitis (TBE) has increased during the last years in Scandinavia, but the underlying mechanism is not understood. TBE human case data reported between 2010 and 2021 were aggregated into postal codes within orebro County, south-central Sweden, along with tick abundance and environmental data to analyse spatial patterns and identify drivers of TBE. We identified a substantial and continuing increase of TBE incidence in orebro County during the study period. Spatial cluster analyses showed significant hotspots (higher number of cases than expected) in the southern and northern parts of orebro County, whereas a cold spot (lower number of cases than expected) was found in the central part comprising orebro municipality. Generalised linear models showed that the risk of acquiring TBE increased by 12.5% and 72.3% for every percent increase in relative humidity and proportion of wetland forest, respectively, whereas the risk decreased by 52.8% for every degree Celsius increase in annual temperature range. However, models had relatively low goodness of fit (R-2 < 0.27). Results suggest that TBE in orebro County is spatially clustered, however variables used in this study, i.e., climatic variables, forest cover, water, tick abundance, sheep as indicator species, alone do not explain this pattern

Prevalence of tick-borne encephalitis virus in questing Ixodes ricinus nymphs in southern Scandinavia and the possible influence of meteorological factors

Ixodes ricinus ticks are Scandinavia's main vector for tick-borne encephalitis virus (TBEV), which infects many people annually. The aims of the present study were (i) to obtain information on the TBEV prevalence in host-seeking I. ricinus collected within the oresund-Kattegat-Skagerrak (oKS) region, which lies in southern Norway, southern Sweden and Denmark; (ii) to analyse whether there are potential spatial patterns in the TBEV prevalence; and (iii) to understand the relationship between TBEV prevalence and meteorological factors in southern Scandinavia. Tick nymphs were collected in 2016, in southern Scandinavia, and screened for TBEV, using pools of 10 nymphs, with RT real-time PCR, and positive samples were confirmed with pyrosequencing. Spatial autocorrelation and cluster analysis was performed with Global Moran's I and SatScan to test for spatial patterns and potential local clusters of the TBEV pool prevalence at each of the 50 sites. A climatic analysis was made to correlate parameters such as minimum, mean and maximum temperature, relative humidity and saturation deficit with TBEV pool prevalence. The climatic data were acquired from the nearest meteorological stations for 2015 and 2016. This study confirms the presence of TBEV in 12 out of 30 locations in Denmark, where six were from Jutland, three from Zealand and two from Bornholm and Falster counties. In total, five out of nine sites were positive from southern Sweden. TBEV prevalence of 0.7%, 0.5% and 0.5%, in nymphs, was found at three sites along the Oslofjord (two sites) and northern Skane region (one site), indicating a potential concern for public health. We report an overall estimated TBEV prevalence of 0.1% in questing I. ricinus nymphs in southern Scandinavia with a region-specific prevalence of 0.1% in Denmark, 0.2% in southern Sweden and 0.1% in southeastern Norway. No evidence of a spatial pattern or local clusters was found in the study region. We found a strong correlation between TBEV prevalence in ticks and relative humidity in Sweden and Norway, which might suggest that humidity has a role in maintaining TBEV prevalence in ticks. TBEV is an emerging tick-borne pathogen in southern Scandinavia, and we recommend further studies to understand the TBEV transmission potential with changing climate in Scandinavia

Landscape effects and spatial patterns of avian influenza virus in Danish wild birds, 2006-2020

Avian influenza (AI) is a contagious disease of birds with zoonotic potential. AI virus (AIV) can infect most bird species, but clinical signs and mortality vary. Assessing the distribution and factors affecting AI presence can direct targeted surveillance to areas at risk of disease outbreaks, or help identify disease hotspots or areas with inadequate surveillance. Using virus surveillance data from passive and active AIV wild bird surveillance, 2006−2020, we investigated the association between the presence of AIV and a range of landscape factors and game bird release. Furthermore, we assessed potential bias in the passive AIV surveillance data submitted by the public, via factors related to public accessibility. Lastly, we tested the AIV data for possible hot‐ and cold spots within Denmark. The passive surveillance data was biased regarding accessibility to areas (distance to roads, cities and coast) compared to random locations within Denmark. For both the passive and active AIV surveillance data, we found significant (p < .01) associations with variables related to coast, wetlands and cities, but not game bird release. We used these variables to predict the risk of AIV presence throughout Denmark, and found high‐risk areas concentrated along the coast and fjords. For both passive and active surveillance data, low‐risk clusters were mainly seen in Jutland and northern Zealand, whereas high‐risk clusters were found in Jutland, Zealand, Funen and the southern Isles such as Lolland and Falster. Our results suggest that landscape affects AIV presence, as coastal areas and wetlands attract waterfowl and migrating birds and therefore might increase the potential for AIV transmission. Our findings have enabled us to create risk maps of AIV presence in wild birds and pinpoint high‐risk clusters within Denmark. This will aid targeted surveillance efforts within Denmark and potentially aid in planning the location of future poultry farms

Spatial data of Ixodes ricinus instar abundance and nymph pathogen prevalence, Scandinavia, 2016-2017

Ticks carry pathogens that can cause disease in both animals and humans, and there is a need to monitor the distribution and abundance of ticks and the pathogens they carry to pinpoint potential high risk areas for tick-borne disease transmission. In a joint Scandinavian study, we measured Ixodes ricinus instar abundance at 159 sites in southern Scandinavia in August-September, 2016, and collected 29,440 tick nymphs at 50 of these sites. We additionally measured abundance at 30 sites in August-September, 2017. We tested the 29,440 tick nymphs in pools of 10 in a Fluidigm real-time PCR chip to screen for 17 different tick-associated pathogens, 2 pathogen groups and 3 tick species. We present data on the geolocation, habitat type and instar abundance of the surveyed sites, as well as presence/absence of each pathogen in all analysed pools from the 50 collection sites and individual prevalence for each site. These data can be used alone or in combination with other data for predictive modelling and mapping of high-risk areas

Variants in genes encoding small GTPases and association with epithelial ovarian cancer susceptibility

Epithelial ovarian cancer (EOC) is the fifth leading cause of cancer mortality in American women. Normal ovarian physiology is intricately connected to small GTP binding proteins of the Ras superfamily (Ras, Rho, Rab, Arf, and Ran) which govern processes such as signal transduction, cell proliferation, cell motility, and vesicle transport. We hypothesized that common germline variation in genes encoding small GTPases is associated with EOC risk. We investigated 322 variants in 88 small GTPase genes in germline DNA of 18,736 EOC patients and 26,138 controls of European ancestry using a custom genotype array and logistic regression fitting log-additive models. Functional annotation was used to identify bio-features and expression quantitative trait loci that intersect with risk variants. One variant, ARHGEF10L (Rho guanine nucleotide exchange factor 10 like) rs2256787, was associated with increased endometrioid EOC risk (OR = 1.33, p = 4.46 x 10(-6)). Other variants of interest included another in ARHGEF10L, rs10788679, which was associated with invasive serous EOC risk (OR = 1.07, p = 0.00026) and two variants in AKAP6 (A-kinase anchoring protein 6) which were associated with risk of invasive EOC (rs1955513, OR = 0.90, p = 0.00033; rs927062, OR = 0.94, p = 0.00059). Functional annotation revealed that the two ARHGEF10L variants were located in super-enhancer regions and that AKAP6 rs927062 was associated with expression of GTPase gene ARHGAP5 (Rho GTPase activating protein 5). Inherited variants in ARHGEF10L and AKAP6, with potential transcriptional regulatory function and association with EOC risk, warrant investigation in independent EOC study populations.Peer reviewe

Variants in genes encoding small GTPases and association with epithelial ovarian cancer susceptibility

Epithelial ovarian cancer (EOC) is the fifth leading cause of cancer mortality in American women. Normal ovarian physiology is intricately connected to small GTP binding proteins of the Ras superfamily (Ras, Rho, Rab, Arf, and Ran) which govern processes such as signal transduction, cell proliferation, cell motility, and vesicle transport. We hypothesized that common germline variation in genes encoding small GTPases is associated with EOC risk. We investigated 322 variants in 88 small GTPase genes in germline DNA of 18,736 EOC patients and 26,138 controls of European ancestry using a custom genotype array and logistic regression fitting log-additive models. Functional annotation was used to identify biofeatures and expression quantitative trait loci that intersect with risk variants. One variant, ARHGEF10L (Rho guanine nucleotide exchange factor 10 like) rs2256787, was associated with increased endometrioid EOC risk (OR = 1.33, p = 4.46 x 10-6). Other variants of interest included another in ARHGEF10L, rs10788679, which was associated with invasive serous EOC risk (OR = 1.07, p = 0.00026) and two variants in AKAP6 (A-kinase anchoring protein 6) which were associated with risk of invasive EOC (rs1955513, OR = 0.90, p = 0.00033; rs927062, OR = 0.94, p = 0.00059). Functional annotation revealed that the two ARHGEF10L variants were located in super-enhancer regions and that AKAP6 rs927062 was associated with expression of GTPase gene ARHGAP5 (Rho GTPase activating protein 5). Inherited variants in ARHGEF10L and AKAP6, with potential transcriptional regulatory function and association with EOC risk, warrant investigation in independent EOC study populations