Detecting disease progression from animal movement using hidden Markov models

An essential part of any disease containment and eradication policy is the implementation of restricted zones, but determining the appropriate size of these zones can be challenging for managers. We designed a new method, based on animal movement, to help assess how large restricted zones should be after a spontaneous outbreak to successfully control infectious diseases in wildlife. Our approach uses first-passage time (FPT) analysis and Cox proportional hazard (CPH) models to calculate and compare the risk of an animal leaving different-sized areas. We illustrate our approach using the example of the African swine fever (ASF) virus and its wild pig reservoir host species, the wild boar (Sus scrofa), and we investigate the feasibility of applying this method to other systems. Using GPS data from 57 wild boar living in the Hainich National Park, Germany, we calculate the time spent by each individual in areas of different sizes using FPT analysis. We apply CPH models on the derived data to compare the risk of leaving areas of different sizes and to assess the effects of season and the sex of the wild boar on the risk of leaving. We conduct survival analyses to estimate the risk of leaving an area over time. Our results indicate that the risk of leaving an area decreases exponentially by 10% for each 100 m increase in radius size so that the differences were more pronounced for small sizes. Furthermore, the probability of leaving increases exponentially with time. Wild boar had a similar risk of leaving an area of a given size throughout the year, except in spring and winter, when females had a much lower risk of leaving. Our findings are in agreement with the literature on wild boar movement, further validating our method, and repeated analyses with location data resampled at different rates gave similar results. Our results may be applicable only to our study area, but they demonstrate the applicability of the proposed method to any ecosystem where wild boar populations are likely to be infected with ASF and where restricted zones should be established accordingly. The outlined approach relies solely on the analysis of movement data and provides a useful tool to determine the optimal size of restricted zones. It can also be applied to future outbreaks of other diseases.

Objective:The purpose of this study was to characterize the circulating Peste des Petits Ruminants virus (PPRV) from slaughtered goats and conduct a phylogenetic analysis of the N gene of PPRV.Materials and Methods:A total of 196 slaughtered goats were investigated at the marketplaces of Mymensingh division from January 2019 to March 2021. Lungs, spleen, and mesenteric lymph nodes were collected for histology and molecular study. In-house developed Reverse-Transcriptase-Polymerase Chain Reaction (RT-PCR) protocols were carried out using designed primer sets (PPRV NF-gctctgtgattgcggctgagc and PPRV NR-cctggtcctccagaatcttggcc). The CLC sequence viewer was used for phylogenetic analysis.Results:Grossly pneumonic lungs, shrinkage spleen, and enlarged mesenteric lymph nodes with hemorrhages were recorded. Both intracytoplasmic and intranuclear inclusion bodies were seen in lymphocytes of the mesenteric lymph node, spleen, and lungs. PPRV was detected in 37 goats (18.9%) by RT-PCR test. The 402-bp amplicon was generated in PPRV-positive cases. The phylogenetic analysis showed that the studied PPRV isolates of the Mymensingh division belonged to lineage IV.Conclusion:The prevalence of PPR was 18.9% in slaughtered goats at marketplaces in the Mymensingh division. Slaughterhouses may be a source of PPRV, and it can be horizontally transmitted from the meat market to the farm. Restricting sick animal movement within the country, mass PPR vaccination campaigns, increased awareness, and improved biosecurity in the meat market may lessen the incidence of PPR in goats.

Peste des petits ruminants (PPR) is primarily a highly contagious morbillivirus infection of small domesticated ruminants. However, it can also infect and cause disease in buffaloes, camels, and a variety of wild ungulates. In camels, it can cause serious disease, although experimental infection often failed to reproduce the natural situation. Clinical disease in wildlife has been observed in various locations of the Arabian Peninsula and in Asia. In numerous cases, there is epidemiological evidence of a spillover of PPR virus from sheep or goats to unusual hosts. Whilst there is clear evidence that a number of wildlife species are susceptible to infection, the actual role of wildlife in the epidemiology of PPR virus remains largely undetermined. Although an enzootic occurrence of PPR in unusual hosts has not been observed up to now, the epidemiological role of these hosts including wildlife populations should not be underestimated and is therefore important in PPR control and final eradication for reaching to PPR zero level.

Emergence of peste des petits ruminants virus lineage IV in Ismailia Province, Egypt

ABSTRACTBackgroundEthiopia has a significant number of sheep and goats, though the benefit gained is little because of several diseases, including Peste des Petits Ruminants (PPR). PPR is a highly contagious and economically important transboundary disease of small ruminants, associated with high morbidity and mortality rates.ObjectivesA cross‐sectional study was conducted to estimate seroprevalence of PPR and identify associated risk factors in four Kebeles of the Pawe district, Northwest Ethiopia.MethodsA total of 334 serum samples (146 from goats and 188 from sheep) were collected and tested for PPRV antibodies using competitive ELISA (c‐ELISA).ResultsOut of a total of 334 blood sera from sheep and goats tested for PPR virus antibodies, 236 (70.7%) were positive. There was no significant difference in prevalence between sheep (71.3%) and goats (69.9%). A significantly higher PPRV seroprevalence was observed in female sheep (75.7%) compared to male sheep (55%). Similarly, female goats had a higher prevalence (74.4%) than male goats (48%) (p value = 0.01). The prevalence was also significantly higher in lactating female sheep (81.8%) and goats (83.3%). Age‐wise, seroprevalence was higher in older sheep (82.2%, odds ratios [OR] = 4.4) and older goats (84.1%, OR = 5.4) than their younger counterparts. The prevalence was higher in Almu Kebele (82.5%) (χ2 = 7.5, p value = 0.05). Flock size, age, body condition, origin and the introduction of new animals were identified as potential risk factors associated with the prevalence.ConclusionsPPR is highly prevalent in the district, indicating significant circulation of the virus in the area. This high prevalence, combined with the regular movement of animals and shared grazing lands in the area, poses a risk for the further spread of the disease. Therefore, priority should be given to the area in control and eradication efforts, along with restrictions on animal movement and targeted vaccination.

Difference in spatiotemporal patterns of wildlife road-crossings and wildlife-vehicle collisions

Peste des petits ruminants (PPR) is a highly contagious disease affecting mainly sheep and goats. Livestock movements contribute to the spread of the disease by introducing it to naive areas or exposing susceptible animals to it in infected regions. Because of its socio-economic impact, the Food and Agriculture Organisation (FAO) and the World Organization for Animal Health (WOAH) have set the goal to eradicate it by 2030, one of the key steps being the improvement of surveillance networks. The present study aimed to provide tools to identify areas that could serve as sentinel nodes, i.e. areas that may be rapidly infected at the onset of epidemics. Using data from a market survey conducted in Northern Nigeria, we reconstructed the small ruminants mobility network and simulated the diffusion of PPR virus through animal movement. From the analysis of simulation outcomes, we investigated which nodes could act as sentinel nodes under specific conditions for disease transmission. We considered several modified networks to get around the problem of data only being available for part of the overall network structure and to account for potential errors made during the field study. For each configuration, we simulated the spread of PPR using a stochastic Susceptible-Infectious (SI) model based on animal movements to assess the epidemics’ extent and the presence of recurrent patterns to identify potential sentinel nodes. We extracted the backbone of the reference network and checked for the presence of sentinel nodes within it. We investigated how the origin (seed) of the epidemics could affect the propagation pattern by comparing and grouping seeds based on their respective transmission paths. Results showed that the isolated backbone contains 45% of sentinel nodes that remain stable or undergo only minor changes in 9 out of 11 configurations. On top of that, the characteristics of sentinel nodes identified in the backbone are not influenced by the severity of the disease. The H index, in-degree, and eigenvector are the most essential variables. This study provides an overview of the major axes of animal movements in Nigeria and the most vulnerable locations that should be prioritized for monitoring livestock diseases like PPR.

Visualizing movement data is challenging: While traditional spatial data can be sufficiently displayed as two‐dimensional plots or maps, movement trajectories require the representation of time in a third dimension. To address this, we present moveVis, an r package, which provides tools to animate movement trajectories, overlaying simultaneous uni‐ or multi‐temporal raster imagery or vector data. moveVis automates the processing of movement and environmental data to turn such into an animation. This includes (a) the regularization of movement trajectories enforcing uniform time instances and intervals across all trajectories, (b) the frame‐wise mapping of movement trajectories onto temporally static or dynamic environmental layers, (c) the addition of customizations, for example, map elements or colour scales and (d) the rendering of frames into an animation encoded as GIF or video file. moveVis is designed to display interactions and concurrencies of animal movement and environmental data. We present examples and use cases, ranging from data exploration to visualizing scientific findings. Static spatial plots of movement data disregard the temporal dimension that distinguishes movement from other spatial data. In contrast, animations allow to display relocation in both time and space. We deem animations a powerful way to visually explore movement data, frame analytical findings and display potential interactions with spatially continuous and temporally dynamic environmental covariates.

Lyantonde District, Uganda, is a recognized hotspot for Peste des Petits Ruminants (PPR) outbreaks. However, the magnitude and risk factors of PPR in this area remain poorly characterized. This study aimed to determine the prevalence of PPR antibodies in goats and sheep and to identify associated risk factors in selected sub-counties of Lyantonde District. A cross-sectional serosurvey was conducted in July 2024 in three purposively selected sub-counties (Lyantonde, Lyakajula, and Kinuuka), chosen for their large small ruminant populations, high livestock trade activity, and active animal movement. Farms without a history of PPR vaccination were randomly selected, and simple random sampling was used to select study animals. Whole blood samples were collected from the jugular vein and analyzed using the ID Screen® PPR competitive ELISA kit to detect virus-specific IgG antibodies. Multivariate analysis was performed using Modified Poisson regression to identify risk factors associated with PPR seroprevalence. Adjusted prevalence ratios (aPRs), 95% confidence intervals (CIs), and p-values were reported. A total of 351 goats and sheep were sampled, with an overall apparent seroprevalence of 42.17% (n = 148). The Rogan-Gladen estimator gave a true prevalence of 44.27%, with goats showing a significantly (p = 0.046) higher prevalence (46.27%) compared to sheep (33.62%). Age was significantly associated with seropositivity. Animals aged > 1-3 years (aPR = 1.86; 95% CI: 1.16-2.97, p = 0.009), and > 3-5 years (aPR = 2.56; 95% CI: 1.54-4.24, p < 0.0001) had higher prevalence ratios compared to those < 1 year. Goats also had higher prevalence ratios than sheep (aPR = 1.59; 95% CI: 1.01-2.53, p = 0.046). Farms reporting wildlife interactions had a 43% higher prevalence ratio (aPR = 1.43; 95% CI: 1.07-1.91, p = 0.015), and acquisition of new animals from other farmers was similarly associated with higher prevalence ratios (aPR = 1.32; 95% CI: 1.02-1.71, p = 0.029). This study shows the high burden of PPR among small ruminants in Lyantonde district, with higher prevalence in goats than sheep and identification of risk factors associated with seropositivity. The study provides baseline evidence of PPR exposure and documents differences by species, age group, animal acquisition practices, and reported wildlife interactions. These findings contribute to improved characterization of PPR epidemiology in Lyantonde district and may inform the design of future surveillance and control activities aimed at reducing PPR burden.

Peste des petits ruminants (PPR) is a highly contagious and devastating viral disease of goats and sheep caused by Peste des petits ruminants virus (PPRV). Despite of its impact on the livelihood of rural African communities, insufficient epidemiological information hampers the implementation of effective PPR control strategies. This study was carried out to determine seroprevalence and risk factors for PPR infection in sheep and goats in Longido, Simanjiro, Ngorongoro, Monduli, Kongwa and Mlele districts using a competitive Enzyme–Linked Immunosorbent Assay and questionnaire to detect PPR antibodies, and to collect information related to the potential risk factors for PPR respectively. A total of 583 serum samples from sheep (n=248), and goats (n=335), and 40 households were involved in questionnare. This study confirmed presence of antibodies to PPRV in sheep and goats in all districts studied; and identified management systems related to movement control to be an important risk factor for the spread of PPR. The results suggest that controlling animal movement and limiting interaction with wildlife could PPR transmission

Infectious diseases result from the interactions of host, pathogens, and, in the case of vector-borne diseases, also vectors. The interactions involve physiological and ecological mechanisms and they have evolved under a given set of environmental conditions. Environmental change, therefore, will alter host-pathogen-vector interactions and, consequently, the distribution, intensity, and dynamics of infectious diseases. Here, we review how climate change may impact infectious diseases of aquatic and terrestrial wildlife. Climate change can have direct impacts on distribution, life cycle, and physiological status of hosts, pathogens and vectors. While a change in either host, pathogen or vector does not necessarily translate into an alteration of the disease, it is the impact of climate change on the interactions between the disease components which is particularly critical for altered disease risks. Finally, climate factors can modulate disease through modifying the ecological networks host-pathogen-vector systems are belonging to, and climate change can combine with other environmental stressors to induce cumulative effects on infectious diseases. Overall, the influence of climate change on infectious diseases involves different mechanisms, it can be modulated by phenotypic acclimation and/or genotypic adaptation, it depends on the ecological context of the host-pathogen-vector interactions, and it can be modulated by impacts of other stressors. As a consequence of this complexity, non-linear responses of disease systems under climate change are to be expected. To improve predictions on climate change impacts on infectious disease, we suggest that more emphasis should be given to the integration of biomedical and ecological research for studying both the physiological and ecological mechanisms which mediate climate change impacts on disease, and to the development of harmonized methods and approaches to obtain more comparable results, as this would support the discrimination of case-specific versus general mechanisms.

Livestock trade significantly contributes to the spread of transboundary animal diseases (TADs), like Peste des Petits Ruminants virus (PPRV), due to the long-distance movement of infected animals. This study investigates the structure and dynamics of the small ruminant trade network across 64 markets and 20 destinations, focusing on market connectivity, trade patterns, and disease risk. Eight key markets were identified due to their significant trading activity and connections. During the study period, 365,261 small ruminants were traded, with 54% directed toward market destinations and the remainder to slaughterhouses or cross-border locations, primarily Somaliland and Kenya. Over 85% of transport to these destinations was by truck, while more than 55% of internal movements were on foot. Trade peaked between July and September, accounting for 42% of the annual trade volume and 46% of cross-border movements. Network analysis revealed 172 distinct trade routes with varying activity levels: 12 persistent, 47 frequent, 42 intermediate, and 69 occasional. The network exhibited low connectivity (density = 0.024) and low reciprocity (0.104), with a negative assortativity (−0.52), indicating smaller markets often connected with larger ones. The network's clustering coefficient was 0.729, and the average path length was 2.216, contrasting with simulated random networks that had a clustering coefficient of 0.047 and an average path length of 3.22. Key markets were identified as “gate-keepers” and “pulse takers,” facilitating connections between isolated and central markets. The epidemic threshold (q) and R0 indicated a high risk of disease spread, especially from July to October. The study found that removing key markets drastically reduced network cohesion, with a 10% removal of central nodes decreasing the giant strongly connected component (GSCC) size by ~80%. Peste des Petits Ruminants (PPR) outbreaks in 2023 correlated strongly with market centrality, highlighting the need for targeted monitoring and control measures. This study underscores the importance of understanding network dynamics to manage trade efficiently and mitigate disease risks in small ruminant populations.

In 1994, the Food and Agriculture Organization undertook to revitalise its activities in the control of transboundary animal disease by establishing a new special programme known as the Emergency Prevention System (EMPRES) against transboundary animal and plant pests and diseases. The emphasis of the EMPRES livestock component is placed on pre-empting outbreaks and losses experienced by agriculture through the enhancement of local capacity to detect and react rapidly to plague events. EMPRES concentrates on the co-ordination of the Global Rinderpest Eradication Programme--a time-bound eradication programme--whilst addressing the progressive control of the most serious epidemic diseases within a broad framework of emergency preparedness. Programme activities are discussed in relation to early warning, early reaction, facilitating research and co-ordination. In addition to rinderpest, particular attention has been paid to contagious bovine pleuropneumonia, a re-emerging disease in Africa targeted for strategic attention, and foot and mouth disease, for which co-ordinated regional control in Latin America and South-East Asia has been initiated. Tactical responses to other disease emergencies such as African swine fever, classical swine fever (hog cholera), Rift Valley fever, peste des petits ruminants and lumpy skin disease are described.

Simple SummaryPeste des petits ruminants (PPR), also known as sheep and goat plague, is a highly contagious animal disease affecting small ruminants and camels. It is caused by a virus belonging to the genus Morbillivirus, family Paramixoviridae. Once newly introduced, the virus can infect up to 90 percent of an animal herd. A PPR outbreak is an emergency due to its rapid spread and high animal mortality rate. This study simulated three control strategies of PPR spread among animals in the United Arab Emirates. These strategies include implementing mass vaccination, ring vaccination and ceased vaccination strategies, combined with or without strict animal movement control simultaneously. The simulation results compared the level of the effectiveness and direct government costs for each of the three strategies. Such results aid the decision-makers in the country and globally in line with the World Animal Health Organization’s goal to eradicate the disease by 2030.Peste des petits ruminants (PPR) is an important infectious viral disease of domestic small ruminants that threatens the food security and sustainable livelihood of farmers across Middle East, Africa, and Asia. The objective of this research is to analyze the disease’s spread and its impacts on direct government costs through conducting three simulations of different control strategies to reduce and quickly eradicate PPR from the United Arab Emirates in the near future. A Modified Animal Disease Spread Model was developed in this study to suit the conditions of the United Arab Emirates. The initial scenario represents when mass vaccination is ceased, and moderate movement restrictions are applied. The second scenario is based on mass vaccination and stamping out the disease, whereas the third simulation scenario assumes mass and ring vaccination when needed, very strict movement control, and stamping out. This study found that the third scenario is the most effective in controlling and eradicating PPR from the UAE. The outbreak duration in days was reduced by 57% and the number of infected animals by 77% when compared to the other scenarios. These results are valuable to the country’s animal health decision-makers and the government’s efforts to report to the World Animal Health Organization (OIE) regarding the progress made towards declaration of the disease’s eradication. They are also useful to other concerned entities in other Middle Eastern, North African, and Asian countries where the disease is spreading.

Peste des petits ruminants (PPR) is a highly contagious viral disease of sheep and goats with high mortality. The disease is of considerable economic importance in countries such as Tanzania, where small ruminant products are important for sustainable livelihoods. This review assesses current knowledge regarding the epidemiology of PPRV in Tanzania, highlighting the challenges with respect to control and suggesting possible interventions. Thirty-three articles were identified after literature searches using Google Scholar and PubMed. Studies revealed that PPRV is endemic in sheep and goats in Tanzania, although seropositivity has also been reported in cattle, camels, buffalo, Grant's gazelle, wildebeest and impala, but with no clinical manifestation. Three lineages (lineage II to IV) of PPRV have been identified in Tanzania, implying at least two separate introductions of the virus. Diagnosis of PPR in Tanzania is mostly by observation of clinical signs and lesions at post mortem. Risk factors in Tanzania include age, sex, species, and close contact of animals from different farms/localities. Although there is an efficacious vaccine available for PPR, poor disease surveillance, low vaccine coverage, and uncontrolled animal movements have been the bane of control efforts for PPR in Tanzania. There is need for collaborative efforts to develop interventions to control and eradicate the disease. The establishment of a national reference laboratory for PPR, conduct of surveillance, the development of high-quality DIVA vaccines, as well as execution of a carefully planned national vaccination campaign may be key to the control and subsequent eradication of PPR in Tanzania and achieving the global goal of eradicating PPR by 2030.