scholarly journals Methods to infer transmission risk factors in complex outbreak data

2011 ◽  
Vol 9 (68) ◽  
pp. 456-469 ◽  
Author(s):  
Simon Cauchemez ◽  
Neil M. Ferguson
Keyword(s):  
Risk Factors ◽  
Missing Data ◽  
Disease Transmission ◽  
Control Strategies ◽  
Model Fitting ◽  
Structured Populations ◽  
Transmission Risk ◽  
Effective Control ◽  
Reconstruction Methods ◽  
History Of

Data collected during outbreaks are essential to better understand infectious disease transmission and design effective control strategies. But analysis of such data is challenging owing to the dependency between observations that is typically observed in an outbreak and to missing data. In this paper, we discuss strategies to tackle some of the ongoing challenges in the analysis of outbreak data. We present a relatively generic statistical model for the estimation of transmission risk factors, and discuss algorithms to estimate its parameters for different levels of missing data. We look at the problem of computational times for relatively large datasets and show how they can be reduced by appropriate use of discretization, sufficient statistics and some simple assumptions on the natural history of the disease. We also discuss approaches to integrate parametric model fitting and tree reconstruction methods in coherent statistical analyses. The methods are tested on both real and simulated datasets of large outbreaks in structured populations.

scholarly journals Applications of percolation theory to fungal spread with synergy

2011 ◽  
Vol 9 (70) ◽  
pp. 949-956 ◽  
Author(s):  
Jonathan J. Ludlam ◽  
Gavin J. Gibson ◽  
Wilfred Otten ◽  
Christopher A. Gilligan
Keyword(s):  
Control Strategies ◽  
Model Fitting ◽  
Structured Populations ◽  
Synergistic Interactions ◽  
Non Invasive ◽  
History Of ◽  
Disease Spreading ◽  
Strict Requirement ◽  
Using Data ◽  
The Impact

There is increasing interest in the use of the percolation paradigm to analyse and predict the progress of disease spreading in spatially structured populations of animals and plants. The wider utility of the approach has been limited, however, by several restrictive assumptions, foremost of which is a strict requirement for simple nearest-neighbour transmission, in which the disease history of an individual is influenced only by that of its neighbours. In a recent paper, the percolation paradigm has been generalized to incorporate synergistic interactions in host infectivity and susceptibility, and the impact of these interactions on the invasive dynamics of an epidemic has been demonstrated. In the current paper, we elicit evidence that such synergistic interactions may underlie transmission dynamics in real-world systems by first formulating a model for the spread of a ubiquitous parasitic and saprotrophic fungus through replicated populations of nutrient sites and subsequently fitting and testing the model using data from experimental microcosms. Using Bayesian computational methods for model fitting, we demonstrate that synergistic interactions are necessary to explain the dynamics observed in the replicate experiments. The broader implications of this work in identifying disease-control strategies that deflect epidemics from invasive to non-invasive regimes are discussed.

Dilution effect and identity effect by wildlife in the persistence and recurrence of bovine tuberculosis

Parasitology ◽  
2014 ◽  
Vol 141 (7) ◽  
pp. 981-987 ◽  
Author(s):  
Z. Y. X. HUANG ◽  
C. XU ◽  
F. VAN LANGEVELDE ◽  
H. H. T. PRINS ◽  
K. BEN JEBARA ◽  
...  
Keyword(s):  
Risk Factors ◽  
Disease Transmission ◽  
Bovine Tuberculosis ◽  
Disease Risk ◽  
Control Strategies ◽  
Dilution Effect ◽  
Effective Control ◽  
African Buffalo ◽  
Mammal Species ◽  
Positive Interaction

SUMMARYCurrent theories on disease-diversity relationships predict a strong influence of host richness on disease transmission. In addition, identity effect, caused by the occurrence of particular species, can also modify disease risk. We tested the richness effect and the identity effects of mammal species on bovine tuberculosis (bTB), based on the regional bTB outbreak data in cattle from 2005–2010 in Africa. Besides, we also tested which other factors were associated with the regional bTB persistence and recurrence in cattle. Our results suggested a dilution effect, where higher mammal species richness (MSR) was associated with reduced probabilities of bTB persistence and recurrence in interaction with cattle density. African buffalo had a positive effect on bTB recurrence and a positive interaction effect with cattle density on bTB persistence, indicating an additive positive identity effect of buffalo. The presence of greater kudu had no effect on bTB recurrence or bTB persistence. Climatic variables only act as risk factors for bTB persistence. In summary, our study identified both a dilution effect and identity effect of wildlife and showed that bTB persistence and recurrence were correlated with different sets of risk factors. These results are relevant for more effective control strategies and better targeted surveillance measures in bTB.

scholarly journals Livestock movement informs the risk of disease spread in traditional production systems in East Africa

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Divine Ekwem ◽  
Thomas A. Morrison ◽  
Richard Reeve ◽  
Jessica Enright ◽  
Joram Buza ◽  
...  
Keyword(s):  
Disease Transmission ◽  
Production Systems ◽  
Control Strategies ◽  
Herd Size ◽  
Transmission Risk ◽  
Disease Spread ◽  
Transmission Potential ◽  
Spatial And Temporal Scales ◽  
Transmission Distance ◽  
Risk Of Disease

AbstractIn Africa, livestock are important to local and national economies, but their productivity is constrained by infectious diseases. Comprehensive information on livestock movements and contacts is required to devise appropriate disease control strategies; yet, understanding contact risk in systems where herds mix extensively, and where different pathogens can be transmitted at different spatial and temporal scales, remains a major challenge. We deployed Global Positioning System collars on cattle in 52 herds in a traditional agropastoral system in western Serengeti, Tanzania, to understand fine-scale movements and between-herd contacts, and to identify locations of greatest interaction between herds. We examined contact across spatiotemporal scales relevant to different disease transmission scenarios. Daily cattle movements increased with herd size and rainfall. Generally, contact between herds was greatest away from households, during periods with low rainfall and in locations close to dipping points. We demonstrate how movements and contacts affect the risk of disease spread. For example, transmission risk is relatively sensitive to the survival time of different pathogens in the environment, and less sensitive to transmission distance, at least over the range of the spatiotemporal definitions of contacts that we explored. We identify times and locations of greatest disease transmission potential and that could be targeted through tailored control strategies.

scholarly journals Global Stability and Optimal Control of Dengue with Two Coexisting Virus Serotypes

MATEMATIKA ◽  
2019 ◽  
Vol 35 (4) ◽  
pp. 149-170
Author(s):  
Afeez Abidemi ◽  
Rohanin Ahmad ◽  
Nur Arina Bazilah Aziz
Keyword(s):  
Optimal Control ◽  
Global Stability ◽  
Disease Transmission ◽  
Deterministic Model ◽  
Control Strategies ◽  
Equilibrium Points ◽  
Effective Control ◽  
Asymptotically Stable ◽  
Globally Asymptotically Stable ◽  
Boundary Equilibrium

This study presents a two-strain deterministic model which incorporates Dengvaxia vaccine and insecticide (adulticide) control strategies to forecast the dynamics of transmission and control of dengue in Madeira Island if there is a new outbreak with a different virus serotypes after the first outbreak in 2012. We construct suitable Lyapunov functions to investigate the global stability of the disease-free and boundary equilibrium points. Qualitative analysis of the model which incorporates time-varying controls with the specific goal of minimizing dengue disease transmission and the costs related to the control implementation by employing the optimal control theory is carried out. Three strategies, namely the use of Dengvaxia vaccine only, application of adulticide only, and the combination of Dengvaxia vaccine and adulticide are considered for the controls implementation. The necessary conditions are derived for the optimal control of dengue. We examine the impacts of the control strategies on the dynamics of infected humans and mosquito population by simulating the optimality system. The disease-freeequilibrium is found to be globally asymptotically stable whenever the basic reproduction numbers associated with virus serotypes 1 and j (j 2 {2, 3, 4}), respectively, satisfy R01,R0j 1, and the boundary equilibrium is globally asymptotically stable when the related R0i (i = 1, j) is above one. It is shown that the strategy based on the combination of Dengvaxia vaccine and adulticide helps in an effective control of dengue spread in the Island.

scholarly journals Potential Distribution Map of Culicoides insignis (Diptera: Ceratopogonidae), Vector of Bluetongue Virus, in Northwestern Argentina

2016 ◽  
Vol 16 (1) ◽  
Author(s):  
Cecilia A. Veggiani Aybar ◽  
Romina A. Díaz Gomez ◽  
María J. Dantur Juri ◽  
Mercedes S. Lizarralde de Grosso ◽  
Gustavo R. Spinelli
Keyword(s):  
Disease Transmission ◽  
Bluetongue Virus ◽  
Potential Distribution ◽  
Control Strategies ◽  
Area Under The Curve ◽  
Transmission Risk ◽  
Distribution Map ◽  
Northwestern Argentina ◽  
Jackknife Test ◽  
Maxent Model

Abstract Culicoides insignis Lutz is incriminated as a vector of bluetongue virus (BTV) to ruminants in America. In South America, almost all countries have serological evidence of BTV infections, but only four outbreaks of the disease have been reported. Although clinical diseases have never been cited in Argentina, viral activity has been detected in cattle. In this study, we developed a potential distribution map of Culicoides insignis populations in northwestern Argentina using Maximum Entropy Modeling (Maxent). For the analyses, information regarding both data of specimen collections between 2003 and 2013, and climatic and environmental variables was used. Variables selection was based on the ecological relevance in relation to Culicoides spp. biology and distribution in the area. The best Maxent model according to the Jackknife test included 53 C. insignis presence records and precipitation of the warmest quarter, altitude, and precipitation of the wettest month. Accuracy was evaluated by the area under the curve (AUC = 0.97). These results provide an important analytical resource of high potential for both the development of suitable control strategies and the assessment of disease transmission risk in the region.

scholarly journals Chronic Wasting Disease Transmission Risk Assessment for Farmed Cervids in Minnesota and Wisconsin

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1586
Author(s):  
James M. Kincheloe ◽  
Dennis N. Makau ◽  
Scott J. Wells ◽  
Amy R. Horn-Delzer
Keyword(s):  
Risk Assessment ◽  
Disease Transmission ◽  
Chronic Wasting Disease ◽  
Control Measures ◽  
Transmission Risk ◽  
Effective Control ◽  
Wasting Disease ◽  
Qualitative Risk Assessment ◽  
Low Uncertainty ◽  
High Uncertainty

CWD (chronic wasting disease) has emerged as one of the most important diseases of cervids and continues to adversely affect farmed and wild cervid populations, despite control and preventive measures. This study aims to use the current scientific understanding of CWD transmission and knowledge of farmed cervid operations to conduct a qualitative risk assessment for CWD transmission to cervid farms and, applying this risk assessment, systematically describe the CWD transmission risks experienced by CWD-positive farmed cervid operations in Minnesota and Wisconsin. A systematic review of literature related to CWD transmission informed our criteria to stratify CWD transmission risks to cervid operations into high-risk low uncertainty, moderate-risk high uncertainty, and negligible-risk low uncertainty categories. Case data from 34 CWD-positive farmed cervid operations in Minnesota and Wisconsin from 2002 to January 2019 were categorized by transmission risks exposure and evaluated for trends. The majority of case farms recorded high transmission risks (56%), which were likely sources of CWD, but many (44%) had only moderate or negligible transmission risks, including most of the herds (62%) detected since 2012. The presence of CWD-positive cervid farms with only moderate or low CWD transmission risks necessitates further investigation of these risks to inform effective control measures.

scholarly journals Assessment of Risk Factors of African Swine Fever in India: Perspectives on Future Outbreaks and Control Strategies

Pathogens ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1044
Author(s):  
Mousumi Bora ◽  
Durlav Prasad Bora ◽  
Mohan Manu ◽  
Nagendra Nath Barman ◽  
Lakshya Jyoti Dutta ◽  
...  
Keyword(s):  
Risk Factors ◽  
Disease Transmission ◽  
Control Strategies ◽  
African Swine Fever ◽  
Small Scale ◽  
Wild Pigs ◽  
Wildlife Reservoirs ◽  
Potential Risk Factors ◽  
And Control ◽  
Near Future

African swine fever (ASF) is one of the most important transboundary diseases of pigs. ASF has been identified in India for the first time in domestic pigs from outbreaks reported in two of the northeastern states, Arunachal Pradesh and Assam in 2020. A total of 11 ASF outbreaks in different regions killed over 3700 pigs and devastated the economy of small-scale livestock owners of both the states. Considering the first outbreak of ASF in India, a generic risk assessment framework was determined to identify potential risk factors that might favor future emergence of the disease. Based on the Indian scenario, we considered population density of host, farming practice, availability of biological vectors and wildlife reservoirs, epidemiological cycles, and international trade to analyze the possibility of future outbreaks of ASF and chances of establishment of endemism. On critical analysis of the identified risk factors associated with ASFV transmission, we observed that the risk factors are well preserved in the Indian geography and might participate in future outbreaks, further disseminating the disease to nearby countries. Since no vaccine is currently available against ASF, the domestic and the wild pigs (wild boars and the endangered pygmy hogs native to India) of this region are under constant threat of infection. For the near future, this region will have to continue to rely on the implementation of preventive measures to avoid the devastating losses that outbreaks can cause. The various adaptive control strategies to minimize the risks associated with the transmission of ASF, keeping our views to Indian settings, have been described. The risk-analysis framework presented in the study will give a further understanding of the dynamics of disease transmission and will help to design control strategies and corresponding measures to minimize the catastrophic consequences of ASF disease.

scholarly journals Epidemic cycles driven by host behaviour

2014 ◽  
Vol 11 (99) ◽  
pp. 20140575 ◽  
Author(s):  
Benjamin M. Althouse ◽  
Laurent Hébert-Dufresne
Keyword(s):  
Sexual Behaviour ◽  
Disease Transmission ◽  
Control Strategies ◽  
Treponema Pallidum ◽  
Structured Populations ◽  
Behavioural Interventions ◽  
Sexually Transmitted ◽  
The Face ◽  
The Usa ◽  
Host Behaviour

Host immunity and demographics (the recruitment of susceptibles via birthrate) have been demonstrated to be a key determinant of the periodicity of measles, pertussis and dengue epidemics. However, not all epidemic cycles are from pathogens inducing sterilizing immunity or are driven by demographics. Many sexually transmitted infections are driven by sexual behaviour. We present a mathematical model of disease transmission where individuals can disconnect and reconnect depending on the infectious status of their contacts. We fit the model to historic syphilis ( Treponema pallidum ) and gonorrhea ( Neisseria gonorrhoeae ) incidence in the USA and explore potential intervention strategies against syphilis. We find that cycles in syphilis incidence can be driven solely by changing sexual behaviour in structured populations. Our model also explains the lack of similar cycles in gonorrhea incidence even if the two infections share the same propagation pathways. Our model similarly illustrates how sudden epidemic outbreaks can occur on time scales smaller than the characteristic demographic time scale of the population and that weaker infections can lead to more violent outbreaks. Behaviour also appears to be critical for control strategies as we found a bigger sensitivity to behavioural interventions than antibiotic treatment. Thus, behavioural interventions may play a larger role than previously thought, especially in the face of antibiotic resistance and low intervention efficacies.

scholarly journals Sheep scab transmission: a spatially explicit dynamic metapopulation model

2021 ◽  
Vol 52 (1) ◽  
Author(s):  
Emily Nixon ◽  
Ellen Brooks-Pollock ◽  
Richard Wall
Keyword(s):  
Sequential Monte Carlo ◽  
Control Strategies ◽  
Model Fitting ◽  
Spatial Location ◽  
Effective Control ◽  
Economic Losses ◽  
Metapopulation Model ◽  
Psoroptes Ovis ◽  
Sheep Scab ◽  
Movement Data

AbstractPsoroptic mange (sheep scab), caused by the parasitic mite, Psoroptes ovis, is an important disease of sheep worldwide. It causes chronic animal welfare issues and economic losses. Eradication of scab has proved impossible in many sheep-rearing areas and recent reports of resistance to macrocyclic lactones, a key class of parasiticide, highlight the importance of improving approaches to scab management. To allow this, the current study aimed to develop a stochastic spatial metapopulation model for sheep scab transmission which can be adapted for use in any geographical region, exhibited here using data for Great Britain. The model uses agricultural survey and sheep movement data to geo-reference farms and capture realistic movement patterns. Reported data on sheep scab outbreaks from 1973 to 1991 were used for model fitting with Sequential Monte Carlo Approximate Bayesian Computation methods. The outbreak incidence predicted by the model was from the same statistical distribution as the reported outbreak data ($${\chi }^{2}$$ χ 2 = 115.3, p = 1) and the spatial location of sheep scab outbreaks predicted was positively correlated with the observed outbreak data by county ($$\tau$$ τ = 0.55, p < 0.001), confirming that the model developed is able to accurately capture the number of farms infected in a year, the seasonality of scab incidence and the spatial patterns seen in the data. This model gives insight into the transmission dynamics of sheep scab and will allow the exploration of more effective control strategies.

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