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Graham, David A.
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Graham, David A.
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Graham, David A.
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- PublicationA modelling framework for the prediction of the herd-level probability of infection from longitudinal data(Peer Community In, 2022-01-07)
; ; ; ; ; he collective control programmes (CPs) that exist for many infectious diseases of farm animals rely on the application of diagnostic testing at regular time intervals for the identification of infected animals or herds. The diversity of these CPs complicates the trade of animals between regions or countries because the definition of freedom from infection differs from one CP to another. In this paper, we describe a statistical model for the prediction of herd-level probabilities of infection from longitudinal data collected as part of CPs against infectious diseases of cattle. The model was applied to data collected as part of a CP against bovine viral diarrhoea virus (BVDV) infection in Loire-Atlantique, France. The model represents infection as a herd latent status with a monthly dynamics. This latent status determines test results through test sensitivity and test specificity. The probability of becoming status positive between consecutive months is modelled as a function of risk factors (when available) using logistic regression. Modelling is performed in a Bayesian framework, using either Stan or JAGS. Prior distributions need to be provided for the sensitivities and specificities of the different tests used, for the probability of remaining status positive between months as well as for the probability of becoming positive between months. When risk factors are available, prior distributions need to be provided for the coefficients of the logistic regression, replacing the prior for the probability of becoming positive. From these prior distributions and from the longitudinal data, the model returns posterior probability distributions for being status positive for all herds on the current month. Data from the previous months are used for parameter estimation. The impact of using different prior distributions and model implementations on parameter estimation was evaluated. The main advantage of this model is its ability to predict a probability of being status positive in a month from inputs that can vary in terms of nature of test, frequency of testing and risk factor availability/presence. The main challenge in applying the model to the BVDV CP data was in identifying prior distributions, especially for test characteristics, that corresponded to the latent status of interest, i.e. herds with at least one persistently infected (PI) animal. The model is available on Github as an R package (https://github.com/AurMad/STOCfree) and can be used to carry out output-based evaluation of disease CPs.204 - PublicationA survey of free-ranging deer in Ireland for serological evidence of exposure to bovine viral diarrhoea virus, bovine herpes virus-1, bluetongue virus and Schmallenberg virusBackground: Deer are an important wildlife species in both the Republic of Ireland and Northern Ireland having colonised most regions across the island of Ireland. In comparison to cattle and sheep which represent the main farmed ruminant species on the island, there is a lack of data concerning their exposure, as measured by the presence of antibodies, to important viral pathogens of ruminants. A study was therefore undertaken to investigate the seroprevalence of wild deer to four viruses, namely bovine viral diarrhoea virus (BVDV), bovine herpesvirus-1 (BoHV-1), Schmallenberg virus (SBV) and bluetongue virus (BTV). Results: Two panels of sera were assembled; Panel 1 comprised 259 samples (202 collected in the Republic of Ireland and 57 in Northern Ireland) between 2013 and 2015, while Panel 2 comprised 131 samples collected in the Republic of Ireland between 2014 and 2015. Overall sika deer (Cervus nippon) were sampled most commonly (54.8%), followed by fallow deer (Dama dama) (35.3%), with red deer (Cervus elaphus) (4.3%) and hybrid species (0.3%) sampled less frequently, with the species not being recorded for the remaining 5.3% of deer sampled. Age was not recorded for 96 of the 390 deer sampled. 196 of the remainder were adults, while 68 and 30 were yearlings and calves, respectively. Using commercially available enzyme-linked immunosorbent assays, true prevalence and 95% confidence intervals were calculated as 9.9%, (6.8-13.0% CI), SBV; 1.5% (0.1-3.0% CI), BoHV-1; 0.0%, 0-1.7% CI), BVDV; and 0.0%, (0.01-0.10% CI), BTV. Conclusions: The results indicate a very low seroprevalence for both BVDV and BoHV-1 in the wild deer tested within the study and, are consistent with a very low prevalence in Ireland. While serological cross-reaction with cervid herpesviruses cannot be excluded, the results in both cases suggest that the presence of these viruses in deer is not a significant risk to their control and eradication from the cattle population. This is important given the ongoing programme to eradicate BVDV in Ireland and deliberations on a national eradication programme for BoHV-1. The SBV results show consistency with those reported from cattle and sheep on the island of Ireland, while the BTV results are consistent with this virus remaining exotic to Ireland. The results provide a baseline against which future surveys of either wild or farmed/captive deer populations can be compared.
Scopus© Citations 18 406 - PublicationA description and qualitative comparison of the elements of heterogeneous bovine viral diarrhea control programs that influence confidence of freedom(Elsevier, 2020-05-01)
; ; ; ; For endemic infections in cattle that are not regulated at the European Union level, such as bovine viral diarrhea virus (BVDV), European Member States have implemented control or eradication programs (CEP) tailored to their specific situations. Different methods are used to assign infection-free status in CEP; therefore, the confidence of freedom associated with the “free” status generated by different CEP are difficult to compare, creating problems for the safe trade of cattle between territories. Safe trade would be facilitated with an output-based framework that enables a transparent and standardized comparison of confidence of freedom for CEP across herds, regions, or countries. The current paper represents the first step toward development of such a framework by seeking to describe and qualitatively compare elements of CEP that contribute to confidence of freedom. For this work, BVDV was used as a case study. We qualitatively compared heterogeneous BVDV CEP in 6 European countries: Germany, France, Ireland, the Netherlands, Sweden, and Scotland. Information about BVDV CEP that were in place in 2017 and factors influencing the risk of introduction and transmission of BVDV (the context) were collected using an existing tool, with modifications to collect information about aspects of control and context. For the 6 participating countries, we ranked all individual elements of the CEP and their contexts that could influence the probability that cattle from a herd categorized as BVDV-free are truly free from infection. Many differences in the context and design of BVDV CEP were found. As examples, CEP were either mandatory or voluntary, resulting in variation in risks from neighboring herds, and risk factors such as cattle density and the number of imported cattle varied greatly between territories. Differences were also found in both testing protocols and definitions of freedom from disease. The observed heterogeneity in both the context and CEP design will create difficulties when comparing different CEP in terms of confidence of freedom from infection. These results highlight the need for a standardized practical methodology to objectively and quantitatively determine confidence of freedom resulting from different CEP around the world.194Scopus© Citations 15 - PublicationThe Irish Programme to Eradicate Bovine Viral Diarrhoea Virus—Organization, Challenges, and Progress(Frontiers Media, 2021-06-01)
; ; ; ; A mandatory national Irish bovine viral diarrhoea (BVD) eradication programme, coordinated by Animal Health Ireland, commenced in 2013. Key decisions and programme review are undertaken by a cross-industry Implementation Group (BVDIG) supported by a Technical Working Group. Ear notch tissue is collected from all new-born calves using modified official identity tags, supplemented by additional blood sampling, including for confirmatory testing of calves with initial positive results and testing of their dams. Testing is delivered by private laboratories in conjunction with the National Reference Laboratory, with all results reported to a central database. This database manages key elements of the programme, issuing results to herdowners by short message service messaging supplemented by letters; assigning and exchanging animal-level statuses with government databases of the Department of Agriculture, Food and the Marine to enable legislated restrictions on animal movements; assigning negative herd status based on test results; generating regular reports for programme management and evaluation and providing herd-specific dashboards for a range of users. Legislation supporting the programme has been in place throughout but has not thus far mandated the slaughter of persistently infected (PI) calves. A key challenge in the early years, highlighted by modeling, was the retention of PI animals by some herd owners. This has largely been resolved by measures including graduated financial supports to encourage their early removal, herd-level movement restrictions, ongoing programme communications and the input of private veterinary practitioners (PVPs). A framework for funded investigations by PVPs in positive herds was developed to identify plausible sources of infection, to resolve the status of all animals in the herd and to agree up to three measures to prevent re-introduction of the virus. The prevalence of PI calves in 2013 was 0.66%, within 11.3% of herds, reducing in each subsequent year, to 0.03 and 0.55%, respectively, at the end of 2020. Recent regulatory changes within the European Union for the first time make provision for official approval of national eradication programmes, or recognition of BVD freedom, and planning is underway to seek approval and, in due course, recognition of freedom within this framework by 2023.267Scopus© Citations 9 - PublicationSTOC Free: An Innovative Framework to Compare Probability of Freedom From Infection in Heterogeneous Control Programmes(Frontiers, 2019-04-26)
; ; ; ; The existence, stage of eradication and design of control programmes (CPs) for diseases that are not regulated by the EU differ between Member States. When freedom from infection is reached (or being pursued), safe trade is essential to protect (or reach) that status. The aim of STOC free, a collaborative project between six countries, is to develop and validate a framework that enables a transparent and standardized comparison of confidence of freedom for CPs across herds, regions or countries. The framework consists of a model combined with a tool to facilitate the collection of the necessary parameters. All relevant actions taken in a CP are included in a Bayesian network model, which allows prior distributions for most parameters. In addition, frequency of occurrence and risk estimates for factors that influence either the probability of introduction or temporary misclassification leading to delayed detection of the infection are included in the model. Bovine viral diarrhoea virus (BVDV) is used as an example disease. Many countries have CPs in place for BVDV and although elements of the CPs are similar, biosecurity measures and testing protocols, including types of tests and testing frequency, as well as target groups, differ widely. Although the initially developed framework is based on BVDV, the aim is to make it sufficiently generic to be adaptable to CPs for other diseases and possibly other species. Thus, STOC free will result in a single general framework, adaptable to multiple disease CPs, which aims to enhance the safety of trade.234Scopus© Citations 9