The impact of the genotype on the prevalence of classical scrapie at population level

Total number and genotypes of animals in holdings selected for the genotype & cull option in the Compulsory Scrapie Flock Scheme (CSFS) in Great Britain were extracted from the National Scrapie Plan data warehouse. The association between various genotype-related measures and scrapie prevalence infection was tested using zero-inflated negative binomial models with the counts of positive cases as dependent variable, and country, number of flocks in the scheme, flock size, surveillance source and the following genotype-related measurements: the centered-log ratios (clr) oof the 15 genotypes, of the proportions of the 5 alleles at codons 136, 154 and 171, of the proportions of the 5 NSP types, and two flock-susceptibility risk indicators, as explanatory variables. A total of 319341 genotyped animals from 168 holdings were included in the analysis. An increased proportion of the ARR/ARR genotype corresponded to a decrease in the number of scrapie cases. ARR/AHQ, AHQ/VRQ, ARH/VRQ and ARQ/VRQ genotypes, NSP type V, ARH, ARQ, AHQ and VRQ alleles and the low and high-susceptibility risk indicators are all associated with an increase risk in the number of scrapie cases

Use of data mining techniques to investigate disease risk classification as a proxy for compromised biosecurity of cattle herds in Wales

<p>Abstract</p> <p>Background</p> <p>Biosecurity is at the forefront of the fight against infectious diseases in animal populations. Few research studies have attempted to identify and quantify the effectiveness of biosecurity against disease introduction or presence in cattle farms and, when done, they have relied on the collection of on-farm data. Data on environmental, animal movement, demographic/husbandry systems and density disease determinants can be collated without requiring additional specific on-farm data collection activities, since they have already been collected for some other purposes. The aim of this study was to classify cattle herds according to their risk of disease presence as a proxy for compromised biosecurity in the cattle population of Wales in 2004 for risk-based surveillance purposes.</p> <p>Results</p> <p>Three data mining methods have been applied: logistic regression, classification trees and factor analysis. Using the cattle holding population in Wales, a holding was considered positive if at least bovine TB or one of the ten most frequently diagnosed infectious or transmissible non-notifiable diseases in England and Wales, according to the Veterinary Investigation Surveillance Report (VIDA) had been diagnosed in 2004. High-risk holdings can be described as open large cattle herds located in high-density cattle areas with frequent movements off to many locations within Wales. Additional risks are associated with the holding being a dairy enterprise and with a large farming area.</p> <p>Conclusion</p> <p>This work has demonstrated the potential of mining various livestock-relevant databases to obtain generic criteria for individual cattle herd biosecurity risk classification. Despite the data and analytical constraints the described risk profiles are highly specific and present variable sensitivity depending on the model specifications. Risk profiling of farms provides a tool for designing targeted surveillance activities for endemic or emerging diseases, regardless of the prior amount of information available on biosecurity at farm level. As the delivery of practical evidence-based information and advice is one of the priorities of Defra's new Animal Health and Welfare Strategy (AHWS), data-driven models, derived from existing databases, need to be developed that can then be used to inform activities during outbreaks of endemic diseases and to help design surveillance activities.</p

Risk mapping of Rinderpest sero-prevalence in Central and Southern Somalia based on spatial and network risk factors

The Somali livestock production system is oriented towards domestic trade and export with seasonal movement patterns of herds/flocks in search of water and pasture and towards export points. The objective of the study is to develop a predictive spatial model of presence of rinderpest.Habka loo diyaariyo xoola soomaliyeed ee loogu talagalay in lagu iibiyo dalka gudihiisa ama dibaddiisa, iyagoo xoolahaas loo kaxaynaayo hadba meeshi biyo iyo baad leh iyo goobtii laga dhoofinayaba. Qasdiga daraasaadkaani wuxuu yahay sidii loo hormarin lahaa habka looga hortegi lahaa cudurrada faafa ee lo'da.Il sistema di produzione di bestiame somalo è orientato verso il commercio interno e l'esportazione con movimenti stagionali delle mandrie/greggi in cerca di acqua e pascoli e verso i luoghi di esportazione. L'obiettivo dello studio è quello di sviluppare un modello spaziale predittivo della presenza di peste bovina

High prevalence of scrapie in a dairy goat herd: tissue distribution of disease-associated PrP and effect of PRNP genotype and age

Following a severe outbreak of clinical scrapie in 2006–2007, a large dairy goat herd was culled and 200 animals were selected for post-mortem examinations in order to ascertain the prevalence of infection, the effect of age, breed and PRNP genotype on the susceptibility to scrapie, the tissue distribution of diseaseassociated PrP (PrP$^{\rm d}$), and the comparative efficiency of different diagnostic methods. As determined by immunohistochemical (IHC) examinations with Bar224 PrP antibody, the prevalence of preclinical infection was very high (72/200; 36.0%), with most infected animals being positive for PrP$^{\rm d}$ in lymphoreticular system (LRS) tissues (68/72; 94.4%) compared to those that were positive in brain samples (38/72; 52.8%). The retropharyngeal lymph node and the palatine tonsil showed the highest frequency of PrP$^{\rm d}$ accumulation (87.3% and 84.5%, respectively), while the recto-anal mucosa-associated lymphoid tissue (RAMALT) was positive in only 30 (41.7%) of the infected goats. However, the efficiency of rectal and palatine tonsil biopsies taken shortly before necropsy was similar. The probability of brain and RAMALT being positive directly correlated with the spread of PrP$^{\rm d}$ within the LRS. The prevalence of infection was influenced by PRNP genetics at codon 142 and by the age of the goats: methionine carriers older than 60 months showed a much lower prevalence of infection (12/78; 15.4%) than those younger than 60 months (20/42; 47.6%); these last showed prevalence values similar to isoleucine homozygotes of any age (40/80; 50.0%). Two of seven goats with definite signs of scrapie were negative for PrP$^{\rm d}$ in brain but positive in LRS tissues, and one goat showed biochemical and IHC features of PrP$^{\rm d}$ different from all other infected goats. The results of this study have implications for surveillance and control policies for scrapie in goats

Explaining the heterogeneous scrapie surveillance figures across Europe: a meta-regression approach

<p>Abstract</p> <p>Background</p> <p>Two annual surveys, the abattoir and the fallen stock, monitor the presence of scrapie across Europe. A simple comparison between the prevalence estimates in different countries reveals that, in 2003, the abattoir survey appears to detect more scrapie in some countries. This is contrary to evidence suggesting the greater ability of the fallen stock survey to detect the disease. We applied meta-analysis techniques to study this apparent heterogeneity in the behaviour of the surveys across Europe. Furthermore, we conducted a meta-regression analysis to assess the effect of country-specific characteristics on the variability. We have chosen the odds ratios between the two surveys to inform the underlying relationship between them and to allow comparisons between the countries under the meta-regression framework. Baseline risks, those of the slaughtered populations across Europe, and country-specific covariates, available from the European Commission Report, were inputted in the model to explain the heterogeneity.</p> <p>Results</p> <p>Our results show the presence of significant heterogeneity in the odds ratios between countries and no reduction in the variability after adjustment for the different risks in the baseline populations. Three countries contributed the most to the overall heterogeneity: Germany, Ireland and The Netherlands. The inclusion of country-specific covariates did not, in general, reduce the variability except for one variable: the proportion of the total adult sheep population sampled as fallen stock by each country. A large residual heterogeneity remained in the model indicating the presence of substantial effect variability between countries.</p> <p>Conclusion</p> <p>The meta-analysis approach was useful to assess the level of heterogeneity in the implementation of the surveys and to explore the reasons for the variation between countries.</p

Prion protein genotype survey confirms low frequency of scrapie-resistant K222 allele in British goat herds

<p>Scrapie in goats is a transmissible, fatal prion disease, which is endemic in the British goat population. The recent success in defining caprine PRNP gene variants that provide resistance to experimental and natural classical scrapie has prompted the authors to conduct a survey of PRNP genotypes in 10 goat breeds and 52 herds to find goats with the resistant K222 allele. They report here the frequencies in 1236 tested animals of the resistance-associated K222 and several other alleles by breed and herd. Eight animals were found to be heterozygous QK222 goats (0.64 per cent genotype frequency, 95 per cent CI 0.28 to 1.27 per cent) but no homozygous KK222 goats were detected. The K222 allele was found in Saanen, Toggenburg and Anglo-Nubian goats. The fact that only a few goats with the K222 allele have been identified does not preclude the possibility to design and implement successful breeding programmes at national level.</p

A quantitative assessment of the prion risk associated with wastewater from carcase-handling facilities

Wastewater from facilities processing livestock that may harbor transmissible spongiform encephalopathies (TSEs) infectivity is permitted under license for application to land where susceptible livestock may have access. Several previous risk assessments have investigated the risk of bovine spongiform encephalopathy (BSE) associated with wastewater effluents; however, the risk of exposure to classical scrapie and atypical scrapie has not been assessed. With the prevalence of certain TSEs (BSE in cattle and classical scrapie in sheep) steadily in decline, and with considerable changes in the structure of carcase-processing industries in Great Britain, a reappraisal of the TSE risk posed by wastewater is required. Our results indicate that the predicted number of new TSE infections arising from the spreading of wastewater on pasture over one year would be low, with a mean of one infection every 1,000 years for BSE in cattle (769, 555,556), and one infection every 30 years (16, 2,500), and 33 years (16, 3,333) for classical and atypical scrapie, respectively. It is assumed that the values and assumptions used in this risk assessment remain constant. For BSE in cattle the main contributors are abattoir and rendering effluent, contributing 35% and 22% of the total number of new BSE infections. For TSEs in sheep, effluent from small incinerators and rendering plants are the major contributors (on average 32% and 31% of the total number of new classical scrapie and atypical scrapie infections). This is a reflection of the volume of carcase material and Category 1 material flow through such facilities

Perinatal mortality in 23 beef herds in Orkney: incidence, risk factors and aetiology

Background: Perinatal mortality in beef calves impacts on profitability and animal welfare, but the incidence and causes in UK herds are not well known. Methods: Data from 11 herds were analysed to establish the risk factors for and incidence of perinatal mortality (full-term calves born dead or died within 48 hours). To establish cause of death, 23 herds in total submitted dead calves for postmortem examination (nine herds submitted all calves, 14 herds submitted calves on an ad hoc basis) and the results were reviewed by a panel. Results: The incidence of perinatal mortality for all 1059 calvings was 5.1 per cent (range 1.6–12.4 per cent across herds; median 4 per cent). The incidence of stillbirth and neonatal mortality was 3.9 per cent (range 0–10.1 per cent) and 1.2 per cent (range 0–2.6 per cent), respectively. Sex of the calf, plurality and level of calving assistance were associated with significantly greater risk of perinatal loss. Parturition-related deaths (n=20), intrauterine infections (n=13), congenital malformations (n=6) and postpartum infections (n=6) were among the diagnosis recorded from 54 calves investigated. Parturition-related deaths and congenital malformations were recorded more commonly from herds submitting all losses than from those submitting on an ad hoc basis. Conclusion: Variation in perinatal incidence across herds exists and many fail to reach the 2 per cent target. Some significant risk factors and common causes of death identified have the potential to decrease perinatal mortality rates through improved herd management

Risk mapping of Rinderpest sero-prevalence in Central and Southern Somalia based on spatial and network risk factors

<p>Abstract</p> <p>Background</p> <p>In contrast to most pastoral systems, the Somali livestock production system is oriented towards domestic trade and export with seasonal movement patterns of herds/flocks in search of water and pasture and towards export points. Data from a rinderpest survey and other data sources have been integrated to explore the topology of a contact network of cattle herds based on a spatial proximity criterion and other attributes related to cattle herd dynamics. The objective of the study is to integrate spatial mobility and other attributes with GIS and network approaches in order to develop a predictive spatial model of presence of rinderpest.</p> <p>Results</p> <p>A spatial logistic regression model was fitted using data for 562 point locations. It includes three statistically significant continuous-scale variables that increase the risk of rinderpest: home range radius, herd density and clustering coefficient of the node of the network whose link was established if the sum of the home ranges of every pair of nodes was equal or greater than the shortest distance between the points. The sensitivity of the model is 85.1% and the specificity 84.6%, correctly classifying 84.7% of the observations. The spatial autocorrelation not accounted for by the model is negligible and visual assessment of a semivariogram of the residuals indicated that there was no undue amount of spatial autocorrelation. The predictive model was applied to a set of 6176 point locations covering the study area. Areas at high risk of having serological evidence of rinderpest are located mainly in the coastal districts of Lower and Middle Juba, the coastal area of Lower Shabele and in the regions of Middle Shabele and Bay. There are also isolated spots of high risk along the border with Kenya and the southern area of the border with Ethiopia.</p> <p>Conclusions</p> <p>The identification of point locations and areas with high risk of presence of rinderpest and their spatial visualization as a risk map will be useful for informing the prioritization of disease surveillance and control activities for rinderpest in Somalia. The methodology applied here, involving spatial and network parameters, could also be applied to other diseases and/or species as part of a standardized approach for the design of risk-based surveillance activities in nomadic pastoral settings.</p

A dynamic model of transmission and elimination of peste des petits ruminants in Ethiopia

Peste des petits ruminants (PPR), a devastating viral disease of sheep and goats, has been targeted by the global community for eradication within the next 15 years. Although an efficacious attenuated live vaccine is available, the lack of knowledge about the transmission potential of PPR virus (PPRV) may compromise eradication efforts. By fitting a metapopulation model simulating PPRV spread to the results of a nationwide serological survey in Ethiopia, we estimated the level of viral transmission in an endemic setting and the vaccination coverage required for elimination. Results suggest that the pastoral production system as a whole acts as a viral reservoir, from which PPRV spills over into the sedentary production system, where viral persistence is uncertain. Estimated levels of PPRV transmission indicate that viral spread could be prevented if the proportion of immune small ruminants is kept permanently above 37% in at least 71% of pastoral village populations. However, due to the high turnover of these populations, maintaining the fraction of immune animals above this threshold would require high vaccine coverage within villages, and vaccination campaigns to be conducted annually. Adapting vaccination strategies to the specific characteristics of the local epidemiological context and small ruminant population dynamics would result in optimized allocation of limited resources and increase the likelihood of PPR eradication