Flock-level risk factors for scrapie in Great Britain: analysis of a 2002 anonymous postal survey

Management of chronic wasting disease in ranched elk: conclusions from a longitudinal three-year study

Chronic wasting disease is a fatal, horizontally transmissible prion disease of cervid species that has been reported in free-ranging and farmed animals in North America, Scandinavia, and Korea. Like other prion diseases, CWD susceptibility is partly dependent on the sequence of the prion protein encoded by the host's PRNP gene; it is unknown if variations in PRNP have any meaningful effects on other aspects of health. Conventional diagnosis of CWD relies on ELISA or IHC testing of samples collected post-mortem, with recent efforts focused on antemortem testing approaches. We report on the conclusions of a study evaluating the role of antemortem testing of rectal biopsies collected from over 570 elk in a privately managed herd, and the results of both an amplification assay (RT-QuIC) and conventional IHC among animals with a several PRNP genotypes. Links between PRNP genotype and potential markers of evolutionary fitness, including pregnancy rates, body condition, and annual return rates were also examined. We found that the RT-QuIC assay identified significantly more CWD positive animals than conventional IHC across the course of the study, and was less affected by factors known to influence IHC sensitivity - including follicle count and PRNP genotype. We also found that several evolutionary markers of fitness were not adversely correlated with specific PRNP genotypes. While the financial burden of the disease in this herd was ultimately unsustainable for the herd owners, our scientific findings and the hurdles encountered will assist future CWD management strategies in both wild and farmed elk and deer.

Prions are affected by evolution at two levels

Prions, infectious proteins, can transmit diseases or be the basis of heritable traits (or both), mostly based on amyloid forms of the prion protein. A single protein sequence can be the basis for many prion strains/variants, with different biological properties based on different amyloid conformations, each rather stably propagating. Prions are unique in that evolution and selection work at both the level of the chromosomal gene encoding the protein, and on the prion itself selecting prion variants. Here, we summarize what is known about the evolution of prion proteins, both the genes and the prions themselves. We contrast the one known functional prion, [Het-s] of Podospora anserina, with the known disease prions, the yeast prions [PSI+] and [URE3] and the transmissible spongiform encephalopathies of mammals.

A Bayesian framework to assess the potential for controlling classical scrapie in sheep flocks using a live diagnostic test

Current strategies to control classical scrapie remove animals at risk of scrapie rather than those known to be infected with the scrapie agent. Advances in diagnostic tests, however, suggest that a more targeted approach involving the application of a rapid live test may be feasible in future. Here we consider the use of two diagnostic tests: recto-anal mucosa-associated lymphatic tissue (RAMALT) biopsies; and a blood-based assay. To assess their impact we developed a stochastic age- and prion protein (PrP) genotype-structured model for the dynamics of scrapie within a sheep flock. Parameters were estimated in a Bayesian framework to facilitate integration of a number of disparate datasets and to allow parameter uncertainty to be incorporated in model predictions. In small flocks a control strategy based on removal of clinical cases was sufficient to control disease and more stringent measures (including the use of a live diagnostic test) did not significantly reduce outbreak size or duration. In medium or large flocks strategies in which a large proportion of animals are tested with either live diagnostic test significantly reduced outbreak size, but not always duration, compared with removal of clinical cases. However, the current Compulsory Scrapie Flocks Scheme (CSFS) significantly reduced outbreak size and duration compared with both removal of clinical cases and all strategies using a live diagnostic test. Accordingly, under the assumptions made in the present study there is little benefit from implementing a control strategy which makes use of a live diagnostic test.

A relevant long-term impact of the circulation of a potentially contaminated vaccine on the distribution of scrapie in Italy. Results from a retrospective cohort study

A sudden increase in the incidence of scrapie in Italy in 1997 was subsequently linked to the use of a potentially infected vaccine against contagious agalactia. The relative risk for the exposed farms ranged between 6 and 40. The aim of this study was to assess the long-term impact of exposure to the potentially scrapie-contaminated vaccine on the Italian classical scrapie epidemic. We carried out a retrospective cohort study, fitting mixed-effects Poisson regression models, dividing national geographic areas into exposure categories on the basis of the vaccine circulation levels. We took into account the sensitivity of the surveillance system applied in the different areas. The population attributable fraction (PAF) was used to assess the impact on the total population of farms associated with the effect of circulation of the vaccine. The provinces where the vaccine was more often sold were noted to have a higher level of disease when compared to those provinces where the vaccine was sold less often (incidence rate ratio [IRR]: 2.7; 95% confidence interval [CI]: 1.1-6.5). The population attributable fraction was high (68.4%). Standardization techniques allowed to account for the potential of geographical variability in the sensitivity of the Italian surveillance system. Although the number of the directly exposed farms was limited, an important long-term impact of the vaccine circulation could be quantified in terms of secondary outbreaks likely due to the exchange of animals from directly exposed flocks.

A Bayesian hierarchical analysis to compare classical and atypical scrapie surveillance data; Wales 2002-2006

We describe the application of Bayesian hierarchical models (BHM) to the analysis of risk of sheep scrapie using data from multiple surveillance sources. More specifically, we analysed data from the test results of three surveillance sources on classical and atypical scrapie in Wales for the period 2002-2006. For each form of scrapie, a BHM was fitted to assess the occurrence of spatial patterns of risk shared by the multiple surveillance sources and the association between covariates and disease. We defined a shared-component model whereby the two types of data sources: exhaustive lists (e.g. reports of clinical cases) and sample-based data sources (e.g. abattoir survey) shared a common spatial pattern of risks at parish level. This shared component was adjusted by a risk-gradient parameter that moderated the individual contribution of the datasets. For both forms of scrapie, the risk-gradient was not significantly different indicating that the sensitivity of the two types of dataset was similar for the two diseases. The spatial patterns of the combinations of data sources appeared similar within disease. However, our results suggest that classical and atypical scrapie differ in their spatial patterns and disease determinants. The joint approach permitted inference from all the available evidence and resulted in robust and less biased estimates of risk, particularly for atypical scrapie where the number of observations was very limited.

A case-control study of atypical scrapie in GB sheep flocks

Wide-scale scrapie surveillance started in 2002 in the EU. As a result, a new form of scrapie was detected which has been referred to as atypical scrapie. Here we present a case-control study conducted on British sheep farms to increase our understanding of the disease and potential risk factors at holding level. Forty case and 120 control holdings were traced from the confirmed atypical results in the scrapie surveillance programme in Great Britain during the period 2002-2007. A detailed questionnaire was completed by interview to record data on holding-specific management variables. A combination of generalized additive, generalized linear and Bayesian models returned 3 variables clearly associated with an increase in the odds of atypical scrapie: presence of two sheep breeds (Welsh Mountain and Cheviot) and flock type (store/fattening flocks). A fourth variable, the number of visits by veterinarians to the holding exerted a protective effect. Various other variables were significantly associated with the outcome, but at a somewhat lower level of confidence; for example, the size of the holding and the presence on the farm of concentrates intended for animals other than sheep.

The role of mathematical modelling in understanding the epidemiology and control of sheep transmissible spongiform encephalopathies: a review

To deal with the incompleteness of observations and disentangle the complexities of transmission much use has been made of mathematical modelling when investigating the epidemiology of sheep transmissible spongiform encephalopathies (TSE) and, in particular, scrapie. Importantly, these modelling approaches allow the incidence of clinical disease to be related to the underlying prevalence of infection, thereby overcoming one of the major difficulties when studying these diseases. Models have been used to investigate the epidemiology of scrapie within individual flocks and at a regional level; to assess the efficacy of different control strategies, especially selective breeding programmes based on prion protein (PrP) genotype; to interpret the results of scrapie surveillance; and to inform the design of surveillance programmes. Furthermore, mathematical modelling has played an important role when assessing the risk to human health posed by the possible presence of bovine spongiform encephalopathy in sheep. Here, we review the various approaches that have been taken when developing and analysing mathematical models for the epidemiology and control of sheep TSE and assess their impact on our understanding of these diseases. We also identify areas that require further work, discuss future challenges and identify data gaps.

The evaluation of exposure risks for natural transmission of scrapie within an infected flock

Background

Although the epidemiology of scrapie has been broadly understood for many years, attempts to introduce voluntary or compulsory controls to eradicate the disease have frequently failed. Lack of precision in defining the risk factors on farm has been one of the challenges to designing control strategies. This study attempted to define which parts of the annual flock management cycle represented the greatest risk of infection to naive lambs exposed to the farm environment at different times.

Results

In VRQ/VRQ lambs exposed to infected sheep at pasture or during lambing, and exposed to the buildings in which lambing took place, the attack rate was high and survival times were short. Where exposure was to pasture alone the number of sheep affected in each experimental group was reduced, and survival times were longer and related to length of exposure.

Conclusion

At the flock level, eradication and control strategies for scrapie must take into account the need to decontaminate buildings used for lambing, and to reduce (or prevent) the exposure of lambs to infected sheep, especially in the later stages of incubation, and at lambing. The potential for environmental contamination from pasture should also be considered. Genotype selection may still prove to be the only viable tool to prevent infection from contaminated pasture, reduce environmental contamination and limit direct transmission from sheep to sheep.

PrP genotype: a flock-level risk factor for scrapie?

Previous epidemiological studies of risk factors for classical scrapie at flock level have identified a variety of management and purchase related variables, along with increased flock size and, in some cases, breed effects. Although known as a risk factor at the individual animal level, PrP genotype frequencies at flock level have not yet been studied. In an unmatched case-control study, three measures of flock-level prion protein (PrP) frequency estimates were investigated with respect to the scrapie status of the flock in 293 British sheep flocks (195 control flocks and 98 case flocks). Flocks with positive frequencies (more than 0 per cent) of two genotypes (VRQ/VRQ and AHQ/VRQ), large frequencies (more than 10 per cent) of the ARR/VRQ genotype, and large frequencies (more than 5.2 per cent) of the VRQ allele were at increased odds of being affected with clinical classical scrapie. When adjusted for flock size, breed and sampling strategy the genotype and allele effects remained, except that for flocks with positive frequencies of VRQ/VRQ. The known effect of increased risk with increased flock size was confirmed. A measure of the flock PrP genotype frequency profile should thus be included in studies of risk factors for scrapie. It could also be integrated into risk-based surveillance strategies for identification of "at-risk-of scrapie" flocks.

Classical sheep scrapie in Great Britain: spatial analysis and identification of environmental and farm-related risk factors

BACKGROUND

Previous studies suggest that the spatial distribution of classical sheep scrapie in Great Britain is uneven and that certain flock characteristics may be associated with occurrence of the disease. However, the existence of areas of high and low disease-risk may also result from differences in the spatial distribution of environmental characteristics. In this study we explored the spatial pattern of classical scrapie in Great Britain between 2002 and 2005 and investigated the association between disease occurrence and various environmental and farm-related risk factors.

RESULTS

Exploratory spatial analysis: South Wales was found to have a higher density of scrapie-positive farms than the rest of Great Britain. In addition, a small cluster of high-risk farms was identified in the center of this region in which clustering of scrapie-positive farms occurred up to a distance of approximately 40 km. SPATIAL MODELLING: A mixed-effects regression model identified flock-size and soil drainage to be significantly associated with the occurrence of scrapie in England and Wales (area under the curve (AUC) 0.71 +/- 0.01, 95% CI 0.68 - 0.74). The predictive risk map based on the estimated association between these factors and disease occurrence showed most of Wales to be at risk of being confirmed positive for scrapie with areas of highest risk in central and south Wales. In England, areas with the highest risk occurred mainly in the north and the midlands.

CONCLUSION

The observed distribution of scrapie in Great Britain exhibited a definite spatial pattern with south Wales identified as an area of high occurrence. In addition both flock (flock size) and environmental variables (soil drainage) were found to be significantly associated with the occurrence of the disease. However, the model's AUC indicated unexplained variation remaining in the model and the source of this variation may lie in farm-level characteristics rather than spatially-varying ones such as environmental factors.

Spatial distribution of the active surveillance of sheep scrapie in Great Britain: an exploratory analysis

Background

This paper explores the spatial distribution of sampling within the active surveillance of sheep scrapie in Great Britain. We investigated the geographic distribution of the birth holdings of sheep sampled for scrapie during 2002 – 2005, including samples taken in abattoir surveys (c. 83,100) and from sheep that died in the field ("fallen stock", c. 14,600). We mapped the birth holdings by county and calculated the sampling rate, defined as the proportion of the holdings in each county sampled by the surveys. The Moran index was used to estimate the global spatial autocorrelation across Great Britain. The contributions of each county to the global Moran index were analysed by a local indicator of spatial autocorrelation (LISA).

Results

The sampling rate differed among counties in both surveys, which affected the distribution of detected cases of scrapie. Within each survey, the county sampling rates in different years were positively correlated during 2002–2005, with the abattoir survey being more strongly autocorrelated through time than the fallen stock survey. In the abattoir survey, spatial indices indicated that sampling rates in neighbouring counties tended to be similar, with few significant contrasts. Sampling rates were strongly correlated with sheep density, being highest in Wales, Southwest England and Northern England. This relationship with sheep density accounted for over 80% of the variation in sampling rate among counties. In the fallen stock survey, sampling rates in neighbouring counties tended to be different, with more statistically significant contrasts. The fallen stock survey also included a larger proportion of holdings providing many samples.

Conclusion

Sampling will continue to be uneven unless action is taken to make it more uniform, if more uniform sampling becomes a target. Alternatively, analyses of scrapie occurrence in these datasets can take account of the distribution of sampling. Combining the surveys only partially reduces uneven sampling. Adjusting the distribution of sampling between abattoirs to reduce the bias in favour of regions with high sheep densities could probably achieve more even sampling. However, any adjustment of sampling should take account of the current understanding of the distribution of scrapie cases, which will be improved by further analysis of this dataset.

A case-control study on the origin of atypical scrapie in sheep, France

Risk factors for this disease suggest a noninfectious origin influenced by genetic and metabolic factors.

A matched case–control study (95 cases and 220 controls) was designed to study risk factors for atypical scrapie in sheep in France. We analyzed contacts with animals from other flocks, lambing and feeding practices, and exposure to toxic substances. Data on the prnp genotype were collected for some case and control animals and included in a complementary analysis. Sheep dairy farms had a higher risk for scrapie (odds ratio [OR] 15.1, 95% confidence interval [CI] 3.3–69.7). Lower risk was associated with organic farms (OR 0.15, 95% CI 0.02–1.26), feeding corn silage (OR 0.16, 95% CI 0.05–0.53), and feeding vitamin and mineral supplements (OR 0.6, 95% CI 0.32–1.14). Genetic effects were quantitatively important but only marginally changed estimates of other variables. We did not find any risk factor associated with an infectious origin of scrapie. Atypical scrapie could be a spontaneous disease influenced by genetic and metabolic factors.

On the question of proportionality of the count of observed scrapie cases and the size of holding

Background

The present paper investigates the question of a suitable basic model for the number of scrapie cases in a holding and applications of this knowledge to the estimation of scrapie-affected holding population sizes and adequacy of control measures within holding. Is the number of scrapie cases proportional to the size of the holding in which case it should be incorporated into the parameter of the error distribution for the scrapie counts? Or, is there a different – potentially more complex – relationship between case count and holding size in which case the information about the size of the holding should be better incorporated as a covariate in the modeling?

Methods

We show that this question can be appropriately addressed via a simple zero-truncated Poisson model in which the hypothesis of proportionality enters as a special offset-model. Model comparisons can be achieved by means of likelihood ratio testing. The procedure is illustrated by means of surveillance data on classical scrapie in Great Britain. Furthermore, the model with the best fit is used to estimate the size of the scrapie-affected holding population in Great Britain by means of two capture-recapture estimators: the Poisson estimator and the generalized Zelterman estimator.

Results

No evidence could be found for the hypothesis of proportionality. In fact, there is some evidence that this relationship follows a curved line which increases for small holdings up to a maximum after which it declines again. Furthermore, it is pointed out how crucial the correct model choice is when applied to capture-recapture estimation on the basis of zero-truncated Poisson models as well as on the basis of the generalized Zelterman estimator. Estimators based on the proportionality model return very different and unreasonable estimates for the population sizes.

Conclusion

Our results stress the importance of an adequate modelling approach to the association between holding size and the number of cases of classical scrapie within holding. Reporting artefacts and speculative biological effects are hypothesized as the underlying causes of the observed curved relationship. The lack of adjustment for these artefacts might well render ineffective the current strategies for the control of the disease.

Within-holding prevalence of sheep classical scrapie in Great Britain

Background

Data from the Compulsory Scrapie Flocks Scheme (CSFS), part of the compulsory eradication measures for the control of scrapie in the EU, have been used to estimate the within-holding prevalence of classical scrapie in Great Britain (GB). Specifically data from one of the testing routes within the CSFS have been used; the initial cull (IC), whereby two options can be applied: the whole flock cull option by which the entire flock is depopulated, and the genotyping and cull of certain genotypes.

Results

Between April 2005 and September 2007, 25,316 suitable samples, submitted from 411 flocks in 213 scrapie-affected holdings in Great Britain, were tested for scrapie. The predicted within-holding prevalence for the initial cull was 0.65% (95% CI: 0.55–0.75). For the whole cull option was 0.47% (95% CI: 0.32–0.68) and for the genotype and cull or mixed option (both options applied in different flocks of the same holding), the predicted within-holding prevalence was 0.7% (95% CI: 0.6–0.83). There were no significant differences in the within-flock prevalence between countries (England, Scotland and Wales) or between CSFS holdings by the surveillance stream that detected the index case. The number of CSFS flocks on a holding did not affect the overall within-holding prevalence of classical scrapie.

Conclusion

These estimates are important in the discussion of the epidemiological implications of the current EU testing programme of scrapie-affected flocks and to inform epidemiological and mathematical models. Furthermore, these estimates may provide baseline data to assist the design of future surveillance activities and control policies with the aim to increase their efficiency.

Epidemiological characteristics of classical scrapie outbreaks in 30 sheep flocks in the United Kingdom

Background

Most previous analyses of scrapie outbreaks have focused on flocks run by research institutes, which may not reflect the field situation. Within this study, we attempt to rectify this deficit by describing the epidemiological characteristics of 30 sheep flocks naturally-infected with classical scrapie, and by exploring possible underlying causes of variation in the characteristics between flocks, including flock-level prion protein (PrP) genotype profile. In total, the study involved PrP genotype data for nearly 8600 animals and over 400 scrapie cases.

Methodology/Principal Findings

We found that most scrapie cases were restricted to just two PrP genotypes (ARQ/VRQ and VRQ/VRQ), though two flocks had markedly different affected genotypes, despite having similar underlying genotype profiles to other flocks of the same breed; we identified differences amongst flocks in the age of cases of certain PrP genotypes; we found that the age-at-onset of clinical signs depended on peak incidence and flock type; we found evidence that purchasing infected animals is an important means of introducing scrapie to a flock; we found some evidence that flock-level PrP genotype profile and flock size account for variation in outbreak characteristics; identified seasonality in cases associated with lambing time in certain flocks; and we identified one case that was homozygous for phenylalanine at codon 141, a polymorphism associated with a very high risk of atypical scrapie, and 28 cases that were heterozygous at this codon.

Conclusions/Significance

This paper presents the largest study to date on commercially-run sheep flocks naturally-infected with classical scrapie, involving 30 study flocks, more than 400 scrapie cases and over 8500 PrP genotypes. We show that some of the observed variation in epidemiological characteristics between farms is related to differences in their PrP genotype profile; although much remains unexplained and may instead be attributed to the stochastic nature of scrapie dynamics.

Evidence of scrapie transmission via milk

Background

The risk of scrapie infection increases with increased duration and proximity of contact between sheep at lambing. Scrapie infectivity has not been detected in milk but cellular prion protein, the precursor of disease-associated prion protein PrP^d, has been found in milk from ruminants. To determine whether milk is able to transmit scrapie, 18 lambs with a prion protein genotype associated with high susceptibility to scrapie (VRQ/VRQ) were fed milk from twelve scrapie-affected ewes of the same genotype, and 15 VRQ/VRQ sheep reared on scrapie-free dams served as controls.

Results

Three lambs fed milk from scrapie-affected ewes were culled due to intercurrent diseases at 43, 44 and 105 days of age respectively, and PrP^d was detected in the distal ileum of the first two lambs, whilst PrP^d was not found in lymphoreticular tissues in the third lamb. A control lamb, housed in a separate pen and culled at 38 days of age, was also negative for PrP^d in a range of tissues. Samples of recto-anal mucosa associated lymphoid tissue collected from the remaining 15 live lambs at seven months of age (between five to seven months after mixing) were positive for PrP^d in the scrapie milk recipients, whereas PrP^d was not detected in the remaining 14 controls at that time. A subsequent sample collected from control lambs revealed PrP^d accumulation in two of five lambs eight months after mixing with scrapie milk recipients suggestive of an early stage of infection via lateral transmission. By contrast, the control sheep housed in the same building but not mixed with the scrapie milk recipients were still negative for PrP^d.

Conclusion

The presence of PrP^d in distal ileum and rectal mucosa indicates transmission of scrapie from ewe to lamb via milk (or colostrum) although it is not yet clear if such cases would go on to develop clinical disease. The high level of infection in scrapie-milk recipients revealed by rectal mucosal testing at approximately seven months of age may be enhanced or supplemented by intra-recipient infection as these lambs were mixed together after feeding with milk from scrapie-affected ewes and we also observed lateral transmission from these animals to lambs weaned from scrapie-free ewes.

Approaches to investigating transmission of spongiform encephalopathies in domestic animals using BSE as an example

Bovine spongiform encephalopathy was a novel spongiform encephalopathy, in an hitherto unaffected species, that had characteristics of a point source epidemic, with an agent that could have been incorporated into a wide variety of feedstuffs and iatrogenically administered to naïve populations, and there was early evidence that it was not restricted to bovines. It was vital to establish, albeit experimentally, which other species might be affected, and whether the epidemic could be maintained by natural transmission, if the source was removed. In contrast, scrapie has been endemic throughout Great Britain for centuries, is maintained naturally (even if we don't know exactly how) and has a known host range. The principles, process and integration of evidence from different types of studies, however, are similar for both of these transmissible spongiform encephalopathies (TSE) and can be applied to any emerging or suspected spongiform encephalopathy. This review discusses the experimental approaches used to determine TSE transmissibility and infectivity and how they relate to natural disease and control measures.