Frequencies of prion protein (PrP) genotypes and distribution of ages in 15 scrapieaffected flocks in Great Britain

Polymorphism of prion protein gene (PRNP) in Nigerian sheep

Polymorphism of the prion protein gene (PRNP) gene determines an animal's susceptibility to scrapie. Three polymorphisms at codons 136, 154, and 171 have been linked to classical scrapie susceptibility, although many variants of PRNP have been reported. However, no study has investigated scrapie susceptibility in Nigerian sheep from the drier agro-climate zones. In this study, we aimed to identify PRNP polymorphism in nucleotide sequences of 126 Nigerian sheep by comparing them with public available studies on scrapie-affected sheep. Further, we deployed Polyphen-2, PROVEAN, and AMYCO analyses to determine the structure changes produced by the non-synonymous SNPs. Nineteen (19) SNPs were found in Nigerian sheep with 14 being non-synonymous. Interestingly, one novel SNP (T718C) was identified. There was a significant difference (P < 0.05) in the allele frequencies of PRNP codon 154 between sheep in Italy and Nigeria. Based on the prediction by Polyphen-2, R154H was probably damaging while H171Q was benign. Contrarily, all SNPs were neutral via PROVEAN analysis while two haplotypes (HYKK and HDKK) had similar amyloid propensity of PRNP with resistance haplotype in Nigerian sheep. Our study provides valuable information that could be possibly adopted in programs targeted at breeding for scrapie resistance in sheep from tropical regions.

Novel Prion Protein Gene Polymorphisms in Awassi Sheep in Three Regions of the Fertile Crescent

Scrapie is a fatal, neurodegenerative disease that affects sheep and goats, and genetic susceptibility to scrapie in sheep is associated with polymorphisms in the prion protein (PRNP) gene. The aim of this study is to identify PRNP polymorphism in Awassi sheep from Türkiye, the Palestinian Authority, and Saudi Arabia. A total of 150 healthy sheep were genotyped for PRNP, using Sanger sequencing. There were seven alleles and eleven genotypes observed based on codons 136, 154, and 171 of PRNP. The ARQ allele was predominant in all populations. The most resistant allele to scrapie, ARR, was present in all three regions. The VRQ allele, associated with the highest susceptibility to scrapie, was detected only in Türkiye at a low frequency. In this study, twenty-seven amino acid substitutions were found. Eight of them (R40Q, G65E, H88L, S98T, A118P, S138T, V192F and L250I) have not been previously reported. These data indicate that sheep breeds close to the sheep domestication center have maintained high genetic diversity in the PRNP region. Our findings on PRNP will provide valuable insights for sheep breeding programs, aiding in the selection of genotypes resistant to scrapie in Türkiye, the Palestinian Authority, and Saudi Arabia.

Molecular cloning and sequence analysis of prion protein gene in Xiji donkey in China

Prion diseases are a group of human and animal neurodegenerative disorders caused by the deposition of an abnormal isoform prion protein (PrP(Sc)) encoded by a single copy prion protein gene (PRNP). Prion disease has been reported in many herbivores but not in Equus and the species barrier might be playing a role in resistance of these species to the disease. Therefore, analysis of genotype of prion protein (PrP) in these species may help understand the transmission of the disease. Xiji donkey is a rare species of Equus not widely reared in Ningxia, China, for service, food and medicine, but its PRNP has not been studied. Based on the reported PrP sequence in GenBank we designed primers and amplified, cloned and sequenced the PRNP of Xiji donkey. The sequence analysis showed that the Xiji donkey PRNP was consisted of an open reading frame of 768 nucleotides encoding 256 amino acids. Amino acid residues unique to donkey as compared with some Equus animals, mink, cow, sheep, human, dog, sika deer, rabbit and hamster were identified. The results showed that the amino acid sequence of Xiji donkey PrP starts with the consensus sequence MVKSH, with almost identical amino acid sequence to the PrP of other Equus species in this study. Amino acid sequence analysis showed high identity within species and close relation to the PRNP of sika deer, sheep, dog, camel, cow, mink, rabbit and hamster with 83.1-99.7% identity. The results provided the PRNP data for an additional Equus species, which should be useful to the study of the prion disease pathogenesis, resistance and cross species transmission.

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.

Regardless the management practices; the increased susceptibility that the non-ARR alleles confer on an individual could be extrapolated at the population level. Increasing prevalence of ARR allele reduces the overall risk of scrapie at population level. At genotype level, the VRQ/VRQ genotype, present a very low frequency in the study population, seems to play a residual effect in the overall risk of scrapie in a flock.

Evidence for maternal transmission of scrapie in naturally affected flocks

It has been known for many years that the offspring of scrapie affected ewes are at increased risk of developing scrapie but whether this is simply the result of an increased genetic susceptibility or transmission of infection has always been unclear. To contribute to clarify this we analysed the data collected in a detailed study of scrapie occurrence in a number of naturally affected commercial sheep flocks in Great Britain (GB) to investigate the association between PrP genotype and parental scrapie status and the incidence of scrapie. Our analyses confirmed the strong association between PrP genotype and the incidence of scrapie found in previous studies and a low incidence of scrapie in animals carrying the ARR allele and a high risk in homozygous VRQ animals. However, we also demonstrate an increased incidence of scrapie in the offspring of scrapie affected ewes controlling for the confounding effect of PrP genotype, but no increased scrapie incidence in the offspring of scrapie affected sires. Our results suggest that some of the increased incidence of scrapie in the offspring of scrapie affected ewes is the result of transmission of infection from mother to offspring. Our results confirm that a breeding policy aimed at decreasing the genetic susceptibility of the population should decrease the incidence of scrapie and that removing the offspring of scrapie affected animals from affected flocks could contribute to the control of this disease.

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.

The impact of sheep breed on the risk of classical scrapie

The risk of classical scrapie in sheep is associated with polymorphisms in the prion protein (PrP) gene. In recent years, large-scale selective breeding programmes for sheep at lower risk of disease have been undertaken across the European Union. We analysed large-scale datasets on scrapie and sheep demography to investigate additional effects of sheep breed on scrapie risk. There was evidence for variation between certain breeds in the scrapie risk of some PrP genotypes, which could be caused by innate breed differences or distinct scrapie strains circulating within them. While the PrP genotypes of cases are generally consistent across breeds, some exceptions provide evidence that scrapie strain may influence affected PrP genotypes to a greater extent than innate breed differences. There was a significant association between the breed-level incidence of scrapie and the frequency of susceptible PrP genotypes in breeds. Our results lend support to selective breeding programmes which aim to reduce the frequency of high-risk PrP genotypes with measures not varying by sheep breed.

Prevalence of sheep infected with classical scrapie in Great Britain: integrating multiple sources of surveillance data for 2002

Estimates for the prevalence of sheep infected with classical scrapie are essential for assessing the efficacy of control strategies that have been implemented in Great Britain (GB). Here a back-calculation approach was used to estimate the prevalence in the GB national flock by integrating data on reported cases and the results of abattoir and fallen stock surveys for 2002. Prevalence estimates ranged from 0.33 to 2.06%, depending on the estimates used for the frequencies of prion protein (PrP) genotypes in the national flock and the stage of incubation at which the diagnostic tests used are able to detect infected animals. The risk of infection was found to be higher than that of clinical disease, especially in those PrP genotypes that have a later age at onset of clinical disease. Moreover, results suggest that a high proportion (more than 55%) of infected animals surviving to disease onset die on farm before clinical signs become apparent, which helps account for the high observed prevalence in the fallen stock compared with the abattoir survey. The analyses indicated that attention needs to be given to identifying the stage of incubation at which diagnostic tests are able to detect infected animals and obtaining better demographic data for the GB national flock.

Breeding programmes for TSE resistance in British sheep. I. Assessing the impact on prion protein (PrP) genotype frequencies

From April 2005, member states of the European Union were required to implement a compulsory breeding programme for resistance to transmissible spongiform encephalopathies (TSEs) in sheep as part of measures to eradicate TSEs from national flocks. In this paper, we assessed the impact of four different breeding strategies on prion protein (PrP) genotype frequencies using a mathematical model which describes in detail gene flow in the British sheep flock. These strategies ranged from the minimum requirements laid down in by EU legislation to compulsory implementation of the current National Scrapie Plan for Great Britain (NSP) ram genotyping scheme. All four strategies were predicted to substantially reduce the frequency of the VRQ allele, which is associated with the highest risk of scrapie, although schemes with more stringent requirements produced a larger reduction. However, there were marked differences in the impact of the strategies on the frequency of other PrP alleles. In particular, restrictions beyond those required by EU legislation were necessary to change the frequency of other PrP alleles substantially. Consequently, a breeding programme which aims to reduce the risk to human health by reducing the frequency of the ARQ allele (associated with the highest risk of BSE in sheep) must place restrictions on ARQ-bearing animals. Similarly, a programme which seeks to increase the frequency of the ARR allele (associated with the lowest risk of TSE) must favour ARR-bearing animals.

A modelling framework to describe the spread of scrapie between sheep flocks in Great Britain

My aim was to develop a stochastic, spatial model describing the spread of scrapie between sheep flocks in Great Britain; I wanted a model, which could subsequently be used to assess the efficacy of different control strategies. The structure of the model reflects the demography of the British sheep flock, including a description of the contact structure between flocks. The dynamics of scrapie were incorporated through two probabilities associated with each flock: of acquiring infection and of experiencing a within-flock outbreak following exposure. The acquisition of infection depends on whether or not a flock buys-in sheep and, if it does, whether or not it trades with an affected flock. Once a flock is exposed, the probability of a within-flock outbreak occurring and its duration depend on the basic reproductive number, the prion-protein (PrP) genotype profile and the flock size. The model was validated using regional data from two postal surveys conducted in 1998 and 2002, which demonstrated that the model captures the spatial dynamics of scrapie (at least at a regional level). Moreover, the predicted distribution for the duration of a within-flock outbreak reflects the duration of outbreaks reported in the literature. Using the model to predict long-term trends in the proportion of affected flocks suggested that, even without control measures beyond the removal of animals with clinical signs, scrapie ultimately will disappear from the national flock, though it is likely to be decades before the disease is eliminated. However, there were scenarios consistent with the available data which suggested that scrapie could remain endemic within the British sheep flock. Consequently, it is essential to take this uncertainty in the long-term dynamics of scrapie into account when considering the efficacy of control strategies. Although control strategies were not explicitly examined, the model suggests two aspects important for control: larger flocks remain affected for longer and provide infection for other, smaller flocks and animal movements must be traceable.

Frequencies of PrP genotypes in 38 breeds of sheep sampled in the National Scrapie Plan for Great Britain

Between October 2001 and January 2003 the prion protein (PrP) genotypes of over 250,000 sheep were determined through the operation of the National Scrapie Plan (NSP); the results for 38 breeds were analysed to provide an estimate of the underlying PrP genotype distribution of the British sheep population. Although there was marked variability among the genotype profiles of the different breeds, several trends emerged. A comparison of the allele frequencies demonstrated that the breeds could be grouped into three categories: breeds dominated by ARR and ARQ in which the frequency of ARR exceeded the frequency of ARQ; breeds dominated by ARR and ARQ in which the frequency of ARQ exceeded the frequency of ARR; and breeds with significant levels of either AHQ, ARH or VRQ. Hill breeds were more likely to have a lower proportion of animals at low risk of scrapie (NSP type 1) and a higher proportion of animals at an intermediate risk of scrapie (NSP type 3) than other breeds. Most breeds had a small proportion of animals at high risk of scrapie (NSP type 5). The frequency of ARR/VRQ (NSP type 4) was variable.

Simulation of the options for a national control programme to eradicate scrapie from Great Britain

Because of the risk to public health posed by the potential presence of bovine spongiform encephalopathy (BSE) in sheep, there are plans to eradicate transmissible spongiform encephalopathies (TSEs) from the British sheep population. We used a mathematical model for the spread of scrapie between sheep flocks to assess the efficacy of five control strategies at eradicating the infection from the national flock. These range from ram-genotyping schemes through whole-flock genotyping with selective culling to whole-flock slaughter. The impact of control was considered under three scenarios for the long-term dynamics of scrapie in GB: two in which scrapie is ultimately eliminated (with different median extinction times) and one in which scrapie remains endemic. Results suggested that it is feasible to eradicate scrapie from the British sheep flock, but that any national control programme will take decades to eliminate the disease and be costly. The most-effective strategy, measured in terms of the probability of eradication and time taken for eradication, was predicted to be whole-flock culling, which was effective under all three scenarios for the long-term dynamics of scrapie. Strategies involving whole-flock genotyping with selective culling were also effective, though they were predicted to take longer to eradicate scrapie than whole-flock culling. Ram-genotyping schemes were effective in some instances, but not for the scenario where scrapie remained endemic in the national flock. At low levels of reporting of clinical disease (< 20%) the probability of eradication within 100 years was predicted to be < 100% and, consequently, low levels of reporting could compromise the effectiveness of a control programme. Moreover, the predicted time taken to eradicate scrapie would increase markedly if the reporting compliance decreased.

Detection of polymorphisms in the prion protein gene in the Belgian sheep population: Some preliminary data

The development of clinical signs of TSE/scrapie in sheep has been linked to polymorphisms in the prion protein (PRNP) gene. The most important polymorphisms appear to be at codons 136, 154, and 171. The objective of this study was to investigate the polymorphisms at these codons in the Belgian sheep population, including clinical healthy animals, healthy animals at the slaughterhouse and animals in TSE/scrapie positive farms (including a Nor98 farm).