Prion protein (PrP) gene polymorphisms associated with natural scrapie cases and their flock-mates in Ireland

Effects on inbreeding of different strategies aimed at eliminating scrapie sensitivity alleles in rare sheep breeds in The Netherlands

The Dutch scrapie eradication programme aims at the exclusive use of homozygous ARR/ARR breeding rams by the end of 2004. As a consequence, breeds with a small population size and a low frequency of the ARR allele may suffer unacceptable losses of genetic diversity and high inbreeding levels. We simulated three breeding strategies to assess their efficacy in eliminating scrapie sensitive alleles and their effect on inbreeding levels. Under mild selection, both homozygous and heterozygous ARR rams were used indiscriminately. Under moderate selection, homozygous ARR rams were used preferably but they were supplemented with heterozygous rams when necessary. Under severe selection, only homozygous rams were used. Severe selection mimics then the proposed eradication programme. Simulations were carried out with allelic frequencies and population parameters of existent rare breeds in The Netherlands. With severe selection all simulated breeds showed unacceptably high inbreeding rates (> 0·5% per year). For some breeds, moderate selection resulted in acceptable inbreeding rates, while for other breeds only mild selection resulted in acceptable rates. The frequency of the ARR allele after 5 years of selection was only slightly lower with moderate selection than with severe selection (0·8% lower on average), but it was clearly lower with mild selection. Based on these simulations, we propose a selection programme where with low frequencies of the ARR allele, mild selection is used initially. Once the ARR frequencies rise to a particular value, the switch can be made to moderate selection. The population size (e.g. below 750, 750 to 3750 and above 3750 ewes) determines the frequency of the ARR allele at which the switch can be made (33%, 25% and 10%, respectively). With even higher ARR frequencies (above 70%, 50% and 33%, respectively) the regime can be changed to severe selection.

Expanding possibilities for intervention against small ruminant lentiviruses through genetic marker-assisted selective breeding

Small ruminant lentiviruses include members that infect sheep (ovine lentivirus [OvLV]; also known as ovine progressive pneumonia virus/maedi-visna virus) and goats (caprine arthritis encephalitis virus [CAEV]). Breed differences in seroprevalence and proviral concentration of OvLV had suggested a strong genetic component in susceptibility to infection by OvLV in sheep. A genetic marker test for susceptibility to OvLV has been developed recently based on the TMEM154 gene with validation data from over 2,800 sheep representing nine cohorts. While no single genotype has been shown to have complete resistance to OvLV, consistent association in thousands of sheep from multiple breeds and management conditions highlight a new strategy for intervention by selective breeding. This genetic marker-assisted selection (MAS) has the potential to be a useful addition to existing viral control measures. Further, the discovery of multiple additional genomic regions associated with susceptibility to or control of OvLV suggests that additional genetic marker tests may be developed to extend the reach of MAS in the future. This review will cover the strengths and limitations of existing data from host genetics as an intervention and outline additional questions for future genetic research in sheep, goats, small ruminant lentiviruses, and their host-pathogen interactions.

Genetic variability of PRNP in Chinese indigenous goats

Polymorphism of the prion protein gene (PRNP) is usually associated with scrapie susceptibility or resistance. To determine the variability of PRNP in Chinese indigenous goat breeds, we isolated genomic DNA from goat blood and amplified and sequenced the coding region of the gene. We identified 10 polymorphic sites that gave rise to 28 haplotypes. Clear frequency differences were found between northern and southern breeds and confirmed by genetic distance analysis, except for the Tangshan dairy goat. Phylogeographic analysis supported the idea that northern and southern breeds might be considered separate clusters, except for the Tangshan dairy goat. The finding of significant differences in allele distribution in northern and southern goats, especially if involved in modulating resistance/susceptibility, needs to be carefully considered for the feasibility of selection plans for resistance to scrapie.

Expression patterns of prion protein gene in differential genotypes sheep: quantification using molecular beacon real-time RT-PCR

Determination of the transcription level of cellular prion protein (PrP(C)) is essential for understanding its role in organisms and revealing mechanism of susceptibility and resistance to scrapie. However, the expression of prion protein (PrP) mRNA in sheep has not been quantified in great detail in digestive tract which is important during scrapie spread through oral route. Herein, we report on measurement of sheep PrP mRNA using absolute quantitative real-time RT-PCR. Total RNA was isolated from five different regions of the central nervous system (CNS), four regions of lymphoid system, eleven regions of digestive tract, and two reproductive organ tissues of eight sheep of two different genotypes (ARR/ARQ and ARH/ARQ) and PrP mRNA was quantified by real-time RT-PCR using molecular beacon. The results showed that highest levels of PrP mRNA were expressed in thalamus and cerebrum (P < 0.01) of CNS examined, followed by cerebellum, spinal cord, and brain stem. In peripheral organs examined, lymph tissue showed moderate level of PrP expression similar to that in digestive tract and reproduction organs. PrP expression levels in the same tissue of different genotype sheep had significant variation. Our study provided the first detail, tissue-specific and genotype-specific data of PrP mRNA expression in sheep for further studies of pathogenesis of prion diseases.

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.

PrP genetics in ruminant transmissible spongiform encephalopathies

Scrapie, bovine spongiform encephalopathy (BSE), and chronic wasting disease (CWD) are prion diseases in ruminants with considerable impact on animal health and welfare. They can also pose a risk to human health and control is therefore an important issue. Prion protein (PrP) genetics may be used to control and eventually eradicate animal prion diseases. The PrP gene in sheep and other representatives of the order Artiodactyles has many polymorphisms of which several are crucial determinants of susceptibility to prion diseases, also known as transmissible spongiform encephalopathies (TSE). This review will present the current understanding of PrP genetics in ruminants highlighting similarity and difference between the species in the context of TSE.

Genetic variability of the PRNP gene in goat breeds from Northern and Southern Italy

AIMS

To determine the variability of the prion protein gene (PRNP) in goats from Northern and Southern Italy.

METHODS AND RESULTS

Genomic DNA isolated from goat blood was polymerase chain reaction (PCR)-amplified for the coding region of the PRNP gene and then sequenced. In total, 13 polymorphic sites were identified: G37V, T110P, G127S, M137I, I142M, I142T, H143R, R154H, P168Q, T194P, R211Q, Q222K and S240P (substitutions I142T and T194P are novel) giving rise to 14 haplotypes. Clear frequency differences between Northern and Southern breeds were found and confirmed by genetic distance analysis.

CONCLUSIONS

Differences in allele distribution were found between Northern and Southern goats, in particular regarding the M142 and K222 alleles, possibly associated to scrapie resistance; philogeographical analysis supported the idea that Northern and Southern breeds may be considered as separate clusters.

SIGNIFICANCE AND IMPACT OF THE STUDY

In Italy only limited studies have been carried out on caprine PRNP genotype distribution; this study is important to fill this lack of information. Moreover the finding of significant differences among allele distributions in Northern and Southern goats, especially if involved in modulating resistance/susceptibility, need to be carefully considered for the feasibility of selection plans for resistance to scrapie.

Advanced survival models for risk-factor analysis in scrapie

Because of the confounding effects of long incubation duration and flock management, accurate epidemiological studies of scrapie outbreaks are difficult to carry out. In this study, 641 Manech red-faced sheep from six scrapie-affected field flocks in Pyrénées Atlantiques, France, were monitored for clinical scrapie over a 6–9 year period. Over this period, 170 scrapie clinical cases were recorded and half of the culled animals were submitted for post-mortem transmissible spongiform encephalopathy diagnosis to assess their infectious status. Collected data were analysed using a ‘mixture cure model’ approach, which allowed for the discriminating effect of PrP genotype and flock origin on incidence and incubation period. Simulations were performed to evaluate the applicability of such a statistical model to the collected data. As expected, ARR heterozygote sheep were less at risk of becoming infected than ARQ/ARQ individuals and had a greater age at clinical onset. Conversely, when compared with ARQ/ARQ, the VRQ haplotype was associated with an increased infection risk, but not a shorter incubation period. Considering the flock effect, we observed that a high incidence rate was not associated with shorter incubation periods and that the incubation period could be significantly different in flocks harbouring similar infection risks. These results strongly support the conclusion that other parameters, such as the nature of the agent or flock management, could interfere with epidemiological dynamics of the infection in scrapie-affected flocks.

Assessment of clinical criteria to diagnose scrapie in Italy

A reliable ante-mortem test for the detection of scrapie in all genotypes has not yet been developed and clinical diagnosis remains a useful tool for surveillance purposes. This paper describes the results of a three-year study in which clinical signs consistent with scrapie were recorded according to standardized criteria in 245 sheep from 21 outbreaks in Italy in order to identify helpful criteria for the diagnosis of the disease. Thirty-seven sheep were scrapie-positive at post-mortem rapid testing, 23 showed weight loss, 20 had proprioceptive deficits, 17 demonstrated ataxia and nibble reflex, and some sheep had a combination of signs. Six scrapie-positive sheep were asymptomatic. The clinical protocol was easy to handle and appears to be a useful tool for improving passive surveillance. The data suggested that positive clinical history, nibble, and nibble combined with proprioceptive positioning deficit have a quite high negative predictive value. The protocol will be proposed as a tool for field inspection in passive surveillance in Italy.

Prion protein gene (PRNP) polymorphisms in Xinjiang local sheep breeds in China

Amino acid polymorphisms of the prion protein (PrP) gene (PRNP), particularly those occurring at codons 136, 154, and 171 have a significant influence on scrapie pathogenesis in many sheep breeds. We isolated blood samples from 222 sheep representing the eight main local sheep breeds in the Xinjiang Autonomous Region, the territory with the most abundant local sheep breeds in China, to identify the PRNP polymorphisms and to determine whether these breeds were at risk for developing scrapie. A new PRNP polymorphism encoding either glycine (G) or arginine (R) at codon 85 as well as eight previously reported polymorphisms at codons 101, 112, 127, 141, 146, 154, 171, and 189 in other sheep breeds were detected. Interestingly, the alanine (A)/V polymorphism at codon 136 was not observed in this study, all sheep being homozygous for A at this position. While the previously identified polymorphism of argine (R) or histidine (H) at codon 154 was detected, the H polymorphism was rare (2.25%). Four polymorphisms at codon 171 encoding glutamine (Q), R, H, or lysine (K) were detected. The predominant ARQ allele occurred at a high frequency of 77.48%, suggesting an increased risk of scrapie in Xinjiang Autonomous Region.

Immunohistochemical studies of scrapie archival material from Irish ARQ/ARQ sheep for evidence of bovine spongiform encephalopathy-derived disease

Since scrapie and bovine spongiform encephalopathy (BSE) in sheep are clinicopathologically indistinguishable, BSE in sheep may have been misdiagnosed as scrapie. Disease-specific prion protein (PrP(d)) patterns in archival tissues of 38 Irish ARQ/ARQ sheep diagnosed as scrapie-affected were compared to those in four Dutch BSE-challenged sheep. When medulla oblongata was immunolabelled with an antibody directed against amino acids 93-99 of ovine prion protein (ovPrP), intraneuronal PrP(d) was apparent in all 38 Irish sheep but was absent in BSE-challenged sheep. When lymphoid follicles were immunolabelled with antibodies directed against amino acids 93-106 of ovPrP, granule clusters of PrP(d) were seen in 34 of the 38 Irish sheep. Follicles of the remaining four archive sheep contained either no PrP(d) or single PrP(d) granules, similar to follicles from BSE-challenged sheep. Based on the medulla results, none of the archival cases had BSE-derived disease. The identification of some scrapie sheep with little or no intrafollicular PrP(d) suggests that this technique may be limited in discriminating between the two diseases.

Diagnosis and PrP genotype target of scrapie in clinically healthy sheep of Massese breed in the framework of a scrapie eradication programme

The application of a selective culling programme in two scrapie affected flocks of Massese breed sheep is described. The genetic susceptibility of this breed and the sensitivity of different diagnostic methods in the pre-clinical diagnosis of scrapie were also investigated. Overall, 2,068 clinically healthy sheep underwent PrP genotyping, providing the basis for selective culling. The prevalence of scrapie infection was investigated in susceptible sheep by two independent diagnostic methods. All the sheep older than 18 months (n = 620) were tested by Prionics Check Western rapid test on the obex, with a prevalence of infection of 3.9%. Furthermore, 385 sheep underwent immunohistochemistry (IHC) on retropharyngeal lymph node (RPLN), with a prevalence of infection of 5.2%. Overall, 32 sheep were diagnosed with pre-clinical scrapie. Of these, 31 were positive by Western blot on the spleen, 29 by IHC on the RPLN and tonsil, 28 by IHC on the obex, 24 by rapid test, and only 18 by IHC on the third eyelid. All the scrapie positive sheep were of the ARQ/ARQ, ARQ/AHQ or ARQ/VRQ genotypes. No significant differences in scrapie prevalence were observed among these genotypes. The estimated risk of the three targeted alleles was also similar, suggesting that in this breed the VRQ allele was not at higher risk for scrapie, compared to the ARQ and AHQ alleles.

Polymorphisms at codons 141 and 154 in the ovine prion protein gene are associated with scrapie Nor98 cases

Until June 2004, thirty-eight scrapie cases with unusual features, designated Nor98, have been diagnosed in Norway. This study investigated the distribution of PrP genotypes among Nor98 cases, their flock-mates and a random sample of Norwegian slaughtered sheep. The PrP genotype distribution of Nor98 cases differed markedly from that of previous cases of classical scrapie. A leucine/phenylalanine polymorphism at codon 141 with hitherto unknown significance to scrapie was strongly associated with Nor98 cases. Twenty of 38 (52.6 %) cases were either homozygous or heterozygous for phenylalanine at codon 141. In contrast, this allele was present in only 10.5 % of the flock-mates and 4.5 % of the random sample of slaughtered sheep. Moreover, the H(154) allele was represented in 24 of 38 (63.2 %) of Nor98 cases, as opposed to 27.0 % of Nor98 flock-mates and 17.0 % of the slaughtered sheep.

Risk of scrapie in British sheep of different prion protein genotype

There is a well-established association between sheep prion protein (PrP) genotype and the risk of death from scrapie. Certain genotypes are clearly associated with susceptibility to the disease and others to resistance. However, there have been no attempts to quantify the disease risk for all 15 PrP genotypes. Here, datasets of the PrP genotypes of nearly 14 000 British sheep and of more than 1500 confirmed scrapie cases were combined to yield an estimate of scrapie risk (reported cases per annum per million sheep of the genotype, or RCAM) for British sheep. The greatest scrapie risk by far, ranging from 225 to 545 RCAM, was for the VRQ-encoding genotypes ARQ/VRQ, ARH/VRQ and VRQ/VRQ. The next greatest risk (37 RCAM) was for the ARQ/ARQ genotype. The ARR/ARR genotype was the only numerically significant genotype for which no scrapie cases have been reported. The AHQ allele conferred resistance and the risk of scrapie in AHQ/VRQ sheep was very low (0·7 RCAM), although there was a higher and moderate risk for the AHQ homozygote (5 RCAM). The ARH allele appeared to confer susceptibility when encoded with VRQ, but possible resistance when encoded with other alleles. Scrapie risk varied with age: for VRQ/VRQ and ARH/VRQ the risk peaked at 2 years of age; that for ARQ/VRQ peaked at 3 years. There was some evidence that, following the lower risk at 4 and 5 years, a second rise occurred from about 6 years. Comparison with other published data indicated that the scrapie risk of certain PrP genotypes may differ between Great Britain and other countries.

The Clinical Neurology of Scrapie in Irish Sheep

One hundred twenty-nine sheep with scrapie were identified from 20 flocks in which scrapie previously had been confirmed. Physical and neurologic examinations were performed on all animals. Videotape recordings were made and reviewed to assess gait. These procedures were repeated in 46 sheep at 2- to 3-week intervals until recumbency or inappetence necessitated euthanasia. Confirmation of scrapie was made by histopathologic and immunohistochemical examinations of brain tissue. The clinical signs most frequently recorded in the 129 animals on initial presentation were hindlimb ataxia (71%), head tremor (61%), altered mental status (57%), positive nibble reflex (51%), crouching posture (51%), teeth grinding (44%), low head carriage (38%), body condition score (BCS) < 1.5 (38%), and conscious proprioceptive deficits of the hindlimbs (36%). Progression of the disease was characterized by an increase in the frequency and severity of ataxia, weakness and hypermetria of the hindlimbs, a decreasing sway response, a decreasing extensor response to thoracolumbar pressure, and a reduction in the BCS. No effect of farm of origin on the clinical presentation could be shown. The presence of a nibble reflex was strongly associated (P < .0005) with prion protein (PrP) genotypes AA136RR154QH171 and AA136RR154QQ171. Logistic regression modeling of groups with associated clinical signs showed that animals with a crouching posture (odds ratio [OR], 20.036) and an abnormal yield to thoracolumbar pressure (OR, 7.117) were at increased risk of ataxia. Pruritus (OR, 0.168) was negatively associated with ataxia. Pruritus (OR, 4.974) and teeth grinding (OR, 4.279) were associated with a positive nibble reflex.

Cases of scrapie with unusual features in Norway and designation of a new type, Nor98

Five cases of scrapie with unusual features have been diagnosed in Norway since 1998. The affected sheep showed neurological signs dominated by ataxia, and had the PrP genotypes homozygous A136 H154 Q171/ A136H154Q171 or heterozygous A136H154Q171/A136R154Q171, which are rarely associated with scrapie. Brain histopathology revealed neuropil vacuolisation essentially in the cerebellar and cerebral cortices; vacuolation was less prominent in the brainstem, and no lesions were observed at the level of the obex. The deposits of PrPSc were mainly in the cortex of the cerebellum and cerebrum, and no PrPSC was detectable by immunohistochemistry and ELISA in the lymphoid tissues investigated. Western blot analysis showed that the glycotype was different from other known scrapie strains and from the BSE strain. From a diagnostic point of view, these features indicate that this type of scrapie, designated Nor98, could have been overlooked and may be of significance for sampling in scrapie surveillance programmes.