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

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

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

Atypical scrapie in sheep from a UK research flock which is free from classical scrapie

Background: In the wake of the epidemic of bovine spongiform encephalopathy the British government established a flock of sheep from which scrapie-free animals are supplied to laboratories for research. Three breeds of sheep carrying a variety of different genotypes associated with scrapie susceptibility/resistance were imported in 1998 and 2001 from New Zealand, a country regarded as free from scrapie. They are kept in a purpose-built Sheep Unit under strict disease security and are monitored clinically and post mortem for evidence of scrapie. It is emphasised that atypical scrapie, as distinct from classical scrapie, has been recognised only relatively recently and differs from classical scrapie in its clinical, neuropathological and biochemical features. Most cases are detected in apparently healthy sheep by post mortem examination.Results: The occurrence of atypical scrapie in three sheep in (or derived from) the Sheep Unit is reported. Significant features of the affected sheep included their relatively high ages (6 y 1 mo, 7 y 9 mo, 9 y 7 mo respectively), their breed (all Cheviots) and their similar PRNP genotypes (AFRQ/AFRQ, AFRQ/ALRQ, and AFRQ/AFRQ, respectively). Two of the three sheep showed no clinical signs prior to death but all were confirmed as having atypical scrapie by immunohistochemistry and Western immunoblotting. Results of epidemiological investigations are presented and possible aetiologies of the cases are discussed.Conclusion: By process of exclusion, a likely explanation for the three cases of atypical scrapie is that they arose spontaneously and were not infected from an exterior source. If correct, this raises challenging issues for countries which are currently regarded as free from scrapie. It would mean that atypical scrapie is liable to occur in flocks worldwide, especially in older sheep of susceptible genotypes. To state confidently that both the classical and atypical forms of scrapie are absent from a population it is necessary for active surveillance to have taken place

A review of cleaning and disinfection guidelines and recommendations following an outbreak of classical scrapie

[EN] Classical scrapie is a prion disease of small ruminants, the infectious agent of which has been shown to be extremely persistent in the environment. Cleaning and disinfection (C&D) after a scrapie outbreak is currently recommended by many governments' veterinary advisors and implemented in most farms affected. Yet, the effectiveness of these procedures remains unclear. The aim of this study was to review existing literature and guidelines regarding farm C&D protocols following classical scrapie outbreaks and assess their effectiveness and the challenges that translation of policy and legislative requirements present at a practical level. A review of the literature was conducted to identify the on-farm C&D protocols used following outbreaks of scrapie, assess those materials with high risk for persistence of the scrapie agent on farms, and review the existing evidence of the effectiveness of recommended C&D protocols. An expert workshop was also organised in Great Britain (GB) to assess: the decision-making process used when implementing C&D protocols on GB farms, the experts' perceptions on the effectiveness of these protocols and changes needed, and their views on potential recommendations for policy and research. Outputs of the literature review revealed that the current recommended protocol for C&D [1 h treatment with sodium hypochlorite containing 20,000 ppm free chlorine or 2 M sodium hydroxide (NaOH)] is based on labo-ratory experiments. Only four field farm experiments have been conducted, indicating a lack of data on effec-tiveness of C&D protocols on farms by the re-occurrence of scrapie infection post re-stocking. Recommendations related to the control of outdoor environment, which are difficult and expensive to implement, vary between countries. The expert workshop concluded that there are no practical, cost-effective C&D alternatives to be considered at this time, with control therefore based on C&D only in combination with additional time restrictions on re-stocking and replacement with non-susceptible livestock or more genetically resistant types, where available. Participants agreed that C&D should still be completed on scrapie affected farms, as it is considered to be "good disease practice" and likely to reduce the levels of the prion protein. Participants felt that any additional protocols developed should not be "too prescriptive" (should not be written down in specific policies) because of significant variation in farm types, farm equipment and installations. Under this scenario, control of classical scrapie on farms should be designed with a level of C&D in combination with re-stocking temporal ban and replacement with livestock of limited susceptibility.The APHA would like to thank all the expert contributions at the workshop. This study was funded by Defra (UK) under Project SE1960 and the Government of education and science of the Generalitat Valenciana (Spain)Alarcon, P.; Marco-Jiménez, F.; Horigan, V.; Ortiz-Pelaez, A.; Rajanayagam, B.; Dryden, A.; Simmons, H.... (2021). A review of cleaning and disinfection guidelines and recommendations following an outbreak of classical scrapie. Preventive Veterinary Medicine. 193:1-9. https://doi.org/10.1016/j.prevetmed.2021.1053881919

Evaluation of a multi-step catalytic co-processing hydrotreatment for the production of renewable fuels using Category 3 animal fat and used cooking oils

An alternative method for the production of renewable fuels from rendered animal fats (pretreated using methods 1–5 or method 7 as described in Annex IV of Commission Regulation (EC) No 2011/142) and used cooking oils, derived from Category 3 animal by-products, was assessed. The method is based on a catalytic co-processing hydrotreatment using a middle distillate followed by a stripping step. The materials must be submitted to a pressure of at least 60 bars and a temperature of at least 270°C for at least 4.7 min. The application focuses on the demonstration of the level of reduction of spores from non-pathogenic spore-forming indicator bacterial species (Bacillus subtilis and Desulfotomaculum kuznetsovii), based on a non-systematic review of published data and additional extrapolation analyses. The EFSA BIOHAZ Panel considers that the application and supporting literature contain sufficient evidence that the proposed alternative method can achieve a reduction of at least 5 log10 in the spores of B. subtilis and a 12 log10 reduction in the spores of C. botulinum. The alternative method under evaluation is considered at least equivalent to the processing methods currently approved in the Commission Regulation (EU) No 2011/142.info:eu-repo/semantics/publishedVersio

Potential BSE risk posed by the use of ruminant collagen and gelatine in feed for non‐ruminant farmed animals

EFSA was requested to estimate the cattle bovine spongiform encephalopathy (BSE) risk (C‐, L‐ and H‐BSE) posed by ruminant collagen and gelatine produced from raw material fit for human consumption, or from material classified as Category 3 animal by‐products (ABP), to be used in feed intended for non‐ruminant animals, including aquaculture animals. Three risk pathways (RP) were identified by which cattle could be exposed to ruminant feed cross‐contaminated with ruminant collagen or gelatine: 1) recycled former foodstuffs produced in accordance with Regulation (EC) No 853/2004 (RP1), 2) technological or nutritional additives or 3) compound feed, produced either in accordance with Regulation (EC) No 853/2004 (RP2a) or Regulation (EU) No 142/2011 (RP2b). A probabilistic model was developed to estimate the BSE infectivity load measured in cattle oral ID50 (CoID50)/kg, in the gelatine produced from the bones and hide of one infected animal older than 30 months with clinical BSE (worst‐case scenario). The amount of BSE infectivity (50th percentile estimate) in a member state (MS) with negligible risk status was 7.6 × 10–2 CoID50/kg, and 3.1 × 10–4 CoID50/kg in a MS with controlled risk status. The assessment considered the potential contamination pathways and the model results (including uncertainties) regarding the current epidemiological situation in the EU and current statutory controls. Given the estimated amount of BSE infectivity to which cattle would be exposed in a single year, and even if all the estimated undetected BSE cases in the EU were used for the production of collagen or gelatine (either using raw materials fit for human consumption or Category 3 ABP raw materials), it was concluded that the probability that no new case of BSE in the cattle population would be generated through any of the three RP is 99–100% (almost certain).info:eu-repo/semantics/publishedVersio

Inactivation of indicator microorganisms and biological hazards by standard and/or alternative processing methods in Category 2 and 3 animal by-products and derived products to be used as organic fertilisers and/or soil improvers

The European Commission requested EFSA to assess if different thermal processes achieve a 5 log10 reduction in Enterococcus faecalis or Salmonella Senftenberg (775W) and (if relevant) a 3 log10 reduction in thermoresistant viruses (e.g. Parvovirus) as well as if different chemical processes achieve a 3 log10 reduction of eggs of Ascaris sp., in eight groups of Category 2 and 3 derived products and animal by-products (ABP). These included (1) ash derived from incineration, co-incineration and combustion; (2) glycerine derived from the production of biodiesel and renewable fuels; (3) other materials derived from the production of biodiesel and renewable fuels; (4) hides and skins; (5) wool and hair; (6) feathers and down; (7) pig bristles; and (8) horns, horn products, hooves and hoof products. Data on the presence of viral hazards and on thermal and chemical inactivation of the targeted indicator microorganisms and biological hazards under relevant processing conditions were extracted via extensive literature searches. The evidence was assessed via expert knowledge elicitation. The certainty that the required log10 reductions in the most resistant indicator microorganisms or biological hazards will be achieved for each of the eight groups of materials mentioned above by the thermal and/or chemical processes was (1) 99–100% for the two processes assessed; (2) 98–100% in Category 2 ABP, at least 90–99% in Category 3 ABP; (3) 90–99% in Category 2 ABP; at least 66–90% in Category 3 ABP; (4) 10–66% and 33–66%; (5) 1–33% and 10–50%; (6) 66–90%; (7) 33–66% and 50–95%; (8) 66–95%, respectively. Data generation on the occurrence and reduction of biological hazards by thermal and/or chemical methods in these materials and on the characterisation of the usage pathways of ABP as organic fertilisers/soil improvers is recommended

Monitoring of chronic wasting disease (CWD) (IV)

The European Commission requested an analysis of the Chronic Wasting Disease (CWD) monitoring programme in Norway, Sweden, Finland, Iceland, Estonia, Latvia, Lithuania and Poland (9 January 2017–28 February 2022). Thirteen cases were detected in reindeer, 15 in moose and 3 in red deer. They showed two phenotypes, distinguished by the presence or absence of detectable disease-associated normal cellular prion protein (PrP) in lymphoreticular tissues. CWD was detected for the first time in Finland, Sweden and in other areas of Norway. In countries where the disease was not detected, the evidence was insufficient to rule out its presence altogether. Where cases were detected, the prevalence was below 1%. The data also suggest that the high-risk target groups for surveillance should be revised, and ‘road kill’ removed. Data show that, in addition to differences in age and sex, there are differences in the prion protein gene (PRNP) genotypes between positive and negative wild reindeer. A stepwise framework has been proposed with expanded minimum background surveillance to be implemented in European countries with relevant cervid species. Additional surveillance may include ad hoc surveys for four different objectives, specific to countries with/without cases, focusing on parallel testing of obex and lymph nodes from adult cervids in high-risk target groups, sustained over time, using sampling units and a data-driven design prevalence. Criteria for assessing the probability of CWD presence have been outlined, based on the definition of the geographical area, an annual assessment of risk of introduction, sustained minimum background surveillance, training and engagement of stakeholders and a surveillance programme based on data-driven parameters. All positive cases should be genotyped. Sample sizes for negative samples have been proposed to detect and estimate the frequency of PRNP polymorphisms. Double-strand sequencing of the entire PRNP open reading frame should be undertaken for all selected samples, with data collated in a centralised collection system at EU level.info:eu-repo/semantics/publishedVersio

Can Geographical Factors Determine the Choices of Farmers in the Ethiopian Highlands to Trade in Livestock Markets?

Proximity and affiliation to the local market appear to be two of the most relevant factors to explain farmer's choices to select a particular trading point. Physical barriers may limit the options , especially in developing countries. A network of villages linked by traders/farmer-traders sharing livestock markets was built with field data collected in 75 villages from 8 kebelles in the Wassona Werna wereda of the Ethiopian Highlands. Two exponential random graph models were fitted with various geographical and demographic attributes of the nodes (dyadic independent model) and three internal network structures (dyadic dependent model). Several diagnostic methods were applied to assess the goodness of fit of the models. The odds of an edge where the distance to the main market Debre Behran and the difference in altitude between two connected villages are both large increases significantly so that villages far away from the main market and at different altitude are more likely to be linked in the network than randomly. The odds of forming an edge between two villages in Abamote or Gudoberet kebelles are approximately 75% lower than an edge between villages in any other kebelles (p<0.05). The conditional log-odds of two villages forming a tie that is not included in a triangle, a 2-star or a 3-star is extremely low, increasing the odds significantly (p<0.05) each time a node is in a 2-star structure and decreasing it when a node is in a 3-star (p<0.05) or in a triangle formation (p<0.05)), conditional on the rest of the network. Two major constraining factors, namely distance and altitude, are not deterrent for the potential contact of susceptible small ruminant populations in the Highlands of Ethiopia