Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Sequence diversity of CV777 PEDV strains
Rasmussen, Thomas Bruun ; Boniotti, Maria Beatrice ; Papetti, Alice ; Grasland, Béatrice ; Frossard, Jean Pierre ; Dastjerdi, Akbar ; Hulst, M.M. ; Hanke, Dennis ; Pohlmann, Anne ; Blome, Sandra ; Poel, W.H.M. van der; Steinbach, Falko ; Blanchard, Yannick ; Lavazza, Antonio ; Bøtner, Anette ; Belsham, Graham J. - \ 2018
PRJEB20818 - ERP023004
Full-length genome sequences of porcine epidemic diarrhoea virus strain CV777; use of NGS to analyse genomic and sub-genomic RNAs
Rasmussen, Thomas Bruun ; Boniotti, Maria Beatrice ; Papetti, Alice ; Grasland, Béatrice ; Frossard, Jean Pierre ; Dastjerdi, Akbar ; Hulst, Marcel ; Hanke, Dennis ; Pohlmann, Anne ; Blome, Sandra ; Poel, Wim H.M. Van Der; Steinbach, Falko ; Blanchard, Yannick ; Lavazza, Antonio ; Bøtner, Anette ; Belsham, Graham J. - \ 2018
PLoS One 13 (2018)3. - ISSN 1932-6203
Porcine epidemic diarrhoea virus, strain CV777, was initially characterized in 1978 as the causative agent of a disease first identified in the UK in 1971. This coronavirus has been widely distributed among laboratories and has been passaged both within pigs and in cell culture. To determine the variability between different stocks of the PEDV strain CV777, sequencing of the full-length genome (ca. 28kb) has been performed in 6 different laboratories, using different protocols. Not surprisingly, each of the different full genome sequences were distinct from each other and from the reference sequence (Accession number AF353511) but they are >99% identical. Unique and shared differences between sequences were identified. The coding region for the surface-exposed spike protein showed the highest proportion of variability including both point mutations and small deletions. The predicted expression of the ORF3 gene product was more dramatically affected in three different variants of this virus through either loss of the initiation codon or gain of a premature termination codon. The genome of one isolate had a substantially rearranged 5´-terminal sequence. This rearrangement was validated through the analysis of sub-genomic mRNAs from infected cells. It is clearly important to know the features of the specific sample of CV777 being used for experimental studies.
Inter-laboratory study to characterize the detection of serum antibodies against porcine epidemic diarrhoea virus
Strandbygaard, Bertel ; Lavazza, Antonio ; Lelli, Davide ; Blanchard, Yannick ; Grasland, Béatrice ; Poder, Sophie Le ; Rose, Nicolas ; Steinbach, Falko ; Poel, Wim H.M. van der; Widén, Frederik ; Belsham, Graham J. ; Bøtner, Anette - \ 2016
Veterinary Microbiology 197 (2016). - ISSN 0378-1135 - p. 151 - 160.
ELISA - PEDV - Porcine coronavirus - Ring trial - Serology

Porcine epidemic diarrhea virus (PEDV) has caused extensive economic losses to pig producers in many countries. It was recently introduced, for the first time, into North America and outbreaks have occurred again in multiple countries within Europe as well. To assess the properties of various diagnostic assays for the detection of PEDV infection, multiple panels of porcine sera have been shared and tested for the presence of antibodies against PEDV in an inter-laboratory ring trial. Different laboratories have used a variety of “in house” ELISAs and also one commercial assay. The sensitivity and specificity of each assay has been estimated using a Bayesian analysis applied to the ring trial results obtained with the different assays in the absence of a gold standard. Although different characteristics were found, it can be concluded that each of the assays used can detect infection of pigs at a herd level by either the early European strains of PEDV or the recently circulating strains (INDEL and non-INDEL). However, not all the assays seem suitable for demonstrating freedom from disease in a country. The results from individual animals, especially when the infection has occurred within an experimental situation, show more variation.

Limited interlaboratory comparison of Schmallenberg virus antibody detection in serum samples.
Poel, W.H.M. van der; Cay, B. ; Zientara, S. ; Steinbach, F. ; Valarcher, J.F. ; Botner, A. ; Mars, M.H. ; Hakze-van der Honing, R.W. van der; Schirrmeier, H. ; Beer, M. - \ 2014
Veterinary Record 174 (2014). - ISSN 0042-4900 - 3 p.
Eight veterinary institutes in seven different countries in Europe participated in a limited interlaboratory comparison trial to evaluate laboratory performances of Schmallenberg virus (SBV) antibody detection in serum. Seven different sheep sera and three different cattle sera were circulated, and all participating institutes were asked to test these sera using SBV antibody detection assay(s) in place in their laboratories. All laboratories within the trial performed a virus neutralisation test (VNT) as well as one or two ELISAs on all samples, and swiftly detected SBV antibodies using these assays. VNT was more sensitive in detecting SBV antibodies than several of the used ELISA assays. Based on the test results, one cattle and one sheep SBV antibody-positive serum were selected to serve as reference sera, which now can be supplied to other laboratories on request.
Scientific Opinion concerning a Multifactorial approach on the use of animal and non-animal-based measures to assess the welfare of pigs
Authie, E. ; Berg, C. ; Bøtner, A. ; Browman, H. ; Capua, I. ; Koeijer, A.A. de; Depner, K. ; Domingo, M. ; Edwards, S. ; Fourichon, C. ; Koenen, F. ; More, S. ; Raj, M.A.B. ; Sihvonen, L. ; Spoolder, H.A.M. ; Stegeman, J.A. ; Thulke, H.H. ; Vågsholm, I. ; Velarde, A. ; Willeberg, P. ; Zientara, S. - \ 2014
EFSA Journal 12 (2014)5. - 101 p.
Pigs have a need for manipulable materials to satisfy a range of behavioural needs, which can be different in different classes of pig. When these needs are not met, a range of adverse welfare consequences result, one of these being an increased risk for tail-biting in weaners and rearing pigs. The ability to control the risk of tail- biting is essential when aiming to avoid tail-docking. Based on available scientific information this Opinion identifies the multiple interactions between risk factors, welfare consequences and animal and non-animal-based measures on the two subjects requested (i) the absence of functional manipulable materials, for pigs at different stages in life and (ii) tail-biting, for weaners and rearing pigs only. An attempt is made to quantify the relationships between the identified interactions by carrying out a statistical analysis of information from available databases, those being an international dataset collected using the Welfare Quality® protocol, which was not designed to evaluate risk factors for tail-biting and therefore, it had limitations in fitness for this analysis, and a large Finnish dataset with undocked pigs. Based on the current state of knowledge, the AHAW Panel proposes two simple tool-boxes for on farm use to assess (i) the functionality of the supplied manipulable material and (ii) the presence and strength of risk factors for tail biting. Both proposed tool-boxes include a combination of the most important resource-based and animal-based measures. Further development and validation of decision–support tools for customised farm assessment is strongly recommended and a proposal for harmonised data collection across the range of European farming circumstances is presented. A series of further recommendations are made by the AHAW Panel.
Scientific Opinion on the use of low atmosphere pressure system (LAPS) for stunning poultry
Authie, E. ; Berg, C. ; Bøtner, A. ; Browman, H. ; Capua, I. ; Koeijer, A.A. de; Depner, K. ; Domingo, M. ; Edwards, S. ; Fourichon, C. ; Koenen, F. ; More, S. ; Raj, M.A.B. ; Sihvonen, L. ; Spoolder, H.A.M. ; Stegeman, J.A. ; Thulke, H.H. ; Vågsholm, I. ; Velarde, A. ; Willeberg, P. ; Zientara, S. - \ 2014
EFSA Journal 12 (2014)1. - 27 p.
The EFSA's Panel on Animal Health and Welfare (AHAW Panel) was asked to deliver a scientific opinion on the use of a low atmosphere pressure system (LAPS) for stunning poultry. Four documents were provided by the European Commission (EC) as the basis for an assessment of the extent to which the LAPS is able to provide a level of animal welfare at least equivalent to that ensured by the current allowed methods for stunning poultry. The LAPS is described as rendering poultry unconscious by gradually reducing oxygen tension in the atmosphere leading to progressive hypoxia in the birds. In order to be allowed in the EU, new stunning methods must ensure 1) absence of pain, distress and suffering until the onset of unconsciousness, and 2) that the animal remains unconscious until death. The submitted studies were peer-reviewed by the AHAW Panel as outlined in its “Guidance on the assessment criteria for studies evaluating the effectiveness of stunning intervention regarding animal protection at the time of killing”. It is unclear from the submitted documents whether the rate of decompression used in LAPS induces unconsciousness and death without causing avoidable pain and suffering in poultry. The assessed studies did not pass the eligibility assessment and, therefore, no further assessment was undertaken.
Scientific Opinion on monitoring procedures at slaughterhouses for sheep and goats
Authie, E. ; Berg, C. ; Bøtner, A. ; Browman, H. ; Capua, I. ; Koeijer, A.A. de; Depner, K. ; Domingo, M. ; Edwards, S. ; Fourichon, C. ; Koenen, F. ; More, S. ; Raj, M.A.B. ; Sihvonen, L. ; Spoolder, H.A.M. ; Stegeman, J.A. ; Thulke, H.H. ; Vågsholm, I. ; Velarde, A. ; Willeberg, P. ; Zientara, S. - \ 2013
EFSA Journal 11 (2013)12. - 65 p.
This scientific opinion proposes toolboxes of welfare indicators for developing monitoring procedures at slaughterhouses for sheep and goats stunned with the head-only electrical method or slaughtered without stunning. In particular, the opinion proposes welfare indicators together with their corresponding outcomes of consciousness, unconsciousness or death. In the case of slaughter with head-only electrical stunning, the opinion proposes a toolbox to assess consciousness at three key stages of monitoring: (a) after electrical stunning and during shackling and hoisting, (b) during neck cutting and (c) during bleeding. For slaughter without stunning, another toolbox is proposed for (a) assessing unconsciousness before releasing the animals from restraint, and (b) confirming death before carcass dressing begins. Various activities—including a systematic literature review, an online survey and stakeholders‘ and hearing experts‘ meetings—were conducted to gather information about the sensitivity, specificity and feasibility of the indicators. On the basis of such information, a methodology was developed to select the most appropriate indicators to be used in the monitoring procedures. The frequency of checking differs according to the role of each person with responsibility for ensuring animal welfare. The personnel performing stunning, shackling, hoisting and/or bleeding will have to check all the animals and confirm that they are not conscious following stunning or before releasing from the restraint. For the animal welfare officer, who has the overall responsibility for animal welfare, a mathematical model for the sampling protocols is proposed, giving some allowance to set the sample size of animals to be checked at a given throughput rate (total number of animals slaughtered in the slaughterhouses) and threshold failure rate (number of potential failures—proportion of animals that are conscious after stunning). Finally, different risk factors and scenarios are proposed to define a =normal‘ or a =reinforced‘ monitoring protocol, according to the needs of the slaughterhouse.
Scientific Opinion on monitoring procedures at slaughterhouses for poultry
Authie, E. ; Berg, C. ; Bøtner, A. ; Browman, H. ; Capua, I. ; Koeijer, A.A. de; Depner, K. ; Domingo, M. ; Edwards, S. ; Fourichon, C. ; Koenen, F. ; More, S. ; Raj, M.A.B. ; Sihvonen, L. ; Spoolder, H.A.M. ; Stegeman, J.A. ; Thulke, H.H. ; Vågsholm, I. ; Velarde, A. ; Willeberg, P. ; Zientara, S. - \ 2013
EFSA Journal 11 (2013)12. - 65 p.
This scientific opinion proposes toolboxes of welfare indicators, and their corresponding outcomes of consciousness, unconsciousness or death, for developing monitoring procedures at slaughterhouses for poultry stunned using electrical waterbaths and gas mixtures or slaughtered without stunning. For waterbath stunning, the opinion proposes a toolbox of indicators for assessing consciousness in poultry at two key stages of monitoring: (a) between the exit from the waterbath stunner and neck cutting and (b) during bleeding. For gas stunning, the opinion proposes a toolbox of indicators for assessing consciousness in poultry at two key stages of monitoring: (a) during shackling and (b) during bleeding. For slaughter without stunning, a toolbox is proposed for confirming death prior to entering scald tanks. Various activities—including a systematic literature review, an online survey and stakeholders‘ and hearing experts‘ meetings—were conducted to gather information about the specificity, sensitivity and feasibility of the indicators. On the basis of such information, a methodology was developed to select the most appropriate indicators to be used in the monitoring procedures. The frequency of checking differs according to the role of each person with responsibility for ensuring poultry welfare. The personnel will have to check all the birds and confirm that they are not conscious following stunning with electrical waterbaths or gas mixtures and that they are dead before entering scald tanks. For the animal welfare officer, a mathematical model for the sampling protocols is proposed, giving some allowance to set the sample size of birds that he/she needs to check at a given throughput rate (total number of birds slaughtered in the slaughterhouses) and threshold failure rate (number of potential failures—birds that are conscious after stunning). Finally, different risk factors and scenarios are proposed to define a =normal‘ or a =reinforced‘ monitoring protocol, according to the needs of the slaughterhouse.
Scientific Opinion on monitoring procedures at slaughterhouses for pigs
Authie, E. ; Berg, C. ; Bøtner, A. ; Browman, H. ; Capua, I. ; Koeijer, A.A. de; Depner, K. ; Domingo, M. ; Edwards, S. ; Fourichon, C. ; Koenen, F. ; More, S. ; Raj, M.A.B. ; Sihvonen, L. ; Spoolder, H.A.M. ; Stegeman, J.A. ; Thulke, H.H. ; Vågsholm, I. ; Velarde, A. ; Willeberg, P. ; Zientara, S. - \ 2013
EFSA Journal 11 (2013)12. - 62 p.
This scientific opinion proposes toolboxes of welfare indicators for developing monitoring procedures at slaughterhouses for pigs stunned with the head-only electrical method or carbon dioxide at high concentration. In particular, the opinion proposes welfare indicators together with their corresponding outcomes of consciousness, unconsciousness or death. The opinion proposes a toolbox of indicators and the outcomes to be used to assess consciousness in pigs at three key stages of monitoring: (a) after stunning and during shackling and hoisting, (b) during sticking and (c) during bleeding. Various activities—including a systematic literature review, an online survey and stakeholders‘ and hearing experts‘ meetings—were conducted to gather information about specificity, sensitivity and feasibility of the indicators that are to be included in the toolboxes for monitoring welfare. On the basis of information gathered during these activities, a methodology was developed to select the most appropriate indicators that could be used in the monitoring procedures. The frequency of checking differs according to the role of each person with responsibility for ensuring animal welfare at slaughter. The personnel performing stunning, shackling, hoisting and/or bleeding will have to check all the animals and confirm that they are not conscious following stunning. For the animal welfare officer, who has the overall responsibility for animal welfare, a mathematical model for the sampling protocols is proposed, giving some allowance to set the sample size of animals that he/she needs to check at a given throughput rate (total number of animals slaughtered in the slaughterhouses) and tolerance level (number of potential failures—animals that are conscious after stunning; animals that are not unconscious or not dead after slaughter without stunning). The model can also be applied to estimate threshold failure rate at a chosen throughput rate and sample size. Finally, different risk factors and scenarios are proposed to define a =normal‘ or a =reinforced‘ monitoring protocol, according to the needs of the slaughterhouse.
Guidance on the assessment criteria for studies evaluating the effectiveness of stunning interventions regarding animal protection at the time of killing
Authie, E. ; Berg, C. ; Bøtner, A. ; Browman, H. ; Capua, I. ; Koeijer, A.A. de; Depner, K. ; Domingo, M. ; Edwards, S. ; Fourichon, C. ; Koenen, F. ; More, S. ; Raj, M.A.B. ; Sihvonen, L. ; Spoolder, H.A.M. ; Stegeman, J.A. ; Thulke, H.H. ; Vågsholm, I. ; Velarde, A. ; Willeberg, P. ; Zientara, S. - \ 2013
EFSA Journal 11 (2013)12. - 41 p.
This guidance defines the assessment process and the criteria that will be applied by the Animal Health and Welfare Panel to studies on known new or modified legal stunning interventions to determine their suitability for further assessment. The criteria that need to be fulfilled are eligibility criteria, reporting quality criteria and methodological quality criteria. The eligibility criteria are based upon the legislation and previously published scientific data. They focus on the intervention and the outcomes of interest, i.e. immediate onset of unconsciousness and insensibility or absence of avoidable pain, distress and suffering until the loss of consciousness and sensibility, and duration of the unconsciousness and insensibility (until death). If a study fulfils the eligibility criteria, it will be assessed regarding a set of reporting quality criteria that are based on the REFLECT and the STROBE statements. As a final step in this first assessment phase, the methodological quality of the submitted study will be assessed. If the criteria regarding eligibility, reporting quality and methodological quality are fulfilled, a full assessment of the animal welfare implications of the proposed alternative stunning intervention, including both pre-stunning and stunning phases, and an evaluation of the quality, strength and external validity of the evidence presented would be carried out at the next level of the assessment. In the case that the criteria regarding eligibility and reporting quality and methodological quality are not fulfilled, the assessment report of the panel will highlight the shortcomings and indicate where improvements are required before the study can be assessed further. In addition to the assessment criteria, the guidance also specifies general aspects applicable to studies on stunning interventions that should be considered when studying the effectiveness of stunning interventions.
Scientific Opinion on monitoring procedures at slaughterhouses for bovines
Authie, E. ; Berg, C. ; Bøtner, A. ; Browman, H. ; Capua, I. ; Koeijer, A.A. de; Depner, K. ; Domingo, M. ; Edwards, S. ; Fourichon, C. ; Koenen, F. ; More, S. ; Raj, M.A.B. ; Sihvonen, L. ; Spoolder, H.A.M. ; Stegeman, J.A. ; Thulke, H.H. ; Vågsholm, I. ; Velarde, A. ; Willeberg, P. ; Zientara, S. - \ 2013
EFSA Journal 11 (2013)12. - 65 p.
This scientific opinion proposes toolboxes of welfare indicators for developing monitoring procedures at slaughterhouses for bovines stunned with penetrative captive bolt or slaughtered without stunning. In particular, the opinion proposes welfare indicators together with their corresponding outcomes of consciousness, unconsciousness or death. In the case of slaughter with captive bolt stunning, the opinion proposes a toolbox of indicators and the outcomes to be used to assess consciousness in bovine animals at three key stages of monitoring: (a) after stunning and during shackling and hoisting; (b) during neck cutting or sticking; and (c) during bleeding. For slaughter of bovines without stunning, a set of indicators and outcomes are proposed in another toolbox to be used for (a) assessing unconsciousness, before releasing bovines from restraint; and (b) confirming death before carcass dressing begins. Various activities—including a systematic literature review, an online survey and stakeholders’ and hearing experts’ meetings—were conducted to gather information about the specificity, sensitivity and feasibility of the indicators that can be included in the toolboxes. The frequency of checking differs according to the role of each person responsible for ensuring animal welfare. Personnel performing stunning, shackling, hoisting and/or bleeding will have to check all the animals and confirm that they are not conscious following stunning or before release from the restraint. For the animal welfare officer, who has the overall responsibility for animal welfare, a mathematical model for the sampling protocols is proposed, giving some allowance to set the sample size of animals that he/she needs to check at a given throughput rate (total number of animals slaughtered in the slaughterhouse) and tolerance level (number of potential failures). Finally, different risk factors and scenarios are proposed to define a ‘normal’ or a ‘reinforced’ monitoring protocol, according to the needs of the slaughterhouse.
Mapping the antigenic structure of porcine parvovirus at the level of peptides
Kamstrup, S. ; Langeveld, J. ; Botner, A. ; Nielsen, J. ; Schaaper, W.M.M. ; Boshuizen, R.S. ; Casal, J.I. ; Hojrup, P. ; Vela, C. ; Meloen, R. ; Dalsgaard, K. - \ 1998
Virus Research 53 (1998). - ISSN 0168-1702 - p. 163 - 173.
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