Short-Term Scientific Missions (STSMs) allow scientists to learn from an institution or laboratory in another COST country – a concept of particular interest to young scientists. In this instance STSMs facilitate Researchers participating in COST Action CA15116 to go to an institution, organisation or research centre in another participating COST Country to foster collaboration and to perform research. Participation of “Early Career Investigators” (ECI) in STSM is particularly encouraged.
Open call Deadlines:
As of 2017 ASF-STOP has an open call for STSMs.This means that you can submit your application at any time you desire. Twice a year we will collect the applications received by those dates, evaluate and award STSMs based on available budget. Criteria for awarding are explained further ahead on this page. Goals for the STSMs and criteria might be adjusted from year to year as the work of ASF-STOP continues.
For 2018/2019 we expect to award a total of 7-8 STSMs. You can send your application any time prior to the collection date.
For more general information on Short-Term Scientific Missions (STSMs), and who can apply for the grants, to which institutions and up to which amounts, please read the information provided on this PDF.
ASF-STOP has presents here a list of partner institutions that are offering STSMs. You are advised to check these possibilities, but you are NOT restricted to these offers. You can take contact with ANY member institution to arrange for an STSM even if that institution is not listed here as offering a STSM.
Purpose of the visit: learning different diagnostic techniques used in the laboratory for ASFV diagnosis and study different methods of epidemiology analysis and risk assessment.
After an extensive spread of the ASF virus (ASFV) genotype II in Eastern Europa, the first case of ASF in Estonia was diagnosed in September 2014. By the end of November 2017, 3540 ASF positive wild boar have been found as well as 26 domestic pig outbreaks have been confirmed.
The disease has spread all over Estonia and only one county out of 15 is still free of the disease. Although ASFV genotype II is circulating in Eastern Europa already for ten years, we know about the virus a lot less than we would like. Therefore, it is crucial to contribute as much as possible to the improvement of molecular typing methods, especially in the affected countries. Up to now, the EURL for ASF (CISA-INIA, Spain) has supported Estonian Veterinary and Food Laboratory (acting also as NRL for ASF in Estonia), sequencing a part of ASFV positive samples. As the result of these analysis, one new CVR variant (CVR2) has been found in Estonia and also, one SNP (single nucleotide polymorphism) within CVR variant 1. Furthermore, has been the great cooperation with the Friedrich-Loeffler-Institut (Germany) with the aim to characterize different virus strains circulating in different regions in Estonia. Up to now, this co-operation has been very fruitful. Based on the results of animal experiments and next generation sequencing (NGS), the association between deletion at the 5’- end of Estonian ASFV strains and attenuated phenotype has raised (Zani et al., 2018-in preparation).
The main goal of the short term scientific mission to the Friedrich-Loeffler-Institut was to strengthen and improve the knowledges of ASFV sequencing and data analysis. Furthermore, to get an overview and basic experience of the NGS approaches.
During two weeks of short term scientific mission genetic characterization of 6 ASFV isolates was performed by PCR and further sequencing throughout the initial analysis of different regions of ASF genome. The regions were i) the C-terminal end of the VP-72 protein coding gene, which differentiates up to 23 distinct genotypes ii) the central variable region (CVR) within the B602Lgene iii) the full E183L gene encoding the p54 protein as a valuable additional genotyping method for molecular epidemiological studies of p72 genotype I viruses, particularly in West Africa where this genotype predominates and iv) the gene K196R coding for the ASFV thymidine kinase. Samples 1 to 5 were obtained from ASFV positive domestic pig samples from Ukraine 2
and sample 6 was an ASFV isolate obtained from an African Ornithodoros porcinus tick.
Secondly, metagenomic analyses of four bovine swab samples were performed using IonTorrent S5 XL NGS platform to get an overview of the important steps and workflow of the next generation sequencing, which can be successfully used for ASF sequencing also.
The purpose of the STSM was to compare different fast molecular techniques, including real-time PCR- and isothermal amplification assays, for the detection of African swine fever virus (ASFV) DNA in field samples obtained in Poland. A fast and reliable diagnosis of such samples is one of the most important measures in the control of ASFV transmission in affected regions, as the application of the fastest and most sensitive diagnostic methods could enable earlier detection of the virus and thus earlier intervention by the competent authorities.
During the STSM, different real-time PCR and isothermal methods for the identification ASFV DNA in Polish field samples were compared. Hence, the OIE recommended real-time PCR with UPL-probe was compared to two new commercial ready-to-use duplex real-time PCR kits (kits A and B – not on the market yet), both containing an internal swine β-actin control. For kit A, samples were analyzed using standard reaction conditions and fast reaction conditions, respectively. For kit B, samples were analyzed using standard reactions conditions, only. In addition, some samples were analyzed using an isothermal amplification assay, cross-priming amplification (CPA) [2]. Amplified product from the CPA reaction were visualized both by using SYBR Green I dye yielding a greenish fluorescence under UV illumination and by using a commercial lateral flow device.
In addition to the evaluation of different methods for the detection of viral DNA in field samples, methods for the isolation and quantification of infectious virus applied at PIWet were introduced. This included virus isolation methods for field isolates in both primary cells and continuous cell lines, and the detection of ASFV infected primary cells by hemadsorption. Finally, the STSM also included an introduction to the diagnostic ASFV laboratory at the Department of Swine Diseases, where hands on experience with handling and pre-processing of blood, tissue and bone marrow samples, DNA extraction methods and serological analysis (ELISA and IPT) have been obtained.
This STSM regards epidemiology of African swine fever (ASF), a viral haemorrhagic disease of domestic pigs and wild boar (Sus scrofa) that causes massive loss of animals due to mortality and the essential eradication control policies. The disease gives rise to animal welfare problems as well as further economic loss from trade restrictions and there are no vaccines.
ASF has been present in Russia and neighbouring countries since 2007 and recently the disease has entered the EU. The evaluation of the risk of introduction of this virus in Europe is needed. For instance, previous European project (ASF-Risk) assessed several pathways in qualitative and quantitative ways: legal imports of live domestic pigs, illegal importation of meat and products, risks of trucks, waste and fomites. However, assessments on ASFv introduction by wild boar are crucial nowadays. Others studies have evaluated the risk of ASFv introduction into the EU by wild boar based on: “natural” movement, abundance rates of wild boar, habitat suitability, resource selection and the density of outbreaks in this species. Anyway, in accordance with the last ASF outbreaks -as those cases in Czech Republic-, wild boar trade by human may play an important role in the introduction pattern for this disease owing to the spatial spread within wild boar populations is slow: 1-2 km/month. In this sense, the proposal STSM was to focus in collection and manipulation of databases regarding the movements of wild boar and the use of this information to explore the risk of ASF virus (ASFv) introduction through legal trade of wild boar among Eastern Europe and some Western European countries.
There is some evidence that legal and illegal movements of live wild boar are happening between ASF infected or at risk countries in Eastern Europe (Hungary, Poland, Ukraine…) and some Western European countries such as France, Spain or Belgium. However, those movements of animals have never been adequately quantified. Quantifying the extent, origin and destination of legal movements is possible by collecting the relevant information and necessary in order to estimate the risk of ASF introduction through this activity in the countries receiving those animals.
According to CA COST Action CA15116 “Understanding and combating African Swine Fever in Europe (ASF-STOP)” main objectives, this proposal pretends (i) determine a methodology of movement surveillance in order to improve the knowledge live wild boar networks into ASF non-infected areas in an European context and (ii) clarify the potential risk of wild boar trade for hunting purposes in ASF spread and maintenance. This information is crucial to assess an activity that poses a serious risk of spread ASF into Western Europe and that is highly relevant to the COST Action and several European institutions on Animal Heath.
Instituto de Investigación en Recursos Cinegéticos (IREC)
04/02/2017
04/14/2017
Details
Researcher Name
Claudia Schulz
Researcher ECI?
Yes
Researchers country
Germany
Researchers Institute
University of Veterinary Medicine Hannover
Host Country
Spain
Host Institute
Instituto de Investigación en Recursos Cinegéticos (IREC)
ITC status
Not From ITC and not in ITC
Description of STSM
The STSM was separated in one week of practical experience at the beautiful Doñana
National Park in Andalusia, Spain, and in one week of data analyses at the IREC, Ciudad Real.
During the first week two Russian colleagues and I were closely supervised and instructed by
Francisco Ruiz-Fons, Pelayo Acevedo and his Master student Pablo Mayordomo Palencia in
different methods to measure density, abundance, activity and speed of wild animals,
particularly of wild boar. The practical methods we learned included camera trapping,
trapping of wild boar with different live traps, perpendicular transects by car and foot,
necropsy of wild boar and the general use of telemeter, radio collars and proximity loggers.
Furthermore, we were instructed to consider which (risk) factors (e.g. habitat, feces
detoriation, sample size, abundance of different animal species) have to be taken into
account before, during and after the performance of field studies.
We conducted various transects with cars and by foot across different habitats and at
different times of the day and night. We learned how to use spotlight, laser distancemeasurement
sensors, GPS devices and the “CyberTracker” software for the detection and
documentation of different wild animal species and their feces.
During the second week, data collected at Doñana National Park and additional exemplary
data were analyzed using free software programs available online. Joaquín Vicente Baños
instructed us about the use of the software “Distance” to analyze data from distance
sampling. We learned how to evaluate which models are most suitable for the calculation of
population density. With Pablo Mayordomo Palencia we analyzed the pictures and videos of
Doñana to calculate speed, activity and density of animal populations. The last days were
dedicated to programming and application of the software programs “CyberTracker”, “qGIS”
and “R software” with Pelayo Acevedo, which allow to set up and analyze representative and
comprehensive field studies, respectively. With the theoretic part of the course, previous
knowledge of the practical field work at Doñana was deepened and beneficially extended.
The whole course has provided us a very valuable and solid background for prospective field
projects in Russia, Iran or elsewhere.
After the two weeks of the STSM, I strongly feel that I can safely apply the different methods
I have learned at the Doñana National Park and at IREC for future field studies.
In conclusion, due to the low number of participants together with the comprehensive
program that was set up for us, the learning success was very efficient - not least because
our supervisors were highly motivated and answered all our questions! Beside the censuring
tools, we learned a lot about the fauna and flora of Doñana and the surrounding of Ciudad
Real and Spanish culture. The organization of the research program, accommodations and
food at all times of the day was excellent. I would like to thank the whole team, particularly
Fran and Pelayo, for this exceptional experience and cordial hospitality!
Introduction of ASF into a free area is generally accompanied by an increased occurrence of fallen animals and thus, hunted wild boar and carcasses are the main target for passive surveillance. However, the encouragement of hunters to report and sample these animals is rather difficult. One part of the problem is the labor- and contact-intensive sampling of decomposed carcasses. Here, pragmatic sampling approaches such as swabs could facilitate sampling actions.
Recently, we were able to show that a blood-soaked forensic livestock swab is suitable for both molecular swine fever diagnosis (Petrov et al., 2014a) and ASFV antibody detection (Blome et al., 2014) under laboratory conditions.
The aim of the short term scientific mission at the Estonian University of Life Sciences was the assessment and validation of this approach under controlled field conditions (proof-of-concept in an affected country). The exercise was done in collaboration with the Estonian Veterinary and Food Laboratory in Tartu, which acts as Estonian National Reference Laboratory (NRL) for ASF and CSF. In the latter, field-collected swab samples were processed and tested by molecular (polymerase chain reaction, PCR) and serological (enzyme-linked immunosorbent assays, ELISA) techniques.
It was foreseen to stay in Tartu for two weeks. During this time, as many swabs as possible should be collected from the field. Should this proof impossible, alternatively archived blood samples at the NRL in Tartu would be the subject of investigations. In the laboratory, nucleic acids should be extracted from the swab followed by routine real-time PCR. In addition, a piece cut from the forensic livestock swab should be used for the ASFV antibody ELISA using the established protocol for filter paper punches.
During the two weeks of the Short Term Scientific Mission only two wild boar carcasses were reported to the Estonian University of Life Sciences (EMU) in Tartu and could thus be directly sampled with the above mentioned livestock swabs. In addition to these samples 42 forensic livestock swabs were soaked in archived samples at the NRL in Tartu.
Recent rapid spread of the African Swine Fever (ASF) in the Northeast Poland during summer 2017
encourages us to prepare risk assessment for the whole country and predict future geographical
transmission paths.
We focus on a predictive stochastic ASF model based on empirical geographical data incorporating
organizational network of regions, empirical forest, swine, and wild boar density as well as
theoretical organizational structure of the pork production supply chain. This project should and as a
decision support system as a tool for epidemiologists and veterinarians in chief.
We used available data on outbreak form OiO and regional information from Statistics Poland (GUS).
We use regression models and social network analysis to investigate the outbreak. We perform early
epidemic growth estimation and simulate landscape-based propagation.
We also realize that up to our knowledge, there are is no scientific quantitative statistical studies to
explain ASF for affected EU countries as Poland, Romania, Lithuania, Czech Republic and Latvia, and
only for Estonia scientific analysis was performed (EFSA-Q-2017-00154).
The result of the cooperation gives novel interdisciplinary insights into understanding of the drivers
of propagation of ASF in Poland as well as new computational and mathematical tools for
reconstruction of the most likely future paths of infection and for the classification of regions into
risk groups.
