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Projects / Programmes source: ARIS

Detection of Influenza A viruses in environmental samples, feed and litter, and setting of an algorithm for the diagnosis of influenza in pigs

Research activity

Code Science Field Subfield
4.04.02  Biotechnical sciences  Veterinarian medicine  Animal pathology and epizootiology 

Code Science Field
B750  Biomedical sciences  Veterinary medicine: surgery, physiology, pathology, clinical studies 

Code Science Field
4.03  Agricultural and Veterinary Sciences  Veterinary science 
Keywords
influenza A viruses, sampling, virus detection, environmental samples, molecular detection, virus isolation, pigs, poultry, wild birds
Evaluation (rules)
source: COBISS
Researchers (23)
no. Code Name and surname Research area Role Period No. of publicationsNo. of publications
1.  20491  Marko Bogataj    Technical associate  2018 - 2021 
2.  17572  PhD Marko Cotman  Veterinarian medicine  Technical associate  2018 - 2021  119 
3.  11184  PhD Alenka Dovč  Veterinarian medicine  Researcher  2018 - 2021  473 
4.  52322  Marjeta Dremelj    Technical associate  2018 - 2021 
5.  18096  Boštjan Flajnik    Technical associate  2018 - 2021 
6.  52924  Martina Germek    Technical associate  2019 - 2021 
7.  21229  PhD Irena Golinar Oven  Veterinarian medicine  Researcher  2018 - 2021  106 
8.  23320  PhD Uroš Krapež  Veterinarian medicine  Researcher  2018 - 2021  181 
9.  21703  Darja Krelj    Technical associate  2018 - 2021 
10.  28450  PhD Urška Kuhar  Veterinarian medicine  Researcher  2018 - 2021  117 
11.  03728  PhD Renata Lindtner Knific  Veterinarian medicine  Researcher  2018 - 2021  110 
12.  32994  PhD Nina Mlakar Hrženjak  Veterinarian medicine  Researcher  2018 - 2021  34 
13.  38981  Jan Plut  Veterinarian medicine  Technical associate  2018 - 2021  60 
14.  24115  PhD Joško Račnik  Veterinarian medicine  Researcher  2018 - 2021  350 
15.  52321  Tjaša Sernel    Technical associate  2018 - 2021 
16.  22446  PhD Brigita Slavec  Veterinarian medicine  Head  2018 - 2021  203 
17.  19156  PhD Marina Štukelj  Veterinarian medicine  Researcher  2018 - 2021  214 
18.  14640  Borut Štumberger  Biology  Technical associate  2019 - 2021  123 
19.  10061  PhD Tomi Trilar  Biology  Researcher  2018 - 2021  1,003 
20.  21502  PhD Al Vrezec  Biology  Researcher  2018 - 2021  1,041 
21.  29352  PhD Marko Zadravec  Veterinarian medicine  Researcher  2018 - 2019  182 
22.  08023  PhD Olga Zorman Rojs  Veterinarian medicine  Researcher  2018 - 2021  423 
23.  50525  PhD Zoran Žlabravec  Veterinarian medicine  Junior researcher  2018 - 2021  42 
Organisations (2)
no. Code Research organisation City Registration number No. of publicationsNo. of publications
1.  0406  University of Ljubljana, Veterinary Faculty  Ljubljana  1627139  10,818 
2.  0614  Slovenian Museum of Natural History  Ljubljana  5052670000  5,891 
Abstract
Before the appearance of highly pathogenic avian influenza (HPAI) virus of subtype H5N1 A/goose/Guangdong (Gs/GD/96) only limited number of outbreaks of HPAI was recorded; the disease was mostly confirmed in domestic poultry and infections in humans with IAV were very rare. The situation changed remarkably due to the appearance of H5N1 virus. According to the official World Health Organisation reports, in the period from 2003 to May 2018 860 cases of human infection with H5N1 were confirmed with very high case-fatality rate of 53 %. Knowing these serious facts, it seems that the fear of the new epidemic could be realistic. Another very important global concern of IAV spread is the fact that outbreaks in poultry are always related to enormous economic losses due to high mortality and financial costs of resolving the outbreaks and have negative impact on animal welfare. Although vaccines against IAV are available on the market, the majority of outbreaks are still resolved on the basis of stamping-out and strict control measurement policy. IAV of subtypes H5 clade 2.3.4.4 spread in 2016 from Russia to EU and caused the largest pandemic in Europe so far. Till August 2017 in domestic poultry 1207 outbreaks from 24 European states were reported and 1590 outbreaks were confirmed in wild birds involving 29 different European countries. In recent outbreaks beside H5N8 also H5N5 of IAV were detected. In Slovenia poultry production is one of the major agricultural sectors, therefore effective protection of this sector against the outbreaks of very contagious infectious diseases such as highly pathogenic avian influenza is of the utmost importance. Although pork production is not so developed as poultry, pig farming is also important, especially in the regions with dense poultry and pig population. It is also very common that on small family farms pigs and poultry are reared together, meaning that there is a possibility of mixing of different IAV strains.  The resulting new virus might then be able also to infect humans.  In Slovenia, two outbreaks of highly pathogenic avian influenza (HPAI) were confirmed, both in free living birds. Both outbreaks (2006 and 2017) were located in north-eastern part of the country, in the region which holds the highest number of poultry and pig farming operations in Slovenia. Till present, very limited data on IAV in pigs are available and no epidemiological studies were performed in the last decade. Knowing that pigs may play an important role in influenza virus evolution and ecology, one of the goals of proposed project is to find out which viral subtypes circulate in pig population. In addition, protocols for surveillance of influenza in pigs will be set for veterinary practitioners and materials for raising awareness among breeders and the public about influenza in pigs will be prepared. The data obtained through this project will thus contribute to an improved on epidemiological picture of AIV circulation in this species also in the whole EU region. In addition, analysis of the obtained data will help the competent authorities in planning effective preventive measures for the control of AIV in pigs in Slovenia. Fast and reliable diagnostic is the key point in detection, prevention and control of contagious diseases. Likewise, it is very important to determine the mode of virus introduction and spread in order to prevent further virus spreading and to check whether preventive measures like cleaning and disinfection were applied adequately and efficiently. Although epidemiological investigations are already a part of national contingency plan in a case of IAV outbreak in poultry, screening of environmental samples and control of efficiency of disinfection are not involved. Within the framework of the proposed project we will determine if non-invasive sampling methods of various environmental samples such as air, floor surfaces and feed can be used for the IAV detection and to optimize these techniques.
Significance for science
Epidemiological data on the prevalence of influenza viruses in pigs in Europe are in comparison with the data on poultry and birds very rare; only a few  studies have been carried out, showing circulation of 3 different subtypes of viruses in some European countries: H1N1, avian origin, and H3N2 and H1N2, human origin. Due to the fact that in our country we do not carry out regular monitoring in this animal species, as well as because of the lower awareness of the professional public, in the last decade there are no data on the prevalence of IAV pigs, nor which AIVs circulate in this population. The data obtained through this project will thus contribute to an improved on epidemiological picture of AIV circulation in this species also in the whole EU region. In addition, analysis of the obtained data will help the competent authorities in planning effective preventive measures for the control of AIV in pigs in Slovenia.   The development of non-invasive sampling methods, which are not currently used for detection of the agents and disease control in practice, and the optimization of diagnostic methods for confirming the causative agents in various matrixes, is an important innovative approach. The use of different patterns in diagnostics, such as absorption coatings and air samples, is currently not described as a routine sampling method for the detection of viruses, and in the literature, there is little data on their performance. We believe that the results obtained under this project will be highlighted in the scientific and professional sphere. In the framework of the project, we will also prepare a protocol for such sampling, which may also be the basis for controlling other viral diseases.
Significance for the country
In Slovenia poultry production is one of the major agricultural sectors, therefore effective protection of this sector against the outbreaks of infectious diseases is of the utmost importance. Within the framework of the project, we will study the IAV's ecology in the area of north east Slovenia, this is an area where intensive poultry farming is highly developed and the poultry population is extremely dense. On the other hand, in this area the population of wild waterfowl is the largest, which represent one of the factors important for the introduction of diseases. Epidemiological survey of the AIV circulation in the mute swan (Cygnus olor) population, one of the most common species of birds infected with AIV viruses in Slovenia, and a survey of their movements will provide information on critical points of possible transmissions in north east region of Slovenia. The analysis of the data obtained from the proposed project will help the competent veterinary authorities and the veterinary profession as well as the poultry industry to plan and implement effective AIV prevention measures on poultry farms. In the framework of the project, a protocol for such sampling for veterinary practitioners will be also prepared.  On the other hand, Slovenian pig farming are in a rather unenviable position; self-supply with pig meat in our country is below 30% . Respiratory diseases are frequent and economically important issue in pig intensive rearing. On a professional basis, this problem  would require in-depth diagnosis, involving various potential infectious agents, but owners often do not decide for it because of limited resources. So, the aetiology of respiratory diseases is often unclear and can lead to the increased use of antimicrobials and unprofitable rearing. We will prepare standard operating procedures for the detection of IAV in pigs and validate molecular methods for the detection of specific virus subtypes occurring in pigs. This brings a significant professional advancement for the veterinary profession and will also help  farmers to improve production results and competitiveness and viability of farming.
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