Projekte in den Förderprogrammen des BMEL, betreut durch den Projektträger BLE (PT BLE)
Ergebnis der Suche
| Titel: | Molecular epidemiology of epizootic diseases using next generation sequencing technology (EPI-SEQ) |
|---|---|
| Beschreibung (dt.): | Ziel ist es, optimierte Methoden zur Untersuchung von Epidemien viraler Tierkrankheiten zu entwickeln und neue Erkenntnisse zur Evolution der Viren zu gewinnen. Am Ende des Projektes werden unter anderem verbesserte Verfahren zur Probenvorbereitung für die Sequenzierung der Virusgenome, für die Datenerhebung und die Sequenzanalyse zur Verfügung stehen. Zu diesem Zweck wird ein internationales Team von Wissenschaftlern unterschiedlichster Disziplinen mit Kenntnissen bei der Untersuchung verschiedenster Aspekte virusbedingter Krankheiten zusammenarbeiten. Die Expertise der beteiligten Wissenschaftler umfasst die molekulare Virologie, Bioinformatik, Modellierung und Evolutionsbiologie. Objekte der Untersuchungen werden verschiedene DNA- und RNA-Viren sein, die in Europa sporadisch Epidemien verursachen (MKSV, AIV, NDV) oder in Wildtieren endemisch sind (CSFV), sowie solche, die Europas Tierpopulationen bedrohen (ASFV, Pockenviren). Von den Genomen dieser Viren, die während vorangegangener Ausbrüche gesammelt wurden oder in vitro unter definierten Bedingungen erzeugt werden, werden zunächst hochauflösende Sequenzdatensätze generiert, die dann in Kombination mit den vorhandenen Daten zur Epidemiologie neue Einblicke in die Ökologie und Evolution der Viren eröffnen werden. Darüber hinaus werden am Ende des Projektes innovative Methoden zur Analyse derartiger Datensätze zur Verfügung stehen. Die erarbeiteten Daten und Werkzeuge werden durch Publikationen und Hinterlegung in den einschlägigen Datenbanken der Wissenschaftsgemeinschaft zur Verfügung gestellt. Neben den bereits genannten Verbesserungen zur Analyse der Evolution und den dadurch erreichten Einblicken in die Evolution der Viren werden durch die gewonnen (Sequenz-) Informationen auch Verbesserungen der molekularen Diagnostik und der Zusammenstellung von Impfstoffen ermöglicht. Nicht zuletzt werden am Ende auch verbesserte Werkzeuge zur Kontrolle endemischer und epidemischer Infektionskrankheiten stehen. |
| Beschreibung (engl.): | Epi-SEQ aims to exploit next generation sequencing (NGS) to generate improved tools that can be used during epidemics of viral diseases threatening livestock industries in Europe. A multidisciplinary team with expertise in molecular virology, bioinformatics, modeling, and evolutionary biology will streamline and validate pipelines for sample preparation, data generation and sequence analysis. The project will target important RNA viruses that cause sporadic epidemics in Europe (FMDV, AIV, NDV), or are endemic in wildlife populations in some EU member states (CSFV), as well as DNA viruses that pose a threat to the EU (ASFV and poxviruses). The project will produce high-resolution sequence data from sample collections held in partner laboratory archives, as well as undertake new in vitro experiments to test specific selection pressures that influence viral evolution. These integrative studies encompassing this spectrum of epidemiology will stimulate the development of innovative tools and provide broad insights into the comparative evolutionary ecology and epidemiology of viruses of human and veterinary importance. The sequence data generated from this project will be made publicly available. Furthermore, the tools that are developed from these studies will be disseminated to a wider audience. Insights from this project will result in: a) Novel information on viral evolution and (sub)populations; b) comparative evolutionary data between viruses with different genome organization (+ vs. - sense RNA, segmented RNA), c) Improved molecular diagnostic assays, based on recognition of suitable sequence motifs; d) Powerful tools for molecular epidemiology; e) Enhanced capacity to optimize the strain composition of vaccines, and match to emerging virus variants; f) More effective tools to control epidemic and endemic infectious diseases. |
| Ergebnis (engl.): | Next-generation sequencing (NGS) techniques offer an unprecedented step-change increase in the amount of sequence data that can be generated from a sample. NGS technologies can determine complete viral genomes with a resolution allowing the quantification of RNA quasispecies variation within samples and can economize the sequencing of large numbers of samples or larger DNA virus genomes. Focusing on important epizootic viral diseases that threaten livestock industries in Europe, the aim of this project is to exploit NGS to generate improved tools that can be used in real-time during epidemics. This work will be undertaken by a multidisciplinary team of scientists from Belgium, Germany, Italy, Sweden, and the United Kingdom with expertise in molecular virology, bioinformatics, mathematical modeling, and evolutionary biology. RNA viruses evolve rapidly and quickly adapt to different environmental pressures escaping host immune defenses, altering their pathogenicity and host range, and evading diagnostic tests. Current methodologies limit the resolution at which we can study the evolutionary dynamics of the complex genomic mixtures (quasispecies) that are typical for these viruses. Archived sample collections representing epizootic outbreaks of pathogens such as foot-andmouth disease virus (FMDV), avian influenza virus (AIV), Newcastle Disease Virus (NDV) and classical Page 1 of 25 emida2-94-2011-11-09-12-27.pdf swine fever virus (CSFV) will be used to monitor the evolution during field outbreaks of disease. Spatiotemporal data collected in the field will be integrated with this genetic data to produce robust models that can be used to reconstruct transmission trees during viral epidemics. Furthermore, in vitro experiments will be performed using FMDV (ss+RNA genome) and AIV (ss segmented-RNA genome) under strong selection pressures. Modeling of the resulting NGS data will provide a framework to describe the wider scale evolutionary patterns that are measured during these field outbreaks. Linking genetic data to viral phenotype will be undertaken by studying DNA viruses with large genomes (ASFV and poxviruses). Although the viruses have relatively stable genomes, their large size poses challenges for sequencing using traditional Sanger approaches. Specific work packages will focus on the improvement and dissemination of technical protocols and on data analysis and dissemination of bioinformatics and modeling tools. Insights from this project will result in: a) Novel information on viral evolution and (sub)populations; b) comparative evolutionary data between viruses with different genome organisation (+ vs. - sense RNA, segmented RNA, c) Improved diagnostic assays, based on an improved recognition of suitable sequence motifs; d) Powerful tools for molecular epidemiology; e) Enhanced capacity to optimize the strain composition of vaccines, and match to emerging virus variants; f) More effective tools to control epidemic and endemic infectious diseases. |
| Laufzeit: | Beginn: 01.05.2012 / Ende: 30.11.2015 |
| Ausf. Einrichtung: | Friedrich-Loeffler-Institut Bundesforschungsinstitut für Tiergesundheit - Institut für Virusdiagnostik, Greifswald |
| Themenfelder: | Tiergesundheit, animal health |
| Förderprogramme: | EU-Forschung |
| Schlagworte: | Tierseuchen, epizootic, Prävention, Prevention, Tierart übergreifend, animal species comprehensive, Virologie, Virology |
| Stichpunkte: | Depidemiologie, Zoonosen |
| Förderkennzeichen: | 2811ERA094 |
| Dokument zum Download: | 11ERA094_Abschlussbericht.pdf (164 KB) |
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