ANIHWA ERA-Net Animal Health and Welfare

Size: px

Start display at page:

Download "ANIHWA ERA-Net Animal Health and Welfare"

Poppy Chase
5 years ago
Views:

ANIHWA ERA-Net Animal Health and Welfare Final Dissemination Conference Epi-SEQ Steven Van Borm steven.vanborm@coda-cerva.be www.episeq.

1 ANIHWA ERA-Net Animal Health and Welfare Final Dissemination Conference Epi-SEQ Steven Van Borm This project has received funding from the European Union s Seventh Framework Programme for research, technological development and demonstration under grant agreement no

2 Molecular epidemiology of epizootic diseases using next generation sequencing technology. 2

3 consortium ANIHWA Dissemination semi Conference 3

4 organisation WP1.Improvement of the technical aspects of NGS platforms and the of technical protocols (FLI Dirk Höper, Martin Beer) Protocol optimisation: from sample to virus representative DNA library (targeted & random approaches) Platform prospection: 3rd generation or single molecule sequencing. NEW: application of technical progress to sequence additional viral genomes WP5. Data analysis, bioinformatics and modelling tools (U. of Glasgow) Construction of data analysis pipelines which distinguish NGS artefacts from underlying genetic variation to enable powerful molecular epidemiology Modelling high resolution epidemiologic/genetic data sets WP6. Dissemination of project results and findings (SLU, Sándor Belák ) WP7. Project management (CODA-CERVA, Steven Van Borm ; SLU, Sándor Belák ) 4

5 organisation WP2. Epidemic and endemic patterns of virus epidemiology (PIR Don King) NGS-based molecular epidemiology of FMD (complete 2001 outbreak) (PIR) NGS-based molecular epidemiology of LPAI and HPAI H7N1 and H7N3 viruses collected during the respective and epidemic waves in Italy (IZSVe) NGS of field H5N1 viruses evolving under vaccination pressure (IZSVe) NEW: NGS of recent HPAI outbreaks, Italy (IZSVe). Investigation of NDV, using NGS to enable multi-genome comparison (SLU-SVA) Comparison of pestivirus chronic (Classical swine fever virus: CSFV) and persistent disease (Bovine viral diarrhea virus: BVDV) with regard to evolution and quasispecies dynamics within the host (FLI) WP3. Linking genetic data to viral phenotype (SLU Sándor Belák ) Development of a reliable, robust and accessible novel molecular epidemiology platform for African Swine Fever Virus (SLU) Studying poxviruses as a model system to dissect virus evolution and relate phenotypic to genetic information (FLI) NEW: NGS of classical swine fever clones (DTU) WP4. Quasispecies characterization of viruses and how they respond to selection (CODA-CERVA, Steven Van Borm) NGS to study experimental evolution of FMDV (antiviral compound)(coda-cerva: Steven Van Borm, Kris De Clercq) Modeling of NGS data from FMDV under strong selection (VAR + PIR + U. Glasgow) NEW: Quasispecies polulation analysis during in vivo host adaptation of West Nile virus (CODA-CERVA, U. Glasgow) 5

6 Output Current situation (no-cost extension until ) 22 peer reviewed publications covering all scientific WP ( for details) WP1 protocol repository realisation of most deliverables (some datasets to be completed and/or analysed) Additional application of developed tools WNV, APMV-6, BTV-27, Bornavirus, PEDV Recent Italian AIV outbreaks Internal workshops on (1) sequencing methods and (2) bioinformatics Epi-SEQ expertise dissemination: technical workshops (spring 2016) EPIZONE workshop basic bioinformatics & NGS COST control avian coronaviruses: training school bioinformatics Review article on NGS applications in veterinary microbiology. 6

7 anihwa 7 Van Borm S et al.(2015). Methods Mol Biol. 1247:

8 anihwa 8 Van Borm S et al.(2015). Methods Mol Biol. 1247:

9 e.g. FMDV (WP1, WP5, WP2) Logan G, Freimanis GL, King DJ, Valdazo-González B, Bachanek-Bankowska K, Sanderson ND, Knowles NJ, King DP, Cottam EM (2014). A universal protocol to generate consensus level genome sequences for foot-and-mouth disease virus and other positive-sense polyadenylated RNA viruses using the Illumina MiSeq. BMC Genomics 15:828. Orton RJ, Wright CF, Morelli MJ, Juleff N, Thébaud G, Knowles NJ, Valdazo- González B, Paton DJ, King DP, Haydon DT (2013). Observing microevolutionary processes of viral populations at multiple scales. Philos Trans R Soc Lond B Biol Sci 368(1614): Orton RJ, Wright CF, Morelli MJ, King DJ, Paton DJ, King DP, Haydon DT (2015). Distinguishing low frequency mutations from RT-PCR and sequence errors in viral deep sequencing data. BMC Genomics. 16: outbreak sample repository 9

10 e.g. AIV (WP1, WP5, WP2) Monne I, Fusaro A, Nelson MI, Bonfanti L, Mulatti P, Hughes J, Murcia PR, Schivo A, Valastro V, Moreno A, Holmes EC, Cattoli G (2014). Emergence of a highly pathogenic avian influenza virus from a low-pathogenic progenitor. J Virol. 88(8): Monne I, Meseko C, Joannis T, Shittu I, Ahmed M, Tassoni L, Fusaro A, Cattoli G. (2015). Highly Pathogenic Avian Influenza A(H5N1) Virus in Poultry, Nigeria, Emerg Infect Dis. 21(7): Fusaro A, Tassoni L, Hughes J, Milani A, Salviato A, Schivo A, Murcia PR, Bonfanti L, Cattoli G, Monne I. (2015). Evolutionary trajectories of two distinct avian influenza epidemics: Parallelisms and divergences. Infect Genet Evol. 34:

11 e.g. BVDV (WP1, WP5, WP2) Jenckel M, Höper D, Schirrmeier H, Reimann I, Goller KV, Hoffmann B, Beer M (2014). Mixed triple: allied viruses in unique recent isolates of highly virulent type 2 bovine viral diarrhea virus detected by deep sequencing. J.Virol. 88 (12)

e.g. Poxviridae (WP1, WP5, WP3) Kalthoff D, Bock WI, Hühn F, Beer M, Hoffmann B (2014). Fatal cowpox virus infection in cotton-top tamarins (Saguinus oedipus) in Germany. Vector Borne Zoonotic Dis.

12 e.g. Poxviridae (WP1, WP5, WP3) Kalthoff D, Bock WI, Hühn F, Beer M, Hoffmann B (2014). Fatal cowpox virus infection in cotton-top tamarins (Saguinus oedipus) in Germany. Vector Borne Zoonotic Dis. 14(4): Hoffmann D, Franke A, Jenckel M, Tamošiūnaitė A, Schluckebier J, Granzow H, Hoffmann B, Fischer S, Ulrich RG, Höper D, Goller K, Osterrieder N, Beer M. (2015). Out of the reservoir: Phenotypic and genotypic characterization of a novel cowpox virus isolated from a common vole. J Virol. pii: JVI

13 e.g. WNV (WP1, WP5, WP4) Dridi M, Rosseel T, Orton R, Johnson P, Lecollinet S, Muylkens B, Lambrecht B, Van Borm S (2015). Next Generation Sequencing shows West Nile virus quasispecies diversification after a single passage in a carrion crow (Corvus corone) in vivo infection model J Gen Virol. 96(10):

14 Conclusions Optimisation of NGS tools Sample preparation and sequencing Bioinformatics, modelling and error correction Prospection of technologies 2nd generation sequencing (Roche 454, Iontorrent, Illumina) 3rd gen. Or single molecule sequencing (Pacbio, Oxford Nanopore sequencing). Application to RNA and DNA virus molecular epidemiology and evolution. Documentation of added value of NGS. Variant detection and number of samples: RNA viruses Larger genomes: DNA viruses Efficient, economical whole genome sequencing of viruses 14

15 Thanks for your attention! The Epi-SEQ consortium 15

NEXT GENERATION SEQUENCING OPENS NEW VIEWS ON VIRUS EVOLUTION AND EPIDEMIOLOGY. 16th International WAVLD symposium, 10th OIE Seminar

NEXT GENERATION SEQUENCING OPENS NEW VIEWS ON VIRUS EVOLUTION AND EPIDEMIOLOGY S. Van Borm, I. Monne, D. King and T. Rosseel 16th International WAVLD symposium, 10th OIE Seminar 07.06.2013 Viral livestock