The objective of this work package is to develop a DNA barcoding method for identification of high priority viruses present in the EU Plant Health Directive and EPPO Plant Health lists of quarantine pathogens.
In order to achieve this aim we will:
- Develop reliable nucleic acid (DNA&RNA) extraction procedures.
- Develop standard operating procedures for identification of viruses including extraction, PCR amplification, sequencing and database searching.
- Task 6.1 Selection and acquisition of targets
- Task 6.2 Nucleic acid extraction
- Task 6.3 Generic primer sets
- Task 6.4 Genome sequencing
- Task 6.5 Generation and validation of Barcode sequences
- Task 6.6 Development and publication of complete protocols.
- D 6.1 List of selected quarantine viruses (Month 6)
- D 6.2 A recommended protocol for nucleic acid extraction for virus infected plant material (Month 9)
- D 6.3 Quarantine viruses (at least two Nepoviruses, Ilarviruses and Criniviruses) acquired by the consortium for primer testing (Month 12)
- D 6.4 Validation data for published (Nepovirus, Ilarvirus Sadawaviruses, Begomoviruses, Tospoviruses and Crinivirus primer sets) and newly designed (three of Torradovirus, Comovirus or Rhabdovirus) generic primer sets with quarantine viruses (Month 18)
- D 6.5 Validated barcode and meta data available for Nepovirus, Ilarvirus, Sadawaviruses, Begomoviruses, Tospoviruses and Crinivirus primers and three of Torradovirus, Comovirus or Rhabdovirus on the project/sequence database (Month 30)
- D 6.6 Complete barcode identification methods written and available for Nepovirus, Ilarvirus, Sadawaviruses, Begomoviruses, Tospoviruses and Crinivirus primers and three of Torradovirus, Comovirus or Rhabdovirus genera (Month 30)
- D 6.7 Genomic sequence available for the un-sequenced viruses (two of, for example: Potato yellowing virus, Aracacha virus B or Potato black ring spot virus ) (Month 36)
- D 6.8 Detailed contingency plan for WP6 (Month 6).