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African Swine Fever roadmap:
Diagnostic Tests

Roadmap for the development of diagnostic tests for ASF

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9

Genome characterization

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Dependencies

Next steps

ASFV genome characterization

Research Question

  • There are a range of viruses’ strains which differ in terms of virulence. Having whole-genome sequences is essential for identifying the host pathogen interactions and how this can be manipulated. Establishing the genomic differences of the various strains will assist in the identification of virulence mechanisms

Research Gaps and Challenges

  • The annotation and analysis of genomes in the size range of ASFV is difficult and requires specialised tools, especially with
    the acquisition of more genome sequences
  • Automation and standardisation of viral genome sequencing for subtyping ASFV strains using NGS pipelines and automatized annotation tolls
  • ASFV sequencing in ticks
  • Identify key variable regions of the genome for epidemiological purposes (without need for WGS in all cases/for all outbreaks)

Solution Routes

  • NGS pipelines or ASFV sequencing
  • Use of bait technology for enrichment of ASFV genomes (e.g. with MyBait-Technology)

Dependencies

  • NGS laboratory with experience in large DNA genomes
  • Combination of different NGS technologies (large reads with MinIon and deep sequencing with standard Illumina or IonTorrent NGS)

State Of the Art

  • To better understand the molecular epidemiology of the recent outbreaks, additional genome markers are under investigation. Among them are different intergenic regions
  • Next-generation sequencing could be aided by enrichment through targeted sequence capture technology. Using current, very robust technologies, it has been possible to develop a comprehensive database, which includes full length genome sequence of large number of isolates to replace the current less meaningful genotype-based classification: https://virology.uvic.ca/organisms/dsdnaviruses/asfarviridae/

Projects

What activities are planned or underway?

Africa's Long Depression: The Growth and Debt Crises of 1975-2000

Planned Completion date 01/03/2027

Participating Country(s):

United KingdomIconUnited Kingdom

Unlocking potential: developing innovative adolescent screening visits for health promotion, prevention and treatment in low-resource settings

Planned Completion date 01/01/2028

Participating Country(s):

United KingdomIconUnited Kingdom