A Deep-Sequencing Workflow for the Fast and Efficient Generation of High-Quality African Swine Fever Virus Whole-Genome Sequences

Viruses. 2019 Sep 11;11(9):846. doi: 10.3390/v11090846.


African swine fever (ASF) is a severe disease of suids caused by African swine fever virus (ASFV). Its dsDNA genome (170-194 kbp) is scattered with homopolymers and repeats as well as inverted-terminal-repeats (ITR), which hamper whole-genome sequencing. To date, only a few genome sequences have been published and only for some are data on sequence quality available enabling in-depth investigations. Especially in Europe and Asia, where ASFV has continuously spread since its introduction into Georgia in 2007, a very low genetic variability of the circulating ASFV-strains was reported. Therefore, only whole-genome sequences can serve as a basis for detailed virus comparisons. Here, we report an effective workflow, combining target enrichment, Illumina and Nanopore sequencing for ASFV whole-genome sequencing. Following this approach, we generated an improved high-quality ASFV Georgia 2007/1 whole-genome sequence leading to the correction of 71 sequencing errors and the addition of 956 and 231 bp at the respective ITRs. This genome, derived from the primary outbreak in 2007, can now serve as a reference for future whole-genome analyses of related ASFV strains and molecular approaches. Using both workflow and the reference genome, we generated the first ASFV-whole-genome sequence from Moldova, expanding the sequence knowledge from Eastern Europe.

Keywords: African swine fever virus (ASFV); Nanopore sequencing; next-generation sequencing (NGS); target enrichment; whole-genome sequencing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • African Swine Fever / virology
  • African Swine Fever Virus / genetics*
  • Animals
  • DNA, Viral / genetics
  • Databases, Nucleic Acid
  • Genetic Variation
  • Genome, Viral*
  • High-Throughput Nucleotide Sequencing / methods*
  • Nanopore Sequencing / methods
  • Swine / virology
  • Viral Proteins / genetics*
  • Whole Genome Sequencing / methods*
  • Workflow


  • DNA, Viral
  • Viral Proteins