A deep-sequencing workflow for the fast and efficient generation of high-quality African swine fever virus whole-genome sequences. Deep-sequencing for high-quality African swine fever virus whole-genome sequences

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 few whole genome sequences are published. Especially in Europe and Asia, where ASFV continuously spreads 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 basis for a detailed virus comparison. Here, we report an effective workflow, combining target enrichment, Illumina and Nanopore sequencing for the generation of ASFV whole-genome sequences. 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 reference for whole-genome analyses of related ASFV strains and molecular approaches. Using both workflow and reference genome, we also generated an ASFV-whole-genome sequence from Moldova that can be used to expand ASFV sequence knowledge.