Abstract
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.
Highlights
Over the last decade, tremendous progress has been made in the field of DNA sequencing [1]
To generate high molecular weight (HMW)-DNA to facilitate long reads through Nanopore sequencing, African swine fever virus (ASFV) Georgia 2007/1 was passaged a second time on porcine primary peripheral blood monocytes (PBMCs) as described elsewhere [54]
The first run resulted in 1,764,078 reads, from which 8438 reads (0.48%) were identified as ASFV-specific by mapping and resulted in a whole-genome sequence
Summary
Tremendous progress has been made in the field of DNA sequencing [1]. We used the described protocol for resequencing of the ASFV Georgia 2007/1 genome, leading to the correction of 71 homopolymer errors and other sequencing artefacts, a longer ITR region and updated annotations [37] of the corrected genome sequence. Using this high-quality sequence as a reference, we used target enrichment in combination with Illumina sequencing and sequenced ASFV directly from organ tissue, thereby providing an ASFV whole-genome sequence from an outbreak in Moldova
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