Next-generation sequencing
For whole-genome sequencing, DNA was extracted from 200 µl of bone-marrow homogenate using the NucleoMagVet kit (Macherey-Nagel, Düren, Germany) according to the manufacturers’ protocol. For rapid generation of sequence information, DNA from the same sample was sequenced on the Illumina MiSeq platform (San Diego, USA) as described elsewhere (Wylezich, Papa, Beer, & Hoper, 2018).
The resulting read data was mapped against a custom database including all ASFV sequences available from International Nucleotide Sequence Database Collaboration (INSDC) databases as of 15th September 2020 using Bowtie2 v.2.3.5.1 (Langmead & Salzberg, 2012) with the highest sensitivity settings followed by de novo assembly of the mapped reads using SPAdes v.3.13 (Antipov, Korobeynikov, McLean, & Pevzner, 2016) with default parameters. The resulting whole-genome sequence was aligned with all other available ASFV whole-genome sequences from INSDC-databases (as of 21st September 2020) using MAFFT v7.388 (Katoh & Standley, 2013) in Geneious Prime v.2019.2.3 (Biomatters, Auckland, New Zealand), annotated on the basis of ASFV Georgia 2007/1 (FR682468.2) using Geneious, and a phylogenetic tree was constructed with IQTREE v 1.6.5 (Hoang, Chernomor, von Haeseler, Minh, & Vinh, 2018; Kalyaanamoorthy, Minh, Wong, von Haeseler, & Jermiin, 2017; Nguyen, Schmidt, von Haeseler, & Minh, 2015). Whole genome sequences from Poland were kindly provided by N. Mazur and G. Woźniakowski ahead of publication in INSDC databases and compared to the ASFV Germany 2020/1 whole-genome sequence using MAFFT v.7.388 with default parameters in Geneious prime.