Next-generation sequencing and phylogenetic analyses
Sequencing resulted in 18.865.783 single-end and 46.020.040 paired-end 300 bp reads from which 1.228.953 reads (1.89%) mapped to the ASFV reference database and were assembled with a coverage of 2082. The ASFV Germany 2020/1 whole-genome sequence encompasses 190,592 bp with a G/C content of 38.4%. Phylogenetically it groups with sequences from ASFV genotype II including all sequences from Eastern Europe, Asia and Belgium (Figure 4). The ASFV Germany 2020/1 sequence shows 99.9% nucleotide sequence identity to the whole-genome sequence of ASFV_Pol17_55892_ C754 (MT847620), which originated from an outbreak south of Warsaw (Piaseczno province, Mazowieckie voivodeship) in 2017 (Mazur-Panasiuk et al., 2020). Furthermore, some characteristic markers e.g. a 14 bp insertion in the O174L gene, a single nucleotide variation in the K145R gene, the MGF 505-5R gene and the K205R gene as well as a one tandem repeat integration in the intergenic region between the genes I73R and I329L described in Poland (Mazur-Panasiuk et al., 2020; Mazur-Panasiuk, Wozniakowski, & Niemczuk, 2019) were also present in ASFV Germany 2020/1. These are in accordance with characteristics found in ASFV sequences from Southern Warsaw and Western Poland (Mazur-Panasiuk et al., 2020; Mazur-Panasiuk et al., 2019) and clearly distinguish ASFV Germany 2020/1 from all other ASFV GTII whole-genome sequences including those from the Czech Republic (LR722600.1), Belgium (LR536725.1), Moldova (LR722599.1) and Georgia (FR682468.2).