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).