Molecular Characterization of African swine fever virus
For ASFV genotyping and assessing the patterns of genetic variation among ASFV positive samples, three regions within the ASFV genome were PCR amplified and sequenced. These were the C-terminal end of theB646L gene encoding the p72 protein, the full length ofE183L gene encoding p54 protein, and CVR within theB602L gene as previously described (Bastos et al., 2003; Lubisi et al., 2005; Phologane et al., 2005 ; Nix et al., 2006; Gallardo et al., 2009). The PCR products were purified using MinElute PCR purification kit (Qiagen) as described by the manufacturer’s protocol and characterized commercially at Macrogen Inc. (Netherlands Europe) using Sanger sequencing method. The assemblage of sequence reads was carried out using the Staden software package (http://staden.sourceforge.net/) and Bioedit (Hall, 1995) with default settings. Confirmation of sequences type was carried out using the BLAST tool, (https://blast.ncbi.nlm.nih.gov/Blast.cgi). Phylogenetic trees were constructed using MEGA X and inferred using Neighbour Joining method for p72 and Minimum Evolution method for p54 (Kumar et al., 2018). ASFV genotypes were retrieved from the Genbank for the construction of the phylogenetic trees for both p72 andp54 . All ASFV sequences from this study were submitted to the Genbank under accession numbers: OL621859- OL621879 for B646Lgene, OL621880- OL621896 for E183L and OL638971-OL638986 for