Molecular Characterization of African swine fever virus genotype II strains from Nigeria
Total nucleic acid was extracted from PPL cultures (using the 5X MagMaxTM Pathogen RNA/DNA kit  was used. For Illumina sequencing,  ASFV genome in the sample was enriched using a custom myBaits ASF target capture kit (Arbor Biosciences, Ann Arbor, MI ) and the sequence libraries were prepared using Nextera XT DNA Library Preparation Kit  (Illumina). Sequencing was performed on an Illumina Miseq instrument using a V2 flow cell with a 500 cycle reagent cartridge (Illumina). The same nucleic acid extract was subjected to Nanopore sequencing using the GridION X5. For library preparation SQK-RPB004 was used and the sample was run on a R9.4 Flowcell. Guppy 4.0.11 with the high-accuracy model was used for base calling. To generate additional data, nucleic acid extracted from 10% tissue homogenate of whole blood from one of the two pigs that died after inoculation with ASFV RV502 (described below) was also subjected to Illumina and Nanopore sequencing. At the end, all data was pooled for analysis.