Complete genome sequencing and comparative phylogenomics of multiple African swine fever virus (ASFV) field isolates of the virulent East African p72 genotype IX viruses. Nine complete genomes of ASFV gen IX viruses

African swine fever virus (ASFV) is a lethal disease of domestic pigs, endemic to wild pigs and Argasidae soft ticks in sub-Saharan Africa. The virus has caused several domestic pig pandemics outside Africa and there is a very strong bias among current genome sequences to derivatives of p72 genotype I and II viruses that have induced epidemics outside Africa. We describe nine novel complete genome IX sequences and provide a phylogenomic analysis of 14 virulent genotype IX viruses from East Africa relative to genomes from other ASFV p72 clades. We also demonstrate differences between these on genotype IX genome sequence and a wild boar cell-passaged variant. The genotype IX genomes cluster with five genomes within East African genotype p72 X. However, genomes from genotypes IX and X are very distinct from those of other p72-genotype. The genotype IX p72 gene-derived primer sequences used for virus diagnosis are distinct from the type primers potentially resulting in reduced sensitivity in surveillance. The novel ASFV IX genomes that we sequenced were generated from DNA isolated directly from field-sampled tissues or primary isolates. We predict that genome sequencing from ASFV field isolates from the indigenous regions of sub-Saharan Africa should become routine, and result in a rapid expansion of knowledge on African ASFV diversity at the whole genome level.