Genome sequencing reveals a highly divergent genotype II African swine fever virus in Nigeria

Abstract

African swine fever is a viral disease with major socioeconomic consequences in countries including Nigeria, where pig farming sustains many livelihoods. Despite the critical role of genomic data in outbreak control, Nigeria has remained underrepresented in global African swine fever virus (ASFV) genomic datasets. Here, we report the first in-country sequencing and genomic analysis of ASFV from recent outbreaks in Nigeria, representing the largest dataset of ASFV genomes generated in Nigeria and Africa to date. Using Oxford Nanopore and Illumina Technology platforms, we assembled 27 whole-genome sequences from field samples collected in Ogun, Osun, and Oyo States. Comparative analyses revealed nearly 100 single-nucleotide polymorphisms (SNPs) in coding regions and more than 250 across coding and non-coding regions, alongside multiple insertions and deletions relative to the Georgia 2007 ASFV reference genome. Notably, we report novel large deletions in variable regions, which may affect genes linked to virulence and host adaptation. Phylogenetic analysis revealed that the Nigerian ASFV genomes form a distinct clade within biotype II, which also diverges considerably from the genome backbone currently utilized for vaccine designs, highlighting the impact of viral divergence on current control measures.