Genomic Characterisation of African Swine Fever Virus Strains in Pigs in South South Nigeria: Genotype Distribution and Virulence Markers

This study provides the first genomic characterisation of African swine fever virus (ASFV) strains from pig outbreaks in South South Nigeria, encompassing Rivers, Bayelsa, Delta, Cross River, Akwa Ibom, and Edo States. African swine fever is a devastating and notifiable viral haemorrhagic disease of pigs for which no commercial vaccine is available, and outbreaks in South South Nigeria cause catastrophic losses to pig farmers in the region. Using a cross-sectional molecular epidemiology design, spleen, lymph node, and blood samples were collected from 120 pigs from 30 farms experiencing acute ASF outbreaks. ASFV was confirmed by real-time PCR. Positive samples were subjected to Sanger sequencing of the B646L gene (p72) for genotypic classification and the E183L gene for serotype determination. Virulence marker analysis including the EP402R (CD2v) gene and the MGF360/505 gene families was performed by PCR. Full genome sequencing was attempted on five representative isolates using Illumina technology. The study addresses a critical gap in ASFV genomic data from Nigeria's South South zone. Findings revealed exclusive detection of ASFV Genotype I in all characterised isolates, which is distinct from the Genotype II strain causing the current European pandemic. CD2v gene analysis showed diversity consistent with serogroup 7 dominant strains. Virulence markers were present in all isolates. The study provides genomic data supporting regional vaccine development and containment strategy design. Keywords: African swine fever virus, genomics, genotyping, South South Nigeria, virulence markers.