Genome sequencing reveals variation of African swine fever virus in Nigerian outbreaks and identification of two major West African viral lineages.

Abstract

African swine fever is a transboundary disease of wild boar and domestic pigs that is caused by the African swine fever virus (ASFV), with a mortality rate of 100 % in naïve animals. The ongoing spread poses a significant threat to food security and economic stability globally. In Nigeria, frequent outbreaks of the disease have been reported since 1997, and genetic analysis of Nigerian ASFV has defined virulent genotypes I and II. The disease has caused a significant impact in the pig-producing regions of the country, resulting in high economic losses. For improved control of the virus, a better knowledge of the virus's genetic diversity is required. Here, we report five complete genome assemblies of ASFV from Nigeria, four genomes assembled with hybrid sequencing platforms and one using the Oxford Nanopore Technology, from different outbreaks between 2020 and 2024. Phylogenetic analysis indicates that these outbreak strains are of genotypes I and II, showing a striking sequence similarity to Benin 97/1 and Nigeria-RV502 of ≥99.90 %. Evolutionary analysis identified CAM1994 and Mauritius MAU/01/2007 to be the closest to the common ancestor of the circulating virus strains in Nigeria. The study reports for the first time the simultaneous occurrence of genotypes I and II in Nigeria. The study documents the evolutionary pattern of the two circulating genotypes in Nigeria and the West African region, allowing monitoring of the transmission dynamics, which will help strengthen surveillance and disease control.