Target capture sequencing for the first Nigerian genotype I African swine fever virus genome

A new study, published in Microbial Genomics (July 2023), reports for the first time the determination of near-complete genomes of African swine fever virus using in-solution hybrid capture sequencing. This represents an important advance in understanding the global evolutionary landscape of African swine fever viruses.

African swine fever is a contagious viral disease that affects domestic pigs and wild boars, causing significant economic losses globally.

After the first outbreak of African swine fever in Nigeria in 1997, there have been frequent reports of the disease in pig-producing regions in the country. To facilitate its control, it is important to understand the genotype and phylogenetic relationship of African swine fever viruses.

Recent genetic analysis of Nigerian African swine fever virus isolates has revealed the presence of both genotypes I and II; this is based on analysis of a few selected genes. Phylogenetic analysis of African swine fever virus whole genomes highlights virus origins and evolution in greater depth.

However, there is currently no information on the African swine fever virus genome from Nigerian isolates, hence this study to fill this gap in knowledge.

Two African swine fever virus–positive samples were detected during a random survey of 150 Nigerian indigenous pig samples collected in 2016.

Near-complete genomes of the two ASFV-positive samples were assembled using in-solution hybrid capture sequencing.

The genome-wide phylogenetic tree assigned these two genomes into p72 genotype I, particularly close to the virulent Benin 97/1 strain.

The two ASFVs share 99.94 and 99.92 % genomic sequence identity to Benin97/1.

These findings provide insight into the origin and relationship of African swine fever virus strains from Nigeria and Italy.

Citation
Adeola, A.C., Luka, P.D., Xiang-Xiang Jiang, Zheng-Fei Cai, Oluwole, O.O., Xian Shi, Oladele, B.M., Olorungbounmi, T.O., Boladuro, B., Omotosho, O., Okoro, V.M.O., Dawuda, P.M., Olaogun, S.C., Sanke, O.J., Hai-Bing Xie, Bishop, R.P., Jianlin Han, Jianbo Li, Ya-Ping Zhang and Min-Sheng Peng. 2023. Target capture sequencing for the first Nigerian genotype I ASFV genome. Microbial Genomics 9(7):001069.

Photo credit: Local pigs in Tay Nguyen, Vietnam (ILRI/Fred Unger)