Characterization of a Novel African Swine Fever Virus p72 Genotype II from Nigeria

Abstract

African swine fever (ASF) is a high-consequence transboundary hemorrhagic fever of swine. It continues to spread across the globe causing socio-economic issues and threatening food security and biodiversity. In 2020, Nigeria reported a major ASF outbreak, killing close to half a million pigs. Based on the partial sequences of the genes B646L (p72) and E183L (p54), the virus responsible for the outbreak was identified as an African swine fever virus (ASFV) p72 genotype II. Here, we report further characterization of ASFV RV502, one of the isolates obtained during the outbreak. The whole genome sequence of this virus revealed a deletion of 6535 bp between the nucleotide positions 11,760-18,295 of the genome, and an apparent reverse complement duplication of the 5' end of the genome at the 3' end. Phylogenetically, ASFV RV502 clustered together with ASFV MAL/19/Karonga and ASFV Tanzania/Rukwa/2017/1 suggesting that the virus responsible for the 2020 outbreak in Nigeria has a South-eastern African origin.

Keywords: African swine fever; Nigeria; West Africa; genotype II.

Figure 1

ASF outbreak map. Affected states based on 2020 WAHIS WOAH reports are marked with blue circles. The states in which the samples were tested at the NCFAD are marked with red circles. The Cross River state that reported ASFV genotype I strain is marked with a triangle.

Figure 2

Diagram showing the sites of deletion and reorganization in the ASFV RV502 genome compared to the ASFV Georgia 2007/1. ASFV RV502 genome is lacking 6535 bp between the nucleotide positions 11,760–18,295 of the genome which includes 14 genes. Additionally, a 688 bp deletion resulted in an in-frame fusion of MGF 110-3L and 110-4L (yellow arrow). A single nucleotide insertion within the MGF 360 1L gene, changed MGF360 1L to the KP360L (red arrow). At the 3′ end of the genome, there is an apparent reverse complement duplication of the 5′ end of the genome, creating an in-frame fusion between MGF 360-21R and 2L, and continues to include a duplication of KP360L (labelled as KP360R).

Figure 3

Maximum-likelihood (ML) phylogenetic tree of 162 ASFV whole genome sequences. Sequences were aligned in MAFFT 7.505 with 1000 bootstrap followed by phylogenetic tree construction using the IQ-TREE. The phylogenetic tree was then visualized using ggtree. The 2020 and 2019 ASFV Nigerian strains sequenced are represented in blue. For clarity, only a limited number of ASFV p72 genotypes are depicted. All sequences belonged to Genotype I are collapsed, the sequences representing different countries are color coded, and the ASFV RV502 sequence (OP672342) is in bold.