Analysis of the Unique Historical Isolate of African Swine Fever Virus Isolate Spencer from Outbreaks in 1951

Abstract

African swine fever (ASF) is a deadly hemorrhagic disease of domestic and wild swine that was first described in the early 20th century after the introduction of European pigs to Kenya. The etiological agent, the African swine fever virus (ASFV), is a large DNA virus within the Asfarviridae family that is broadly categorized epidemiologically into genotypes based on the nucleotide sequence of B646L, the gene encoding the major capsid protein p72. ASF outbreaks in Africa have been linked historically to 25 genotypes by p72 nucleotide analysis and, recently, to 6 genotypes by amino acid comparison, whereas global outbreaks of ASF outside of Africa have only been linked to 2 genotypes: genotype I, which led to an outbreak in Europe during the 1960s that later spread to South America, and genotype II, responsible for the current pandemic that began in Georgia in 2007 and has since spread to Europe, Asia, and Hispaniola. Here, we present an analysis of the genome of ASFV Spencer, an isolate that was collected in 1951 near Johannesburg, South Africa. While nucleotide analysis of Spencer indicates the p72 coding sequence is unique, differentiating from the closest reference by five nucleotides, the predicted amino acid sequence indicates that it is 100% homologous to contemporary genotype 1. Full genome analysis reveals it is more similar to Mkuzi1979 and encodes genes that share similarity with either genotype 1 or genotype 2 outbreak strains.

Keywords: 1951; ASFV; African swine fever; African swine fever virus; South Africa.

Figure 1

Nucleotide alignment of the p72 coding region. The region highlighted in yellow indicates the 478 C-terminal region used in the historic genotype classification. A royal blue bar graph beneath each sequence indicates nucleotide conservation.

Figure 2

Predicted amino acid alignment of the p72 coding region. Amino acid variations are highlighted. A royal blue bar graph beneath each sequence indicates nucleotide conservation.

Figure 3

Phylogenetic tree constructed using the UPGMA method showing the relationships based on average nucleotide identity between Spencer and historic isolates. Scale indicates branch length.

Figure 4

MGF 110 coding region of Spencer, Mkuzi1979, Georgia 2007/1, K49, and L60Mkuzi1979. Arrows indicate the coding direction of predicted ORFs belonging to MGF_110 (gray), MGF_100 (blue), MGF_360 (peach), or non-MGF (green) families. Dark gray ORFs indicate MGF_110 fusion proteins. Genomic deletions are represented by the absence of a black line. Royal blue bar graph beneath the figure indicates nucleotide conservation.

Figure 5

Venn diagram indicating the number of identical genes predicted to be encoded by Mkuzi1979, Georgia 2007/1, and K49 as compared to Spencer.