Genomic analysis of highly virulent Georgia 2007/1 isolate of African swine fever virus

Abstract

African swine fever is widespread in Africa but has occasionally been introduced into other continents. In June 2007, African swine fever was isolated in the Caucasus Region of the Republic of Georgia and subsequently in neighboring countries (Armenia, Azerbaijan, and 9 states of the Russian Federation). Previous data for sequencing of 3 genes indicated that the Georgia 2007/1 isolate is closely related to isolates of genotype II, which has been identified in Mozambique, Madagascar, and Zambia. We report the complete genomic coding sequence of the Georgia 2007/1 isolate and comparison with other isolates. A genome sequence of 189,344 bp encoding 166 open reading frames (ORFs) was obtained. Phylogeny based on concatenated sequences of 125 conserved ORFs showed that this isolate clustered most closely with the Mkuzi 1979 isolate. Some ORFs clustered differently, suggesting that recombination may have occurred. Results provide a baseline for monitoring genomic changes in this virus.

Figure 1

Comparison of the Georgia 2007/1 African swine fever virus (ASFV) isolate genome with those of other ASFV isolates. ASFV phylogeny midpoint was rooted in a neighbor-joining tree on the basis of 125 conserved open reading frame regions (40,810 aa) from 12 taxa. Node values show percentage bootstrap support (n = 1,000). The isolates shown and accession numbers are Kenya AY261360, Malawi Lil20/1 AY261361, Tengani AY261364, Warmbaths AY261365, Pretorisuskop AY261363, Warthog AY261366, Warmbaths AY261365, Mkuzi AY261362, OurT88/3 a.m.712240, BA71V NC_001659, Benin97/1 a.m.712239, and E75 FN557520. Scale bar indicates nucleotide substitutions per site.

Figure 2

Phylogenetic trees of 4 of the most divergent African swine fever virus proteins. A) C-type lectin EP153R, B) A238L, C) CD2-like protein EP402R, D) structural protein K177R (P22). Evolutionary history was inferred by using the neighbor-joining method. The bootstrap consensus tree inferred from 1,000 replicates is taken to represent the evolutionary history of the proteins analyzed. Branches corresponding to partitions reproduced in <50% bootstrap replicates are collapsed. The percentage of replicate trees in which the associated proteins clustered in the bootstrap test (1,000 replicates) are shown next to the branches. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. All positions containing gaps and missing data were eliminated from the dataset (complete deletion option). There were 224 positions in the final dataset. Phylogenetic analyses were conducted in MEGA4 (27). Scale bars indicate amino acid substitutions per site.