Abstract
BackgroundTwo novel avipoxviruses from South Africa have been sequenced, one from a Feral Pigeon (Columba livia) (FeP2) and the other from an African penguin (Spheniscus demersus) (PEPV). We present a purpose-designed bioinformatics pipeline for analysis of next generation sequence data of avian poxviruses and compare the different avipoxviruses sequenced to date with specific emphasis on their evolution and gene content.ResultsThe FeP2 (282 kbp) and PEPV (306 kbp) genomes encode 271 and 284 open reading frames respectively and are more closely related to one another (94.4%) than to either fowlpox virus (FWPV) (85.3% and 84.0% respectively) or Canarypox virus (CNPV) (62.0% and 63.4% respectively). Overall, FeP2, PEPV and FWPV have syntenic gene arrangements; however, major differences exist throughout their genomes. The most striking difference between FeP2 and the FWPV-like avipoxviruses is a large deletion of ~16 kbp from the central region of the genome of FeP2 deleting a cc-chemokine-like gene, two Variola virus B22R orthologues, an N1R/p28-like gene and a V-type Ig domain family gene. FeP2 and PEPV both encode orthologues of vaccinia virus C7L and Interleukin 10. PEPV contains a 77 amino acid long orthologue of Ubiquitin sharing 97% amino acid identity to human ubiquitin.ConclusionsThe genome sequences of FeP2 and PEPV have greatly added to the limited repository of genomic information available for the Avipoxvirus genus. In the comparison of FeP2 and PEPV to existing sequences, FWPV and CNPV, we have established insights into African avipoxvirus evolution. Our data supports the independent evolution of these South African avipoxviruses from a common ancestral virus to FWPV and CNPV.
Highlights
Two novel avipoxviruses from South Africa have been sequenced, one from a Feral Pigeon (Columba livia) (FeP2) and the other from an African penguin (Spheniscus demersus) (PEPV)
The genomes of only three avipoxviruses have been published; a pathogenic American strain of fowlpox virus (FPVUS) [9], an attenuated European strain of fowlpox virus derived from European FWPV HP1 passaged over 400 times in chick embryo fibroblasts (FP9) [10], and a virulent canarypox virus isolated from a canary (CNPVATCC VR-111) [11]
Inverted Terminal Repeats (ITRs) The FeP2 and penguinpox virus (PEPV) genomes, like most other poxviruses, contain two identical inverted repeated sequences at their termini (ITR). These are 4,682 bp in FeP2 and 5,766 bp in PEPV, both of which are shorter than the ITRs of the other sequenced avipoxviruses (FPVUS: 9,520 bp, FP9: 10,158 bp and Canarypox virus (CNPV): 6,491 bp)
Summary
Two novel avipoxviruses from South Africa have been sequenced, one from a Feral Pigeon (Columba livia) (FeP2) and the other from an African penguin (Spheniscus demersus) (PEPV). Comparison of the CNPV and FWPV genomes reveals overall synteny in genome arrangement with similar genetic complements. They do exhibit significant differences in the terminal, variable regions as well as in three internal, variable regions which is in contrast to the conservation of central genomic regions in other Chordopoxviruses (ChPVs). These variable regions within the conserved central region of the genomes occur near the junctions of areas that were identified in FWPV as rearranged relative to other ChPVs and contain genes involved in virus-host interactions [9,11]. Avipoxviruses are considerably divergent from other ChPVs [9,11] and may constitute a separate subfamily within the Poxviridae family [11,12,13]
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