title: The complete genome sequences of poxviruses isolated from a penguin and a pigeon in South Africa and comparison to other sequenced avipoxviruses.
abstract: BACKGROUND
  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). 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.
  
  
  RESULTS
  The 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.
  
  
  CONCLUSIONS
  The 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.
authors.forename: Kristy
authors.initials: K
authors.lastname: Offerman
authors.forename: Olivia
authors.initials: O
authors.lastname: Carulei
authors.forename: Anelda Philine
authors.initials: AP
authors.lastname: van der Walt
authors.forename: Nicola
authors.initials: N
authors.lastname: Douglass
authors.affiliation: Division of Medical Virology, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa. Anna-Lise.Williamson@uct.ac.za.
authors.forename: Anna-Lise
authors.initials: AL
authors.lastname: Williamson
mesh_terms: D000818:Animals; D018150:Avipoxvirus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D001715:Bird Diseases / Q000821:virology*; D010856:Columbidae; D019143:Evolution, Molecular; D023061:Gene Order; D016679:Genome, Viral; D008969:Molecular Sequence Data; D010802:Phylogeny; D011213:Poxviridae Infections / Q000662:veterinary* / Q000821:virology; D017422:Sequence Analysis, DNA; D013019:South Africa; D046429:Spheniscidae; D026801:Synteny