Skip directly to site content Skip directly to page options Skip directly to A-Z link Skip directly to A-Z link Skip directly to A-Z link
Volume 17, Number 4—April 2011
Research

Genomic Analysis of Highly Virulent Georgia 2007/1 Isolate of African Swine Fever Virus

David A.G. Chapman, Alistair C. Darby, Melissa Da Silva, Chris Upton, Alan D. Radford, and Linda K. DixonComments to Author 
Author affiliations: Author affiliations: Institute for Animal Health, Woking, UK (D.A.G. Chapman, L.K. Dixon); University of Liverpool, Neston, UK (A.C. Darby, A. Radford); University of Victoria, Victoria, British Columbia, Canada (M. Da Silva, C. Upton)

Main Article

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 re

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.

Main Article

References
  1. Costard  S, Wieland  B, de Glanville  W, Jori  F, Rowlands  R, Vosloo  W, African swine fever: how can global spread be prevented? Philos Trans R Soc Lond B Biol Sci. 2009;364:2683–96. DOIPubMedGoogle Scholar
  2. Dixon  LK, Escribano  JM, Martins  C, Rock  DL, Salas  ML, Wilkinson  PJ. Asfarviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA, editors. Virus taxonomy: eighth report of the International Committee on Taxonomy of Viruses. London: Elsevier/Academic Press; 2005. p. 135–43.
  3. Rojo  G, Garcia-Beato  R, Vinuela  E, Salas  ML, Salas  J. Replication of African swine fever virus DNA in infected cells. Virology. 1999;257:524–36. DOIPubMedGoogle Scholar
  4. Iyer  LM, Balaji  S, Koonin  EV, Aravind  L. Evolutionary genomics of nucleo-cytoplasmic large DNA viruses. Virus Res. 2006;117:156–84. DOIPubMedGoogle Scholar
  5. ProMED-mail. African swine fever—Russia (05): (KB), conf., culled. 2010 Apr 6 [cited 2011 Jan 6]. http://www.promedmail.org, archive no. 20100406.1107.
  6. Bastos  ADS, Penrith  ML, Cruciere  C, Edrich  JL, Hutchings  G, Roger  F, Genotyping field strains of African swine fever virus by partial p72 gene characterisation. Arch Virol. 2003;148:693–706. DOIPubMedGoogle Scholar
  7. Rowlands  RJ, Michaud  V, Heath  L, Hutchings  G, Oura  C, Vosloo  W, African swine fever virus isolate, Georgia, 2007. Emerg Infect Dis. 2008;14:1870–4. DOIPubMedGoogle Scholar
  8. Rutherford  K, Parkhill  J, Crook  J, Horsnell  T, Rice  P, Rajandream  MA, Artemis: sequence visualization and annotation. Bioinformatics. 2000;16:944–5. DOIPubMedGoogle Scholar
  9. Salzberg  SL, Delcher  AL, Kasif  S, White  O. Microbial gene identification using interpolated Markov models. Nucleic Acids Res. 1998;26:544–8. DOIPubMedGoogle Scholar
  10. Tcherepanov  V, Ehlers  A, Upton  C. Genome annotation transfer utility (GATU): rapid annotation of viral genomes using a closely related reference genome. BMC Genomics. 2006;7:150. DOIPubMedGoogle Scholar
  11. Upton  C, Hogg  D, Perrin  D, Boone  M, Harris  NL. Viral genome organizer: a system for analyzing complete viral genomes. Virus Res. 2000;70:55–64. DOIPubMedGoogle Scholar
  12. Ronaghi  M. Pyrosequencing sheds light on DNA sequencing. Genome Res. 2001;11:3–11. DOIPubMedGoogle Scholar
  13. Ronaghi  M, Uhlen  M, Nyren  P. A sequencing method based on real-time pyrophosphate. Science. 1998;281:363. DOIPubMedGoogle Scholar
  14. Chapman  DAG, Tcherepanov  V, Upton  C, Dixon  LK. Comparison of the genome sequences of nonpathogenic and pathogenic African swine fever virus isolates. J Gen Virol. 2008;89:397–408. DOIPubMedGoogle Scholar
  15. Yáñez  RJ, Rodriguez  JM, Nogal  ML, Yuste  L, Enriquez  C, Rodriguez  JF, Analysis of the complete nucleotide sequence of African swine fever virus. Virology. 1995;208:249–78. DOIPubMedGoogle Scholar
  16. Yozawa  T, Kutish  GF, Afonso  CL, Lu  Z, Rock  DL. Two novel multigene families, 530 and 300, in the terminal variable regions of African swine fever virus genome. Virology. 1994;202:997–1002. DOIPubMedGoogle Scholar
  17. Boinas  FS, Hutchings  GH, Dixon  LK, Wilkinson  PJ. Characterization of pathogenic and non-pathogenic African swine fever virus isolates from Ornithodoros erraticus inhabiting pig premises in Portugal. J Gen Virol. 2004;85:2177–87. DOIPubMedGoogle Scholar
  18. Zsak  L, Borca  MV, Risatti  GR, Zsak  A, French  RA, Lu  Z, Preclinical diagnosis of African swine fever in contact-exposed swine by a real-time PCR assay. J Clin Microbiol. 2005;43:112–9. DOIPubMedGoogle Scholar
  19. Haresnape  JM, Wilkinson  PJ. A study of African swine fever virus–infected ticks (Ornithodoros moubata) collected from 3 villages in the ASF enzootic area of Malawi following an outbreak of the disease in domestic pigs. Epidemiol Infect. 1989;102:507–22. DOIPubMedGoogle Scholar
  20. Pan  IC. African swine fever virus: generation of subpopulations with altered immunogenicity and virulence following passage in cell cultures. J Vet Med Sci. 1992;54:43–52.PubMedGoogle Scholar
  21. Borca  MV, Carrillo  C, Zsak  L, Laegreid  WW, Kutish  GF, Neilan  JG, Deletion of a CD2-like gene, 8-DR, from African swine fever virus affects viral infection in domestic swine. J Virol. 1998;72:2881–9.PubMedGoogle Scholar
  22. Hurtado  C, Granja  AG, Bustos  MJ, Nogal  ML, de Buitrago  GG, de Yebenes  VG, The C-type lectin homologue gene (EP153R) of African swine fever virus inhibits apoptosis both in virus infection and in heterologous expression. Virology. 2004;326:160–70. DOIPubMedGoogle Scholar
  23. Goatley  LC, Marron  MB, Jacobs  SC, Hammond  JM, Miskin  JE, Abrams  CC, Nuclear and nucleolar localization of an African swine fever virus protein, I14L, that is similar to the herpes simplex virus-encoded virulence factor ICP34.5. J Gen Virol. 1999;80:525–35.PubMedGoogle Scholar
  24. Sussman  MD, Lu  Z, Kutish  G, Afonso  CL, Roberts  P, Rock  DL. Identification of an African swine fever virus gene with similarity to a myeloid differentiation primary response gene and a neurovirulence-associated gene of herpes simplex virus. J Virol. 1992;66:5586–9.PubMedGoogle Scholar
  25. Zsak  L, Lu  Z, Kutish  GF, Neilan  JG, Rock  DL. An African swine fever virus virulence-associated gene NL-S with similarity to the herpes simplex virus ICP34.5 gene. J Virol. 1996;70:8865–71.PubMedGoogle Scholar
  26. Camacho  A, Vinuela  E. Protein p22 of African swine fever virus: an early structural protein that is incorporated into the membrane of infected cells. Virology. 1991;181:251–7. DOIPubMedGoogle Scholar
  27. Tamura  K, Dudley  J, Nei  M, Kumar  S. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol. 2007;24:1596–9. DOIPubMedGoogle Scholar
  28. Neilan  JG, Zsak  L, Lu  Z, Kutish  GF, Afonso  CL, Rock  DL. Novel swine virulence determinant in the left variable region of the African swine fever virus genome. J Virol. 2002;76:3095–104. DOIPubMedGoogle Scholar
  29. de Villiers  EP, Gallardo  C, Arias  M, da Silva  M, Upton  C, Martin  R, Phylogenomic analysis of 11 complete African swine fever virus genome sequences. Virology. 2010;400:128–36. DOIPubMedGoogle Scholar

Main Article

Page created: July 25, 2011
Page updated: July 25, 2011
Page reviewed: July 25, 2011
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.
file_external