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Comparative analysis of the complete genome sequences of Kenyan African swine fever virus isolates within p72 genotypes IX and X

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Abstract

Twelve complete African swine fever virus (ASFV) genome sequences are currently publicly available and these include only one sequence from East Africa. We describe genome sequencing and annotation of a recent pig-derived p72 genotype IX, and a tick-derived genotype X isolate from Kenya using the Illumina platform and comparison with the Kenya 1950 isolate. The three genomes constitute a cluster that was phylogenetically distinct from other ASFV genomes, but 98–99 % conserved within the group. Vector-based compositional analysis of the complete genomes produced a similar topology. Of the 125 previously identified ‘core’ ASFV genes, two ORFs of unassigned function were absent from the genotype IX sequence which was 184 kb in size as compared to 191 kb for the genotype X. There were multiple differences among East African genomes in the 360 and 110 multicopy gene families. The gene corresponding to 360-19R has transposed to the 5′ variable region in both genotype X isolates. Additionally, there is a 110 ORF in the tick-derived genotype X isolate formed by fusion of 13L and 14L that is unique among ASFV genomes. In future, functional analysis based on the variations in the multicopy families may reveal whether they contribute to the observed differences in virulence between genotpye IX and X viruses.

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Acknowledgments

We are grateful to the CSIRO-AusAID Africa-Australia Food Security Initiative and to INIA, Spain under research agreement TF069018 for funding. We are particularly grateful to Dr. Bruce Pengelly of CSIRO for his support of this project. CU and CF were supported by an NSERC Discovery grant. We thank Dr. Harry Noyes and the Liverpool University Centre for Genomics technical advice relating to genome sequencing and template amplification. This is ILRI publication number 92–9146–365–5.

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Authors and Affiliations

  1. International Livestock Research Institute (ILRI), PO Box 30709, Nairobi, 00100, Kenya

    Richard P. Bishop, Etienne P. de Villiers & Edward A. Okoth

  2. Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada

    Clare Fleischauer & Chris Upton

  3. EU Reference Laboratory for ASF, CISA-INIA, Valdeolmos, 28130, Madrid, Spain

    Marisa Arias & Carmina Gallardo

Authors
  1. Richard P. Bishop
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  2. Clare Fleischauer
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  3. Etienne P. de Villiers
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  4. Edward A. Okoth
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  5. Marisa Arias
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  6. Carmina Gallardo
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  7. Chris Upton
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Correspondence to Richard P. Bishop.

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Edited by William Dundon.

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Bishop, R.P., Fleischauer, C., de Villiers, E.P. et al. Comparative analysis of the complete genome sequences of Kenyan African swine fever virus isolates within p72 genotypes IX and X. Virus Genes 50, 303–309 (2015). https://doi.org/10.1007/s11262-014-1156-7

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  • DOI: https://doi.org/10.1007/s11262-014-1156-7

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