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Sequence analysis and evaluation of the NS3/A gene region of bluetongue virus isolates from South Africa

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Abstract

Phylogenetic networks and sequence analysis allow a more accurate understanding of the serotypes, genetic relationships and epidemiology of viruses. Based on gene sequences of the conserved segment 10 (NS3), bluetongue virus (BTV) can be divided into five topotypes. In this molecular epidemiology study, segment 10 sequence data of 11 isolates obtained from the Virology Section of the Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, were analyzed and compared to sequence data of worldwide BTV strains available in the GenBank database. The consensus nucleotide sequences of NS3/A showed intermediate levels of variation, with the nucleotide sequence identity ranging from 79.72 % to 100 %. All 11 strains demonstrated conserved amino acid characteristics. Phylogenetic networks were used to identify BTV topotypes. The phylogeny obtained from the nucleotide sequence data of the NS3/A-encoding gene presented three major and two minor topotypes. The clustering of strains from different geographical areas into the same group indicated spatial spread of the segment 10 genes, either through gene reassortment or through the introduction of new strains from other geographical areas via trade. The effect of reassortment and genetic drift on BTV and the importance of correct serotyping to identify viral strains are highlighted.

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Acknowledgments

We thank the University of Pretoria, Department Veterinary Tropical Diseases, for giving us the opportunity to do the work. Dr. Melvyn Quan, Mr. Louwrens Snyman, Dr. Peter Coetzee and Miss Karen Eberhson are acknowledged for their assistance, and Dr. Otto Koekemoer, for information on sequences. Funding was received from the National Research Foundation and the Meat Industry Trust.

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Authors and Affiliations

  1. Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort, 0110, South Africa

    Jumari Steyn & Estelle Hildegard Venter

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  1. Jumari Steyn
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  2. Estelle Hildegard Venter
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Correspondence to Jumari Steyn or Estelle Hildegard Venter.

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This study was approved by the Research Committee (V079/12).

Conflict of interest

The authors declare that they have no financial or personal relationships which may have inappropriately influenced the outcomes and conclusions they may have drawn.

Additional information

Nucleotide sequences are available in the GenBank database under the following accession numbers: BTV-2 is KJ506696, BTV-7 is KJ506695, BTV-8 is KJ506703, BTV-11 is KJ506694, BTV-16 is KJ506697, BTV-19 is KJ506699, BTV-20 is KJ506702, BTV-21 is KJ506701, BTV-22 is KJ506698, BTV-22 is KJ506700, BTV-S299 is KJ506704.

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Steyn, J., Venter, E.H. Sequence analysis and evaluation of the NS3/A gene region of bluetongue virus isolates from South Africa. Arch Virol 161, 947–957 (2016). https://doi.org/10.1007/s00705-015-2741-3

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