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Phylogenomic characterization of historic lumpy skin disease virus isolates from South Africa

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Abstract

The poxvirus lumpy skin disease virus (LSDV) is the causative agent of the vexatious lumpy skin disease, which predominantly affects cattle and water buffalo. It has been endemic to South Africa since the 1950s, and in 1960, a live attenuated vaccine was commercially released for use in the country to mitigate the spread of this transboundary disease. This vaccine (Neethling/vaccine/LW-1959) was generated from serial passages of the prototype lumpy skin disease virus strain Neethling-WC/RSA/1957, which was isolated in 1957 from an outbreak in the Western Cape province of South Africa and was subsequently used to prove the infectious nature of the virus and the resulting disease in cattle. In this study, we determined the complete genome sequence of the LSDV prototype strain Neethling-WC/RSA/1957, as well as three other LSDV isolates from the 1950s, one wild-type isolate from the 1970s, and a commercial vaccine produced in 1988 (LW-1959). Phylogenomic analysis showed that all six sequences were in cluster 1.1, along with previous sequences of the vaccine strain, the oldest known isolate (LSDV/Haden/RSA/1954), and virulent viruses isolated in the 1990s from South Africa. Seven single-nucleotide polymorphisms were identified between the Neethling-WC/RSA/1957 strain and the vaccine strain (LW-1959), providing new insights into virus attenuation and possible markers for DIVA assays.

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Fig. 1
Fig. 2

Data availability

Information on the country of origin, year of isolation, and GenBank accession number for each of the six genome sequences from this study is provided in Table 1.

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Acknowledgements

We thank Dr. Wallace and Ms. Wemmer for critical reading of this manuscript.

Funding

No specific funding was obtained for this study.

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Authors and Affiliations

  1. Agricultural Research Council-Onderstepoort Veterinary Institute, 100 old Soutpan Road, Onderstepoort, 0110, South Africa

    Antoinette van Schalkwyk, Pravesh Kara & Livio Heath

  2. Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville, 7535, South Africa

    Antoinette van Schalkwyk

Authors
  1. Antoinette van Schalkwyk
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  2. Pravesh Kara
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  3. Livio Heath
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All authors contributed to the study conception and design. All authors read and approved the final manuscript.

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Correspondence to Antoinette van Schalkwyk.

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van Schalkwyk, A., Kara, P. & Heath, L. Phylogenomic characterization of historic lumpy skin disease virus isolates from South Africa. Arch Virol 167, 2063–2070 (2022). https://doi.org/10.1007/s00705-022-05515-6

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