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Genome sequence characterization of the unique recombinant vaccine-like lumpy skin disease virus strain Kurgan/2018

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Abstract

In 2018, the molecular epidemiology of lumpy skin disease in Russia was characterized by a surge in novel recombinant vaccine-like strains causing outbreaks along the southern border, spreading in an easterly direction. Currently, five distinct novel recombinant vaccine-like lineages have been described, designated as clusters 2.1 to 2.5. Based on the complete genome sequence analysis of the causative lumpy skin disease virus (Kurgan/Russia/2018), obtained from an eponymous outbreak, the genome was shown to be composed of a Neethling vaccine strain virus as the dominant parental strain and KSGPO vaccine virus as its minor parental strain. These features are similar to those of Saratov/Russia/2017 and Tyumen/Russia/2018, representing clusters 2.1 and 2.4, respectively. However, Kurgan/Russia/2018 has 16 statistically significant recombination events unique to this sequence, contributing to the phylogenetic clustering of Kurgan/Russia/2018 in yet another cluster designed cluster 2.6, based on analysis involving the complete genome sequences.

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Data Availability

All findings reported herein are available within the published article. The genome sequence reported here is available in the GenBank database under the accession number OR194148. The raw reads used for the assembly of the genome sequence of the Kurgan/2018 strain are the property of the funder, and permission to publish the NGS reads has not been granted to the authors.

References

  1. Abutarbush SM, Ababneh MM, Al Zoubi IG, Al Sheyab OM, Al Zoubi MG, Alekish MO, Al Gharabat R (2013) J. Lumpy skin disease in Jordan: disease emergence, clinical signs, complications and preliminary-associated economic losses. Transbound Emerg Dis 62:549–554

    Article  PubMed  Google Scholar 

  2. Tulman ER, Afonso CL, Lu Z, Kutish Zl, Rock GF (2001) Genome of lumpy skin disease virus. J Virol 15:7122–7130. https://doi.org/10.1128/JVI.75.15.7122-7130.2001

    Article  Google Scholar 

  3. Van Schalkwyk A, Byadovskaya O, Shumilova I, Wallace DB, Sprygin A (2022) Estimating evolutionary changes between highly passaged and original parental lumpy skin disease virus strains. Transbound Emerg Dis 69(4):e486–e496. https://doi.org/10.1111/tbed.14326Epub 2021 Oct 6. PMID: 34555250

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  5. Sprygin A, Babin Y, Pestova Y, Kononova S, Wallace DB, Van Schalkwyk A, Byadovskaya O, Diev V, Lozovoy D, Kononov A (2018) Analysis and insights into recombination signals in lumpy skin disease virus recovered in the field. PLoS One. 13(12):e0207480. https://doi.org/10.1371/journal.pone.0207480. eCollection 2018

  6. Sprygin A, Van Schalkwyk A, Shumilova I, Nesterov A, Kononova S, Prutnikov P, Byadovskaya O, Kononov A (2020) Full-length genome characterization of a novel recombinant vaccine-like lumpy skin disease virus strain detected during the climatic winter in Russia, 2019. Arch Virol 165:2675–2677

    Article  CAS  PubMed  Google Scholar 

  7. Krotova A, Byadovskaya O, Shumilova I, Zinyakov N, van Schalkwyk A, Sprygin A (2022) Molecular characterization of a novel recombinant lumpy skin disease virus isolated during an outbreak in Tyumen, Russia, in 2019. Transbound Emerg Dis 69:e2312–e2317. https://doi.org/10.1111/tbed.14574

    Article  CAS  PubMed  Google Scholar 

  8. Ma J, Yuan Y, Shao J, Sun M, He W, Chen J, Liu Q (2022) Genomic characterization of lumpy skin disease virus in southern China. Transbound Emerg Dis 69(5):2788–2799. https://doi.org/10.1111/tbed.14432Epub 2022 Feb 25. PMID: 34927369

    Article  CAS  PubMed  Google Scholar 

  9. Vandenbussche F, Mathijs E, Philips W, Saduakassova M, De Leeuw I, Sultanov A, Haegeman A, De Clercq K (2022). Recombinant LSDV strains in Asia: vaccine spillover or natural emergence?. Viruses 14(7):1429

  10. Krotova A, Mazloum A, Byadovskaya O, Sprygin A (2022) Phylogenetic analysis of lumpy skin disease virus isolates in Russia in 2019–2021. Arch Virol 167:1693–1699

    Article  CAS  PubMed  Google Scholar 

  11. Krotova A, Byadovskaya O, Shumilova I, van Schalkwyk A, Sprygin A (2022) An in-depth bioinformatic analysis of the novel recombinant lumpy skin disease virus strains: from unique patterns to established lineage. BMC Genomics 23(1):396. https://doi.org/10.1186/s12864-022-08639-w

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Kononova S, Kononov A, Shumilova I et al (2021) A lumpy skin disease virus which underwent a recombination event demonstrates more aggressive growth in primary cells and cattle than the classical field isolate. Transbound Emerg Dis 68:1377–1383. https://doi.org/10.1111/tbed.13798

    Article  CAS  PubMed  Google Scholar 

  13. Shumilova I, Krotova A, Nesterov A, Byadovskaya O, van Schalkwyk A, Sprygin A (2022) Overwintering of recombinant lumpy skin disease virus in northern latitudes. Russia Transbound Emerg Dis 69:e3239–e3243

    CAS  PubMed  Google Scholar 

  14. Shumilova I, Nesterov A, Byadovskaya O, Prutnikov P, Wallace DB, Mokeeva M, Pronin V, Kononov A, Chvala I, Sprygin A (2022) A Recombinant Vaccine-like Strain of Lumpy Skin Disease Virus Causes Low-Level Infection of Cattle through Virus-Inoculated Feed. Pathogens 11(8):920. https://doi.org/10.3390/pathogens11080920

    Article  PubMed  PubMed Central  Google Scholar 

  15. Nesterov A, Mazloum A, Byadovskaya O, Shumilova I, Van Schalkwyk A, Krotova A, Sprygin A (2022) Experimentally controlled study indicates that the naturally occurring recombinant vaccine-like lumpy skin disease strain Udmurtiya/2019, detected during freezing winter in northern latitudes, is transmitted via indirect contact. Front Vet Sci 9:1651

    Article  Google Scholar 

  16. Krotova A, Mazloum A, van Schalkwyk A, Prokhvatilova L, Gubenko O, Byadovskaya O, Chvala I, Sprygin A (2023) The Characterization and Differentiation of Recombinant Lumpy Skin Disease Isolates Using a Region within ORF134. Appl Microbiol 3:35–44. https://doi.org/10.3390/applmicrobiol3010003

    Article  Google Scholar 

  17. Haegeman A, De Leeuw I, Philips W, De Regge N (2023) Development and Validation of a New DIVA Real-Time PCR Allowing to Differentiate Wild-Type Lumpy Skin Disease Virus Strains, Including the Asian Recombinant Strains, from Neethling-Based Vaccine Strains. Viruses 15(4):870

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Kononov A, Prutnikov P, Bjadovskaya O, Kononova S, Rusaleev V, Pestova Y, Sprygin A (2020) Emergence of a New Lumpy Skin Disease Virus Variant in Kurgan Oblast, Russia, in 2018. Arch Virol 165:1343–1356. https://doi.org/10.1007/s00705-020-04607-5

    Article  CAS  Google Scholar 

  19. Alexander S, Olga B, Svetlana K, Valeriy Z, Yana P, Pavel P, Aleksandr K (2019) A real-time PCR screening assay for the universal detection of lumpy skin disease virus DNA. BMC Res Notes 12(1):1–5

    Article  Google Scholar 

  20. Mazloum A, van Schalkwyk A, Shotin A, Zinyakov N, Igolkin A, Chernishev R, Debeljak Z, Korennoy F, Sprygin AV (2023). Whole-genome sequencing of African swine fever virus from wild boars in the Kaliningrad region reveals unique and distinguishing genomic mutations. Front Vet Sci 9:1019808

  21. Krotova A, Shalina K, Mazloum A, Kwon D, Van Schalkwyk A, Byadovskaya O, Sprygin A (2022) Genetic characterization of sheep pox virus strains from outbreaks in Central Russia in 2018–2019. Transbound Emerg Dis 69(6):e3430–e3435

    Article  CAS  PubMed  Google Scholar 

  22. Heath L, van der Walt E, Varsani A, Martin DP (2006) Recombination patterns in aphthoviruses mirror those found in other picornaviruses. J Virol 80:11827–11832 pmid:16971423

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, Ingersoll R, Sheppard HW, Ray SC (1999) Full-length human immunodeficiency virus type 1 genomes from subtype C-infected sero-converters in India, with evidence of inter-subtype recombination. J Virol 73(1):152–160 pmid:9847317

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:547–1549

    Article  Google Scholar 

  25. Sprygin A, Mazloum A, van Schalkwyk A, Babiuk S (2022) Capripoxviruses, leporipoxviruses, and orthopoxviruses: Occurrences of recombination. Front Microbiol 13:978829

    Article  PubMed  PubMed Central  Google Scholar 

  26. Sudhakar SB, Mishra N, Kalaiyarasu S, Ahirwar K, Chatterji S, Parihar O, Singh VP, Sanyal A (2023) Lumpy Skin Disease Virus Infection in Free-Ranging Indian Gazelles (Gazella bennettii), Rajasthan, India. Emerg Infect Dis 29(7):1407–1410. https://doi.org/10.3201/eid2907.230043

    Article  PubMed  PubMed Central  Google Scholar 

  27. Ren S, Chen H, Yuan L, Yang X, Afera TB, Rehman ZU, Wang H, Wang X, Ma C, Lin Y, Qiu X, Yin X, Sun Y (2023) Phylogenetic and pathogenic characterization of lumpy skin disease virus circulating in China. Virology 585:127–138. https://doi.org/10.1016/j.virol.2023.06.008

    Article  CAS  PubMed  Google Scholar 

  28. Kumar A, Venkatesan G, Kushwaha A, Poulinlu G, Saha T, Ramakrishnan MA, Dhar P, Kumar GS, Singh RK (2023) Genomic characterization of Lumpy Skin Disease virus (LSDV) from India: Circulation of Kenyan-like LSDV strains with unique kelch-like proteins. Acta Trop 241:106838. https://doi.org/10.1016/j.actatropica.2023.106838

    Article  CAS  PubMed  Google Scholar 

  29. Kononova S, Kononov A, Shumilova I, Byadovskaya O, Nesterov A, Prutnikov P, Babiuk S, Sprygin A (2021) A lumpy skin disease virus which underwent a recombination event demonstrates more aggressive growth in primary cells and cattle than the classical field isolate. Transbound Emerg Dis 68(3):1377–1383. https://doi.org/10.1111/tbed.13798

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

The authors thank Dmitry Kwon and Alena Krotova for excellent technical assistance.

Funding

This work was supported by grant no. 075-15-2021-1054 from the Ministry of Education and Science of Russia to implement the objectives of the Federal Scientific and Technical Program for the Development of Genetic Technologies during 2019–2027.

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Authors and Affiliations

  1. Federal Center for Animal Health, Vladimir, Russia

    Alexander Sprygin, Ali Mazloum, Olga Byadovskaya & Ilya Chvala

  2. Agricultural Research Council – Onderstepoort Veterinary Institute, Pretoria, South Africa

    Antoinette van Schalkwyk

Authors
  1. Alexander Sprygin
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  2. Antoinette van Schalkwyk
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  3. Ali Mazloum
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  4. Olga Byadovskaya
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  5. Ilya Chvala
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Contributions

All authors contributed equally in preparing the manuscript and have read and agreed to the published version.

Corresponding author

Correspondence to Alexander Sprygin.

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Ethics statement

This research was conducted on clinical diagnostic samples submitted for diagnostic testing. No work with animals was performed in this study.

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The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

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Communicated by William G Dundon

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Sprygin, A., van Schalkwyk, A., Mazloum, A. et al. Genome sequence characterization of the unique recombinant vaccine-like lumpy skin disease virus strain Kurgan/2018. Arch Virol 169, 23 (2024). https://doi.org/10.1007/s00705-023-05938-9

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