Sequencing and Analysis of Lumpy Skin Disease Virus Whole Genomes Reveals a New Viral Subgroup in West and Central Africa

Ismar R Haga¹, Barbara B Shih^{2

3}, Gessica Tore¹, Noemi Polo¹, Paolo Ribeca^{1

4

5

6

7}, Delgerzul Gombo-Ochir⁸, Gansukh Shura⁸, Tsagaan Tserenchimed⁸, Bazarragchaa Enkhbold⁸, Dulam Purevtseren⁸, Gerelmaa Ulziibat⁸, Batchuluun Damdinjav⁹, Lama Yimer^{10

11}, Fufa D Bari¹¹, Daniel Gizaw¹², Adeyinka Jeremy Adedeji¹³, Rebecca Bitiyong Atai¹³, Jolly Amoche Adole¹³, Banenat Bajehson Dogonyaro¹³, Pradeep Lakpriya Kumarawadu¹⁴, Carrie Batten¹, Amanda Corla¹, Graham L Freimanis¹, Chandana Tennakoon¹, Andy Law², Samantha Lycett², Tim Downing¹, Philippa M Beard^{1

15}

Affiliations

¹ The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK.
² The Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, Midlothian EH25 9RG, UK.
³ Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YW, UK.
⁴ UK Health Security Agency, 61 Colindale Ave, London NW9 5EQ, UK.
⁵ NIHR Health Protection Research Unit in Genomics and Enabling Data, Mathematics Institute, Zeeman Builing, University of Warwick, Coventry CV4 7AL, UK.
⁶ NIHR Health Protection Research Unit in Gastrointestinal Infections, Ronald Ross Building, University of Liverpool, Liverpool L69 7BE, UK.
⁷ Biomathematics and Statistics Scotland, James Maxwell Clerk Building, Peter Guthrie Tait Road, Kings Buildings, Edinburgh EH9 3FD, UK.
⁸ Laboratory of Transboundary Animal Disease Diagnosis and Surveillance, State Central Veterinary Laboratory, Zaisan, Ulaanbaatar 17024, Mongolia.
⁹ General Authority for Veterinary Service, Ministry of Food, Agriculture and Light Industry, Ulaanbaatar 13381, Mongolia.
¹⁰ School of Veterinary Medicine, Wollega University, Nekemte P.O. Box 395, Ethiopia.
¹¹ College of Veterinary Medicine and Agriculture, Addis Ababa University, Bishoftu P.O. Box 3434, Ethiopia.
¹² Animal Health Institute (AHI), Sebata P.O. Box 04, Ethiopia.
¹³ National Veterinary Research Institute, Vom 930103, Nigeria.
¹⁴ Department of Animal Production and Health, Gatambe, Peradeniya 20400, Sri Lanka.
¹⁵ School of Life Sciences, Keele University, Staffordshire ST5 5BG, UK.

PMID: 38675899
PMCID: PMC11053774
DOI: 10.3390/v16040557

Sequencing and Analysis of Lumpy Skin Disease Virus Whole Genomes Reveals a New Viral Subgroup in West and Central Africa

Ismar R Haga et al. Viruses. 2024.

. 2024 Apr 3;16(4):557.

doi: 10.3390/v16040557.

Authors

Affiliations

¹ The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK.
² The Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, Midlothian EH25 9RG, UK.
³ Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YW, UK.
⁴ UK Health Security Agency, 61 Colindale Ave, London NW9 5EQ, UK.
⁵ NIHR Health Protection Research Unit in Genomics and Enabling Data, Mathematics Institute, Zeeman Builing, University of Warwick, Coventry CV4 7AL, UK.
⁶ NIHR Health Protection Research Unit in Gastrointestinal Infections, Ronald Ross Building, University of Liverpool, Liverpool L69 7BE, UK.
⁷ Biomathematics and Statistics Scotland, James Maxwell Clerk Building, Peter Guthrie Tait Road, Kings Buildings, Edinburgh EH9 3FD, UK.
⁸ Laboratory of Transboundary Animal Disease Diagnosis and Surveillance, State Central Veterinary Laboratory, Zaisan, Ulaanbaatar 17024, Mongolia.
⁹ General Authority for Veterinary Service, Ministry of Food, Agriculture and Light Industry, Ulaanbaatar 13381, Mongolia.
¹⁰ School of Veterinary Medicine, Wollega University, Nekemte P.O. Box 395, Ethiopia.
¹¹ College of Veterinary Medicine and Agriculture, Addis Ababa University, Bishoftu P.O. Box 3434, Ethiopia.
¹² Animal Health Institute (AHI), Sebata P.O. Box 04, Ethiopia.
¹³ National Veterinary Research Institute, Vom 930103, Nigeria.
¹⁴ Department of Animal Production and Health, Gatambe, Peradeniya 20400, Sri Lanka.
¹⁵ School of Life Sciences, Keele University, Staffordshire ST5 5BG, UK.

PMID: 38675899
PMCID: PMC11053774
DOI: 10.3390/v16040557

Abstract

Lumpy skin disease virus (LSDV) is a member of the capripoxvirus (CPPV) genus of the Poxviridae family. LSDV is a rapidly emerging, high-consequence pathogen of cattle, recently spreading from Africa and the Middle East into Europe and Asia. We have sequenced the whole genome of historical LSDV isolates from the Pirbright Institute virus archive, and field isolates from recent disease outbreaks in Sri Lanka, Mongolia, Nigeria and Ethiopia. These genome sequences were compared to published genomes and classified into different subgroups. Two subgroups contained vaccine or vaccine-like samples ("Neethling-like" clade 1.1 and "Kenya-like" subgroup, clade 1.2.2). One subgroup was associated with outbreaks of LSD in the Middle East/Europe (clade 1.2.1) and a previously unreported subgroup originated from cases of LSD in west and central Africa (clade 1.2.3). Isolates were also identified that contained a mix of genes from both wildtype and vaccine samples (vaccine-like recombinants, grouped in clade 2). Whole genome sequencing and analysis of LSDV strains isolated from different regions of Africa, Europe and Asia have provided new knowledge of the drivers of LSDV emergence, and will inform future disease control strategies.

Keywords: cattle; lumpy skin disease virus; poxvirus.

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Conflict of interest statement

The authors declare no conflicts of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

Figures

**Figure 1**
Core genome phylogenies for (A) all 22 LSDV samples and (B) clade 1.2 only (18 samples). (A) The clade 1.1 Neethling strain was distinct from the clade 2 Hong Kong/Mongolia isolates. (B) Clade 1.2 was divided into three groups: clade 1.2.2 related to Kenyan sheep and goat pox (KSGP) vaccines (blue, n = 6), clade 1.2.3 linked to west and central Africa (green, n = 5) and clade 1.2.1 with samples from the Middle East and east Africa (red, n = 7). Bootstraps with values > 90 are shown.

**Figure 2**
Phylogenies of the (A) central (67,250 to 99,575 bp) and (B) adjacent core genome regions (13,851–66,966 and 99,608–106,910 bp, concatenated). (A) At the central core genome, clade 2’s Hong Kong and the Mongolia pair (grey) had ancestry more like clade 1.2.2 (clade 1.2.2 in blue, clade 1.2.3 in green, clade 1.2.1 in red). (B) At the adjacent core genome regions, clade 2 was more like Neethling (clade 1.1).

**Figure 3**
Geographic distribution of the LSDV strains. Colour designations: clade 1.2.1 red, clade 1.2.2 blue, clade 1.2.3 green, and clade 2 yellow.

See this image and copyright information in PMC

References

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BB/R002606/1, BB/R008833/1, BB/X011038/1, BB/X011046/1, BB/CCG2250, BB/CCG1780/1, BBS/E/RL/230002C, BBS/E/RL/230002D, , BBS/E/I/00007039, /1, BB/IDG2250/1,/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom

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Sequencing and Analysis of Lumpy Skin Disease Virus Whole Genomes Reveals a New Viral Subgroup in West and Central Africa

Affiliations

Sequencing and Analysis of Lumpy Skin Disease Virus Whole Genomes Reveals a New Viral Subgroup in West and Central Africa

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

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MeSH terms

Grants and funding

LinkOut - more resources

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