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Mishra R, Biswas SK, Nandi S, Mahajan S, Sai Balaji KG, Gairola V, Poloju D, Gulzar S, Singh KP, Singh RK, Sharma GK. Deciphering the genetic landscape of lumpy skin disease: Unraveling variable virulence through comprehensive genome sequence analysis in India. Virology 2024; 596:110123. [PMID: 38805805 DOI: 10.1016/j.virol.2024.110123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/10/2024] [Accepted: 05/22/2024] [Indexed: 05/30/2024]
Abstract
Lumpy Skin Disease (LSD), a poxvirus disease affecting cattle, emerged in India in 2019 and intensified in 2022, resulting in significant economic losses for dairy farmers. There was unusual shift in mortality and morbidity patterns during the second wave. A comprehensive genetic study conducted, analyzing samples from 2019 to 2022 revealed circulation of two distinct subclades (subclade 1.2a and 1.2b) in India, with the latter showing a different pattern in morbidity and mortality. Notably, the Ankyrin repeats gene-based analysis could differentiate animals with varying clinical scores. Genetic variations were significant, with unique deletions identified, including a 12-nucleotide deletion in the GPCR gene in virus isolates collected during 2022 outbreaks, not reported earlier in Indian LSDV strains. A crucial finding was a significant 95-nucleotide deletion in the Functional Resolution Sequence (FRS) repeats of LSDV genomes from 2022 outbreaks, absent in 2019 samples. These deletions may have influenced the virus's virulence in India.
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Affiliation(s)
- R Mishra
- Center for Animal Disease Research and Diagnosis, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India.
| | - S K Biswas
- Center for Animal Disease Research and Diagnosis, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India.
| | - S Nandi
- Center for Animal Disease Research and Diagnosis, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India.
| | - S Mahajan
- Division of Veterinary Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India.
| | - K G Sai Balaji
- Center for Animal Disease Research and Diagnosis, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India.
| | - V Gairola
- Center for Animal Disease Research and Diagnosis, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India; Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA.
| | - D Poloju
- Center for Animal Disease Research and Diagnosis, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India.
| | - S Gulzar
- Center for Animal Disease Research and Diagnosis, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India.
| | - K P Singh
- Center for Animal Disease Research and Diagnosis, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India.
| | - R K Singh
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India.
| | - G K Sharma
- Center for Animal Disease Research and Diagnosis, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, 243122, India
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Makalo MJR, Settypalli TBK, Meki IK, Bakhoum MT, Ahmed HO, Phalatsi MS, Ramatla T, Onyiche TE, Nionzima-Bohloa L, Metlin A, Dhingra M, Cattoli G, Lamien CE, Thekisoe OMM. Genetic Characterization of Lumpy Skin Disease Viruses Circulating in Lesotho Cattle. Viruses 2024; 16:762. [PMID: 38793643 PMCID: PMC11125814 DOI: 10.3390/v16050762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Lumpy skin disease is one of the fast-spreading viral diseases of cattle and buffalo that can potentially cause severe economic impact. Lesotho experienced LSD for the first time in 1947 and episodes of outbreaks occurred throughout the decades. In this study, eighteen specimens were collected from LSD-clinically diseased cattle between 2020 and 2022 from Mafeteng, Leribe, Maseru, Berea, and Mohales' Hoek districts of Lesotho. A total of 11 DNA samples were analyzed by PCR and sequencing of the extracellular enveloped virus (EEV) glycoprotein, G-protein-coupled chemokine receptor (GPCR), 30 kDa RNA polymerase subunit (RPO30), and B22R genes. All nucleotide sequences of the above-mentioned genes confirmed that the PCR amplicons of clinical samples are truly LSDV, as they were identical to respective LSDV isolates on the NCBI GenBank. Two of the elevem samples were further characterized by whole-genome sequencing. The analysis, based on both CaPV marker genes and complete genome sequences, revealed that the LSDV isolates from Lesotho cluster with the NW-like LSDVs, which includes the commonly circulating LSDV field isolates from Africa, the Middle East, the Balkans, Turkey, and Eastern Europe.
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Affiliation(s)
- Mabusetsa Joseph Raporoto Makalo
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2531, South Africa; (T.R.); (T.E.O.); (O.M.M.T.)
- Department of Livestock Services, Ministry of Agriculture, Food Security, and Nutrition, Private A82, Maseru, Lesotho;
| | - Tirumala Bharani Kumar Settypalli
- Animal Production and Health Laboratory, Animal Production and Health Section, Joint FAO/IAEA Division, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, P.O. Box 100, 1400 Vienna, Austria; (T.B.K.S.); (I.K.M.); (H.O.A.); (G.C.); (C.E.L.)
| | - Irene Kasindi Meki
- Animal Production and Health Laboratory, Animal Production and Health Section, Joint FAO/IAEA Division, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, P.O. Box 100, 1400 Vienna, Austria; (T.B.K.S.); (I.K.M.); (H.O.A.); (G.C.); (C.E.L.)
| | - Mame Thierno Bakhoum
- Laboratoire National de l’Elevage et de Recherches Vétérinaires ISRA/LNERV(LNERV), BP 2057, Dakar, Senegal;
| | - Hatem Ouled Ahmed
- Animal Production and Health Laboratory, Animal Production and Health Section, Joint FAO/IAEA Division, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, P.O. Box 100, 1400 Vienna, Austria; (T.B.K.S.); (I.K.M.); (H.O.A.); (G.C.); (C.E.L.)
| | | | - Tsepo Ramatla
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2531, South Africa; (T.R.); (T.E.O.); (O.M.M.T.)
| | - ThankGod Emmanuel Onyiche
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2531, South Africa; (T.R.); (T.E.O.); (O.M.M.T.)
- Department of Veterinary Parasitology and Entomology, University of Maiduguri, P. M. B. 1069, Maiduguri 600230, Nigeria
| | - Lineo Nionzima-Bohloa
- Department of Livestock Services, Ministry of Agriculture, Food Security, and Nutrition, Private A82, Maseru, Lesotho;
| | - Artem Metlin
- Food and Agriculture Organization of the United Nations, Viale delle Terme di Caracalla, 00153 Rome, Italy; (A.M.); (M.D.)
| | - Madhur Dhingra
- Food and Agriculture Organization of the United Nations, Viale delle Terme di Caracalla, 00153 Rome, Italy; (A.M.); (M.D.)
| | - Giovanni Cattoli
- Animal Production and Health Laboratory, Animal Production and Health Section, Joint FAO/IAEA Division, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, P.O. Box 100, 1400 Vienna, Austria; (T.B.K.S.); (I.K.M.); (H.O.A.); (G.C.); (C.E.L.)
| | - Charles Euloge Lamien
- Animal Production and Health Laboratory, Animal Production and Health Section, Joint FAO/IAEA Division, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, P.O. Box 100, 1400 Vienna, Austria; (T.B.K.S.); (I.K.M.); (H.O.A.); (G.C.); (C.E.L.)
| | - Oriel Matlhahane Molifi Thekisoe
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2531, South Africa; (T.R.); (T.E.O.); (O.M.M.T.)
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Haga IR, Shih BB, Tore G, Polo N, Ribeca P, Gombo-Ochir D, Shura G, Tserenchimed T, Enkhbold B, Purevtseren D, Ulziibat G, Damdinjav B, Yimer L, Bari FD, Gizaw D, Adedeji AJ, Atai RB, Adole JA, Dogonyaro BB, Kumarawadu PL, Batten C, Corla A, Freimanis GL, Tennakoon C, Law A, Lycett S, Downing T, Beard PM. Sequencing and Analysis of Lumpy Skin Disease Virus Whole Genomes Reveals a New Viral Subgroup in West and Central Africa. Viruses 2024; 16:557. [PMID: 38675899 PMCID: PMC11053774 DOI: 10.3390/v16040557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 03/02/2024] [Accepted: 03/05/2024] [Indexed: 04/28/2024] Open
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.
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Grants
- 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, Biotechnology and Biological Sciences Research Council
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Affiliation(s)
- Ismar R. Haga
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (I.R.H.); (N.P.); (P.R.); (C.B.); (G.L.F.); (C.T.); (T.D.)
| | - Barbara B. Shih
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, Midlothian EH25 9RG, UK; (B.B.S.); (A.L.); (S.L.)
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YW, UK
| | - Gessica Tore
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (I.R.H.); (N.P.); (P.R.); (C.B.); (G.L.F.); (C.T.); (T.D.)
| | - Noemi Polo
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (I.R.H.); (N.P.); (P.R.); (C.B.); (G.L.F.); (C.T.); (T.D.)
| | - Paolo Ribeca
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (I.R.H.); (N.P.); (P.R.); (C.B.); (G.L.F.); (C.T.); (T.D.)
- UK Health Security Agency, 61 Colindale Ave, London NW9 5EQ, UK
- NIHR Health Protection Research Unit in Genomics and Enabling Data, Mathematics Institute, Zeeman Builing, University of Warwick, Coventry CV4 7AL, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, Ronald Ross Building, University of Liverpool, Liverpool L69 7BE, UK
- Biomathematics and Statistics Scotland, James Maxwell Clerk Building, Peter Guthrie Tait Road, Kings Buildings, Edinburgh EH9 3FD, UK
| | - Delgerzul Gombo-Ochir
- Laboratory of Transboundary Animal Disease Diagnosis and Surveillance, State Central Veterinary Laboratory, Zaisan, Ulaanbaatar 17024, Mongolia; (D.G.-O.); (G.S.); (T.T.); (B.E.); (D.P.); (G.U.)
| | - Gansukh Shura
- Laboratory of Transboundary Animal Disease Diagnosis and Surveillance, State Central Veterinary Laboratory, Zaisan, Ulaanbaatar 17024, Mongolia; (D.G.-O.); (G.S.); (T.T.); (B.E.); (D.P.); (G.U.)
| | - Tsagaan Tserenchimed
- Laboratory of Transboundary Animal Disease Diagnosis and Surveillance, State Central Veterinary Laboratory, Zaisan, Ulaanbaatar 17024, Mongolia; (D.G.-O.); (G.S.); (T.T.); (B.E.); (D.P.); (G.U.)
| | - Bazarragchaa Enkhbold
- Laboratory of Transboundary Animal Disease Diagnosis and Surveillance, State Central Veterinary Laboratory, Zaisan, Ulaanbaatar 17024, Mongolia; (D.G.-O.); (G.S.); (T.T.); (B.E.); (D.P.); (G.U.)
| | - Dulam Purevtseren
- Laboratory of Transboundary Animal Disease Diagnosis and Surveillance, State Central Veterinary Laboratory, Zaisan, Ulaanbaatar 17024, Mongolia; (D.G.-O.); (G.S.); (T.T.); (B.E.); (D.P.); (G.U.)
| | - Gerelmaa Ulziibat
- Laboratory of Transboundary Animal Disease Diagnosis and Surveillance, State Central Veterinary Laboratory, Zaisan, Ulaanbaatar 17024, Mongolia; (D.G.-O.); (G.S.); (T.T.); (B.E.); (D.P.); (G.U.)
| | - Batchuluun Damdinjav
- General Authority for Veterinary Service, Ministry of Food, Agriculture and Light Industry, Ulaanbaatar 13381, Mongolia;
| | - Lama Yimer
- School of Veterinary Medicine, Wollega University, Nekemte P.O. Box 395, Ethiopia;
- College of Veterinary Medicine and Agriculture, Addis Ababa University, Bishoftu P.O. Box 3434, Ethiopia;
| | - Fufa D. Bari
- College of Veterinary Medicine and Agriculture, Addis Ababa University, Bishoftu P.O. Box 3434, Ethiopia;
| | - Daniel Gizaw
- Animal Health Institute (AHI), Sebata P.O. Box 04, Ethiopia;
| | - Adeyinka Jeremy Adedeji
- National Veterinary Research Institute, Vom 930103, Nigeria; (A.J.A.); (R.B.A.); (J.A.A.); (B.B.D.)
| | - Rebecca Bitiyong Atai
- National Veterinary Research Institute, Vom 930103, Nigeria; (A.J.A.); (R.B.A.); (J.A.A.); (B.B.D.)
| | - Jolly Amoche Adole
- National Veterinary Research Institute, Vom 930103, Nigeria; (A.J.A.); (R.B.A.); (J.A.A.); (B.B.D.)
| | | | | | - Carrie Batten
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (I.R.H.); (N.P.); (P.R.); (C.B.); (G.L.F.); (C.T.); (T.D.)
| | - Amanda Corla
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (I.R.H.); (N.P.); (P.R.); (C.B.); (G.L.F.); (C.T.); (T.D.)
| | - Graham L. Freimanis
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (I.R.H.); (N.P.); (P.R.); (C.B.); (G.L.F.); (C.T.); (T.D.)
| | - Chandana Tennakoon
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (I.R.H.); (N.P.); (P.R.); (C.B.); (G.L.F.); (C.T.); (T.D.)
| | - Andy Law
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, Midlothian EH25 9RG, UK; (B.B.S.); (A.L.); (S.L.)
| | - Samantha Lycett
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, Midlothian EH25 9RG, UK; (B.B.S.); (A.L.); (S.L.)
| | - Tim Downing
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (I.R.H.); (N.P.); (P.R.); (C.B.); (G.L.F.); (C.T.); (T.D.)
| | - Philippa M. Beard
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (I.R.H.); (N.P.); (P.R.); (C.B.); (G.L.F.); (C.T.); (T.D.)
- School of Life Sciences, Keele University, Staffordshire ST5 5BG, UK
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4
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Xie S, Cui L, Liao Z, Zhu J, Ren S, Niu K, Li H, Jiang F, Wu J, Wang J, Wu J, Song B, Wu W, Peng C. Genomic analysis of lumpy skin disease virus asian variants and evaluation of its cellular tropism. NPJ Vaccines 2024; 9:65. [PMID: 38514651 PMCID: PMC10957905 DOI: 10.1038/s41541-024-00846-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 02/21/2024] [Indexed: 03/23/2024] Open
Abstract
Lumpy skin disease virus (LSDV) is a poxvirus that mainly affects cattle and can lead to symptoms such as severe reduction in milk production as well as infertility and mortality, which has resulted in dramatic economic loss in affected countries in Africa, Europe, and Asia. In this study, we successfully isolated two strains of LSDV from different geographical regions in China. Comparative genomic analyses were performed by incorporating additional LSDV whole genome sequences reported in other areas of Asia. Our analyses revealed that LSDV exhibited an 'open' pan-genome. Phylogenetic analysis unveiled distinct branches of LSDV evolution, signifying the prevalence of multiple lineages of LSDV across various regions in Asia. In addition, a reporter LSDV expressing eGFP directed by a synthetic poxvirus promoter was generated and used to evaluate the cell tropism of LSDV in various mammalian and avian cell lines. Our results demonstrated that LSDV replicated efficiently in several mammalian cell lines, including human A549 cells. In conclusion, our results underscore the necessity for strengthening LSD outbreak control measures and continuous epidemiological surveillance.
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Affiliation(s)
- Shijie Xie
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine (CVM), China Agricultural University, Beijing, 100193, China
| | - Lianxin Cui
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine (CVM), China Agricultural University, Beijing, 100193, China
| | - Zhiyi Liao
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine (CVM), China Agricultural University, Beijing, 100193, China
| | - Junda Zhu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine (CVM), China Agricultural University, Beijing, 100193, China
| | - Shuning Ren
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine (CVM), China Agricultural University, Beijing, 100193, China
| | - Kang Niu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine (CVM), China Agricultural University, Beijing, 100193, China
| | - Hua Li
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine (CVM), China Agricultural University, Beijing, 100193, China
| | - Fei Jiang
- China Animal Disease Control Center, Beijing, 102618, China
| | - Jiajun Wu
- China Animal Disease Control Center, Beijing, 102618, China
| | - Jie Wang
- Xinjiang Key Laboratory of Animal Infectious Diseases/Institute of Veterinary Medicine, Xinjiang Academy of Animal Sciences, Urumqi, 830013, China
| | - Jian Wu
- Xinjiang Key Laboratory of Animal Infectious Diseases/Institute of Veterinary Medicine, Xinjiang Academy of Animal Sciences, Urumqi, 830013, China
| | - Baifen Song
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine (CVM), China Agricultural University, Beijing, 100193, China
| | - Wenxue Wu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine (CVM), China Agricultural University, Beijing, 100193, China.
| | - Chen Peng
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine (CVM), China Agricultural University, Beijing, 100193, China.
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5
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Sudhakar SB, Mishra N, Kalaiyarasu S, Sharma RK, Ahirwar K, Vashist VS, Agarwal S, Sanyal A. Emergence of lumpy skin disease virus (LSDV) infection in domestic Himalayan yaks (Bos grunniens) in Himachal Pradesh, India. Arch Virol 2024; 169:51. [PMID: 38374459 DOI: 10.1007/s00705-024-05994-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/02/2024] [Indexed: 02/21/2024]
Abstract
In this study, we investigated and confirmed natural lumpy skin disease virus (LSDV) infection in Himalayan yaks (Bos grunniens) in Himachal Pradesh, India, based on clinical manifestations and results of genome detection, antibody detection, virus isolation, and nucleotide sequencing. Subsequent phylogenetic analysis based on complete GPCR, RPO30, and EEV gene sequences revealed that the LSDV isolates from these yaks and local cattle belonged to LSDV subcluster 1.2.1 rather than the dominant subcluster 1.2.2, which is currently circulating in India, suggesting a separate recent introduction. This is the first report of natural LSDV infection in yaks in India, expanding the known host range of LSDV. Further investigations are needed to assess the impact of LSDV infection in yaks.
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Affiliation(s)
- Shashi Bhushan Sudhakar
- ICAR-National Institute of High Security Animal Diseases, Anand Nagar, Bhopal, Madhya Pradesh, 462 022, India
| | - Niranjan Mishra
- ICAR-National Institute of High Security Animal Diseases, Anand Nagar, Bhopal, Madhya Pradesh, 462 022, India.
| | - Semmannan Kalaiyarasu
- ICAR-National Institute of High Security Animal Diseases, Anand Nagar, Bhopal, Madhya Pradesh, 462 022, India
| | - Ram Krishan Sharma
- Veterinary Hospital, Cheog, Theog-171209, Shimla, Himachal Pradesh, India
| | - Khusboo Ahirwar
- ICAR-National Institute of High Security Animal Diseases, Anand Nagar, Bhopal, Madhya Pradesh, 462 022, India
| | - Vikram S Vashist
- State Veterinary Hospital Complex, Cart Road, Shimla, Himachal Pradesh, 171001, India
| | - Sonam Agarwal
- ICAR-National Institute of High Security Animal Diseases, Anand Nagar, Bhopal, Madhya Pradesh, 462 022, India
| | - Aniket Sanyal
- ICAR-National Institute of High Security Animal Diseases, Anand Nagar, Bhopal, Madhya Pradesh, 462 022, India
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Suwankitwat N, Deemagarn T, Bhakha K, Songkasupa T, Vitoonpong R, Trakunjaroonkit P, Rodphol S, Nuansrichay B, Chintapitaksakul L, Wongsarattanasin K, Kwon OK, Kang HE, Shin YK. Complete Genomic Characterization of Lumpy Skin Disease Virus Isolates from Beef Cattle in Lopburi Province, Central Thailand, during 2021-2022. Vet Sci 2023; 11:10. [PMID: 38250916 PMCID: PMC10818611 DOI: 10.3390/vetsci11010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/08/2023] [Accepted: 12/18/2023] [Indexed: 01/23/2024] Open
Abstract
Lumpy skin disease (LSD) is a viral infection that impacts the cattle industry. The most efficient approach to prevent disease involves the utilization of live-attenuated LSD vaccines (LAVs), which stands out as the most successful method. However, LAVs might be subjected to changes to their genomes during replication that increase viral infectivity or virulence. The objective of this study was to monitor alterations in the genetic characteristics of the lumpy skin disease virus (LSDV) in beef cattle following the administration of LAVs in Lopburi Province of Central Thailand. A total of four skin samples from LSD cases were collected from non-vaccinated animals that exhibited LSD clinical symptoms from two distinct districts, spanning three subdistricts within the region. The samples of cattle were analyzed using real-time PCR targeting the LSDV074 p32 gene, the virus was isolated, and the entire genome sequences were evaluated through a single nucleotide polymorphisms (SNPs) analysis, and phylogenetic trees were assembled. The investigations revealed that LSDVs from two isolates from Chai Badan district exhibited significant mutations in the open reading frame (ORF) 023 putative protein, while another two isolates from Lam Sonthi district had a change in the untranslated region (UTR). For a result, the most proficient disease diagnosis and control should be evaluated on viral genetics on a regular basis.
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Affiliation(s)
- Nutthakarn Suwankitwat
- National Institute of Animal Health, Department of Livestock Development, Bangkok 10900, Thailand; (T.D.); (K.B.); (T.S.); (R.V.); (P.T.); (S.R.); (B.N.); (L.C.)
| | - Taweewat Deemagarn
- National Institute of Animal Health, Department of Livestock Development, Bangkok 10900, Thailand; (T.D.); (K.B.); (T.S.); (R.V.); (P.T.); (S.R.); (B.N.); (L.C.)
| | - Kultyarat Bhakha
- National Institute of Animal Health, Department of Livestock Development, Bangkok 10900, Thailand; (T.D.); (K.B.); (T.S.); (R.V.); (P.T.); (S.R.); (B.N.); (L.C.)
| | - Tapanut Songkasupa
- National Institute of Animal Health, Department of Livestock Development, Bangkok 10900, Thailand; (T.D.); (K.B.); (T.S.); (R.V.); (P.T.); (S.R.); (B.N.); (L.C.)
| | - Ratchaneekorn Vitoonpong
- National Institute of Animal Health, Department of Livestock Development, Bangkok 10900, Thailand; (T.D.); (K.B.); (T.S.); (R.V.); (P.T.); (S.R.); (B.N.); (L.C.)
| | - Pannaporn Trakunjaroonkit
- National Institute of Animal Health, Department of Livestock Development, Bangkok 10900, Thailand; (T.D.); (K.B.); (T.S.); (R.V.); (P.T.); (S.R.); (B.N.); (L.C.)
| | - Sureenipa Rodphol
- National Institute of Animal Health, Department of Livestock Development, Bangkok 10900, Thailand; (T.D.); (K.B.); (T.S.); (R.V.); (P.T.); (S.R.); (B.N.); (L.C.)
| | - Bandit Nuansrichay
- National Institute of Animal Health, Department of Livestock Development, Bangkok 10900, Thailand; (T.D.); (K.B.); (T.S.); (R.V.); (P.T.); (S.R.); (B.N.); (L.C.)
| | - Lerdchai Chintapitaksakul
- National Institute of Animal Health, Department of Livestock Development, Bangkok 10900, Thailand; (T.D.); (K.B.); (T.S.); (R.V.); (P.T.); (S.R.); (B.N.); (L.C.)
| | - Khanin Wongsarattanasin
- Animal Health Development Group, Lopburi Provincial Livestock Office, Department of Livestock Development, Lopburi 15000, Thailand;
| | - Oh-Kyu Kwon
- Animal and Plant Quarantine Agency, Ministry of Agriculture, Food and Rural Affairs, Gimcheon-si 39660, Gyeongsangbuk-do, Republic of Korea; (O.-K.K.); (H.-E.K.)
| | - Hae-Eun Kang
- Animal and Plant Quarantine Agency, Ministry of Agriculture, Food and Rural Affairs, Gimcheon-si 39660, Gyeongsangbuk-do, Republic of Korea; (O.-K.K.); (H.-E.K.)
| | - Yeun-Kyung Shin
- Animal and Plant Quarantine Agency, Ministry of Agriculture, Food and Rural Affairs, Gimcheon-si 39660, Gyeongsangbuk-do, Republic of Korea; (O.-K.K.); (H.-E.K.)
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Van Borm S, Dellicour S, Martin DP, Lemey P, Agianniotaki EI, Chondrokouki ED, Vidanovic D, Vaskovic N, Petroviċ T, Laziċ S, Koleci X, Vodica A, Djadjovski I, Krstevski K, Vandenbussche F, Haegeman A, De Clercq K, Mathijs E. Complete genome reconstruction of the global and European regional dispersal history of the lumpy skin disease virus. J Virol 2023; 97:e0139423. [PMID: 37905838 PMCID: PMC10688313 DOI: 10.1128/jvi.01394-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 10/02/2023] [Indexed: 11/02/2023] Open
Abstract
IMPORTANCE Lumpy skin disease virus (LSDV) has a complex epidemiology involving multiple strains, recombination, and vaccination. Its DNA genome provides limited genetic variation to trace outbreaks in space and time. Sequencing of LSDV whole genomes has also been patchy at global and regional scales. Here, we provide the first fine-grained whole genome sequence sampling of a constrained LSDV outbreak (southeastern Europe, 2015-2017), which we analyze along with global publicly available genomes. We formally evaluate the past occurrence of recombination events as well as the temporal signal that is required for calibrating molecular clock models and subsequently conduct a time-calibrated spatially explicit phylogeographic reconstruction. Our study further illustrates the importance of accounting for recombination events before reconstructing global and regional dynamics of DNA viruses. More LSDV whole genomes from endemic areas are needed to obtain a comprehensive understanding of global LSDV dispersal dynamics.
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Affiliation(s)
- Steven Van Borm
- Scientific Directorate Animal Infectious Diseases, Sciensano, Brussels, Belgium
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Darren P. Martin
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Philippe Lemey
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Eirini I. Agianniotaki
- National Reference Laboratory for Capripoxviruses, Department of Molecular Diagnostics, FMD, Virological, Rickettsial and Exotic Diseases, Directorate of Athens Veterinary Center, Ministry of Rural Development and Food, Athens, Greece
| | - Eleni D. Chondrokouki
- National Reference Laboratory for Capripoxviruses, Department of Molecular Diagnostics, FMD, Virological, Rickettsial and Exotic Diseases, Directorate of Athens Veterinary Center, Ministry of Rural Development and Food, Athens, Greece
| | - Dejan Vidanovic
- Department for laboratory diagnostics, Veterinary Specialized Institute, Kraljevo, Serbia
| | - Nikola Vaskovic
- Department for laboratory diagnostics, Veterinary Specialized Institute, Kraljevo, Serbia
| | - Tamaš Petroviċ
- Department for Virology, Scientific Veterinary Institute, Novi Sad, Serbia
| | - Sava Laziċ
- Department for Virology, Scientific Veterinary Institute, Novi Sad, Serbia
| | - Xhelil Koleci
- Faculty of Veterinary Medicine, The Agricultural University of Tirana, Tirana, Albania
| | - Ani Vodica
- Animal Health Department, Food Safety and Veterinary Institute, Tirana, Albania
| | - Igor Djadjovski
- Faculty of Veterinary Medicine, Ss. Cyril and Methodius University in Skopje, Skopje, Macedonia
| | - Kiril Krstevski
- Faculty of Veterinary Medicine, Ss. Cyril and Methodius University in Skopje, Skopje, Macedonia
| | - Frank Vandenbussche
- Scientific Directorate Animal Infectious Diseases, Sciensano, Brussels, Belgium
| | - Andy Haegeman
- Scientific Directorate Animal Infectious Diseases, Sciensano, Brussels, Belgium
| | - Kris De Clercq
- Scientific Directorate Animal Infectious Diseases, Sciensano, Brussels, Belgium
| | - Elisabeth Mathijs
- Scientific Directorate Animal Infectious Diseases, Sciensano, Brussels, Belgium
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