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Berguido FJ, Kangethe RT, Shell W, Wijewardana V, Grabherr R, Cattoli G, Lamien CE. Different Neutralizing Antibody Responses of Heterologous Sera on Sheeppox and Lumpy Skin Disease Viruses. Viruses 2024; 16:1127. [PMID: 39066289 PMCID: PMC11281510 DOI: 10.3390/v16071127] [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: 06/12/2024] [Revised: 07/03/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
Sheeppox virus (SPPV), goatpox virus (GTPV), and lumpy skin disease virus (LSDV) are the three members of the genus Capripoxvirus within the Poxviridae family and are the etiologic agents of sheeppox (SPP), goatpox (GTP), and lumpy skin disease (LSD), respectively. LSD, GTP, and SPP are endemic in Africa and Asia, causing severe disease outbreaks with significant economic losses in livestock. Incursions of SPP and LSD have occurred in Europe. Vaccination with live attenuated homologous and heterologous viruses are routinely implemented to control these diseases. Using the gold standard virus neutralization test, we studied the ability of homologous and heterologous sera to neutralize the SPPV and LSDV. We found that LSD and SPP sera effectively neutralize their homologous viruses, and GTP sera can neutralize SPPV. However, while LSD sera effectively neutralizes SPPV, SPP and GTP sera cannot neutralize the LSDV to the same extent. We discuss the implications of these observations in disease assay methodology and heterologous vaccine efficacy.
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Affiliation(s)
- Francisco J. Berguido
- Animal Production and Health Laboratory, Joint FAO/IAEA Centre, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Wagramer Strasse 5, P.O. Box 100, 1400 Vienna, Austria (C.E.L.)
- Institute of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Richard Thiga Kangethe
- Animal Production and Health Laboratory, Joint FAO/IAEA Centre, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Wagramer Strasse 5, P.O. Box 100, 1400 Vienna, Austria (C.E.L.)
| | - Wendy Shell
- Institute for Veterinary Disease Control, AGES—Austrian Agency for Health and Food Safety, Robert Koch-Gasse 17, 2340 Mödling, Austria
| | - Viskam Wijewardana
- Animal Production and Health Laboratory, Joint FAO/IAEA Centre, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Wagramer Strasse 5, P.O. Box 100, 1400 Vienna, Austria (C.E.L.)
| | - Reingard Grabherr
- Institute of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Giovanni Cattoli
- Animal Production and Health Laboratory, Joint FAO/IAEA Centre, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Wagramer Strasse 5, P.O. Box 100, 1400 Vienna, Austria (C.E.L.)
| | - Charles Euloge Lamien
- Animal Production and Health Laboratory, Joint FAO/IAEA Centre, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Wagramer Strasse 5, P.O. Box 100, 1400 Vienna, Austria (C.E.L.)
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2
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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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3
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Sendow I, Meki IK, Dharmayanti NLPI, Hoerudin H, Ratnawati A, Settypalli TBK, Ahmed HO, Nuradji H, Saepulloh M, Adji RS, Fairusya N, Sari F, Anindita K, Cattoli G, Lamien CE. Molecular characterization of recombinant LSDV isolates from 2022 outbreak in Indonesia through phylogenetic networks and whole-genome SNP-based analysis. BMC Genomics 2024; 25:240. [PMID: 38438878 PMCID: PMC10913250 DOI: 10.1186/s12864-024-10169-6] [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: 09/25/2023] [Accepted: 02/28/2024] [Indexed: 03/06/2024] Open
Abstract
Lumpy skin disease (LSD) is a transboundary viral disease of cattle and water buffaloes caused by the LSD virus, leading to high morbidity, low mortality, and a significant economic impact. Initially endemic to Africa only, LSD has spread to the Middle East, Europe, and Asia in the past decade. The most effective control strategy for LSD is the vaccination of cattle with live-attenuated LSDV vaccines. Consequently, the emergence of two groups of LSDV strains in Asian countries, one closely related to the ancient Kenyan LSDV isolates and the second made of recombinant viruses with a backbone of Neethling-vaccine and field isolates, emphasized the need for constant molecular surveillance. This current study investigated the first outbreak of LSD in Indonesia in 2022. Molecular characterization of the isolate circulating in the country based on selected LSDV-marker genes: RPO30, GPCR, EEV glycoprotein gene, and B22R, as well as whole genome analysis using several analytical tools, indicated the Indonesia LSDV isolate as a recombinant of LSDV_Neethling_vaccine_LW_1959 and LSDV_NI-2490. The analysis clustered the Indonesia_LSDV with the previously reported LSDV recombinants circulating in East and Southeast Asia, but different from the recombinant viruses in Russia and the field isolates in South-Asian countries. Additionally, this study has demonstrated alternative accurate ways of LSDV whole genome analysis and clustering of isolates, including the recombinants, instead of whole-genome phylogenetic tree analysis. These data will strengthen our understanding of the pathogens' origin, the extent of their spread, and determination of suitable control measures required.
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Affiliation(s)
- Indrawati Sendow
- Research Center for Veterinary Science, Research Organization for Health, National Research and Innovation Agency, West Java, Indonesia
| | - Irene Kasindi Meki
- Animal Production and Health Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Wagramer Strasse 5, A-1400, Vienna, P.O. Box 100, Austria.
| | - Ni Luh Putu Indi Dharmayanti
- Research Center for Veterinary Science, Research Organization for Health, National Research and Innovation Agency, West Java, Indonesia
| | - Heri Hoerudin
- Research Center for Veterinary Science, Research Organization for Health, National Research and Innovation Agency, West Java, Indonesia
| | - Atik Ratnawati
- Research Center for Veterinary Science, Research Organization for Health, National Research and Innovation Agency, West Java, Indonesia
| | - Tirumala Bharani K Settypalli
- Animal Production and Health Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Wagramer Strasse 5, A-1400, Vienna, P.O. Box 100, Austria
| | - Hatem Ouled Ahmed
- Animal Production and Health Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Wagramer Strasse 5, A-1400, Vienna, P.O. Box 100, Austria
| | - Harimurti Nuradji
- Research Center for Veterinary Science, Research Organization for Health, National Research and Innovation Agency, West Java, Indonesia
| | - Muharam Saepulloh
- Research Center for Veterinary Science, Research Organization for Health, National Research and Innovation Agency, West Java, Indonesia
| | - Rahmat Setya Adji
- Research Center for Veterinary Science, Research Organization for Health, National Research and Innovation Agency, West Java, Indonesia
| | - Nuha Fairusya
- Research Center for Veterinary Science, Research Organization for Health, National Research and Innovation Agency, West Java, Indonesia
| | | | | | - Giovanni Cattoli
- Animal Production and Health Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Wagramer Strasse 5, A-1400, Vienna, P.O. Box 100, Austria
| | - Charles Euloge Lamien
- Animal Production and Health Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Wagramer Strasse 5, A-1400, Vienna, P.O. Box 100, Austria
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Yadav P, Kumar A, Nath SS, Devasurmutt Y, Shashidhar G, Joshi M, Puvar A, Sharma S, Raval J, Pandit R, Chavda P, Nagaraj S, Revanaiah Y, Patil D, Raval SK, Raval J, Kanani A, Thakar F, Kumar N, Reddy GBM, Joshi C, Gulati BR, Tatu U. Unravelling the genomic origins of lumpy skin disease virus in recent outbreaks. BMC Genomics 2024; 25:196. [PMID: 38373902 PMCID: PMC10875885 DOI: 10.1186/s12864-024-10061-3] [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: 09/17/2023] [Accepted: 01/29/2024] [Indexed: 02/21/2024] Open
Abstract
Lumpy skin disease virus (LSDV) belongs to the genus Capripoxvirus and family Poxviridae. LSDV was endemic in most of Africa, the Middle East and Turkey, but since 2015, several outbreaks have been reported in other countries. In this study, we used whole genome sequencing approach to investigate the origin of the outbreak and understand the genomic landscape of the virus. Our study showed that the LSDV strain of 2022 outbreak exhibited many genetic variations compared to the Reference Neethling strain sequence and the previous field strains. A total of 1819 variations were found in 22 genome sequences, which includes 399 extragenic mutations, 153 insertion frameshift mutations, 234 deletion frameshift mutations, 271 Single nucleotide polymorphisms (SNPs) and 762 silent SNPs. Thirty-eight genes have more than 2 variations per gene, and these genes belong to viral-core proteins, viral binding proteins, replication, and RNA polymerase proteins. We highlight the importance of several SNPs in various genes, which may play an essential role in the pathogenesis of LSDV. Phylogenetic analysis performed on all whole genome sequences of LSDV showed two types of variants in India. One group of the variant with fewer mutations was found to lie closer to the LSDV 2019 strain from Ranchi while the other group clustered with previous Russian outbreaks from 2015. Our study highlights the importance of genomic characterization of viral outbreaks to not only monitor the frequency of mutations but also address its role in pathogenesis of LSDV as the outbreak continues.
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Affiliation(s)
- Priya Yadav
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Ankeet Kumar
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Sujith S Nath
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Yashas Devasurmutt
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | | | - Madhvi Joshi
- Gujarat Biotechnology Research Centre, Gandhinagar, 382011, India
| | - Apurvasinh Puvar
- Gujarat Biotechnology Research Centre, Gandhinagar, 382011, India
| | - Sonal Sharma
- Gujarat Biotechnology Research Centre, Gandhinagar, 382011, India
| | - Janvi Raval
- Gujarat Biotechnology Research Centre, Gandhinagar, 382011, India
| | | | - Priyank Chavda
- Gujarat Biotechnology Research Centre, Gandhinagar, 382011, India
| | - Sudeep Nagaraj
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bangalore, 560064, India
| | - Yogisharadhya Revanaiah
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bangalore, 560064, India
| | - Deepak Patil
- Kamdhenu University, Gandhinagar, Gujarat, India
| | - S K Raval
- Kamdhenu University, Gandhinagar, Gujarat, India
| | - Jigar Raval
- Kamdhenu University, Gandhinagar, Gujarat, India
| | | | | | - Naveen Kumar
- National Centre for Veterinary Type Cultures, ICAR-NRC on Equines, Sirsa Road, Hisar, Haryana, 125001, India
| | | | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre, Gandhinagar, 382011, India
| | - Baldev Raj Gulati
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bangalore, 560064, India
| | - Utpal Tatu
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India.
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Berguido FJ, Chibssa TR, Loitsch A, Liu Y, Krstevski K, Djadjovski I, Tuppurainen E, Petrović T, Vidanović D, Caufour P, Settypalli TBK, Grünwald-Gruber C, Grabherr R, Diallo A, Cattoli G, Lamien CE. Harnessing Attenuation-Related Mutations of Viral Genomes: Development of a Serological Assay to Differentiate between Capripoxvirus-Infected and -Vaccinated Animals. Viruses 2023; 15:2318. [PMID: 38140559 PMCID: PMC10747038 DOI: 10.3390/v15122318] [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: 10/20/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
Sheeppox, goatpox, and lumpy skin disease caused by the sheeppox virus (SPPV), goatpox virus (GTPV), and lumpy skin disease virus (LSDV), respectively, are diseases that affect millions of ruminants and many low-income households in endemic countries, leading to great economic losses for the ruminant industry. The three viruses are members of the Capripoxvirus genus of the Poxviridae family. Live attenuated vaccines remain the only efficient means for controlling capripox diseases. However, serological tools have not been available to differentiate infected from vaccinated animals (DIVA), though crucial for proper disease surveillance, control, and eradication efforts. We analysed the sequences of variola virus B22R homologue gene for SPPV, GTPV, and LSDV and observed significant differences between field and vaccine strains in all three capripoxvirus species, resulting in the truncation and absence of the B22R protein in major vaccines within each of the viral species. We selected and expressed a protein fragment present in wildtype viruses but absent in selected vaccine strains of all three species, taking advantage of these alterations in the B22R gene. An indirect ELISA (iELISA) developed using this protein fragment was evaluated on well-characterized sera from vaccinated, naturally and experimentally infected, and negative cattle and sheep. The developed wildtype-specific capripox DIVA iELISA showed >99% sensitivity and specificity for serum collected from animals infected with the wildtype virus. To the best of our knowledge, this is the first wildtype-specific, DIVA-capable iELISA for poxvirus diseases exploiting changes in nucleotide sequence alterations in vaccine strains.
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Affiliation(s)
- Francisco J. Berguido
- Animal Production and Health Laboratory, Animal Production and Health Section, Joint FAO/IAEA Division, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, WagramerStrasse 5, P.O. Box 100, 1400 Vienna, Austria
- Institute of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | | | - Angelika Loitsch
- Austrian Agency for Health and Food Safety (AGES), Spargelfeldstrasse 191, 1220 Vienna, Austria
| | - Yang Liu
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Kiril Krstevski
- Faculty of Veterinary Medicine, Ss. Cyril and Methodius University in Skopje, 1000 Skopje, North Macedonia
| | - Igor Djadjovski
- Faculty of Veterinary Medicine, Ss. Cyril and Methodius University in Skopje, 1000 Skopje, North Macedonia
| | - Eeva Tuppurainen
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, 17493 Greifswald, Germany
| | - Tamaš Petrović
- Scientific Veterinary Institute “Novi Sad”, 21000 Novi Sad, Serbia
| | - Dejan Vidanović
- Veterinary Specialized Institute Kraljevo, Zicka 34, 36103 Kraljevo, Serbia
| | - Philippe Caufour
- UMR ASTRE Cirad-Inrae, University of Montpellier (I-MUSE), 34398 Montpellier, France
| | - Tirumala Bharani K. 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, WagramerStrasse 5, P.O. Box 100, 1400 Vienna, Austria
| | - Clemens Grünwald-Gruber
- Core Facility Mass Spectrometry, University of Natural Resources and Life Sciences Vienna, 1190 Vienna, Austria
| | - Reingard Grabherr
- Institute of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Adama Diallo
- Independent Researcher, Hahngasse, 24-26, 02/07, 1090 Vienna, Austria
| | - 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, WagramerStrasse 5, P.O. Box 100, 1400 Vienna, Austria
| | - 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, WagramerStrasse 5, P.O. Box 100, 1400 Vienna, Austria
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Desingu PA, Rubeni TP, Nagarajan K, Sundaresan NR. Sign of APOBEC editing, purifying selection, frameshift, and in-frame nonsense mutations in the microevolution of lumpy skin disease virus. Front Microbiol 2023; 14:1214414. [PMID: 38033577 PMCID: PMC10682384 DOI: 10.3389/fmicb.2023.1214414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 10/25/2023] [Indexed: 12/02/2023] Open
Abstract
The lumpy skin disease virus (LSDV), which mostly affects ruminants and causes huge-economic loss, was endemic in Africa, caused outbreaks in the Middle East, and was recently detected in Russia, Serbia, Greece, Bulgaria, Kazakhstan, China, Taiwan, Vietnam, Thailand, and India. However, the role of evolutionary drivers such as codon selection, negative/purifying selection, APOBEC editing, and genetic variations such as frameshift and in-frame nonsense mutations in the LSDVs, which cause outbreaks in cattle in various countries, are still largely unknown. In the present study, a frameshift mutation in LSDV035, LSDV019, LSDV134, and LSDV144 genes and in-frame non-sense mutations in LSDV026, LSDV086, LSDV087, LSDV114, LSDV130, LSDV131, LSDV145, LSDV154, LSDV155, LSDV057, and LSDV081 genes were revealed among different clusters. Based on the available complete genome sequences, the prototype wild-type cluster-1.2.1 virus has been found in other than Africa only in India, the wild-type cluster-1.2.2 virus found in Africa were spread outside Africa, and the recombinant viruses spreading only in Asia and Russia. Although LSD viruses circulating in different countries form a specific cluster, the viruses detected in each specific country are distinguished by frameshift and in-frame nonsense mutations. Furthermore, the present study has brought to light that the selection pressure for codons usage bias is mostly exerted by purifying selection, and this process is possibly caused by APOBEC editing. Overall, the present study sheds light on microevolutions in LSDV, expected to help in future studies towards disturbed ORFs, epidemiological diagnostics, attenuation/vaccine reverts, and predicting the evolutionary direction of LSDVs.
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Affiliation(s)
| | - T. P. Rubeni
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - K. Nagarajan
- Department of Veterinary Pathology, Madras Veterinary College, Chennai, India
- Veterinary and Animal Sciences University (TANUVAS), Chennai, India
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Mazloum A, Van Schalkwyk A, Babiuk S, Venter E, Wallace DB, Sprygin A. Lumpy skin disease: history, current understanding and research gaps in the context of recent geographic expansion. Front Microbiol 2023; 14:1266759. [PMID: 38029115 PMCID: PMC10652407 DOI: 10.3389/fmicb.2023.1266759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 09/28/2023] [Indexed: 12/01/2023] Open
Abstract
Lumpy skin disease is recognized as a transboundary and emerging disease of cattle, buffaloes and other wild ruminants. Being initially restricted to Africa, and since 1989 the Middle East, the unprecedented recent spread across Eurasia demonstrates how underestimated and neglected this disease is. The initial identification of the causative agent of LSD as a poxvirus called LSD virus, was well as findings on LSDV transmission and epidemiology were pioneered at Onderstepoort, South Africa, from as early as the 1940s by researchers such as Weiss, Haig and Alexander. As more data emerges from an ever-increasing number of epidemiological studies, previously emphasized research gaps are being revisited and discussed. The currently available knowledge is in agreement with the previously described South African research experience that LSDV transmission can occur by multiple routes, including indirect contact, shared water sources and arthropods. The virus population is prone to molecular evolution, generating novel phylogenetically distinct variants resulting from a diverse range of selective pressures, including recombination between field and homologous vaccine strains in cell culture that produce virulent recombinants which pose diagnostic challenges. Host restriction is not limited to livestock, with certain wild ruminants being susceptible, with unknown consequences for the epidemiology of the disease.
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Affiliation(s)
- Ali Mazloum
- Federal Center for Animal Health, Vladimir, Russia
| | - Antoinette Van Schalkwyk
- Agricultural Research Council – Onderstepoort Veterinary Institute, Onderstepoort, South Africa
- Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Shawn Babiuk
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB, Canada
| | - Estelle Venter
- College of Public Health, Medical and Veterinary Sciences, Discipline Veterinary Science, James Cook University, Townsville, QLD, Australia
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - David B. Wallace
- Agricultural Research Council – Onderstepoort Veterinary Institute, Onderstepoort, South Africa
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
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Putty K, Rao PL, Ganji VK, Dutta D, Mondal S, Hegde NR, Srivastava A, Subbiah M. First complete genome sequence of lumpy skin disease virus directly from a clinical sample in South India. Virus Genes 2023; 59:317-322. [PMID: 36689139 DOI: 10.1007/s11262-023-01967-3] [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: 08/29/2022] [Accepted: 01/11/2023] [Indexed: 01/24/2023]
Abstract
Lumpy skin disease (LSD), a notifiable disease listed by the World Organization for Animal Health and a fast fast-moving transboundary viral disease infecting cattle and buffaloes, was reported in India in 2019 and has since rapidly spread across the country. This study reports the first complete genome sequence and analysis of a pathogenic LSD virus (LSDV) from India (LSDV/208/PVNRTVU/2020) obtained by direct sequencing of a suspected clinical sample using Illumina and Nanopore sequencing technologies. The complete genome sequence of LSDV/208/PVNRTVU/2020 is 150445 bp long, codes for 156 putative genes and carries identical 2254 bp inverted terminal repeats at either ends. The unique features reported in the LSDV isolates from the recent outbreaks in Asia, namely, the insertions of 12 nucleotides in the viral G-protein coupled receptor (GPCR) and 27 nucleotides leading to duplication of 9 aminoacids in the extracellular enveloped virus-specific (EEV) genes were also conserved in LSDV/208/PVNRTVU/2020. Phylogenetic analysis of the complete genome sequence of LSDV/208/PVNRTVU/2020 revealed its close relation with Kenyan strains and clustered away from vaccine strains. Further analysis showed evidence of strong purifying selection without any recombination events. The data presented in this study could be useful for designing effective strategies such as developing rapid diagnostics and vaccines to control LSD.
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Affiliation(s)
- Kalyani Putty
- Department of Veterinary Biotechnology, PVNR Telangana Veterinary University, Hyderabad, Telangana, 500030, India
| | - Pachineella Lakshmana Rao
- National Institute of Animal Biotechnology, Gachibowli, Hyderabad, Telangana, 500032, India
- Graduate Studies, Regional Center for Biotechnology, Faridabad, 121001, India
| | - Vishweshwar Kumar Ganji
- Department of Veterinary Biotechnology, PVNR Telangana Veterinary University, Hyderabad, Telangana, 500030, India
| | - Devasmita Dutta
- National Institute of Animal Biotechnology, Gachibowli, Hyderabad, Telangana, 500032, India
| | - Subhajit Mondal
- National Institute of Animal Biotechnology, Gachibowli, Hyderabad, Telangana, 500032, India
| | - Nagendra R Hegde
- National Institute of Animal Biotechnology, Gachibowli, Hyderabad, Telangana, 500032, India
| | - Anand Srivastava
- National Institute of Animal Biotechnology, Gachibowli, Hyderabad, Telangana, 500032, India
| | - Madhuri Subbiah
- National Institute of Animal Biotechnology, Gachibowli, Hyderabad, Telangana, 500032, India.
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9
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Wei YR, Ma WG, Wang P, Wang W, Su XH, Yang XY, Mi XY, Wu JY, Huang J. Retrospective genomic analysis of the first Lumpy skin disease virus outbreak in China (2019). Front Vet Sci 2023; 9:1073648. [PMID: 36713885 PMCID: PMC9879060 DOI: 10.3389/fvets.2022.1073648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/13/2022] [Indexed: 01/14/2023] Open
Abstract
Lumpy skin disease caused by Lumpy skin disease virus (LSDV) is a severe systemic disease affecting cattle and other ruminants. Lumpy skin disease was first reported in northwest China in August 2019 and has severely threatened the cattle breeding industry in China. However, there have been limited genomic studies of LSDV from the first outbreak and its subsequent epidemics. This study aims to characterize the comparative genomic evolution of the LSDV strain from the first outbreak in China. The etiological agent was isolated in a Madin-Darby bovine kidney cell culture and subsequently identified by PCR and Sanger sequencing of six selected genes. The genome sequence was determined using Illumina sequencing and analyzed through genome alignment and phylogenetic tree. The results showed that all six genes were successfully amplified and genetically clustered into LSDV. The virus presented the highest homology to strain China/GD01/2020, which shared 100% identities among 150 open reading frames (ORFs), and 97.1-99.7% identities among additional 6 ORFs. Bayesian inference tree analysis revealed that the virus shared a common ancestor with LSDV strains from China and Vietnam. The study provides an additional genomic data for LSDV tracking and control in China and neighboring countries.
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Affiliation(s)
- Yu-Rong Wei
- Xinjiang Key Laboratory of Animal Infectious Diseases, Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, China
| | - Wen-Ge Ma
- Xinjiang Key Laboratory of Animal Infectious Diseases, Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, China
| | - Ping Wang
- Xinjiang Key Laboratory of Animal Infectious Diseases, Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, China
| | - Wen Wang
- Center for Animal Disease Prevention and Control of Xinjiang, Urumqi, China
| | - Xiao-Hui Su
- Center for Animal Disease Prevention and Control of Xinjiang, Urumqi, China
| | - Xue-Yun Yang
- Xinjiang Key Laboratory of Animal Infectious Diseases, Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, China
| | - Xiao-Yun Mi
- Xinjiang Key Laboratory of Animal Infectious Diseases, Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, China
| | - Jian-Yong Wu
- Xinjiang Key Laboratory of Animal Infectious Diseases, Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, China
| | - Jiong Huang
- Xinjiang Key Laboratory of Animal Infectious Diseases, Institute of Veterinary Medicine, Xinjiang Academy of Animal Science, Urumqi, China,*Correspondence: Jiong Huang ✉
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10
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Lumpy Skin Disease Outbreaks in Africa, Europe, and Asia (2005-2022): Multiple Change Point Analysis and Time Series Forecast. Viruses 2022; 14:v14102203. [PMID: 36298758 PMCID: PMC9611638 DOI: 10.3390/v14102203] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/01/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022] Open
Abstract
LSD is an important transboundary disease affecting the cattle industry worldwide. The objectives of this study were to determine trends and significant change points, and to forecast the number of LSD outbreak reports in Africa, Europe, and Asia. LSD outbreak report data (January 2005 to January 2022) from the World Organization for Animal Health were analyzed. We determined statistically significant change points in the data using binary segmentation, and forecast the number of LSD reports using auto-regressive moving average (ARIMA) and neural network auto-regressive (NNAR) models. Four significant change points were identified for each continent. The year between the third and fourth change points (2016-2019) in the African data was the period with the highest mean of number of LSD reports. All change points of LSD outbreaks in Europe corresponded with massive outbreaks during 2015-2017. Asia had the highest number of LSD reports in 2019 after the third detected change point in 2018. For the next three years (2022-2024), both ARIMA and NNAR forecast a rise in the number of LSD reports in Africa and a steady number in Europe. However, ARIMA predicts a stable number of outbreaks in Asia, whereas NNAR predicts an increase in 2023-2024. This study provides information that contributes to a better understanding of the epidemiology of LSD.
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11
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Sprygin A, Mazloum A, van Schalkwyk A, Babiuk S. Capripoxviruses, leporipoxviruses, and orthopoxviruses: Occurrences of recombination. Front Microbiol 2022; 13:978829. [PMID: 36274700 PMCID: PMC9584655 DOI: 10.3389/fmicb.2022.978829] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Poxviruses are double-stranded DNA viruses with several members displaying restricted host ranges. They are genetically stable with low nucleotide mutation rates compared to other viruses, due to the poxviral high-fidelity DNA polymerase. Despite the low accumulation of mutations per replication cycle, poxvirus genomes can recombine with each other to generate genetically rearranged viruses through recombination, a process directly associated with replication and the aforementioned DNA polymerase. Orthopoxvirus replication is intimately tethered to high frequencies of homologous recombination between co-infecting viruses, duplicated sequences of the same virus, and plasmid DNA transfected into poxvirus-infected cells. Unfortunately, the effect of these genomic alterations on the cellular context for all poxviruses across the family Poxviridae remains elusive. However, emerging sequence data on currently circulating and archived poxviruses, such as the genera orthopoxviruses and capripoxviruses, display a wide degree of divergence. This genetic variability cannot be explained by clonality or genetic drift alone, but are probably a result of significant genomic alterations, such as homologous recombination, gene loss and gain, or gene duplications as the major selection forces acting on viral progeny. The objective of this review is to cross-sectionally overview the currently available findings on natural and laboratory observations of recombination in orthopoxviruses, capripoxviruses, and leporipoxviruses, as well as the possible mechanisms involved. Overall, the reviewed available evidence allows us to conclude that the current state of knowledge is limited in terms of the relevance of genetic variations across even a genus of poxviruses as well as fundamental features governing and precipitating intrinsic gene flow and recombination events.
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Affiliation(s)
- Alexander Sprygin
- Federal Center for Animal Health, Vladimir, Russia
- *Correspondence: Alexander Sprygin,
| | - Ali Mazloum
- Federal Center for Animal Health, Vladimir, Russia
| | | | - Shawn Babiuk
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB, Canada
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12
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Development and Optimization of Indirect ELISAs for the Detection of Anti-Capripoxvirus Antibodies in Cattle, Sheep, and Goat Sera. Microorganisms 2022; 10:microorganisms10101956. [PMID: 36296232 PMCID: PMC9608586 DOI: 10.3390/microorganisms10101956] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/05/2022] Open
Abstract
Sheeppox (SPP), goatpox (GTP), and lumpy skin disease (LSD) are economically significant pox diseases of ruminants, caused by sheeppox virus (SPPV), goatpox virus (GTPV), and lumpy skin disease virus (LSDV), respectively. SPPV and GTPV can infect both sheep and goats, while LSDV mainly affects cattle. The recent emergence of LSD in Asia and Europe and the repeated incursions of SPP in Greece, Bulgaria, and Russia highlight how these diseases can spread outside their endemic regions, stressing the urgent need to develop high-throughput serological surveillance tools. We expressed and tested two recombinant truncated proteins, the capripoxvirus homologs of the vaccinia virus C-type lectin-like protein A34 and the EEV glycoprotein A36, as antigens for an indirect ELISA (iELISA) to detect anti-capripoxvirus antibodies. Since A34 outperformed A36 by showing no cross-reactivity to anti-parapoxvirus antibodies, we optimized an A34 iELISA using two different working conditions, one for LSD in cattle and one for SPP/GTP in sheep and goats. Both displayed sound sensitivities and specificities: 98.81% and 98.72%, respectively, for the LSD iELISA, and 97.68% and 95.35%, respectively, for the SPP/GTP iELISA, and did not cross-react with anti-parapoxvirus antibodies of cattle, sheep, and goats. These assays could facilitate the implementation of capripox control programs through serosurveillance and the screening of animals for trade.
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13
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Seerintra T, Saraphol B, Wankaew S, Piratae S. Molecular identification and characterization of Lumpy skin disease virus emergence from cattle in the northeastern part of Thailand. J Vet Sci 2022; 23:e73. [PMID: 36038191 PMCID: PMC9523339 DOI: 10.4142/jvs.22111] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/07/2022] [Accepted: 07/05/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Lumpy skin disease (LSD), a disease transmitted by direct and indirect contact with infected cattle, is caused by the Lumpy skin disease virus (LSDV). The disease affects cattle herds in Africa, Europe, and Asia. The clinical signs of LSD range from mild to the appearance of nodules and lesions in the skin leading to severe symptoms that are sometimes fatal with significant livestock economic losses. OBJECTIVES This study aimed to characterize LSDV strains in the blood of infected cattle in Thailand based on the GPCR gene and determine the phylogenetic relationship of LSDV Thailand isolates with published sequences available in the database. METHODS In total, the blood samples of 120 cattle were collected from different farms in four provinces in the northeastern part of Thailand, and the occurrence of LSDV was examined by PCR based on the P32 antigen gene. The genetic diversity of LSDV based on the GPCR gene was analyzed. RESULTS Polymerase chain reaction assays based on the P32 antigen gene showed that 4.17% (5/120) were positive for LSDV. All positive blood samples were amplified successfully for the GPCR gene. Phylogenetic analysis showed that LSDV Thailand isolates clustered together with LSDVs from China and Russia. CONCLUSIONS The LSD outbreak in Thailand was confirmed, and a phylogenetic tree was constructed to infer the branching pattern of the GPCR gene from the presence of LSDV in Thailand. This is the first report on the molecular characterization of LSDV in cattle in Thailand.
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Affiliation(s)
- Tossapol Seerintra
- Faculty of Veterinary Sciences, Mahasarakham University, Maha Sarakham 44000, Thailand
| | - Bhuripit Saraphol
- Faculty of Veterinary Sciences, Mahasarakham University, Maha Sarakham 44000, Thailand
| | - Sitthichai Wankaew
- Laboratory of Veterinary teaching hospital of Mahasarakham University, Maha Sarakham 44000, Thailand
| | - Supawadee Piratae
- One Health Research Unit, Faculty of Veterinary Sciences, Mahasarakham University, Maha Sarakham 44000, Thailand
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14
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Krotova A, Byadovskaya O, Shumilova I, van Schalkwyk A, Sprygin A. An in-depth bioinformatic analysis of the novel recombinant lumpy skin disease virus strains: from unique patterns to established lineage. BMC Genomics 2022; 23:396. [PMID: 35610557 PMCID: PMC9131581 DOI: 10.1186/s12864-022-08639-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/16/2022] [Indexed: 11/26/2022] Open
Abstract
Background Since the first description of lumpy skin disease virus (LSDV) in Africa in the 1920’s, it has brazenly spread beyond Africa into the Middle East, Europe and most recently Asia. In 2017 the first atypical LSDV recombinant strain was reported in Russia, composed of both a live-attenuated Neethling vaccine strain and Kenyan vaccine strain. An increase in LSDV research enabled a public release of numerous full genome sequences of unique recombinant LSDV strains from Kazakhstan, Russia, China and Vietnam. Prior to the recombinant strain first described in China in 2019, every new recombinant strain was genetically unique and each of these recombinants clustered in a monophyletic lineage. In this work, we provide the complete genome sequences of two novel recombinant strains of LSDV from Russia and attempt to gain more insight into genomic composition of all the recombinant strains currently available. This analysis will provide new insight into the global molecular epidemiology of LSDV. Results By sequencing and analyzing two novel recombinant strains Khabarovsk/2020 and Tomsk/2020, this study investigates the differences and similarities of all five the available recombinant LSDV lineages from different countries based on the SNPs inherited from the aforementioned parental strains. A total of seven recombinant strains: LSDV/Russia/Saratov/2017, LSDV/Russia/Udmurtya/2019, LSDV/KZ-Kostanay/Kazakhstan/2018, LSDV/Russia/Tyumen/2019, LSDV/GD01/China/2020 Khabarovsk/2020 and Tomsk/2020 were examined. It was observed that strains isolated prior to 2020 were composed of unique combinations of open reading frames, whilst from 2020 onwards all circulating strains in Russia and South-Eastern Asia belonged to a single lineage radiating out in the region. The first representative of this lineage is LSDV/GD01/China/2020. Interestingly, the other four unique recombinant strains as well as the newly established lineage, exhibit consistent patterns of targeted selection pointing to regions constantly selected for during the recombination-driven processes. Conclusion This study highlights the inexplicable emergence of novel recombinant strains to be unique introductions of sibling viruses, with the most recent recombinant lineage establishing as the dominant strain across the south eastern Asian countries as evidenced by full genome sequence data. Overall, these findings indicate that LSDVs are subjected to accelerated evolutionary changes due to recombination in the face of homologous live attenuated vaccines as well as the slow genetic drift commonly observed in capripoxviruses curculatign in the field with hardly any genetic changes over decades. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08639-w.
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15
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Molecular Characterization and Phylogenetic Analysis of Lumpy Skin Disease Virus Collected from Outbreaks in Northern Thailand in 2021. Vet Sci 2022; 9:vetsci9040194. [PMID: 35448692 PMCID: PMC9025784 DOI: 10.3390/vetsci9040194] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/31/2022] [Accepted: 04/15/2022] [Indexed: 02/01/2023] Open
Abstract
Understanding molecular epidemiology is essential for the improvement of lumpy skin disease (LSD) eradication and control strategies. The objective of this study was to perform a molecular characterization and phylogenetic analysis of lumpy skin disease virus (LSDV) isolated from dairy cows presenting LSD-like clinical signs in northern Thailand. The skin nodules were collected from 26 LSD-suspected cows involved in six outbreaks during the period from July to September of 2021. LSDVs were confirmed from clinical samples using the polymerase chain reaction (PCR). The PCR-positive samples were subsequently amplified and sequenced using a G-protein-coupled chemokine receptor (GPCR) gene for molecular characterization and phylogenetic analyses. All 26 samples were positive for LSDV by PCR. A phylogenetic analysis indicated that the 24 LSDV isolates obtained from cattle in northern Thailand were closely related to other LSDV sequences acquired from Asia (China, Hong Kong, and Vietnam). On the other hand, two LSDV isolates of the cows presenting LSD-like clinical signs after vaccination were clustered along with LSDV Neethling-derived vaccines. The outcomes of this research will be beneficial in developing effective control strategies for LSDV.
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