Molecular characterization of recombinant LSDV isolates from 2022 outbreak in Indonesia through phylogenetic networks and whole-genome SNP-based analysis
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 dec...
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| Format: | Article |
| Language: | English |
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BMC
2024-03-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-024-10169-6 |
| _version_ | 1827328560220602368 |
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| author | Indrawati Sendow Irene Kasindi Meki Ni Luh Putu Indi Dharmayanti Heri Hoerudin Atik Ratnawati Tirumala Bharani K. Settypalli Hatem Ouled Ahmed Harimurti Nuradji Muharam Saepulloh Rahmat Setya Adji Nuha Fairusya Faralinda Sari Katamtama Anindita Giovanni Cattoli Charles Euloge Lamien |
| author_facet | Indrawati Sendow Irene Kasindi Meki Ni Luh Putu Indi Dharmayanti Heri Hoerudin Atik Ratnawati Tirumala Bharani K. Settypalli Hatem Ouled Ahmed Harimurti Nuradji Muharam Saepulloh Rahmat Setya Adji Nuha Fairusya Faralinda Sari Katamtama Anindita Giovanni Cattoli Charles Euloge Lamien |
| author_sort | Indrawati Sendow |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-07T15:19:23Z |
| format | Article |
| id | doaj.art-d1fb7a3f17b8400e84a7007111d65b8c |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-07T15:19:23Z |
| publishDate | 2024-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-d1fb7a3f17b8400e84a7007111d65b8c2024-03-05T17:46:11ZengBMCBMC Genomics1471-21642024-03-0125111210.1186/s12864-024-10169-6Molecular characterization of recombinant LSDV isolates from 2022 outbreak in Indonesia through phylogenetic networks and whole-genome SNP-based analysisIndrawati Sendow0Irene Kasindi Meki1Ni Luh Putu Indi Dharmayanti2Heri Hoerudin3Atik Ratnawati4Tirumala Bharani K. Settypalli5Hatem Ouled Ahmed6Harimurti Nuradji7Muharam Saepulloh8Rahmat Setya Adji9Nuha Fairusya10Faralinda Sari11Katamtama Anindita12Giovanni Cattoli13Charles Euloge Lamien14Research Center for Veterinary Science, Research Organization for Health, National Research and Innovation AgencyAnimal Production and Health Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy AgencyResearch Center for Veterinary Science, Research Organization for Health, National Research and Innovation AgencyResearch Center for Veterinary Science, Research Organization for Health, National Research and Innovation AgencyResearch Center for Veterinary Science, Research Organization for Health, National Research and Innovation AgencyAnimal Production and Health Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy AgencyAnimal Production and Health Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy AgencyResearch Center for Veterinary Science, Research Organization for Health, National Research and Innovation AgencyResearch Center for Veterinary Science, Research Organization for Health, National Research and Innovation AgencyResearch Center for Veterinary Science, Research Organization for Health, National Research and Innovation AgencyResearch Center for Veterinary Science, Research Organization for Health, National Research and Innovation AgencyRegional Livestock ServicesDisease Investigator Center Bukit TinggiAnimal Production and Health Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy AgencyAnimal Production and Health Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy AgencyAbstract 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.https://doi.org/10.1186/s12864-024-10169-6LSDVWhole genome sequencingRecombinantPhylogenetic networkSNP |
| spellingShingle | Indrawati Sendow Irene Kasindi Meki Ni Luh Putu Indi Dharmayanti Heri Hoerudin Atik Ratnawati Tirumala Bharani K. Settypalli Hatem Ouled Ahmed Harimurti Nuradji Muharam Saepulloh Rahmat Setya Adji Nuha Fairusya Faralinda Sari Katamtama Anindita Giovanni Cattoli Charles Euloge Lamien Molecular characterization of recombinant LSDV isolates from 2022 outbreak in Indonesia through phylogenetic networks and whole-genome SNP-based analysis BMC Genomics LSDV Whole genome sequencing Recombinant Phylogenetic network SNP |
| title | Molecular characterization of recombinant LSDV isolates from 2022 outbreak in Indonesia through phylogenetic networks and whole-genome SNP-based analysis |
| title_full | Molecular characterization of recombinant LSDV isolates from 2022 outbreak in Indonesia through phylogenetic networks and whole-genome SNP-based analysis |
| title_fullStr | Molecular characterization of recombinant LSDV isolates from 2022 outbreak in Indonesia through phylogenetic networks and whole-genome SNP-based analysis |
| title_full_unstemmed | Molecular characterization of recombinant LSDV isolates from 2022 outbreak in Indonesia through phylogenetic networks and whole-genome SNP-based analysis |
| title_short | Molecular characterization of recombinant LSDV isolates from 2022 outbreak in Indonesia through phylogenetic networks and whole-genome SNP-based analysis |
| title_sort | molecular characterization of recombinant lsdv isolates from 2022 outbreak in indonesia through phylogenetic networks and whole genome snp based analysis |
| topic | LSDV Whole genome sequencing Recombinant Phylogenetic network SNP |
| url | https://doi.org/10.1186/s12864-024-10169-6 |
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