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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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2
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Di Giuseppe A, Zenobio V, Dall'Acqua F, Di Sabatino D, Calistri P. Lumpy Skin Disease. Vet Clin North Am Food Anim Pract 2024; 40:261-276. [PMID: 38811129 DOI: 10.1016/j.cvfa.2024.01.002] [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] [Indexed: 05/31/2024] Open
Abstract
Lumpy skin disease (LSD) is a contagious non-zoonotic viral disease of cattle. The disease raises great concern due to the recent rapid spread toward free countries and reoccurrence in countries where control and preventive measures had achieved eradication. Deep nodules involving skin, subcutaneous tissue, and occasionally muscles are localized mostly in the head, neck, perineum, genitalia, udder, and limbs. LSD can cause large economic losses mainly because of the decline in milk production and the decrease in hide value, in addition to the ban of movement of animals and animal products.
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Affiliation(s)
- Alessandra Di Giuseppe
- Veterinary Operations Center for Epidemiology, Programming, Information (COVEPI), Istituto Zooprofilattico dell'Abruzzo e del Molise "G. Caporale" or Experimental Zooprophylactic Institute of Abruzzo and Molise "G. Caporale", Teramo, Italy.
| | - Valentina Zenobio
- Istituto Zooprofilattico Sperimentaledell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | - Francesca Dall'Acqua
- Istituto Zooprofilattico Sperimentaledell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | - Daria Di Sabatino
- Istituto Zooprofilattico Sperimentaledell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | - Paolo Calistri
- Istituto Zooprofilattico Sperimentaledell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
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3
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Shumilova I, Prutnikov P, Mazloum A, Krotova A, Tenitilov N, Byadovskaya O, Chvala I, Prokhvatilova L, Sprygin A. Subclinical infection caused by a recombinant vaccine-like strain poses high risks of lumpy skin disease virus transmission. Front Vet Sci 2024; 11:1330657. [PMID: 38628945 PMCID: PMC11019024 DOI: 10.3389/fvets.2024.1330657] [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: 10/31/2023] [Accepted: 02/26/2024] [Indexed: 04/19/2024] Open
Abstract
Lumpy skin disease (LSD) is a transboundary viral infection, affecting cattle with characteristic manifestations involving multiple body systems. A distinctive characteristic of lumpy skin disease is the subclinical disease manifestation wherein animals have viremia and shed the virus through nasal and ocular discharges, while exhibiting no nodules but enlarged lymph nodes that are easily oversighted by inexperienced vets. Further research on the role of subclinically ill animals in the transmission of LSD virus (LSDV) can contribute to the development of more effective tools to control the disease worldwide. Thus, this study aims to determine the potential role of subclinical infection in virus transmission in a non-vector-borne manner. To achieve this, we inoculated animals with the recombinant vaccine-like strain (RVLS) Udmurtiya/2019 to cause clinical and subclinical LSDV infection. After the disease manifestation, we relocated the subclinically ill animals to a new clean facility followed by the introduction of another five animals to determine the role of RVLS-induced subclinical infection in the virus transmission via direct/indirect contact. After the introduction of the naïve animals to the relocated subclinically ill ones in a shared airspace, two introduced animals contracted the virus (clinically and subclinically), showing symptoms of fever, viremia, and seroconversion in one animal, while three other introduced animals remained healthy and PCR-negative until the end of the study. In general, the findings of this study suggest the importance of considering LSDV subclinical infection as a high-risk condition in disease management and outbreak investigations.
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4
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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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5
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Sprygin A, van Schalkwyk A, Mazloum A, Byadovskaya O, Chvala I. Genome sequence characterization of the unique recombinant vaccine-like lumpy skin disease virus strain Kurgan/2018. Arch Virol 2024; 169:23. [PMID: 38193946 DOI: 10.1007/s00705-023-05938-9] [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: 07/20/2023] [Accepted: 11/06/2023] [Indexed: 01/10/2024]
Abstract
In 2018, the molecular epidemiology of lumpy skin disease in Russia was characterized by a surge in novel recombinant vaccine-like strains causing outbreaks along the southern border, spreading in an easterly direction. Currently, five distinct novel recombinant vaccine-like lineages have been described, designated as clusters 2.1 to 2.5. Based on the complete genome sequence analysis of the causative lumpy skin disease virus (Kurgan/Russia/2018), obtained from an eponymous outbreak, the genome was shown to be composed of a Neethling vaccine strain virus as the dominant parental strain and KSGPO vaccine virus as its minor parental strain. These features are similar to those of Saratov/Russia/2017 and Tyumen/Russia/2018, representing clusters 2.1 and 2.4, respectively. However, Kurgan/Russia/2018 has 16 statistically significant recombination events unique to this sequence, contributing to the phylogenetic clustering of Kurgan/Russia/2018 in yet another cluster designed cluster 2.6, based on analysis involving the complete genome sequences.
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Affiliation(s)
| | | | - Ali Mazloum
- Federal Center for Animal Health, Vladimir, Russia
| | | | - Ilya Chvala
- Federal Center for Animal Health, Vladimir, Russia
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6
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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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7
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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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8
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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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9
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Schlosser-Perrin L, Holzmuller P, Fernandez B, Miotello G, Dahmani N, Neyret A, Bertagnoli S, Armengaud J, Caufour P. Constitutive proteins of lumpy skin disease virion assessed by next-generation proteomics. J Virol 2023; 97:e0072323. [PMID: 37737587 PMCID: PMC10617387 DOI: 10.1128/jvi.00723-23] [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: 05/24/2023] [Accepted: 06/10/2023] [Indexed: 09/23/2023] Open
Abstract
IMPORTANCE Lumpy skin disease virus (LSDV) is the causative agent of an economically important cattle disease which is notifiable to the World Organisation for Animal Health. Over the past decades, the disease has spread at an alarming rate throughout the African continent, the Middle East, Eastern Europe, the Russian Federation, and many Asian countries. While multiple LDSV whole genomes have made further genetic comparative analyses possible, knowledge on the protein composition of the LSDV particle remains lacking. This study provides for the first time a comprehensive proteomic analysis of an infectious LSDV particle, prompting new efforts toward further proteomic LSDV strain characterization. Furthermore, this first incursion within the capripoxvirus proteome represents one of very few proteomic studies beyond the sole Orthopoxvirus genus, for which most of the proteomics studies have been performed. Providing new information about other chordopoxviruses may contribute to shedding new light on protein composition within the Poxviridae family.
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Affiliation(s)
- Léo Schlosser-Perrin
- UMR ASTRE, CIRAD, INRAE, University of Montpellier (I-MUSE), Montpellier, France
| | - Philippe Holzmuller
- UMR ASTRE, CIRAD, INRAE, University of Montpellier (I-MUSE), Montpellier, France
| | - Bernard Fernandez
- UMR ASTRE, CIRAD, INRAE, University of Montpellier (I-MUSE), Montpellier, France
| | - Guylaine Miotello
- Département Médicaments et Technologies pour la Santé, Université Paris Saclay, CEA, INRAE, Bagnols-sur-Cèze, France
| | - Noureddine Dahmani
- UMR ASTRE, CIRAD, INRAE, University of Montpellier (I-MUSE), Montpellier, France
| | - Aymeric Neyret
- CEMIPAI, University of Montpellier, UAR3725 CNRS, Montpellier, France
| | | | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé, Université Paris Saclay, CEA, INRAE, Bagnols-sur-Cèze, France
| | - Philippe Caufour
- UMR ASTRE, CIRAD, INRAE, University of Montpellier (I-MUSE), Montpellier, France
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10
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Kumar R, Chander Y, Verma A, Tripathi BN, Barua S, Kumar N. TA novel HRM-based gap-qRT-PCR for identification and quantitation of the vaccine and field strain(s) of lumpy skin disease virus. J Immunol Methods 2023:113521. [PMID: 37392930 DOI: 10.1016/j.jim.2023.113521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/03/2023]
Abstract
Lumpy skin disease (LSD) has become the most important animal health problem in India due to high morbidity, mortality and production losses. A homologous live-attenuated LSD vaccine (Lumpi-ProVacInd) was recently developed by using a local LSD virus (LSDV) strain (LSDV/2019/India/Ranchi) in India which is likely to replace the existing practice of vaccinating cattle with goatpox vaccine. It is essential to differentiate the vaccine and field strains, if a live-attenuated vaccine has been used for control and eradication of the disease, particularly in endemic areas. As compared to the prevailing vaccine and field/virulent strains, the Indian vaccine strain (Lumpi-ProVacInd) has a unique deletion of 801 nucleotides in its inverted terminal repeat (ITR) region. We exploited this unique feature and developed a novel high resolution melting-based gap quantitative real-time PCR (HRM-gap-qRT-PCR) for rapid identification and quantitation of the vaccine and field strain(s) of LSDV.
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Affiliation(s)
- Ram Kumar
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Yogesh Chander
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Assim Verma
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Bhupendra N Tripathi
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India; Animal Science Division, Indian Council of Agricultural Research, New Delhi, India
| | - Sanjay Barua
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India
| | - Naveen Kumar
- National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India.
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11
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Kumar A, Venkatesan G, Kushwaha A, Poulinlu G, Saha T, Ramakrishnan MA, Dhar P, Kumar GS, Singh RK. Genomic characterization of Lumpy Skin Disease virus (LSDV) from India: Circulation of Kenyan-like LSDV strains with unique kelch-like proteins. Acta Trop 2023; 241:106838. [PMID: 36796571 DOI: 10.1016/j.actatropica.2023.106838] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/18/2022] [Accepted: 01/15/2023] [Indexed: 02/17/2023]
Abstract
Lumpy skin disease (LSD) is an economically important poxviral disease endemic to Asia, Europe, and Africa. Recently, LSD has spread to naïve countries, including India, China, Bangladesh, Pakistan, Myanmar, Vietnam, and Thailand. Here, we describe the complete genomic characterization of LSDV from India, LSDV-WB/IND/19 isolated from an LSD affected calf in 2019 determined by Illumina next-generation sequencing (NGS). The LSDV-WB/IND/19 has a genome size of 150,969 bp encoding 156 putative ORFs. Phylogenetic analysis based on complete genome sequence suggested that LSDV-WB/IND/19 is closely related to Kenyan LSDV strains with 10-12 variants with non-synonymous changes confined to LSD_019, LSD_049, LSD_089, LSD_094, LSD_096, LSD_140, and LSD_144 genes. In contrast to complete kelch-like proteins in Kenyan LSDV strains, LSDV-WB/IND/19 LSD_019 and LSD_144 genes were found to encode truncated versions (019a, 019b, and 144a, 144b). LSD_019a and LSD_019b proteins of LSDV-WB/IND/19 resemble that of wild-type LSDV strains based on SNPs and the C-terminal part of LSD_019b except for deletion at K229, whereas the LSD_144a and LSD_144b proteins resemble that of Kenyan LSDV strains based on SNPs, however, C-terminal part of LSD_144a resembles that of vaccine-associated LSDV strains due to premature truncation. The NGS findings were confirmed by Sanger sequencing of these genes in Vero cell isolate as well as in the original skin scab along with similar findings in another Indian LSDV from scab specimen. LSD_019 and LSD_144 genes are thought to modulate virulence and host range in capripoxviruses. This study demonstrates the circulation of unique LSDV strains in India and highlights the importance of constant monitoring of the molecular evolution of LSDV and associated factors in the region in light of the emergence of recombinant LSDV strains.
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Affiliation(s)
- Amit Kumar
- Pox Virus Laboratory, Division of Virology, ICAR-Indian Veterinary Research Institute (IVRI), Mukteswar, Uttarakhand, India.
| | - Gnanavel Venkatesan
- ICAR-Indian Veterinary Research Institute (IVRI), Bengaluru campus, Karnataka, India
| | - Anand Kushwaha
- Pox Virus Laboratory, Division of Virology, ICAR-Indian Veterinary Research Institute (IVRI), Mukteswar, Uttarakhand, India
| | - G Poulinlu
- Pox Virus Laboratory, Division of Virology, ICAR-Indian Veterinary Research Institute (IVRI), Mukteswar, Uttarakhand, India
| | - Tapabrata Saha
- Block Animal Health Centre, Chhatna, Bankura, West Bengal, India
| | - M A Ramakrishnan
- ICAR-Indian Veterinary Research Institute (IVRI), Bengaluru campus, Karnataka, India
| | - Pronab Dhar
- ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Uttar Pradesh, India
| | - G Sai Kumar
- ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Uttar Pradesh, India
| | - R K Singh
- ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, Uttar Pradesh, India
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Nesterov A, Mazloum A, Byadovskaya O, Shumilova I, Van Schalkwyk A, Krotova A, Kirpichenko V, Donnik I, Chvala I, Sprygin A. Experimentally controlled study indicates that the naturally occurring recombinant vaccine-like lumpy skin disease strain Udmurtiya/2019, detected during freezing winter in northern latitudes, is transmitted via indirect contact. Front Vet Sci 2022; 9:1001426. [PMID: 36337212 PMCID: PMC9632959 DOI: 10.3389/fvets.2022.1001426] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 10/04/2022] [Indexed: 08/21/2023] Open
Abstract
Lumpy skin disease (LSD) caused by LSD virus (LSDV), is a member of the poxvirus genus Capripoxvirus. It is classified as a notifiable disease by the World Organization for Animal Health (WOAH) based on its potential for rapid spread and global economic impact. Due to these characteristics, the mode of LSDV transmission has prompted intensive research efforts. Previous experimental studies using the virulent vaccine-derived recombinant LSDV strain Saratov/2017, demonstrated that this strain has the capacity for transmission in a vector-proof environment. This study demonstrated that a second novel recombinant vaccine-derived LSDV strain Udmurtiya/2019, can infect bulls in contact with diseased animals, in the absence of insect vectors. Bulls were housed in an insect proof animal biosafety level 3 facility, where half the animals were inoculated intravenously with the recombinant LSDV (Udmurtiya/2019), whilst the remaining five animals were mock-inoculated but kept in contact with the inoculated group. Both the infected / inoculated group (IN) and uninfected / incontact group (IC), were monitored for 41 days with continuous registration of body temperature, observations for clinical signs and collection of blood samples and nasal swabs for testing of LSDV presence using real-time PCR. Results indicated that cohabitation of animals from both groups was sufficient to transmit the virus from the IN to the IC-group, with the onset of clinical signs including pyrexia (~41°C) and classical LSD nodular skin lesions starting at 10 dpi for the IN group and 16 dpi for the IC-group. Additionally, the presence of LSDV genomes as well as anti-LSDV antibodies were detected in swabs, blood and serum samples from animals belonging to both groups. These results provides additional evidence of LSDV transmission in a controlled environment without direct contact between diseased and healthy animals, yet in the absence of vectors. Based on these observations, the question concerning a hypothetical relation between mutations in the virus genome and its mode of transmission gains more importance and requires additional investigations with direct comparisons between classical and novel recombinant LSDV strains.
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Affiliation(s)
| | - Ali Mazloum
- Federal Center for Animal Health, Vladimir, Russia
| | | | | | - Antoinette Van Schalkwyk
- Agricultural Research Council—Onderstepoort Veterinary Institute, Pretoria, South Africa
- Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | | | | | | | - Ilya Chvala
- Federal Center for Animal Health, Vladimir, Russia
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13
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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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Byadovskaya O, Prutnikov P, Shalina K, Babiuk S, Perevozchikova N, Korennoy F, Chvala I, Kononov A, Sprygin A. The changing epidemiology of lumpy skin disease in Russia since the first introduction from 2015 to 2020. Transbound Emerg Dis 2022; 69:e2551-e2562. [PMID: 35583857 DOI: 10.1111/tbed.14599] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 05/06/2022] [Accepted: 05/14/2022] [Indexed: 12/24/2022]
Abstract
Lumpy skin disease (LSD) is an economically important transboundary disease affecting cattle, causing large economic losses such as decreased production and trade restrictions. LSD has been a historically neglected disease since it previously caused disease limited to the African continent. Currently, the epidemiology of LSD virus is based on how the disease is transmitted in tropical and sub-tropical climates. The understanding of its epidemiology in hemiboreal climates is not well understood and needs urgent attention to expand the current knowledge. In this study, the epidemiological findings on LSD in Russia over a 6-year period are summarized and discussed. A total of 471 outbreaks were identified spanning over a 9000 km range. The outbreaks of LSD occur primarily in small holder farms (backyard) compared to commercial farms between mid-May through mid-November including weather conditions with snow and freezing temperatures that preclude vector activity. Mortality and morbidity varied across the 6 years ranging from 1.19% to 61.8% and 0% to 50%, respectively, with a tendency to decline from 2015 to 2020. The geographic pattern of spread was assessed by means of directionality, indicating a northward movement from 2015 to 2016, with a consequent East turn in 2017 through Siberia to the Far East by 2020. All cases occurred along the border with Kazakhstan. Mathematical modelling showed that the disease tended to form statistically verified annual spatiotemporal clusters in 2016-2018, whereas in 2019 and 2020 such segregation was not evident. The trend of spread was mainly either from south to north or from south to a north-east direction.
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Affiliation(s)
| | | | | | - Shawn Babiuk
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Canada
| | | | | | - Ilya Chvala
- Federal Center for Animal Health, Vladimir, Russia
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15
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Shumilova I, Nesterov A, Byadovskaya O, Prutnikov P, Wallace DB, Mokeeva M, Pronin V, Kononov A, Chvala I, Sprygin A. A Recombinant Vaccine-like Strain of Lumpy Skin Disease Virus Causes Low-Level Infection of Cattle through Virus-Inoculated Feed. Pathogens 2022; 11:pathogens11080920. [PMID: 36015041 PMCID: PMC9414542 DOI: 10.3390/pathogens11080920] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/28/2022] [Accepted: 08/09/2022] [Indexed: 12/18/2022] Open
Abstract
Since 1989, lumpy skin disease of cattle (LSD) has spread out of Africa via the Middle East northwards and eastwards into Russia, the Far East and South-East Asia. It is now threatening to become a worldwide pandemic, with Australia possibly next in its path. One of the research gaps on the disease concerns its main mode of transmission, most likely via flying insect vectors such as biting flies or mosquitoes. Direct or indirect contact transmission is possible, but appears to be an inefficient route, although there is evidence to support the direct contact route for the newly detected recombinant strains first isolated in Russia. In this study, we used experimental bulls and fed them via virus-inoculated feed to evaluate the indirect contact route. To provide deeper insights, we ran two parallel experiments using the same design to discover differences that involved classical field strain Dagestan/2015 LSDV and recombinant vaccine-like Saratov/2017. Following the attempted indirect contact transmission of the virus from the inoculated feed via the alimentary canal, all bulls in the Dagestan/2015 group remained healthy and did not seroconvert by the end of the experiment, whereas for those in the Saratov/2017 recombinant virus group, of the five bulls fed on virus-inoculated feed, three remained clinically healthy, while two displayed evidence of a mild infection. These results provide support for recombinant virus transmission via the alimentary canal. In addition, of particular note, the negative control in-contact bull in this group exhibited a biphasic fever at days 10 and 20, developed lesions from day 13 onwards, and seroconverted by day 31. Two explanations are feasible here: one is the in-contact animal was somehow able to feed on some of the virus-inoculated bread left over from adjacent animals, but in the case here of the individual troughs being used, that was not likely; the other is the virus was transmitted from the virus-fed animals via an airborne route. Across the infected animals, the virus was detectable in blood from days 18 to 29 and in nasal discharge from days 20 to 42. Post-mortem and histological examinations were also indicative of LSDV infection, supporting further evidence for rapid, in F transmission of this virus. This is the first report of recombinant LSDV strain transmitting via the alimentary mode.
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Affiliation(s)
- Irina Shumilova
- Federal State-Financed Institution, Federal Center for Animal Health, 600901 Vladimir, Russia
| | - Alexander Nesterov
- Federal State-Financed Institution, Federal Center for Animal Health, 600901 Vladimir, Russia
| | - Olga Byadovskaya
- Federal State-Financed Institution, Federal Center for Animal Health, 600901 Vladimir, Russia
| | - Pavel Prutnikov
- Federal State-Financed Institution, Federal Center for Animal Health, 600901 Vladimir, Russia
| | - David B. Wallace
- Agricultural Research Council–Onderstepoort Veterinary Institute, Private Bag X5, Onderstepoort, Pretoria 0002, South Africa
- Department Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X4, Onderstepoort, Pretoria 0002, South Africa
| | - Maria Mokeeva
- Federal State-Financed Institution, Federal Center for Animal Health, 600901 Vladimir, Russia
| | - Valeriy Pronin
- Federal State-Financed Institution, Federal Center for Animal Health, 600901 Vladimir, Russia
| | - Aleksandr Kononov
- Federal State-Financed Institution, Federal Center for Animal Health, 600901 Vladimir, Russia
| | - Ilya Chvala
- Federal State-Financed Institution, Federal Center for Animal Health, 600901 Vladimir, Russia
| | - Alexander Sprygin
- Federal State-Financed Institution, Federal Center for Animal Health, 600901 Vladimir, Russia
- Correspondence:
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Krotova A, Mazloum A, Byadovskaya O, Sprygin A. Phylogenetic analysis of lumpy skin disease virus isolates in Russia in 2019-2021. Arch Virol 2022; 167:1693-1699. [PMID: 35666394 DOI: 10.1007/s00705-022-05487-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/15/2022] [Indexed: 11/25/2022]
Abstract
Lumpy skin disease continues to pose a threat to countries in the East and Asia-Pacific regions. Although only occasional LSDV outbreaks have been reported recently in Russia, these have been mainly restricted to the Far East region of the country. An increase in the number of outbreaks in South East Asia has been attributed to recombinant vaccine-like LSDV strains. In this scenario, it is epidemiologically important to perform phylogenetic analysis to track the distribution of LSDV worldwide at the genetic level to understand routes of migration and molecular evolution patterns. In this study, we investigated the RPO30 and GPCR gene regions of LSDV isolates associated with outbreaks in 2019-2021 in Siberia and the Far East region of Russia. The inferred phylogeny confirms the recombinant origin of these sequenced isolates. Based on sequences of these selected loci, the isolates from 2019 differed from isolates detected in Russia in the past and from isolates from Asian countries, while the isolates from 2020 and 2021 exhibited a high degree of similarity to the Asian isolates. These findings indicate that recombinant LSDV strains continue to persist and additionally point to the establishment of a specific lineage of recombinant isolates in the region. Full genome sequencing is still needed to gain more information about how the circulating isolates are related to each other.
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Affiliation(s)
| | - Ali Mazloum
- Federal Center for Animal Health, Vladimir, Russia
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17
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van Schalkwyk A, Kara P, Heath L. Phylogenomic characterization of historic lumpy skin disease virus isolates from South Africa. Arch Virol 2022; 167:2063-2070. [PMID: 35792935 DOI: 10.1007/s00705-022-05515-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/16/2022] [Indexed: 11/02/2022]
Abstract
The poxvirus lumpy skin disease virus (LSDV) is the causative agent of the vexatious lumpy skin disease, which predominantly affects cattle and water buffalo. It has been endemic to South Africa since the 1950s, and in 1960, a live attenuated vaccine was commercially released for use in the country to mitigate the spread of this transboundary disease. This vaccine (Neethling/vaccine/LW-1959) was generated from serial passages of the prototype lumpy skin disease virus strain Neethling-WC/RSA/1957, which was isolated in 1957 from an outbreak in the Western Cape province of South Africa and was subsequently used to prove the infectious nature of the virus and the resulting disease in cattle. In this study, we determined the complete genome sequence of the LSDV prototype strain Neethling-WC/RSA/1957, as well as three other LSDV isolates from the 1950s, one wild-type isolate from the 1970s, and a commercial vaccine produced in 1988 (LW-1959). Phylogenomic analysis showed that all six sequences were in cluster 1.1, along with previous sequences of the vaccine strain, the oldest known isolate (LSDV/Haden/RSA/1954), and virulent viruses isolated in the 1990s from South Africa. Seven single-nucleotide polymorphisms were identified between the Neethling-WC/RSA/1957 strain and the vaccine strain (LW-1959), providing new insights into virus attenuation and possible markers for DIVA assays.
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Affiliation(s)
- Antoinette van Schalkwyk
- Agricultural Research Council-Onderstepoort Veterinary Institute, 100 old Soutpan Road, Onderstepoort, 0110, South Africa. .,Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville, 7535, South Africa.
| | - Pravesh Kara
- Agricultural Research Council-Onderstepoort Veterinary Institute, 100 old Soutpan Road, Onderstepoort, 0110, South Africa
| | - Livio Heath
- Agricultural Research Council-Onderstepoort Veterinary Institute, 100 old Soutpan Road, Onderstepoort, 0110, South Africa
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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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Krotova A, Byadovskaya O, Shumilova I, Zinyakov N, van Schalkwyk A, Sprygin A. Molecular characterization of a novel recombinant lumpy skin disease virus isolated during an outbreak in Tyumen, Russia, in 2019. Transbound Emerg Dis 2022; 69:e2312-e2317. [PMID: 35488786 DOI: 10.1111/tbed.14574] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/11/2022] [Accepted: 04/26/2022] [Indexed: 11/30/2022]
Abstract
Lumpy skin disease virus causes a debilitating pox disease of domesticated cattle and water buffalos. In the last decade, LSDV has spread from Africa into the Middle East, Europe and most recently Asia. As of 2017 atypical outbreaks caused by novel LSDV strains were reported in Russia, followed by China and Vietnam between 2018 and 2020. In this work we describe another unique recombinant LSDV strain recovered from Tyumen, Russia in 2019. Typing of the virus using currently available qPCR protocols produced inconclusive results and subsequently the complete genome of the isolate was determined. The consensus genome contained statistically significant signals of possible recombination events between parental strains KSGPO-240/Kenya/1958 and the live attenuated vaccine LW/1958. The novel strain carries 25 unique breakpoints different from the known recombinant strains. Additionally, the findings reiterate the importance of complete genome sequencing when analysing outbreak samples caused in particular by mosaic LSDV, in contrast to only performing specified qPCRs. This article is protected by copyright. All rights reserved.
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Shumilova I, Krotova A, Nesterov A, Byadovskaya O, van Schalkwyk A, Sprygin A. Overwintering of recombinant lumpy skin disease virus in northern latitudes, Russia. Transbound Emerg Dis 2022; 69:e3239-e3243. [PMID: 35298087 DOI: 10.1111/tbed.14521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/02/2022] [Accepted: 03/15/2022] [Indexed: 11/27/2022]
Abstract
Lumpy skin disease is an emerging transboundary infection demonstrating a great range expansion worldwide recently. With many knowledge gaps, there is a lack of understanding how lumpy skin disease virus (LSDV), including naturally occurring vaccine-like LSDV, is capable of surviving under different climatic conditions. In this study we describe a recombinant vaccine-like LSDV from an outbreak in Saratov region of Russia in 2019, where the first recombinant Saratov/2017 was documented. Although, the two isolates were two years apart, Saratov/2019 seems to be clonally derived from Saratov/2017 with accrual of mutations characteristic of circulating under selective conditions. The obtained findings demonstrate the persistence of LSDV during winter and successful overwintering in in cold climate, necessitating an objective need for deeper research into LSDV biology. This article is protected by copyright. All rights reserved.
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