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Complete Genome Sequence of the Lumpy Skin Disease Virus Recovered from the First Outbreak in the Northern Caucasus Region of Russia in 2015.

ABSTRACT: We report here the complete genome sequence of a lumpy skin disease virus (LSDV) isolate obtained in the Northern Caucasus region of Russia in 2015. The LSDV/Russia/Dagestan/2015 genome sequence grouped with field LSDV isolates found in Serbia and Greece, suggesting the monophyletic origin of LSDV isolates that recently affected countries in the Northern Hemisphere.

SUBMITTER: Sprygin A

PROVIDER: S-EPMC6386575 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature

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Complete Genome Sequence of the Lumpy Skin Disease Virus Recovered from the First Outbreak in the Northern Caucasus Region of Russia in 2015.

Sprygin Alexander A Babin Yuriy Y Pestova Yana Y Kononova Svetlana S Byadovskaya Olga O Kononov Aleksandr A

Microbiology resource announcements 20190221 8

We report here the complete genome sequence of a lumpy skin disease virus (LSDV) isolate obtained in the Northern Caucasus region of Russia in 2015. The LSDV/Russia/Dagestan/2015 genome sequence grouped with field LSDV isolates found in Serbia and Greece, suggesting the monophyletic origin of LSDV isolates that recently affected countries in the Northern Hemisphere. ...[more]

PMID: 30834374

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Project description:Lumpy skin disease virus (LSDV) is the causative agent of lumpy skin disease (LSD) that has been recently reported in the South-East and North Asian parts of the Russian Federation. During 2017-2019, there were more than 30 LSD outbreaks in Saratov Region despite active inoculation of cattle with heterologous vaccine. Importantly, the first case of the novel recombinant LSDV strain was reported here in 2017. This study aimed to determine the main clonal lineage(s) of LSDV strains circulated within Saratov Region and other regions of Russia since the first introduction of LSDV. The molecular typing and subtyping based on the coding regions of the G-protein-coupled chemokine receptor (GPCR) gene resulted in a discrimination of all outbreak-related LSDV strains into two main types, such as Type I and Type II, and subtypes Ia-d and IIa-g. Phylogenetically, eleven LSDV lineages were revealed in Russia including the five ones in Saratov Region. They were the following: (i) the Neethling wild Type Ia/2017; (ii) the recombinant Saratov IIc/2017/2019; (iii) the specific Dergachevskyi IId/2017; (iv) the Khvalynsky IIg/2018, and (v) the Haden-Type IIa lineage for the six LSDV strains detected in cattle immunized with heterologous vaccine during the last LSD outbreak in the Saratov Region, Nesterovo Village, in 2019 (Nesterovo-2019 strains). A single LSDV strain detected in Saratov Region in 2017 had the same Type Ia that was identified in 2016 in the bordered Republic of Kazakhstan. Phylogeographic analysis demonstrated three nominal clusters of LSDV types in the following Russian Federation territories: (I) the Central European part; (II) the South-East of the European part; (III) the North Asian part. Cluster I was represented by mainly Type I strains, while both Clusters 2 and 3 contained predominantly Type II strains. The Clusters I and II partially overlapped, while Cluster 3 was separate. Multiple introductions of LSDV into Saratov Region in 2017-2019 using GPCR-based molecular typing and subtyping were revealed. This scheme is a promising tool for molecular discrimination of LSDV strains derived from both vaccinated and unvaccinated against LSD cattle as well as for molecular epidemiology.

Project description:BackgroundLumpy skin disease (LSD) is an important viral disease causing significant economic losses in commercial livestock production. In mid-2019, an outbreak of LSD has been reported in cattle population from different parts of Bangladesh including Chattogram division. A cross-sectional surveillance study was undertaken from August 2019 to December 2019 to investigate the prevalence and associated risk factors of LSD in cattle in Chattogram district.MethodsA total of 3,327 cattle from 19 commercial farms were examined for the LSD specific skin lesions and associated risk factors. A total of 120 skin biopsies were collected from the suspected animal for the confirmation of the disease using molecular detection and histopathological examination. Partial genome sequencing and phylogenetic analyses were performed on selected viral isolates.ResultsThe overall clinical prevalence of LSD in the study population was 10% (95% confidence interval [CI]: 9.4%-11%) where the highest farm level outbreak frequency was 63.33% (95% CI: 45.51%-78.13%) and the lowest 4.22% (95% CI: 3.39%-5.25%). Crossbred and female cattle showed a significantly higher prevalence of the disease compared to their counterparts. Introduction of new animals in farms was found to be one of the most significant risk factors in the transmission of the disease. All suspected skin biopsies were positive for LSD virus (LSDV) infection with granulomatous and pyogranulomatous dermatitis was revealed on histopathology. Phylogenetic analysis based on the inverted terminal repeat region of the LSDV gene suggested that the locally circulating strain was closely related to the strains isolated from the Middle East and North African countries.ConclusionsThe data generated in this study would be beneficial to the field veterinarians and animal health decision makers in the country as well as it will aid in taking appropriate measures to prevent further relapse or outbreak of this disease in future.

Dataset Information

Complete Genome Sequence of the Lumpy Skin Disease Virus Recovered from the First Outbreak in the Northern Caucasus Region of Russia in 2015.

Publications

Complete Genome Sequence of the Lumpy Skin Disease Virus Recovered from the First Outbreak in the Northern Caucasus Region of Russia in 2015.

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