Full-length genome characterization of a novel recombinant vaccine-like lumpy skin disease virus strain detected during
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Full‑length genome characterization of a novel recombinant vaccine‑like lumpy skin disease virus strain detected during the climatic winter in Russia, 2019 Alexander Sprygin1 · Antoinette Van Schalkwyk2 · Irina Shumilova1 · Alexander Nesterov1 · Svetlana Kononova1 · Pavel Prutnikov1 · Olga Byadovskaya1 · Aleksandr Kononov1 Received: 22 April 2020 / Accepted: 26 June 2020 © Springer-Verlag GmbH Austria, part of Springer Nature 2020
Abstract An uncharacteristic outbreak of lumpy skin disease was reported in the Republic of Udmurtiya, Russia, during the climatic winter of March 2019. The causative lumpy skin disease virus (LSDV_Udmurtiya_Russia_2019) was shown to be a recombinant composed of a live attenuated Neethling-type vaccine strain as the dominant parental strain and a Kenyan KSGP/ NI-2490-like virus as its minor parental strain, with 24 statistically significant recombination events that are not identical to those in LSDV Saratov/2017, in which 27 events were identified. Lumpy skin disease virus (LSDV) is a threat to the global livestock cattle industry, inflicting a burden on farmers and affected administrative units [1]. The causative agent is a double-stranded DNA virus of the genus Capripoxvirus, family Poxviridae [2]. Transmission of LSDV seems to be mediated by biting insects and, possibly, certain species of ticks [3]. The first 2019 outbreak in Russia was documented in the Republic of Udmurtiya in early March, when climatic winter was still occurring. The temperatures during the start and end of this outbreak were freezing (below zero Celsius), and no insect activity was possible. The goal of this study was thus to perform full genome sequencing of the strain and characterize its genetic background.
Provenance of the virus material
Handling Editor: William G Dundon.
On the 7th of March 2019, the first outbreak of LSD of the year was reported in the Republic of Udmurtiya in the Russian Federation (56.704273 N, 51.97163 E). The farm had over 5000 animals divided into three units. Three days after the first unit of 100 animals was transferred to sheltered outdoor conditions, five animals showed clinical signs of LSD: skin nodules over the body measuring 0.5–1 cm in diameter, nasal discharge, and fever. Following the identification of a LSD outbreak, all of the animals received an emergency sheep pox-based vaccine. Climatic winter conditions persisted during this period with freezing temperatures during the day and night. The farm experiencing the outbreak had no animal rotation, nor were new animals imported within the preceding four months prior to the outbreak. The virus was cultured on lamb testis cells and purified through a sucrose cushion as described previously [4]. Genomic DNA was extracted and sequenced on a MiSeq benchtop sequencer (Illumina, USA) as described [4].
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00705-020-04756-7) contains supplementary material, which is available to authorized users.
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