Phylogenetic analysis of lumpy skin disease virus isolates in Russia in 2019-2021

Genome sequence characterization of the unique recombinant vaccine-like lumpy skin disease virus strain Kurgan/2018

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.

Lumpy skin disease: history, current understanding and research gaps in the context of recent geographic expansion

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.

Constitutive proteins of lumpy skin disease virion assessed by next-generation proteomics

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.

Development and application of a real-time polymerase chain reaction assay to detect lumpy skin disease virus belonging to the Kenyan sheep and goat pox group

Lumpy skin disease (LSD) outbreaks in Southeast and South Asia are attributed to different lineages of LSD virus (LSDV). Variants belonging to the novel recombinant cluster 2.5 circulate in China and Thailand, while a Kenyan sheep and goat pox (KSGP) strain from cluster 1.1 circulates in India, Pakistan, and Bangladesh. The clusters representing these circulating strains are vastly different. However, if their distribution encroaches into each other's ranges, it will be impossible to differentiate between them due to the lack of suitable molecular tools. Thus, fit-for-purpose molecular tools are in demand to effectively and timeously diagnose and investigate the epidemiology of LSDVs in a region. These could significantly contribute to the phylogenetic delineation of LSDVs and the development of preventive measures against transboundary spillovers. This work aimed to develop a real-time polymerase chain reaction assay targeting open reading frame LW032, capable of specifically detecting KSGP-related isolates and recombinant LSDV strains containing the KSGP backbone. The analytical specificity was proven against the widest possible panel of recombinant vaccine-like LSDV strains known to date. The amplification efficiency was 91.08%, and the assay repeatability had a cycle threshold variation of 0.56-1.1 over five repetitions across three runs. This KSGP-specific assay is reliable and fast and is recommended for use in LSDV epidemiological studies where the accurate detection of KSGP genetic signatures is a priority, particularly in regions where KSGP-like and other lineages are circulating.

Genotyping tool for salmonid gill pox virus (SGPV) obtained from farmed and wild Atlantic salmon (Salmo salar)

Poxviruses are common viruses found in vertebrate species. In 2006, the first poxvirus associated with salmon, salmonid gill poxvirus (SGPV), was identified during an outbreak of gill disease at a smolt production site in northern Norway and at two marine farms in western Norway. Poxviruses had previously been detected in ayu (Plecoglossus altivelis) and koi carp (Cyprinus carpio). In all three fish species, poxviruses are associated with gill disease. It has not been possible to culture SGPV from Norway, and little is known about its virulence. However, the association between SGPV and gill disease in salmon has shown the need for molecular tools to identify reservoirs and transmission routes. Sequencing the genome of a second isolate of SGPV has made it possible to compare variable regions between two strains of the virus, showing the presence of a large number of variable regions that exhibit both variable numbers of tandem repeats and intra-ORF variation. We present eight regions that are suitable for distinguishing strains of SGPV and determining their phylogenetic relationship, and these were used to compare SGPV isolates obtained from both farmed and wild salmon in fresh and sea water. The prevalence of the virus was found to be higher in wild salmon in rivers than in returning wild salmon collected from traps in Norwegian fjords. Genotyping based on the eight selected variable regions, suggests the presence of geographically distinct isolates in freshwater among both farmed and wild salmon, while SGPV from marine farms shows high local diversity and a wide geographical distribution of similar strains of the virus.

Evidence of lumpy skin disease virus infection in camels

Countries in the Indian subcontinent are currently facing a deadly epidemic of lumpy skin disease (LSD).  LSD is primarily a disease of cattle. Buffaloes may sometimes develop mild illness, however, other domestic animals are considered resistant to LSD. We confirmed the LSDV infection in camels as evidenced by skin nodules on the body surface of the affected camels, isolation of LSD virus (LSDV) and amplification of LSDV-specific gene segments from the skin nodules (PCR), nucleotide sequencing of the viral genome and, demonstration of anti-LSDV antibodies in serum. Phylogenetic analysis based on nucleotide sequencing of ORF011, ORF012 and ORF036 revealed that the virus (LSDV/Camel/India/2022/Bikaner) is related to the historical NI-2490/Kenya/KSGP-like field strains which are predominantly circulating in the Indian subcontinent. This is the first report wherein LSDV has been to infect camels.

The Characterization and Differentiation of Recombinant Lumpy Skin Disease Isolates Using a Region within ORF134

The recent description and characterization of several novel and unique lumpy skin disease virus (LSDV) strains have revealed the inadequacy of current techniques for differentiating between vaccine- and wild-type viruses. The lack of reliable sequencing targets for promptly distinguishing circulating recombinant vaccine-like strains (RVLSs) highlights the need to develop a single and simple differentiation tool. In this study, we analyzed the available LSDV whole-genome sequences and identified a 705-bp region in open reading frame (ORF) LW134. Based on a single run of nucleotide sequencing and phylogenetic analysis, the region with 13 informative single nucleotide polymorphisms (SNPs) was capable of accurately segregating the novel RVLSs into the same five clusters previously confirmed by whole-genome sequencing. In addition, archived RVLSs from Russia were analyzed for further characterization using the newly described single PCR and sequencing assay. The ORF LW134 assay identified one archived RVLS as a novel cluster distinct from the previously described five clusters, while clustering the remaining samples into previously designated lineages, demonstrating the reliability of the assay. The novel PCR and sequencing assays described in this study have great potential for accurately delineating the molecular and evolutionary affiliation of circulating RVLSs.

Evidence of Lumpy Skin Virus DNA in Blood-Feeding Flies During Outbreaks in Russia in 2018-2019

In this study we report the testing of blood-feeding and synanthropic flies captured near animals affected by lumpy skin disease virus (LSDV) in Russia during the outbreaks in the Kurgan region in 2018 and Saratov region in 2019. The insects of interest were the stable fly Stomoxys calcitrans, Tabanidae horse flies, Culicoides midges and the house fly Musca domestica examined as individuals or pools. The obtained findings demonstrate that viral DNA was found in pools of S.calcitrans and M. domestica and in the head and abdomen of stable flies. This is the first report of LSDV DNA detection in Tabanidae flies from the field. The presented data are envisaged to help further guide the search for putative vectors of LSDV in different climatic regions and interpret laboratory-controlled experiments on vector-borne transmission of LSDV.