Analysis of vaccine-like lumpy skin disease virus from flies near the western border of China

In-silico characterization of LSDV132 protein divulged its BCL-2-like nature

Lumpy skin disease virus (LSDV) belongs to Poxviridae family. This virus possesses various proteins which impart potential functions to it including assembly of newly synthesized viruses in the replication cycle and forming their structure. LSDV132 protein is also one of such proteins. Its key characteristics were unknown because, no any relevant study was reported about it. This study aimed to investigate its characteristic features and essential functions using several bioinformatics techniques. These analyses included physiochemical characterization and exploring the crucial functional and structural perspectives. Upon analysis of the physiochemical properties, the instability index was computed to be 30.89% which proposed LSDV132 protein to be a stable protein. Afterwards, the phosphorylation sites were explored. Several sites were found in this regard which led to the hypothesis that it might be involved in the regulation of apoptosis and cell signaling, among other cellular processes. Furthermore, the KEGG analysis and the analysis of protein family classification confirmed that the LSDV132 protein possessed Poxvirus-BCL-2-like motifs, indicating that it might be responsible in modulating the apoptosis of host cells. This crucial finding suggested that the protein under study possessed BCL-2-like features. Proceeding this very important finding, the molecular docking analysis was performed. In this context, various viral BCL-2 inhibitors were retrieved from the ChEMBL database for docking purpose. The docking results revealed that pelcitoclax exhibited best docking scores i.e., -9.1841 kcal/mol, among all of the other docked complexes. This fact signified that this compound might serve as an inhibitor of LSDV132 protein.

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.

Lumpy Skin Disease: A Systematic Review of Mode of Transmission, Risk of Emergence and Risk Entry Pathway

The spread of lumpy skin disease (LSD) to free countries over the last 10 years, particularly countries in Europe, Central and South East Asia, has highlighted the threat of emergence in new areas or re-emergence in countries that achieved eradication. This review aimed to identify studies on LSD epidemiology. A focus was made on hosts, modes of transmission and spread, risks of outbreaks and emergence in new areas. In order to summarize the research progress regarding the epidemiological characteristics of LSD virus over the last 40 years, the Preferred Reporting Items for Systematic reviews and Meta-Analyses statement guidelines were followed, via two databases, i.e., PubMed (biomedical literature) and Scopus (peer-reviewed literature including scientific journals, books, and conference proceedings). A total of 86 scientific articles were considered and classified according to the type of epidemiological study, i.e., experimental versus observational. The main findings and limitations of the retrieved articles were summarized: buffaloes are the main non-cattle hosts, the main transmission mode is mechanical, i.e., via blood-sucking vectors, and stable flies are the most competent vectors. Vectors are mainly responsible for a short-distance spread, while cattle trade spread the virus over long distances. Furthermore, vaccine-recombinant strains have emerged. In conclusion, controlling animal trade and insects in animal transport trucks are the most appropriate measures to limit or prevent LSD (re)emergence.

Lumpy Skin Disease—An Emerging Cattle Disease in Europe and Asia

Lumpy skin disease virus (LSDV) is a member of the Capripoxvirus genus, mainly infecting cattle and buffalo, which until relatively recently was only endemic in parts of Africa and then spread to the Middle East and lately Europe and Asia. Lumpy skin disease (LSD) is a notifiable disease with a serious impact on the beef industry as it causes mortality of up to 10% and has impacts on milk and meat production, as well as fertility. The close serological relationship between LSDV, goat poxvirus (GTPV) and sheep poxvirus (SPPV) has led to live attenuated GTPV and SPPV vaccines being used to protect against LSD in some countries. There is evidence that the SPPV vaccine does not protect from LSD as well as the GTPV and LSDV vaccines. One of the LSD vaccines used in Eastern Europe was found to be a combination of different Capripoxviruses, and a series of recombination events in the manufacturing process resulted in cattle being vaccinated with a range of recombinant LSDVs resulting in virulent LSDV which spread throughout Asia. It is likely that LSD will become endemic throughout Asia as it will be very challenging to control the spread of the virus without widespread vaccination.

Retrospective genomic analysis of the first Lumpy skin disease virus outbreak in China (2019)

Lumpy skin disease caused by Lumpy skin disease virus (LSDV) is a severe systemic disease affecting cattle and other ruminants. Lumpy skin disease was first reported in northwest China in August 2019 and has severely threatened the cattle breeding industry in China. However, there have been limited genomic studies of LSDV from the first outbreak and its subsequent epidemics. This study aims to characterize the comparative genomic evolution of the LSDV strain from the first outbreak in China. The etiological agent was isolated in a Madin-Darby bovine kidney cell culture and subsequently identified by PCR and Sanger sequencing of six selected genes. The genome sequence was determined using Illumina sequencing and analyzed through genome alignment and phylogenetic tree. The results showed that all six genes were successfully amplified and genetically clustered into LSDV. The virus presented the highest homology to strain China/GD01/2020, which shared 100% identities among 150 open reading frames (ORFs), and 97.1-99.7% identities among additional 6 ORFs. Bayesian inference tree analysis revealed that the virus shared a common ancestor with LSDV strains from China and Vietnam. The study provides an additional genomic data for LSDV tracking and control in China and neighboring countries.

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.

Molecular and histopathological characterization of lumpy skin disease in cattle in northern Vietnam during the 2020-2021 outbreaks

Lumpy skin disease (LSD) is a serious emerging infectious disease in cattle caused by a virus of the family Poxviridae. According to the Department of Animal Health, LSD first occurred in Vietnam at the end of October 2020 in Cao Bang and Lang Son provinces. So far, the disease has infected over 63,000 animals, resulting in 9170 deaths occurring in 32 different provinces in northern and central Vietnam. In this study, skin samples from lumpy skin disease virus (LSDV)-infected cattle from the northern provinces of Vietnam displaying clinical symptoms including fever (> 40 °C), runny nose, drooling, and skin lesions were used for genetic characterization and histopathology. Genetic analysis of the partial P32 (LSDV074), partial F (LSDV117), complete RPO30 (LSDV035), and complete G-protein-coupled-chemokine-like receptor (GPCR) (LSDV011) genes showed that all Vietnamese LSDV strains belonged to the genus Capripoxvirus and were closely related to LSDV strains isolated in China. Microscopic examination of the skin lesions showed thickening of the epidermal layer of the skin and hair follicles, hyperplasia of sebaceous glands, intracytoplasmic inclusion bodies, and hemorrhages in the mesoderm.

Capripoxviruses, leporipoxviruses, and orthopoxviruses: Occurrences of recombination

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.

Risk factors associated with lumpy skin disease in cattle in West Kazakhstan

Lumpy skin disease is an important emerging disease posing a threat to the livestock industry worldwide. Moreover, factors involved in disease transmission in the field and at farm level remain unidentified. This research was based on a cross-sectional study using a questionnaire administered through face-to-face interviews with affected farmers. From January 2021 to July 2021, 543 households were visited in four provinces of the West Kazakhstan region to assess the prevalence of LSD and its associated risk factors. Animal and farm level risk factors were examined using univariable and multivariable mixed effect logistic regression. At animal level, the factors associated with LSD outbreaks include herd size Medium OR = 0.68, (95% CI: 0.54-0.84); large OR = 0.63, (95% CI: 0.49-0.81), purchasing animals OR = 11.67, (95% CI: 8.87-15.35), and selling animals during LSD outbreak OR = 1.24, (95% CI: 1.06-1.45). The overall animal level and herd level LSD prevalence were 10.2% (95% CI: 9.6 -0.10.9) and 49.2% (95% CI: 45.0 - 53.4) respectively. Our study demonstrates the dissemination of LSDV from primary outbreaks to new areas and risk factors associated with LSD in Kazakhstan. This finding will enhance knowledge on disease epidemiology and help develop coordinated actions in prevention and control of the possible LSD outbreaks.

Genomic characterization of lumpy skin disease virus in southern China

Lumpy skin disease virus (LSDV) is of high economic importance and has spread rapidly to many European and Asian countries in recent years. LSDV was introduced to China in 2019 and have caused severe outbreaks in several provinces. Here, we detected an LSDV strain (GD01/2020) from a cattle farm with typical LSD symptoms in Guangdong, southern China using a novel quantitative real-time PCR assay targeting the viral GPCR gene. We obtained the whole genomic sequence of GD01/2020 through metagenomic analysis. The GD01/2020 was highly homologous to the LSDVs isolated in Xinjiang, China in 2019, and distinct from all the LSDVs identified in other countries, in their sequences of GPCR and RPO30 genes. The GD01/2020 was a vaccine-recombinant strain, but distinct from two recombinant LSDVs identified in Russia. At least 25 putative recombination events between a vaccine strain and a field strain were identified in the genome of GD01/2020, which could affect the virulence and transmissibility of the virus. These results suggested that a virulent vaccine-recombinant LSDV from an unknown origin was introduced into Xinjiang, China in 2019 and spread to Guangdong, China in 2020.

Molecular characterization of a novel subgenotype of lumpy skin disease virus strain isolated in Inner Mongolia of China

BACKGROUND

The outbreak of Lumpy skin disease (LSD) in cattle caused by LSD virus (LSDV) was first reported in August 2019 in China. Since then, several LSD outbreaks have been reported in seven different provinces of China. Until now, several Lumpy skin disease virus (LSDV) strains from China have been reported and sequenced including LSDV/Xinjiang/2019 (MN598005.1), China/GD01/2020 (MW355944.1), and LSDV/Hongkong/2021 (MW732649.1). In October 2020, more than 1,700 cattle imported from Chile arrived in Xilingol, Inner Mongolia, and were diagnosed with LSD. Currently, limited data on the origin of the virus is available.

METHODS

Nucleotide sequences of the ORF11, ORF36, ORF74, ORF117, ORF126 genes and the complete genome of LSDV strains and isolates were downloaded from NCBI database. MEGA7.0 was used to perform phylogenetic analysis with Neighbor-Joining (NJ). DNASTAR software is used to analyze homologous comparison analysis with related genes of reference strains included in Genbank.

RESULTS

Compared with other strains isolated from China, the results of full genome sequence analysis showed the LSDV/NMG/2020 strain belonged to the recombinant strains. The LSDV/NMG/2020 strain is different from the current LSDV field isolates in Africa, the Middle East, Europe, and the newly emerged LSDV Russia variants. Based on the identities of P32, RPO30, EEV, GPCR and LSDV117 genes (99.8%, 99%, 99.8%, 99% and 98.7%), the sub-cluster recombinant containing LSDV/NMG/2020 strain is phylogenetically closer to the Russia strain (Saratov/2017).

CONCLUSIONS

In this study, we reported a new isolated LSDV strain named LSDV/NMG/2020. The results of genomic characterization and phylogenetic analysis demonstrated that the LSDV/NMG/2020 isolate was a vaccine-like recombinant strain.

Genetic and phylogenetic analysis of lumpy skin disease viruses (LSDV) isolated from the first and subsequent field outbreaks in India during 2019 reveals close proximity with unique signatures of historical Kenyan NI-2490/Kenya/KSGP-like field strains

Lumpy skin disease (LSD), an economically important viral disease of cattle caused by lumpy skin disease virus (LSDV) has recently spread into South and East Asia. LSD emerged in India in August 2019, first in Odisha State and spread to other areas, but there is scanty data on source and molecular epidemiology of LSDV involved in the initial outbreaks. Here we report genetic relationships and molecular features of LSDV, causing outbreaks in cattle spanning seven districts in Odisha and West Bengal States during August-December, 2019. Twelve LSDV isolates obtained using lamb testis cells were sequenced and analysed in four complete genes, GPCR, RPO30, P32 and EEV. The phylogenetic analysis revealed that all the Indian LSDV isolates from 2019 outbreaks are very closely related (99.7%-100%) to the historical Kenyan NI-2490/Kenya/KSGP-like field strains. Importantly, our results demonstrated that LSDV strains involved in 2019 outbreaks in India and Bangladesh are very similar in GPCR (99.7%), RPO30 (100%) and partial EEV (100%) sequences, indicating a common exotic source of LSDV introduction. Additionally, a 12-nucleotide insertion was found in GPCR gene of LSDV strains from 2019 outbreaks in India and Bangladesh. The findings of this study highlight the importance of continuous monitoring and molecular characterization of LSDV strains. These data should be useful while developing diagnostic and control strategies against LSD in India.

Recombinant LSDV Strains in Asia: Vaccine Spillover or Natural Emergence?

From 2017 to 2019, several vaccine-like recombinant strains of lumpy skin disease virus (LSDV) were discovered in Kazakhstan and neighbouring regions of Russia and China. Shortly before their emergence, the authorities in Kazakhstan launched a mass vaccination campaign with the Neethling-based Lumpivax vaccine. Since none of the other countries in the affected region had used a homologous LSDV vaccine, it was soon suspected that the Lumpivax vaccine was the cause of these unusual LSDV strains. In this study, we performed a genome-wide molecular analysis to investigate the composition of two Lumpivax vaccine batches and to establish a possible link between the vaccine and the recent outbreaks. Although labelled as a pure Neethling-based LSDV vaccine, the Lumpivax vaccine appears to be a complex mixture of multiple CaPVs. Using an iterative enrichment/assembly strategy, we obtained the complete genomes of a Neethling-like LSDV vaccine strain, a KSGP-like LSDV vaccine strain and a Sudan-like GTPV strain. The same analysis also revealed the presence of several recombinant LSDV strains that were (almost) identical to the recently described vaccine-like LSDV strains. Based on their InDel/SNP signatures, the vaccine-like recombinant strains can be divided into four groups. Each group has a distinct breakpoint pattern resulting from multiple recombination events, with the number of genetic exchanges ranging from 126 to 146. The enormous divergence of the recombinant strains suggests that they arose during seed production. The recent emergence of vaccine-like LSDV strains in large parts of Asia is, therefore, most likely the result of a spillover from animals vaccinated with the Lumpivax vaccine.

An in-depth bioinformatic analysis of the novel recombinant lumpy skin disease virus strains: from unique patterns to established lineage

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.

Characterization of Lumpy skin disease virus isolated from a giraffe in Vietnam

While investigating a giraffe death in a Vietnamese zoo, we successfully identified and isolated lumpy skin disease virus (LSDV) from skin nodule biopsies and ruptured nodule wound swab samples. Phylogenetic analysis indicated that the isolate obtained in this study was closely related to the previous Vietnamese and Chinese LSDV strains from cattle. This is the first report on the genome detection and isolation of LSDV in a diseased giraffe in Vietnam. Further study is needed to better understand the epidemiology of this disease in wildlife. This article is protected by copyright. All rights reserved.

Overwintering of recombinant lumpy skin disease virus in northern latitudes, Russia

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.

Coding-Complete Sequences of Recombinant Lumpy Skin Disease Viruses Collected in 2020 from Four Outbreaks in Northern Vietnam

Lumpy skin disease virus (LSDV) causes a severe, systemic, and economically important disease in cattle. Here, we report coding-complete sequences of recombinant LSDVs from four outbreaks in October and November 2020 in northeastern Vietnam.

The Importance of Quality Control of LSDV Live Attenuated Vaccines for Its Safe Application in the Field

Vaccination is an effective approach to prevent, control and eradicate diseases, including lumpy skin disease (LSD). One of the measures to address farmer hesitation to vaccinate is guaranteeing the quality of vaccine batches. The purpose of this study was to demonstrate the importance of a quality procedure via the evaluation of the LSD vaccine, Lumpivax (Kevevapi). The initial PCR screening revealed the presence of wild type LSD virus (LSDV) and goatpox virus (GTPV), in addition to vaccine LSDV. New phylogenetic PCRs were developed to characterize in detail the genomic content and a vaccination/challenge trial was conducted to evaluate the impact on efficacy and diagnostics. The characterization confirmed the presence of LSDV wild-, vaccine- and GTPV-like sequences in the vaccine vial and also in samples taken from the vaccinated animals. The analysis was also suggestive for the presence of GTPV-LSDV (vaccine/wild) recombinants. In addition, the LSDV status of some of the animal samples was greatly influenced by the differentiating real-PCR used and could result in misinterpretation. Although the vaccine was clinically protective, the viral genomic content of the vaccine (being it multiple Capripox viruses and/or recombinants) and the impact on the diagnostics casts serious doubts of its use in the field.