Complete Coding Sequence of Lumpy Skin Disease Virus Isolated from Kinmen Island, Taiwan, in 2020

Molecular characterization of recombinant LSDV isolates from 2022 outbreak in Indonesia through phylogenetic networks and whole-genome SNP-based analysis

Lumpy skin disease (LSD) is a transboundary viral disease of cattle and water buffaloes caused by the LSD virus, leading to high morbidity, low mortality, and a significant economic impact. Initially endemic to Africa only, LSD has spread to the Middle East, Europe, and Asia in the past decade. The most effective control strategy for LSD is the vaccination of cattle with live-attenuated LSDV vaccines. Consequently, the emergence of two groups of LSDV strains in Asian countries, one closely related to the ancient Kenyan LSDV isolates and the second made of recombinant viruses with a backbone of Neethling-vaccine and field isolates, emphasized the need for constant molecular surveillance. This current study investigated the first outbreak of LSD in Indonesia in 2022. Molecular characterization of the isolate circulating in the country based on selected LSDV-marker genes: RPO30, GPCR, EEV glycoprotein gene, and B22R, as well as whole genome analysis using several analytical tools, indicated the Indonesia LSDV isolate as a recombinant of LSDV_Neethling_vaccine_LW_1959 and LSDV_NI-2490. The analysis clustered the Indonesia_LSDV with the previously reported LSDV recombinants circulating in East and Southeast Asia, but different from the recombinant viruses in Russia and the field isolates in South-Asian countries. Additionally, this study has demonstrated alternative accurate ways of LSDV whole genome analysis and clustering of isolates, including the recombinants, instead of whole-genome phylogenetic tree analysis. These data will strengthen our understanding of the pathogens' origin, the extent of their spread, and determination of suitable control measures required.

Sign of APOBEC editing, purifying selection, frameshift, and in-frame nonsense mutations in the microevolution of lumpy skin disease virus

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.

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.

The first study on the impact of lumpy skin disease outbreaks on monthly milk production on dairy farms in Khon Kaen, Thailand

Background and Aim

Outbreaks of lumpy skin disease (LSD) have resulted in substantial economic losses to the dairy industry in Thailand. This study aimed to determine the influence of LSD outbreaks on monthly milk production levels.

Materials and Methods

Milk production for dairy farms located in Khon Kaen Province, Thailand, belonging to the Khon Kaen Dairy Cooperative, was affected by LSD outbreaks from May to August of 2021. The resulting data were analyzed using general linear mixed models.

Results

It was estimated that the LSD outbreak caused economic losses totaling 2,413,000 Thai Baht (68,943 USD) over the outbreak period. The monthly farm milk production level in May differed from the levels in June and August. Dairy farmers experienced losses between 8.23 and 9.96 tons of milk each month, which equated to between 4180 and 14,440 Thai Baht (119.43 and 412.57 USD) in monthly income.

Conclusion

This study demonstrated that LSD outbreaks on dairy farms resulted in significant farm milk production losses. Our findings will increase awareness among authorities and stakeholders in the dairy industry of Thailand, as well as to assist in the prevention of future LSD outbreaks and minimize the negative impacts of LSD.

Genomic characterization of Lumpy Skin Disease virus (LSDV) from India: Circulation of Kenyan-like LSDV strains with unique kelch-like proteins

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.

Rapid Spread and Genetic Characterisation of a Recently Emerged Recombinant Lumpy Skin Disease Virus in Thailand

Simple Summary

Lumpy skin disease (LSD) is an economically important disease of cattle caused by LSD virus (LSDV), a member of poxviruses. It had never been found in Thailand before March 2021, but has since spread broadly to various provinces. Regional veterinarians have collected samples from the LSD cattle and submitted them for diagnosis as a part of disease surveillance during the outbreaks. Our study aimed to monitor the distribution of the outbreaks by recording the LSD cases based on clinical signs and laboratory tests up to June 2022, and characterise the causative agent virologically and genetically. Outbreak maps were created to illustrate the rapid temporal distribution of the LSD index cases in each province of Thailand. We detected two distant origins of the outbreaks. LSDV DNA was confirmed in blood, milk, and skin samples collected from sick animals by real-time PCR. LSDV was proven to be the causative virus based on serological, virological, and pathological diagnoses. By genetic analysis, the Thai LSDV is a recombinant virus derived from a vaccine strain previously appearing in China and Vietnam. Its genetic material is a mosaic hybrid genome containing the vaccine virus DNA as the backbone interspersed with DNA fragments of a field strain.

Abstract

The emergence of the lumpy skin disease virus (LSDV) was first detected in north-eastern Thailand in March 2021. Since then, the abrupt increase of LSD cases was observed throughout the country as outbreaks have spread rapidly to 64 out of a total of 77 provinces within four months. Blood, milk, and nodular skin samples collected from affected animals have been diagnosed by real-time PCR targeting the p32 gene. LSDV was isolated by primary lamb testis (PLT) cells, followed by Madin-Darby bovine kidney (MDBK) cells, and confirmed by immunoperoxidase monolayer assay (IPMA). Histopathology and immunohistochemistry (IHC) of a skin lesion showed inclusion bodies in keratinocytes and skin epithelial cells. Phylogenetic analyses of RPO30 and GPCR genes, and the whole genome revealed that Thai viruses were closely related to the vaccine-derived recombinant LSDV strains found previously in China and Vietnam. Recombination analysis confirmed that the Thai LSDV possesses a mosaic hybrid genome containing the vaccine virus DNA as the backbone and a field strain DNA as the minor donor. This is an inclusive report on the disease distributions, complete diagnoses, and genetic characterisation of LSDV during the first wave of LSD outbreaks in Thailand.

Coding-Complete Genome Sequence of a Lumpy Skin Disease Virus Isolated during the 2021 Thailand Outbreak

Lumpy skin disease (LSD) is an economically devastating and transboundary disease in cattle. Here, we report the coding-complete genome sequence of the LSDV72/PrachuapKhiriKhan/Thailand/2021 strain, which was isolated from an affected cow during the first LSD outbreak in Thailand in 2021. The sequence will be beneficial for future genomic studies of the virus.

Spatio-temporal patterns of lumpy skin disease outbreaks in dairy farms in northeastern Thailand

In 2021–2022, there were numerous outbreaks of lumpy skin disease (LSD) affecting cattle farms across Thailand. This circumstance was the country's first encounter with an LSD outbreak. Thus, a better understanding of LSD epidemiology is necessary. The aim of this study was to determine the spatio-temporal patterns of the LSD outbreaks in dairy farming areas. Data from LSD outbreak investigations collected from dairy farms in Khon Kean province, northeastern Thailand, were analyzed using spatio-temporal models including space-time permutation, Poisson, and Bernoulli models. LSD outbreaks were found in 133 out of 152 dairy farms from May to July, 2021. The majority of dairy farms (n = 102) were affected by the LSD outbreaks in June. The overall herd attack, morbidity and mortality rates were 87, 31, and 0.9%, respectively. According to the results of all models, the most likely clusters were found in the northern part of the study area. The space-time permutation and Poisson model identified 15 and 6 spatio-temporal outbreak clusters, respectively, while the Bernoulli model detected only one cluster. The most likely clusters from those models cover radii of 1.59, 4.51, and 4.44 km, respectively. All farms included in the cluster identified by the space-time permutation model were also included in the cluster identified by the Poisson model, implying that both models detected the same outbreak area. Furthermore, the study results suggested that farmers who own farms within a one km radius of the LSD outbreak farm should be advised to implement more stringent insect vector control measures to prevent disease spread. This study provides better insights into the spatio-temporal pattern of clusters of LSD in the outbreak area. The findings of this study can support authorities in formulating strategies to prevent and control future outbreaks as well as prioritizing resource allocation to high-risk areas.

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.