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

Genomic analysis and spatiotemporal distribution of newly emerging lumpy skin disease virus in malaysia identify recombinant strain from transboundary spread

Lumpy skin disease is a transboundary viral disease affecting bovine species. This disease had never been recorded in Malaysia prior to May of 2021, and had spread to 65 of 92 districts in Peninsular Malaysia by December of the same year. In this study, we conducted a whole-genome sequencing, phylogenetic analysis and geographical mapping of the outbreak from lumpy skin disease virus isolated from the first wave of outbreaks to better understand the origin, transmission, and genetic diversity of the virus. The whole genome sequences of these isolates were deposited in GenBank with accession number PP145891 and PP145892. Malaysia LSDV isolates were found clustered with recombinant strains in clade 2.5, particularly subclade 2.5.1, which included strains from China, Vietnam, Thailand, and Indonesia. The spread of the disease in Malaysia was closely linked to cross-border cattle movements from Thailand, as evidenced by the spatiotemporal distribution of the outbreaks. This study emphasizes the need for ongoing genomic surveillance to detect emerging variants and inform targeted control strategies, including vaccination and cross-border cooperation to curb future outbreaks.

Evaluation of an interferon-gamma release assay for early detection of lumpy skin disease virus infection and vaccination in cattle

Lumpy skin disease virus (LSDV) causes a nodular dermatitis in cattle and has high economic consequences in affected areas. Detection of LSDV exposure mostly relies on the humoral immune response, while the cell-mediated immune (CMI) response, an important hallmark of the immune reaction to LSDV, is neglected. We collected samples during 3 weeks post-vaccination of cattle with a Neethling-based live attenuated vaccine (LAV) and during 4 weeks post-LSDV infection under experimental conditions to i) investigate the development of the CMI response, ii) optimize an interferon-gamma release assay (IGRA) by comparing two matrices (whole blood and PBMCs) and different stimuli, and iii) evaluate the usefulness of an IGRA for detection of infection and vaccination. The CMI response to the Neethling LAV was detectable in all animals from 10 days post-vaccination, and importantly, preceded the detection of antibodies. A uniform CMI response to infection was already detected at its plateau level at 7 days post-infection in all animals and also preceded antibody detection. Whole blood and PBMCs allowed efficient IFN-γ secretion, but the IFN-γ response was significantly higher in PBMCs. Heat-inactivated antigen proved to be the stimulus of choice for LSD IGRA, providing increased sensitivity of the test and allowing its performance under BSL2 conditions. Under several conditions, LSDV IGRA showed a specificity of up to 100%. The LSD IGRA could be a powerful immunoassay for early detection of LSD and post-vaccination monitoring, making it worthwhile to explore its diagnostic characteristics in more animals and under field conditions.IMPORTANCEThe immune reaction to lumpy skin disease virus (LSDV) infection or vaccination is currently assessed with serological tests prone to suboptimal sensitivity, long processing time, and the necessity of biosafety level (BSL) 3 laboratories. Furthermore, the delayed or absent seroconversion indicates a need for an alternative immunoassay detecting immune reactions to LSDV exposure applicable in BSL2 settings. Seeing the known importance of cell-mediated immune (CMI) response against poxvirus infections, we evaluated the suitability of the interferon-gamma release assay (IGRA) test for detection of LSDV infection and vaccination. IGRA allowed early detection of the CMI response to LSDV infection (within 7 days) and vaccination (within 10 days) with a Neethling-based live attenuated vaccine, and the CMI response preceded the detection of seroconversion. Whole blood and heat-inactivated antigen increased IGRA sensitivity, making it suitable for application in BSL2 laboratories. This assay overcomes the downsides of currently available immunoassays, and these results encourage its further evaluation.

Whole Genome Sequencing of Lumpy Skin Disease Virus from 2021-2023 in Eastern Eurasia Reveals No More Recombination Signals in the Circulating Pool of Strains

Having spanned thousands of kilometers from Africa through Europe, the Middle East, Central Asia through to the south eastern part of Eurasia in the recent decade, lumpy skin disease virus has now become entrenched in China, Thailand, Vietnam, and South Korea. In light of discovered findings on recombination, cluster 2.5 lineage strains are now dominant and continue to spread throughout Southeast Asia. To gain a better picture of the phylogenetic landscape in the field, whole genome sequencing of 11 LSDV isolates from Russia and Mongolia collected from 2021 to 2023 has been attempted to see the dynamics of recombination signals, as was shown for LSDV circulating in 2017-2019 in Russia and Kazakhstan. Deep sequencing performed direct from skin nodules along with data retrieved from Genbank provides the most recent update on molecular epidemiology of LSDV and demonstrates that no more mosaic variant of LSDV has been observed, and cluster 2.5 lineage is now the dominant lineage currently on the rise in the region with its own patterns of monophyletic evolution. These discoveries may help future investigations aimed at epidemiological surveillance and virus tracking in the context of currently identified lineages worldwide.

Progress in diagnostic methods and vaccines for lumpy skin disease virus: a path towards understanding the disease

Lumpy skin disease (LSD) is caused by Lumpy Skin disease virus (LSDV) belonging to the genus Capripoxvirus (CaPV). The disease is widespread in Africa, the Middle East and Asia and has been present in Egypt since 1988. LSD is mainly transmitted by blood-sucking insects. LSD is clinically distinguished by a high fever, skin nodules, and swollen Lymph nodes. Detecting sub-clinical disease can be challenging however, prompt laboratory investigations are vital. Skin lesions are the main source of infection, although the virus is shed through many excretions and discharges including semen. Disease confirmation in clinical laboratories includes detection of viral nucleic acid, antigen and antibody levels. Simple, adaptable, and quick assays for detecting LSDV are required for control measures. Vaccination, together with controlled quarantine and vector control measures, may be beneficial for preventing disease spread. Presently, a range of live attenuated vaccines, have been used in the field with different levels of protection and side effects. With high levels of vaccination coverage, attenuated Neethling vaccines have successfully eradicated of LSDV in Europe. Inactivated LSDV vaccines have also been demonstrated effective in experimental infections. Furthermore, due to its large genome, LSDV is being exploited as a vaccine delivery element, generating an innovative composite with additional viral genes by DNA recombination. Vaccines developed on this basis have the potential to prevent a wide range of diseases and have been demonstrated to be effective in experimental settings. In this review, we emphasizethe advances in diagnostic methods and vaccines developed last decade, thereby providing a basis for future research into various aspects of LSDV and providing information for possibility of disease elimination.

Deciphering the genetic landscape of lumpy skin disease: Unraveling variable virulence through comprehensive genome sequence analysis in India

Lumpy Skin Disease (LSD), a poxvirus disease affecting cattle, emerged in India in 2019 and intensified in 2022, resulting in significant economic losses for dairy farmers. There was unusual shift in mortality and morbidity patterns during the second wave. A comprehensive genetic study conducted, analyzing samples from 2019 to 2022 revealed circulation of two distinct subclades (subclade 1.2a and 1.2b) in India, with the latter showing a different pattern in morbidity and mortality. Notably, the Ankyrin repeats gene-based analysis could differentiate animals with varying clinical scores. Genetic variations were significant, with unique deletions identified, including a 12-nucleotide deletion in the GPCR gene in virus isolates collected during 2022 outbreaks, not reported earlier in Indian LSDV strains. A crucial finding was a significant 95-nucleotide deletion in the Functional Resolution Sequence (FRS) repeats of LSDV genomes from 2022 outbreaks, absent in 2019 samples. These deletions may have influenced the virus's virulence in India.

Genetic Characterization of Lumpy Skin Disease Viruses Circulating in Lesotho Cattle

Lumpy skin disease is one of the fast-spreading viral diseases of cattle and buffalo that can potentially cause severe economic impact. Lesotho experienced LSD for the first time in 1947 and episodes of outbreaks occurred throughout the decades. In this study, eighteen specimens were collected from LSD-clinically diseased cattle between 2020 and 2022 from Mafeteng, Leribe, Maseru, Berea, and Mohales' Hoek districts of Lesotho. A total of 11 DNA samples were analyzed by PCR and sequencing of the extracellular enveloped virus (EEV) glycoprotein, G-protein-coupled chemokine receptor (GPCR), 30 kDa RNA polymerase subunit (RPO30), and B22R genes. All nucleotide sequences of the above-mentioned genes confirmed that the PCR amplicons of clinical samples are truly LSDV, as they were identical to respective LSDV isolates on the NCBI GenBank. Two of the elevem samples were further characterized by whole-genome sequencing. The analysis, based on both CaPV marker genes and complete genome sequences, revealed that the LSDV isolates from Lesotho cluster with the NW-like LSDVs, which includes the commonly circulating LSDV field isolates from Africa, the Middle East, the Balkans, Turkey, and Eastern Europe.

Subclinical infection caused by a recombinant vaccine-like strain poses high risks of lumpy skin disease virus transmission

Lumpy skin disease (LSD) is a transboundary viral infection, affecting cattle with characteristic manifestations involving multiple body systems. A distinctive characteristic of lumpy skin disease is the subclinical disease manifestation wherein animals have viremia and shed the virus through nasal and ocular discharges, while exhibiting no nodules but enlarged lymph nodes that are easily oversighted by inexperienced vets. Further research on the role of subclinically ill animals in the transmission of LSD virus (LSDV) can contribute to the development of more effective tools to control the disease worldwide. Thus, this study aims to determine the potential role of subclinical infection in virus transmission in a non-vector-borne manner. To achieve this, we inoculated animals with the recombinant vaccine-like strain (RVLS) Udmurtiya/2019 to cause clinical and subclinical LSDV infection. After the disease manifestation, we relocated the subclinically ill animals to a new clean facility followed by the introduction of another five animals to determine the role of RVLS-induced subclinical infection in the virus transmission via direct/indirect contact. After the introduction of the naïve animals to the relocated subclinically ill ones in a shared airspace, two introduced animals contracted the virus (clinically and subclinically), showing symptoms of fever, viremia, and seroconversion in one animal, while three other introduced animals remained healthy and PCR-negative until the end of the study. In general, the findings of this study suggest the importance of considering LSDV subclinical infection as a high-risk condition in disease management and outbreak investigations.

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.

Complete genome reconstruction of the global and European regional dispersal history of the lumpy skin disease virus

IMPORTANCE

Lumpy skin disease virus (LSDV) has a complex epidemiology involving multiple strains, recombination, and vaccination. Its DNA genome provides limited genetic variation to trace outbreaks in space and time. Sequencing of LSDV whole genomes has also been patchy at global and regional scales. Here, we provide the first fine-grained whole genome sequence sampling of a constrained LSDV outbreak (southeastern Europe, 2015-2017), which we analyze along with global publicly available genomes. We formally evaluate the past occurrence of recombination events as well as the temporal signal that is required for calibrating molecular clock models and subsequently conduct a time-calibrated spatially explicit phylogeographic reconstruction. Our study further illustrates the importance of accounting for recombination events before reconstructing global and regional dynamics of DNA viruses. More LSDV whole genomes from endemic areas are needed to obtain a comprehensive understanding of global LSDV dispersal dynamics.

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.

Development of the isothermal recombinase polymerase amplification assays for rapid detection of the genus Capripoxvirus

Sheeppox virus (SPPV), goatpox virus (GTPV) and lumpy skin disease virus (LSDV) belong to the genus Capripoxvirus (CaPV), and are important pathogens of sheep, goat and cattle, respectively. Rapid and reliable detection of CaPV is critical to prevent its spread and promote its eradication. This study aimed to develop the recombinase polymerase amplification (RPA) assays combined with real-time fluorescence (real-time RPA) and naked-eye visible lateral flow strip (LFS RPA) for rapid detection of CaPV. Both developed RPA assays worked well at 39 °C within 20 min. They were highly specific for the detection of GTPV, SPPV and LSDV, while no cross-reactivity was observed for other non-targeted pathogens and genomic DNA of goat, sheep and cattle. The limit of detection for real-time RPA and LFS RPA were 1.0 × 102 and 1.0 × 101 copies per reaction, respectively. In the artificially contaminated samples with GTPV, the detection results of RPA assays were consistent with those of real-time PCR. For 15 clinical samples, LSDV was detected by real-time RPA, LFS RPA and real-time PCR in 13, 15 and 15 samples, respectively. The developed RPA assays were specific, sensitive, and user-friendly for the rapid detection of CaPV, and could be a better alternative method applied in low-resources settings.