Phylogenetic and pathogenic characterization of lumpy skin disease virus circulating in China

Lumpy skin disease virus suppresses the antiviral response of bovine peripheral blood mononuclear cells that support viral dissemination

Lumpy skin disease virus (LSDV) causes a severe emerging and transboundary disease in cattle. Infection with LSDV leads to the development of widespread dermal nodules. In addition to the skin, LSDV resides in multiple internal organs and can be isolated from the blood of infected cattle. We have characterised the tropism, replication, and dissemination of both a field isolate of LSDV and an attenuated vaccine strain in vitro. To study virus infection and dissemination in living cells, we generated recombinant viruses that express a green fluorescent protein (GFP) under a synthetic viral promoter. The recombinant LSDVs expressing GFP displayed replication kinetics similar to their parental strains in a bovine kidney cell line. These LSDV-GFP strains also replicated effectively in a bovine macrophage cell line and primary bovine foreskin cells, showing no apparent differences between the field isolate and the vaccine strain. Bovine peripheral blood mononuclear cells (PBMCs) infected with either LSDV-GFP strain displayed specific viral-driven GFP fluorescence and significant viral gene expression. However, these infected PBMCs did not support substantial viral DNA replication or the release of infectious progeny. Further analysis of the anti-viral response revealed that heat-treated LSDV, but not infectious viruses, induced the expression of interferon-stimulated genes (ISGs) in PBMCs. Thus, although LSDV did not replicate productively in PBMCs, it evaded the anti-viral response of these cells. Finally, we demonstrated that despite the lack of productive replication, infected PBMCs effectively transmitted LSDV to recipient permissive cells in co-culture, leading to the formation of infection foci. This suggests a potential role for PBMCs in the dissemination of LSDV.

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.

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.

Comparative RNA sequencing analysis of three Capripoxvirus infections in an immortalized hTERT-bOEC cell model

Capripoxviruses (CaPVs), such as lumpy skin disease, sheep pox, and goat pox, cause significant production and economic losses and are major constraints to the growth of livestock production in endemic areas. Understanding the pathogenic mechanism of CaPVs and their translation into clinical applications depends on the availability of a suitable cell line. In this study, we used a lentiviral packaging system to establish an immortalized hTERT-bOEC cell line by ectopic introduction of human telomerase reverse transcriptase (hTERT). Western blotting, indirect immunofluorescence, and flow cytometry analyses revealed that hTERT was successfully integrated into the genome of hTERT-bOEC cells. Crucially, this hTERT-bOEC cell line was highly susceptible to LSDV, SPPV, and GTPV infections. Establishing hTERT-bOECs is critical for basic research, clinical application, and vaccine development related to CaPVs. Furthermore, RNA-seq analyses revealed a similar differential expression of genes and enrichment of signaling pathways to CaPV infections in hTERT-bOECs. Real-time quantitative qPCR further confirmed the top five up-regulated and down-regulated differentially expressed genes among the CaPV infections. Transcriptome analyses provide deep insight into the biological characteristics of the replication process in CaPV infections.

Analysis of Gene Differences Between F and B Epidemic Lineages of Bandavirus Dabieense

The prevalence of SFTS is becoming increasingly widespread and is expected to become a significant security issue. The article discusses the prevalence regions and genetic differences in two SFTSV lineages, so as to provide a scientific data basis for the clinical control and prevention of fever with thrombocytopenia syndrome. The literature involving SFTSV patients from 2009 to 2023 and SFTSV complete genome sequences uploaded by NCBI were collected and sorted out, based on time and SFTSV lineage division, we analyzed viral gene sequence. SFTSV patient data were continuously reported from 2009 to 2023, involving five countries including China, South Korea, Japan, Thailand, and Vietnam. There are obvious lineage and host divisions between the SFTSV lineages prevalent in China and abroad. The sources of B-lineage SFTSV samples are mainly concentrated in South Korea, Japan, and the middle and lower reaches of Hubei or Zhejiang in China, with half of the samples coming from humans and half from animals, and the F series SFTSV samples were mainly collected from provinces such as Anhui and Henan in China, with the main source being human patients. The F-lineage SFTSV is the highest proportion in the middle and upper provinces in China. The B lineage has recently appeared in Zhejiang and Taiwan and is prevalent abroad. Using prediction software based on molecular structure prediction technology, analyze the differences between the B and F lineages of SFTSV through prediction methods such as nucleotide mutations, gene recombination, mutation sites, and evolution rates. Conclusively, the differences in SFTSV between B and F lineages may be related to gene recombination of M and L fragments, it was also found that the B lineage had a lower recombination rate and mutation rate than the F lineage, and the evolutionary rate was prominently different. Comparative analysis of the differences in two SFTSV lineage genes could further understand the epidemic status of SFTSV and provide help and more insights for the prevention of the spread of specific types of SFTSV.

Viromics-based precision diagnosis of reproductive abnormalities in cows reveals a reassortant Akabane disease virus

BACKGROUND

At the end of 2021, an epidemic of reproductive abnormalities in cows occurred in Jilin Province, China, posing an urgent need for a rapid diagnosis.

RESULTS

To identify the cause of the disease, a total of 172 samples were collected from 21 dead calves and 45 aborting or pregnant cows in 10 farms across the province. Routine PCR or RT-PCR detection did not find any common abortion-related agents. We then employed the viromics-based precision diagnosis method to analyze these samples, and the read-based annotation showed signals of an Akabane disease virus (AKAV) in some libraries. To further identify the virus, nested RT-PCR detection revealed that 52.3% (11/21) of dead calves and 26.6% (12/45) of cows were positive for the virus. Phylogenetic analysis of the partial fragments showed that the S segment of the virus was 100% identical to the Chinese strain TJ2016, but its M and L segments shared 94.3% and 96.5% identities with an Israeli strain.

CONCLUSIONS

The viromic and molecular results suggested that these animals were infected with a reassortant AKAV. Coupled with the clinical signs, the virus should be responsible for the epizootic, highlighting that molecular and serological surveys of the virus in cows during early pregnancy, as well as ecological investigation in its arthropod vectors, are necessary.

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.

Platform establishment of the Cre-loxP recombination system for genetic manipulation of the Lumpy skin disease virus

Lumpy skin disease virus (LSDV) is a rapidly emerging pathogen in Asia, including China. Genetic manipulation of the LSDV is essential for the elucidation of the pathogenic mechanism and biological function of the LSDV-encoded protein. In this study, we established a platform for the Cre-loxP recombination system under a modified early-late H5 promoter of the VACV for quick construction of the recombinant LSDV virus. The recombinant virus, LSDV-EGFP-ΔTK, was purified and obtained using serial limited dilution and picking the single cells methods. Using the lentiviral package system, a Cre recombinase enzyme stable expression MDBK cell line was established to supply the Cre recombinase for the reporter gene excision. A genetically stable, safe TK gene-deleted LSDV (LSDV-ΔTK) was constructed using homologous recombination and the Cre-loxP system. It was purified using limited dilution in the MDBK-Cre cell line. Establishing the Cre-loxP recombination system will enable sequential deletion of the interested genes from the LSDV genome and genetic manipulation of the LSDV genome, providing technical support and a platform for developing the attenuated LSDV vaccine.

Emergence of Lumpy Skin Disease Virus Infection in Yaks, Cattle-Yaks, and Cattle on the Qinghai-Xizang Plateau of China

Lumpy skin disease (LSD) is a viral disease caused by lumpy skin disease virus (LSDV), which mainly infects cattle and can cause huge economic losses. In May 2023, yaks, cattle-yaks, and cattle in Tibet (Xizang), China, developed fever, skin nodules, and severe discharges and were suspected to be cases of LSD. Samples from these animals were analyzed using molecular biology and serological methods. The RPO30, P32, and GPCR genes were amplified by PCR and sequenced, and the whole genome of the virus was determined using viral metagenomics technology. Sequencing results showed that it was indeed an LSDV infection, and enzyme-linked immunosorbent assay results confirmed the presence of LSDV antibodies. The whole genome phylogenetic tree shows that LSDV/CHINA/Tibet/2023 is different from the previous epidemic strains in China, but clusters with India 2022 strain. This is the first report of LSD in yaks, cattle-yaks, and cattle on the highest altitude plateau in the world.

Identification of the murine osteoblastic cell MC3T3-E1 as a permissive cell line in response to lumpy skin disease virus

Lumpy skin disease virus (LSDV) is a rapidly emerging pathogen in China. Screening suitable cells for LSDV replication is vital for future research on pathogenic mechanisms and vaccine development. Previous comparative studies have identified that the rodent-derived BHK21 is a highly susceptible cell model to LSDV infection. Using western blot, indirect immune-fluorescence assay, flow cytometry, and transmission electron microscopy methods, this study is the first to identify the murine osteoblastic cell line MC3T3-E1 as a novel permissive cell model for LSDV infection. The establishment of MC3T3-E1 as a suitable infectious cell model enhances our understanding of the species range and cell types of the permissive cells and nonpermissive that support LSDV replication. It is helpful to accelerate future research on the pathogenesis, clinical application, and vaccine development of LSDV.

Genomic analysis of lumpy skin disease virus asian variants and evaluation of its cellular tropism

Lumpy skin disease virus (LSDV) is a poxvirus that mainly affects cattle and can lead to symptoms such as severe reduction in milk production as well as infertility and mortality, which has resulted in dramatic economic loss in affected countries in Africa, Europe, and Asia. In this study, we successfully isolated two strains of LSDV from different geographical regions in China. Comparative genomic analyses were performed by incorporating additional LSDV whole genome sequences reported in other areas of Asia. Our analyses revealed that LSDV exhibited an 'open' pan-genome. Phylogenetic analysis unveiled distinct branches of LSDV evolution, signifying the prevalence of multiple lineages of LSDV across various regions in Asia. In addition, a reporter LSDV expressing eGFP directed by a synthetic poxvirus promoter was generated and used to evaluate the cell tropism of LSDV in various mammalian and avian cell lines. Our results demonstrated that LSDV replicated efficiently in several mammalian cell lines, including human A549 cells. In conclusion, our results underscore the necessity for strengthening LSD outbreak control measures and continuous epidemiological surveillance.

Lumpy skin disease virus ORF127 protein suppresses type I interferon responses by inhibiting K63-linked ubiquitination of tank binding kinase 1

Lumpy skin disease (LSD) is a severe animal infectious disease caused by lumpy skin disease virus (LSDV), inducing extensive nodules on the cattle mucosa or the scarfskin. LSDV genome encodes multiple proteins to evade host innate immune response. However, the underlying molecular mechanisms are poorly understood. In this study, we found that LSDV could suppress the expression of IFN-β and interferon-stimulated genes (ISGs) in MDBK cells during the early stage of infection. Subsequently, an unbiased screen was performed to screen the LSDV genes with inhibitory effects on the type I interferon (IFN-I) production. ORF127 protein was identified as one of the strongest inhibitory effectors on the expression of IFN-β and ISGs, meanwhile, the 1-43 aa of N-terminal of ORF127 played a vital role in suppressing the expression of IFN-β. Overexpression of ORF127 could significantly promote LSDV replication through inhibiting the production of IFN-β and ISGs in MDBK cells. Mechanism study showed that ORF127 specifically interacted with TBK1 and decreased the K63-linked polyubiquitination of TBK1 which suppressed the phosphorylation of TBK1 and ultimately decreased the production of IFN-β. In addition, truncation mutation analysis indicated that the 1-43 aa of N-terminal of ORF127 protein was the key structural domain for its interaction with TBK1. In short, these results validated that ORF127 played a negative role in regulating IFN-β expression through cGAS-STING signaling pathway. Taken together, this study clarified the molecular mechanism of ORF127 gene antagonizing IFN-I-mediated antiviral, which will helpfully provide new strategies for the treatment and prevention of LSD.

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.