Structure of the recombinant RNA polymerase from African Swine Fever Virus

Regulation of detoxifying enzymes expression and restriction of picorna-like virus infection by natural polysaccharide extracts in Drosophila cells

The world is currently witnessing a rise in viral infections, while the availability of antiviral drugs remains limited. Traditional Chinese medicine (TCM) has historically served as a valuable source of novel compounds for disease treatment. In this study, we assessed the antiviral potential of various TCM compounds using Drosophila melanogaster as a model organism. Our findings reveal that natural polysaccharide extracts, prepared from 10 commonly used medicinal herbs or fungi, exhibit antiviral activity against two picorna-like viruses. Importantly, the antiviral effect is not directly attributable to the compound itself but is instead mediated by cellular responses induced by treatment with the extract. We observed that the polysaccharide extract triggers a broad transcriptional response, which partially overlaps with NF-κB pathway activation in Drosophila. However, the antiviral activity of the extract was independent of classical innate immune pathways, such as RNA interference or NF-κB signaling. Instead, the extract appears to uniquely stimulate detoxification pathways, including upregulation of cytochrome P450 and glutathione S-transferase genes, which correlates with its antiviral effects.

Advances in African swine fever virus molecular biology and host interactions contributing to new tools for control

African swine fever virus (ASFV) causes a frequently fatal hemorrhagic disease in domestic pigs and wild boar. The spread from Africa to Georgia in 2007 initiated a pandemic affecting many European and most Asian countries. This has had a very high socio-economic impact and threatens global food security. The virus is a large, complex, cytoplasmic DNA virus, the only member of the Asfarviridae family and codes for 170-190 proteins. Many of these have unknown functions and do not resemble other viruses or host proteins. This complexity has hindered the development of vaccines and other tools for control. The intensity of research has increased since the spread of ASFV in Europe and Asia, leading to rapid advances in knowledge. This review summarizes recent research, including the determination by cryogenic electron microscopy of the virus capsid structure and virion proteome. Novel information on the virus replication cycle, including mechanisms of virus entry into cells and the identification of host endosomal proteins important for entry, is summarized. Multiple, novel virus immune evasion proteins and their targets in the type I interferon response and inflammation pathways have been identified. The potential for the application of this knowledge to developing novel control tools, including modified live vaccines and other interventions targeting critical virus processes or host interactions, is discussed.

Preparation of a new monoclonal antibody against D205R protein of African swine fever virus and identification of its linear antigenic epitope

African swine fever virus (ASFV), a highly contagious virus with a double-stranded DNA genome, is notorious for causing severe hemorrhagic fever in pigs, often leading to mortality rates as high as 100 %. First identified in Kenya in 1921, the virus has since spread globally, with a significant outbreak in China in 2018, causing extensive economic losses in the swine industry. The D205R protein (pD205R) of ASFV, classified as a non-structural protein, plays a role in the transcription of viral genes and is associated with ASFV RNA polymerase. However, the specific function of this protein remains unclear. To gain a deeper insight into the structure, function, and mechanisms of interaction between pD205R and the host, we successfully expressed the pD205R protein and generated a monoclonal antibody (mAb), designated 3G6G1, targeting this protein. The mAb 3G6G1 can be utilized for indirect immunofluorescence (IFA) and Western blotting (WB) detection of ASFV strains. Through the evaluation of the reactivity of antibodies against a series of truncated pD205R fragments, we identified the epitope recognized by mAb 3G6G1 as residing within the amino acid sequence 96 VLSKKNI 102. Bioinformatics analysis indicated that this antigenic epitope possesses a high antigenic index and is highly conserved. These findings will establish a foundation for further research into the function of the D205R protein and its role in the interaction between ASFV and its host.

Structural basis of RNA polymerase complexes in African swine fever virus

African swine fever virus is highly contagious and causes a fatal infectious disease in pigs, resulting in a significant global impact on pork supply. The African swine fever virus RNA polymerase serves as a crucial multifunctional protein complex responsible for genome transcription and regulation. Therefore, it is essential to investigate its structural and functional characteristics for the prevention and control of African swine fever. Here, we determine the structures of endogenous African swine fever virus RNA polymerase in both nucleic acid-free and elongation states. The African swine fever virus RNA polymerase shares similarities with the core of typical RNA polymerases, but possesses a distinct subunit M1249L. Notably, the dynamic binding mode of M1249L with RNA polymerase, along with the C-terminal tail insertion of M1249L in the active center of DNA-RNA scaffold binding, suggests the potential of M1249L to regulate RNA polymerase activity within cells. These results are important for understanding the transcription cycle of the African swine fever virus and for developing antiviral strategies.

Transcription regulation of African swine fever virus: dual role of M1249L

African swine fever virus (ASFV), which poses significant risks to the global economy, encodes a unique host-independent transcription system. This system comprises an eight-subunit RNA polymerase (vRNAP), temporally expressed transcription factors and transcript associated proteins, facilitating cross-species transmission via intermediate host. The protein composition of the virion and the presence of transcription factors in virus genome suggest existence of distinct transcription systems during viral infection. However, the precise mechanisms of transcription regulation remain elusive. Through analyses of dynamic transcriptome, vRNAP-associated components and cell-based assay, the critical role of M1249L in viral transcription regulation has been highlighted. Atomic-resolution structures of vRNAP-M1249L supercomplex, exhibiting a variety of conformations, have uncovered the dual functions of M1249L. During early transcription, M1249L could serve as multiple temporary transcription factors with C-terminal domain acting as a switcher for activation/inactivation, while during late transcription it aids in the packaging of the transcription machinery. The structural and functional characteristics of M1249L underscore its vital roles in ASFV transcription, packaging, and capsid assembly, presenting novel opportunities for therapeutic intervention.

Genetic Variations of African Swine Fever Virus: Major Challenges and Prospects

African swine fever (ASF) is a contagious viral disease affecting pigs and wild boars. It typically presents as a hemorrhagic fever but can also manifest in various forms, ranging from acute to asymptomatic. ASF has spread extensively globally, significantly impacting the swine industry. The complex and highly variable character of the ASFV genome makes vaccine development and disease surveillance extremely difficult. The overall trend in ASFV evolution is towards decreased virulence and increased transmissibility. Factors such as gene mutation, viral recombination, and the strain-specificity of virulence-associated genes facilitate viral variations. This review deeply discusses the influence of these factors on viral immune evasion, pathogenicity, and the ensuing complexities encountered in vaccine development, disease detection, and surveillance. The ultimate goal of this review is to thoroughly explore the genetic evolution patterns and variation mechanisms of ASFV, providing a theoretical foundation for advancement in vaccine and diagnostic technologies.

Transcription termination and readthrough in African swine fever virus

Introduction

African swine fever virus (ASFV) is a nucleocytoplasmic large DNA virus (NCLDV) that encodes its own host-like RNA polymerase (RNAP) and factors required to produce mature mRNA. The formation of accurate mRNA 3' ends by ASFV RNAP depends on transcription termination, likely enabled by a combination of sequence motifs and transcription factors, although these are poorly understood. The termination of any RNAP is rarely 100% efficient, and the transcriptional "readthrough" at terminators can generate long mRNAs which may interfere with the expression of downstream genes. ASFV transcriptome analyses reveal a landscape of heterogeneous mRNA 3' termini, likely a combination of bona fide termination sites and the result of mRNA degradation and processing. While short-read sequencing (SRS) like 3' RNA-seq indicates an accumulation of mRNA 3' ends at specific sites, it cannot inform about which promoters and transcription start sites (TSSs) directed their synthesis, i.e., information about the complete and unprocessed mRNAs at nucleotide resolution.

Methods

Here, we report a rigorous analysis of full-length ASFV transcripts using long-read sequencing (LRS). We systematically compared transcription termination sites predicted from SRS 3' RNA-seq with 3' ends mapped by LRS during early and late infection.

Results

Using in-vitro transcription assays, we show that recombinant ASFV RNAP terminates transcription at polyT stretches in the non-template strand, similar to the archaeal RNAP or eukaryotic RNAPIII, unaided by secondary RNA structures or predicted viral termination factors. Our results cement this T-rich motif (U-rich in the RNA) as a universal transcription termination signal in ASFV. Many genes share the usage of the same terminators, while genes can also use a range of terminators to generate transcript isoforms varying enormously in length. A key factor in the latter phenomenon is the highly abundant terminator readthrough we observed, which is more prevalent during late compared with early infection.

Discussion

This indicates that ASFV mRNAs under the control of late gene promoters utilize different termination mechanisms and factors to early promoters and/or that cellular factors influence the viral transcriptome landscape differently during the late stages of infection.