scholarly journals Transcriptome view of a killer: African swine fever virus

2020 ◽  
Vol 48 (4) ◽  
pp. 1569-1581 ◽  
Author(s):  
Gwenny Cackett ◽  
Michal Sýkora ◽  
Finn Werner
Keyword(s):  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Fever Virus ◽  
Single Nucleotide ◽  
Dna Viruses ◽  
Temporal Regulation ◽  
Global Agriculture ◽  
Nucleocytoplasmic Large Dna Viruses ◽  
Nucleotide Resolution ◽  
Single Nucleotide Resolution

African swine fever virus (ASFV) represents a severe threat to global agriculture with the world's domestic pig population reduced by a quarter following recent outbreaks in Europe and Asia. Like other nucleocytoplasmic large DNA viruses, ASFV encodes a transcription apparatus including a eukaryote-like RNA polymerase along with a combination of virus-specific, and host-related transcription factors homologous to the TATA-binding protein (TBP) and TFIIB. Despite its high impact, the molecular basis and temporal regulation of ASFV transcription is not well understood. Our lab recently applied deep sequencing approaches to characterise the viral transcriptome and gene expression during early and late ASFV infection. We have characterised the viral promoter elements and termination signatures, by mapping the RNA-5′ and RNA-3′ termini at single nucleotide resolution. In this review, we discuss the emerging field of ASFV transcripts, transcription, and transcriptomics.

Architecture of African swine fever virus and implications for viral assembly

Science ◽  
2019 ◽  
Vol 366 (6465) ◽  
pp. 640-644 ◽  
Author(s):  
Nan Wang ◽  
Dongming Zhao ◽  
Jialing Wang ◽  
Yangling Zhang ◽  
Ming Wang ◽  
...  
Keyword(s):  
Vaccine Development ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Fever Virus ◽  
Capsid Proteins ◽  
Dna Viruses ◽  
Capsid Shell ◽  
Nucleocytoplasmic Large Dna Viruses ◽  
Swine Disease ◽  
Capsid Stability

African swine fever virus (ASFV) is a giant and complex DNA virus that causes a highly contagious and often lethal swine disease for which no vaccine is available. Using an optimized image reconstruction strategy, we solved the ASFV capsid structure up to 4.1 angstroms, which is built from 17,280 proteins, including one major (p72) and four minor (M1249L, p17, p49, and H240R) capsid proteins organized into pentasymmetrons and trisymmetrons. The atomic structure of the p72 protein informs putative conformational epitopes, distinguishing ASFV from other nucleocytoplasmic large DNA viruses. The minor capsid proteins form a complicated network below the outer capsid shell, stabilizing the capsid by holding adjacent capsomers together. Acting as core organizers, 100-nanometer-long M1249L proteins run along each edge of the trisymmetrons that bridge two neighboring pentasymmetrons and form extensive intermolecular networks with other capsid proteins, driving the formation of the capsid framework. These structural details unveil the basis of capsid stability and assembly, opening up new avenues for African swine fever vaccine development.

scholarly journals Pacmanvirus, a New Giant Icosahedral Virus at the Crossroads between Asfarviridae and Faustoviruses

2017 ◽  
Vol 91 (14) ◽  
Author(s):  
Julien Andreani ◽  
Jacques Yaacoub Bou Khalil ◽  
Madhumati Sevvana ◽  
Samia Benamar ◽  
Fabrizio Di Pinto ◽  
...  
Keyword(s):  
African Swine Fever Virus ◽  
Acanthamoeba Castellanii ◽  
Genomic Analysis ◽  
African Swine Fever ◽  
Fever Virus ◽  
Dna Virus ◽  
Dna Viruses ◽  
Content Type ◽  
Double Stranded Dna ◽  
Protein Locus

ABSTRACT African swine fever virus, a double-stranded DNA virus that infects pigs, is the only known member of the Asfarviridae family. Nevertheless, during our isolation and sequencing of the complete genome of faustovirus, followed by the description of kaumoebavirus, carried out over the past 2 years, we observed the emergence of previously unknown related viruses within this group of viruses. Here we describe the isolation of pacmanvirus, a fourth member in this group, which is capable of infecting Acanthamoeba castellanii. Pacmanvirus A23 has a linear compact genome of 395,405 bp, with a 33.62% G+C content. The pacmanvirus genome harbors 465 genes, with a high coding density. An analysis of reciprocal best hits shows that 31 genes are conserved between African swine fever virus, pacmanvirus, faustovirus, and kaumoebavirus. Moreover, the major capsid protein locus of pacmanvirus appears to be different from those of kaumoebavirus and faustovirus. Overall, comparative and genomic analyses reveal the emergence of a new group or cluster of viruses encompassing African swine fever virus, faustovirus, pacmanvirus, and kaumoebavirus. IMPORTANCE Pacmanvirus is a newly discovered icosahedral double-stranded DNA virus that was isolated from an environmental sample by amoeba coculture. We describe herein its structure and replicative cycle, along with genomic analysis and genomic comparisons with previously known viruses. This virus represents the third virus, after faustovirus and kaumoebavirus, that is most closely related to classical representatives of the Asfarviridae family. These results highlight the emergence of previously unknown double-stranded DNA viruses which delineate and extend the diversity of a group around the asfarvirus members.

scholarly journals Identification of a functional small non-coding RNA encoded by African swine fever virus

2019 ◽  
Author(s):  
Laura E. M. Dunn ◽  
Alasdair Ivens ◽  
Christopher L. Netherton ◽  
David A. G. Chapman ◽  
Philippa M. Beard
Keyword(s):  
Small Rnas ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Fever Virus ◽  
Dna Viruses ◽  
Log Reduction ◽  
Complex Interactions ◽  
Non Coding Rna ◽  
Haemorrhagic Disease ◽  
Cellular Components

AbstractAfrican swine fever virus (ASFV) causes a lethal haemorrhagic disease of domestic pigs, to which there is no vaccine available. ASFV has a large, double-stranded DNA genome that encodes over 150 proteins. Replication takes place in the cytoplasm of the cell and involves complex interactions with host cellular components including small non-coding RNAs (sncRNAs). A number of DNA viruses are known to manipulate sncRNA either by encoding their own or disrupting host sncRNA. In order to investigate the interplay between ASFV and sncRNAs, study of host and viral small RNAs extracted from ASFV-infected primary porcine macrophages (PAMs) was undertaken. We discovered that ASFV infection had only a modest effect on host miRNAs, with only 6 miRNAs differentially expressed during infection. The data also revealed 3 potential novel small RNAs encoded by ASFV, ASFVsRNA1-3. Further investigation of ASFVsRNA2 detected it in lymphoid tissue from pigs with ASF. Overexpression of ASFVsRNA2 led to up to a 1 log reduction in ASFV growth indicating that ASFV utilises a virally-encoded small RNA to disrupt its own replication. This study describes the modest impact of ASFV on host sncRNAs and the identification of a functional ASFV-encoded sncRNA.ImportanceAfrican swine fever (ASF) poses a major threat to pig populations and food security worldwide. The disease is endemic in Africa and Eastern Europe and rapidly emerging into Asia where it has led to the deaths of millions of pigs in the past 12 months. The development of safe and effective vaccines to protect pigs against ASF has been hindered by lack of understanding of the complex interactions between ASFV and the host cell. We focused our work on characterising the interactions between ASFV and sncRNAs. We found only modest changes to host sncRNA abundance after ASFV infection, and discovered a functional ASFV-encoded sncRNA. The knowledge from this study can be exploited to develop more effective ASFV vaccines that take advantage of the sncRNA system.

scholarly journals Temporal Transcriptome and Promoter Architecture of the African Swine Fever Virus

2019 ◽  
Author(s):  
Gwenny Cackett ◽  
Dorota Matelska ◽  
Michal Sýkora ◽  
Raquel Portugal ◽  
Michal Malecki ◽  
...  
Keyword(s):  
African Swine Fever Virus ◽  
Transcription Termination ◽  
African Swine Fever ◽  
Promoter Sequence ◽  
Transcription Unit ◽  
Fever Virus ◽  
Regulation Of Transcription ◽  
Alternative Promoters ◽  
Nucleotide Resolution ◽  
Global Threat

AbstractThe African Swine Fever Virus causes haemorrhagic fever in domestic pigs and presents the biggest global threat to animal farming in recorded history. Despite its importance, very little is known the mechanisms and temporal regulation of transcription in ASFV. Here we report the first detailed viral transcriptome analysis of ASFV during early and late infection of Vero cells. In addition to total RNA sequencing, we have characterised the transcription start sites and transcription termination sites at nucleotide-resolution, revealing the distinct DNA consensus motifs of early and late promoters, as well as the sequence determinants for transcription termination. ASFV can utilise alternative promoters to generate distinct proteins from the same transcription unit that differ with respect to the polypeptide N-terminus. Finally, our results reveal that the ASFV-RNAP undergoes transcript slippage at the 5’ end of transcription units that in a promoter sequence-specific manner results in the addition of 5’-AT and 5’-ATAT tails to mRNAs.

scholarly journals The main DNA viruses significantly affecting pig livestock

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Carlos Díaz ◽  
Vladimír Celer ◽  
Ivo Frébort
Keyword(s):  
Immune System ◽  
Pseudorabies Virus ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Fever Virus ◽  
Host Immune System ◽  
Dna Virus ◽  
Dna Viruses ◽  
Double Stranded Dna ◽  
Porcine Circoviruses

AbstractSwine DNA viruses have developed unique mechanisms for evasion of the host immune system, infection and DNA replication, and finally, construction and release of new viral particles. This article reviews four classes of DNA viruses affecting swine: porcine circoviruses, African swine fever virus, porcine parvoviruses, and pseudorabies virus. Porcine circoviruses belonging to the Circoviridae family are small single-stranded DNA viruses causing different diseases in swine including poly-weaning multisystemic wasting syndrome, porcine dermatitis and nephropathy syndrome, and porcine respiratory disease complex. African swine fever virus, the only member of the Asfivirus genus in the Asfarviridae family, is a large double-stranded DNA virus and for its propensity to cause high mortality, it is currently considered the most dangerous virus in the pig industry. Porcine parvoviruses are small single-stranded DNA viruses belonging to the Parvoviridae family that cause reproductive failure in pregnant gilts. Pseudorabies virus, or suid herpesvirus 1, is a large double-stranded DNA virus belonging to the Herpesviridae family and Alphaherpesvirinae subfamily. Recent findings including general as well as genetic classification, virus structure, clinical syndromes and the host immune system responses and vaccine protection are described for all four swine DNA virus classes.

scholarly journals The Mimivirus L375 Nudix enzyme hydrolyzes the 5’ mRNA cap

2021 ◽  
Author(s):  
Grace Kago ◽  
Susan Parrish
Keyword(s):  
African Swine Fever Virus ◽  
Sequence Similarity ◽  
African Swine Fever ◽  
Host Protein ◽  
Mrna Turnover ◽  
Dna Viruses ◽  
Mrna Decapping ◽  
Double Stranded Dna ◽  
Nucleocytoplasmic Large Dna Viruses ◽  
Host Protein Synthesis

AbstractThe giant Mimivirus is a member of the nucleocytoplasmic large DNA viruses (NCLDV), a group of diverse viruses that contain double-stranded DNA (dsDNA) genomes that replicate primarily in eukaryotic hosts. Two members of the NCLDV, Vaccinia Virus (VACV) and African Swine Fever Virus (ASFV), both synthesize Nudix enzymes that have been shown to decap mRNA, a process thought to accelerate viral and host mRNA turnover and promote the shutoff of host protein synthesis. Mimivirus encodes two Nudix enzymes in its genome, denoted as L375 and L534. Importantly, L375 exhibits sequence similarity to ASFV-DP and eukaryotic Dcp2, two Nudix enzymes shown to possess mRNA decapping activity. In this work, we demonstrate that recombinant Mimivirus L375 cleaves the 5’ m7GpppN mRNA cap, releasing m7GDP as a product. L375 did not significantly cleave mRNAs containing an unmethylated 5’GpppN cap, indicating that this enzyme specifically hydrolyzes methylated-capped transcripts. A point mutation in the L375 Nudix motif completely eliminated cap hydrolysis, showing that decapping activity is dependent on this motif. Addition of methylated cap derivatives or uncapped RNA inhibited L375 decapping activity, suggesting that L375 recognizes its substrate through interaction with both the mRNA cap and RNA body.

scholarly journals The Mimivirus L375 Nudix enzyme hydrolyzes the 5’ mRNA cap

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0245820
Author(s):  
Grace Kago ◽  
Susan Parrish
Keyword(s):  
African Swine Fever Virus ◽  
Sequence Similarity ◽  
African Swine Fever ◽  
Host Protein ◽  
Mrna Turnover ◽  
Dna Viruses ◽  
Mrna Decapping ◽  
Double Stranded Dna ◽  
Nucleocytoplasmic Large Dna Viruses ◽  
Host Protein Synthesis

The giant Mimivirus is a member of the nucleocytoplasmic large DNA viruses (NCLDV), a group of diverse viruses that contain double-stranded DNA (dsDNA) genomes that replicate primarily in eukaryotic hosts. Two members of the NCLDV, Vaccinia Virus (VACV) and African Swine Fever Virus (ASFV), both synthesize Nudix enzymes that have been shown to decap mRNA, a process thought to accelerate viral and host mRNA turnover and promote the shutoff of host protein synthesis. Mimivirus encodes two Nudix enzymes in its genome, denoted as L375 and L534. Importantly, L375 exhibits sequence similarity to ASFV-DP and eukaryotic Dcp2, two Nudix enzymes shown to possess mRNA decapping activity. In this work, we demonstrate that recombinant Mimivirus L375 cleaves the 5’ m7GpppN mRNA cap, releasing m7GDP as a product. L375 did not significantly cleave mRNAs containing an unmethylated 5’GpppN cap, indicating that this enzyme specifically hydrolyzes methylated-capped transcripts. A point mutation in the L375 Nudix motif completely eliminated cap hydrolysis, showing that decapping activity is dependent on this motif. Addition of uncapped RNA significantly reduced L375 decapping activity, suggesting that L375 may recognize its substrate through interaction with the RNA body.

scholarly journals The determinants of African Swine Fever Virus Virulence – the Georgia 2007/1 strain and the host macrophage response

2021 ◽  
Author(s):  
Gwenny Cackett ◽  
Raquel Portugal ◽  
Dorota Matelska ◽  
Linda Dixon ◽  
Finn Werner
Keyword(s):  
Gene Expression ◽  
African Swine Fever Virus ◽  
Case Fatality ◽  
African Swine Fever ◽  
Fever Virus ◽  
Host Cells ◽  
Macrophage Response ◽  
Transcription Start Sites ◽  
Nucleotide Resolution ◽  
Cap Analysis

African swine fever virus (ASFV) has a major global economic impact. With a case fatality in domestic pigs approaching 100%, it currently presents the largest threat to animal farming. Although genomic differences between attenuated and highly virulent ASFV strains have been identified the molecular determinants for virulence at the level of gene expression have remained opaque. Here we characterise the transcriptome of ASFV genotype II Georgia 2007/1 (GRG) during infection of the physiologically relevant host cells, porcine macrophages. In this study Cap Analysis Gene Expression sequencing (CAGE-seq) was used to map the 5’ ends of mRNAs at nucleotide resolution, transcription start sites (TSSs) and the global promoter landscape of GRG at early and late times, 5 and 16 hours, post-infection. We then compared transcriptomic maps between the GRG isolate against the lab-attenuated BA71V strain. GRG-specific transcripts identified potential determinants of virulence including members of early expressed multi-gene family members (MGFs), including two we newly characterised in MGF 100 (I7L and I8L). We have importantly shown the response of the host transcriptome to infection, which highlighted a pro-inflammatory immune response with the upregulation of NF-kB activated genes, innate immunity- as well as lysosome components such as S100 proteins.

Genetic markers of the African swine fever virus

2020 ◽  
Vol 23 (04) ◽  
pp. 21-26
Author(s):  
A.K. Sibgatullova ◽  
◽  
M.E. Vlasov ◽  
I.A. Titov ◽  
◽  
...  
Keyword(s):  
Genetic Markers ◽  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Fever Virus
Sign in / Sign up

Export Citation Format

Share Document