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

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.

Download Full-text

The main DNA viruses significantly affecting pig livestock

Journal of Veterinary Research ◽

10.2478/jvetres-2021-0001 ◽

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.

Download Full-text

Structural Insight into African Swine Fever Virus A179L-Mediated Inhibition of Apoptosis

Journal of Virology ◽

10.1128/jvi.02228-16 ◽

2017 ◽

Vol 91 (6) ◽

Cited By ~ 26

Author(s):

Suresh Banjara ◽

Sofia Caria ◽

Linda K. Dixon ◽

Mark G. Hinds ◽

Marc Kvansakul

Keyword(s):

Crystal Structures ◽

African Swine Fever Virus ◽

Three Dimensional ◽

African Swine Fever ◽

Fever Virus ◽

Structural Basis ◽

Dna Virus ◽

Content Type ◽

Antiapoptotic Proteins ◽

Apoptosis Inhibition

ABSTRACT Programmed cell death is a tightly controlled process critical for the removal of damaged or infected cells. Pro- and antiapoptotic proteins of the Bcl-2 family are pivotal mediators of this process. African swine fever virus (ASFV) is a large DNA virus, the only member of the Asfarviridae family, and harbors A179L, a putative Bcl-2 like protein. A179L has been shown to bind to several proapoptotic Bcl-2 proteins; however, the hierarchy of binding and the structural basis for apoptosis inhibition are currently not understood. We systematically evaluated the ability of A179L to bind proapoptotic Bcl-2 family members and show that A179L is the first antiapoptotic Bcl-2 protein to bind to all major death-inducing mammalian Bcl-2 proteins. We then defined the structural basis for apoptosis inhibition of A179L by determining the crystal structures of A179L bound to both Bid and Bax BH3 motifs. Our findings provide a mechanistic understanding for the potent antiapoptotic activity of A179L by identifying it as the first panprodeath Bcl-2 binder and serve as a platform for more-detailed investigations into the role of A179L during ASFV infection. IMPORTANCE Numerous viruses have acquired strategies to subvert apoptosis by encoding proteins capable of sequestering proapoptotic host proteins. African swine fever virus (ASFV), a large DNA virus and the only member of the Asfarviridae family, encodes the protein A179L, which functions to prevent apoptosis. We show that A179L is unusual among antiapoptotic Bcl-2 proteins in being able to physically bind to all core death-inducing mammalian Bcl-2 proteins. Currently, little is known regarding the molecular interactions between A179L and the proapoptotic Bcl-2 members. Using the crystal structures of A179L bound to two of the identified proapoptotic Bcl-2 proteins, Bid and Bax, we now provide a three-dimensional (3D) view of how A179L sequesters host proapoptotic proteins, which is crucial for subverting premature host cell apoptosis.

Download Full-text

Inhibition of a Large Double-Stranded DNA Virus by MxA Protein

Journal of Virology ◽

10.1128/jvi.00781-08 ◽

2008 ◽

Vol 83 (5) ◽

pp. 2310-2320 ◽

Cited By ~ 45

Author(s):

Christopher L. Netherton ◽

Jennifer Simpson ◽

Otto Haller ◽

Thomas E. Wileman ◽

Haru-Hisa Takamatsu ◽

...

Keyword(s):

Rna Viruses ◽

African Swine Fever Virus ◽

African Swine Fever ◽

Vero Cells ◽

Dna Virus ◽

Dna Viruses ◽

Double Stranded Dna ◽

Late Protein ◽

B Virus ◽

Negative Sense

ABSTRACT Increasing evidence points to the importance of the interferon (IFN) response in determining the host range and virulence of African swine fever virus (ASFV). Infection with attenuated strains of ASFV leads to the upregulation of genes controlled by IFN pathways, including myxovirus resistance (Mx) genes that are potent effectors of the antiviral state. Mx gene products are known to inhibit the replication of many negative-sense single-stranded RNA viruses, as well as double-stranded RNA viruses, positive-sense single-stranded RNA viruses, and the reverse-transcribing DNA virus hepatitis B virus. Here, we provide data that extend the known range of viruses inhibited by Mx to include the large double-stranded DNA viruses. Stably transfected Vero cells expressing human MxA protein did not support ASFV plaque formation, and virus replication in these cells was reduced 100-fold compared with that in control cells. In contrast, ASFV replication in cells expressing MxB protein or a mutant MxA protein was similar to that in control Vero cells. There was a drastic reduction in ASFV late protein synthesis in MxA-expressing cells, correlating with the results of previous work on the effect of IFN on viral replication. Strikingly, the inhibition of ASFV replication was linked to the recruitment of MxA protein to perinuclear viral assembly sites, where the protein surrounded the virus factories. Interactions between ASFV and MxA were similar to those seen between MxA and different RNA viruses, suggesting a common inhibitory mechanism.

Download Full-text

African Swine Fever Virus Gets Undressed: New Insights on the Entry Pathway

Journal of Virology ◽

10.1128/jvi.01906-16 ◽

2016 ◽

Vol 91 (4) ◽

Cited By ~ 7

Author(s):

Germán Andrés

Keyword(s):

African Swine Fever Virus ◽

Structural Complexity ◽

African Swine Fever ◽

Low Ph ◽

Fever Virus ◽

Dna Virus ◽

Alternative Pathways ◽

Entry Pathway ◽

A Genome ◽

Inner Envelope

ABSTRACT African swine fever virus (ASFV) is a large, multienveloped DNA virus composed of a genome-containing core successively wrapped by an inner lipid envelope, an icosahedral protein capsid, and an outer lipid envelope. In keeping with this structural complexity, recent studies have revealed an intricate entry program. This Gem highlights how ASFV uses two alternative pathways, macropinocytosis and clathrin-mediated endocytosis, to enter into the host macrophage and how the endocytosed particles undergo a stepwise, low pH-driven disassembly leading to inner envelope fusion and core delivery in the cytoplasm.

Download Full-text

Crystal Structure of African Swine Fever Virus pS273R Protease and Implications for Inhibitor Design

Journal of Virology ◽

10.1128/jvi.02125-19 ◽

2020 ◽

Vol 94 (10) ◽

Author(s):

Guobang Li ◽

Xiaoxia Liu ◽

Mengyuan Yang ◽

Guangshun Zhang ◽

Zhengyang Wang ◽

...

Keyword(s):

Crystal Structure ◽

Structural Information ◽

African Swine Fever Virus ◽

African Swine Fever ◽

Hydrolytic Activity ◽

Viral Disease ◽

Fever Virus ◽

Dna Virus ◽

Core Domain ◽

The Core

ABSTRACT African swine fever (ASF) is a highly contagious hemorrhagic viral disease of domestic and wild pigs that is responsible for serious economic and production losses. It is caused by the African swine fever virus (ASFV), a large and complex icosahedral DNA virus of the Asfarviridae family. Currently, there is no effective treatment or approved vaccine against the ASFV. pS273R, a specific SUMO-1 cysteine protease, catalyzes the maturation of the pp220 and pp62 polyprotein precursors into core-shell proteins. Here, we present the crystal structure of the ASFV pS273R protease at a resolution of 2.3 Å. The overall structure of the pS273R protease is represented by two domains named the “core domain” and the N-terminal “arm domain.” The “arm domain” contains the residues from M1 to N83, and the “core domain” contains the residues from N84 to A273. A structure analysis reveals that the “core domain” shares a high degree of structural similarity with chlamydial deubiquitinating enzyme, sentrin-specific protease, and adenovirus protease, while the “arm domain” is unique to ASFV. Further, experiments indicated that the “arm domain” plays an important role in maintaining the enzyme activity of ASFV pS273R. Moreover, based on the structural information of pS273R, we designed and synthesized several peptidomimetic aldehyde compounds at a submolar 50% inhibitory concentration, which paves the way for the design of inhibitors to target this severe pathogen. IMPORTANCE African swine fever virus, a large and complex icosahedral DNA virus, causes a deadly infection in domestic pigs. In addition to Africa and Europe, countries in Asia, including China, Vietnam, and Mongolia, were negatively affected by the hazards posed by ASFV outbreaks in 2018 and 2019, at which time more than 30 million pigs were culled. Until now, there has been no vaccine for protection against ASFV infection or effective treatments to cure ASF. Here, we solved the high-resolution crystal structure of the ASFV pS273R protease. The pS273R protease has a two-domain structure that distinguishes it from other members of the SUMO protease family, while the unique “arm domain” has been proven to be essential for its hydrolytic activity. Moreover, the peptidomimetic aldehyde compounds designed to target the substrate binding pocket exert prominent inhibitory effects and can thus be used in a potential lead for anti-ASFV drug development.

Download Full-text

Transcriptome view of a killer: African swine fever virus

Biochemical Society Transactions ◽

10.1042/bst20191108 ◽

2020 ◽

Vol 48 (4) ◽

pp. 1569-1581 ◽

Cited By ~ 1

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.

Download Full-text

Exceptionally diverse morphotypes and genomes of crenarchaeal hyperthermophilic viruses

Biochemical Society Transactions ◽

10.1042/bst0320204 ◽

2004 ◽

Vol 32 (2) ◽

pp. 204-208 ◽

Cited By ~ 60

Author(s):

D. Prangishvili ◽

R.A. Garrett

Keyword(s):

Aquatic Ecosystems ◽

African Swine Fever Virus ◽

African Swine Fever ◽

Open Reading Frames ◽

Dna Viruses ◽

Double Stranded Dna ◽

Sequence Patterns ◽

Hydrothermal Environments ◽

Homologous Orfs ◽

Reading Frames

The remarkable diversity of the morphologies of viruses found in terrestrial hydrothermal environments with temperatures >80°C is unprecedented for aquatic ecosystems. The best-studied viruses from these habitats have been assigned to novel viral families: Fuselloviridae, Lipothrixviridae and Rudiviridae. They all have double-stranded DNA genomes and infect hyperthermophilic crenarchaea of the orders Sulfolobales and Thermoproteales. Representatives of the different viral families share a few homologous ORFs (open reading frames). However, about 90% of all ORFs in the seven sequenced genomes show no significant matches to sequences in public databases. This suggests that these hyperthermophilic viruses have exceptional biochemical solutions for biological functions. Specific features of genome organization, as well as strategies for DNA replication, suggest that phylogenetic relationships exist between crenarchaeal rudiviruses and the large eukaryal DNA viruses: poxviruses, the African swine fever virus and Chlorella viruses. Sequence patterns at the ends of the linear genome of the lipothrixvirus AFV1 are reminiscent of the telomeric ends of linear eukaryal chromosomes and suggest that a primitive telomeric mechanism operates in this virus.

Download Full-text

Crystal Structure of African Swine Fever Virus dUTPase Reveals a Potential Drug Target

mBio ◽

10.1128/mbio.02483-19 ◽

2019 ◽

Vol 10 (5) ◽

Cited By ~ 5

Author(s):

Changyao Li ◽

Yan Chai ◽

Hao Song ◽

Changjiang Weng ◽

Jianxun Qi ◽

...

Keyword(s):

Plasmodium Falciparum ◽

Mycobacterium Tuberculosis ◽

High Resolution ◽

Drug Design ◽

Active Site ◽

African Swine Fever Virus ◽

African Swine Fever ◽

Fever Virus ◽

Potential Drug ◽

Content Type

ABSTRACT E165R, a highly specific dUTP nucleotidohydrolase (dUTPase) encoded by the African swine fever virus (ASFV) genome, is required for productive replication of ASFV in swine macrophages. Here, we solved the high-resolution crystal structures of E165R in its apo state and in complex with its product dUMP. Structural analysis explicitly defined the architecture of the active site of the enzyme as well as the interaction between the active site and the dUMP ligand. By comparing the ASFV E165R structure with dUTPase structures from other species, we found that the active site of E165R is highly similar to those of dUTPases from Mycobacterium tuberculosis and Plasmodium falciparum, against which small-molecule chemicals have been developed, which could be the potential drug or lead compound candidates for ASFV. Our results provide important basis for anti-ASFV drug design by targeting E165R. IMPORTANCE African swine fever virus (ASFV), an Asfivirus affecting pigs and wild boars with up to 100% case fatality rate, is currently rampaging throughout China and some other countries in Asia. There is an urgent need to develop therapeutic and preventive reagents against the virus. Our crystallographic and biochemical studies reveal that ASFV E165R is a member of trimeric dUTP nucleotidohydrolase (dUTPase) family that catalyzes the hydrolysis of dUTP into dUMP. Our apo-E165R and E165R-dUMP structures reveal the constitutive residues and the configuration of the active center of this enzyme in rich detail and give evidence that the active center of E165R is very similar to that of dUTPases from Plasmodium falciparum and Mycobacterium tuberculosis, which have already been used as targets for designing drugs. Therefore, our high-resolution structures of E165R provide useful structural information for chemotherapeutic drug design.

Download Full-text

Faustovirus, an Asfarvirus-Related New Lineage of Giant Viruses Infecting Amoebae

Journal of Virology ◽

10.1128/jvi.00115-15 ◽

2015 ◽

Vol 89 (13) ◽

pp. 6585-6594 ◽

Cited By ~ 128

Author(s):

Dorine Gaëlle Reteno ◽

Samia Benamar ◽

Jacques Bou Khalil ◽

Julien Andreani ◽

Nicholas Armstrong ◽

...

Keyword(s):

African Swine Fever Virus ◽

African Swine Fever ◽

Fever Virus ◽

Open Reading Frames ◽

Gene Repertoire ◽

Significant Similarity ◽

Content Type ◽

Genes Encoding ◽

Giant Viruses ◽

Almost All

ABSTRACTGiant viruses are protist-associated viruses belonging to the proposed orderMegavirales; almost all have been isolated fromAcanthamoebaspp. Their isolation in humans suggests that they are part of the human virome. Using a high-throughput strategy to isolate new giant viruses from their original protozoan hosts, we obtained eight isolates of a new giant viral lineage fromVermamoebavermiformis, the most common free-living protist found in human environments. This new lineage was proposed to be the faustovirus lineage. The prototype member, faustovirus E12, forms icosahedral virions of ≈200 nm that are devoid of fibrils and that encapsidate a 466-kbp genome encoding 451 predicted proteins. Of these, 164 are found in the virion. Phylogenetic analysis of the core viral genes showed that faustovirus is distantly related to the mammalian pathogen African swine fever virus, but it encodes ≈3 times more mosaic gene complements. About two-thirds of these genes do not show significant similarity to genes encoding any known proteins. These findings show that expanding the panel of protists to discover new giant viruses is a fruitful strategy.IMPORTANCEBy usingVermamoeba, a protist living in humans and their environment, we isolated eight strains of a new giant virus that we named faustovirus. The genomes of these strains were sequenced, and their sequences showed that faustoviruses are related to but different from the vertebrate pathogen African swine fever virus (ASFV), which belongs to the familyAsfarviridae. Moreover, the faustovirus gene repertoire is ≈3 times larger than that of ASFV and comprises approximately two-thirds ORFans (open reading frames [ORFs] with no detectable homology to other ORFs in a database).

Download Full-text