Diverse Trajectories Drive the Expression of a Giant Virus in the Oomycete Plant Pathogen Phytophthora parasitica

Giant viruses of amoebas, recently classified in the class Megaviricetes, are a group of viruses that can infect major eukaryotic lineages. We previously identified a set of giant virus sequences in the genome of Phytophthora parasitica, an oomycete and a devastating major plant pathogen. How viral insertions shape the structure and evolution of the invaded genomes is unclear, but it is known that the unprecedented functional potential of giant viruses is the result of an intense genetic interplay with their hosts. We previously identified a set of giant virus sequences in the genome of P. parasitica, an oomycete and a devastating major plant pathogen. Here, we show that viral pieces are found in a 550-kb locus and are organized in three main clusters. Viral sequences, namely RNA polymerases I and II and a major capsid protein, were identified, along with orphan sequences, as a hallmark of giant viruses insertions. Mining of public databases and phylogenetic reconstructions suggest an ancient association of oomycetes and giant viruses of amoeba, including faustoviruses, African swine fever virus (ASFV) and pandoraviruses, and that a single viral insertion occurred early in the evolutionary history of oomycetes prior to the Phytophthora–Pythium radiation, estimated at ∼80 million years ago. Functional annotation reveals that the viral insertions are located in a gene sparse region of the Phytophthora genome, characterized by a plethora of transposable elements (TEs), effectors and other genes potentially involved in virulence. Transcription of viral genes was investigated through analysis of RNA-Seq data and qPCR experiments. We show that most viral genes are not expressed, and that a variety of mechanisms, including deletions, TEs insertions and RNA interference may contribute to transcriptional repression. However, a gene coding a truncated copy of RNA polymerase II along a set of neighboring sequences have been shown to be expressed in a wide range of physiological conditions, including responses to stress. These results, which describe for the first time the endogenization of a giant virus in an oomycete, contribute to challenge our view of Phytophthora evolution.

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Differential Effect of the Deletion of African Swine Fever Virus Virulence-Associated Genes in the Induction of Attenuation of the Highly Virulent Georgia Strain

Viruses ◽

10.3390/v11070599 ◽

2019 ◽

Vol 11 (7) ◽

pp. 599 ◽

Cited By ~ 14

Author(s):

Elizabeth Ramirez-Medina ◽

Elizabeth Vuono ◽

Vivian O’Donnell ◽

Lauren G. Holinka ◽

Ediane Silva ◽

...

Keyword(s):

Protective Immunity ◽

Gene Deletion ◽

African Swine Fever Virus ◽

African Swine Fever ◽

Early Death ◽

Fever Virus ◽

Differential Behavior ◽

Viral Genes ◽

The Uk ◽

Highly Virulent

African swine fever virus (ASFV) is the etiological agent of an often lethal disease of domestic pigs, African swine fever (ASF). The ASFV Georgia 2007 isolate (ASFV-G) is responsible for the current epidemic situation in Europe and Asia. Genetically modified ASFVs containing deletions of virulence-associated genes have produced attenuated phenotypes and induced protective immunity in swine. Here we describe the differential behavior of two viral genes, NL (DP71L) and UK (DP96R), both originally described as being involved in virus virulence. Deletion of either of these genes efficiently attenuated ASFV strain E70. We demonstrated that deletion of the UK gene from the ASFV-G genome did not decrease virulence when compared to the parental virus. Conversely, deletion of the NL gene produced a heterogeneous response, with early death in one of the animals and transient fever in the other animals. With this knowledge, we attempted to increase the safety profile of the previously reported experimental vaccine ASFV-GΔ9GL/ΔUK by deleting the NL gene. A triple gene-deletion virus was produced, ASFV-GΔ9GL/ΔNL/ΔUK. Although ASFV-GΔ9GL/ΔNL/ΔUK replicated in primary cell cultures of swine macrophages, it demonstrated a severe replication deficiency in pigs, failing to induce protection against challenge with parental ASFV-G.

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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).

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DNA segment of African Swine Fever Virus first detected in hard ticks from sheep and bovine

10.1101/485060 ◽

2018 ◽

Author(s):

Ze Chen ◽

Xiaofeng Xu ◽

Xiaojun Yang ◽

Weihao Dou ◽

Xiufeng Jin ◽

...

Keyword(s):

African Swine Fever Virus ◽

African Swine Fever ◽

Fever Virus ◽

Control Measures ◽

Single Amino Acid ◽

Small Rna Sequencing ◽

Hard Ticks ◽

Wide Range ◽

Prevention And Control Measures ◽

And Control

In this study, we aimed to detect viruses in hard ticks using the small RNA sequencing based method. A 235-bp DNA segment was detected in Dermacentor nuttalli (hard ticks) and D. silvarum (hard ticks) from sheep and bovine, respectively. The detected 235-bp segment had an identity of 99% to a 235-bp DNA segment of African Swine Fever Virus (ASFV) and contained three single nucleotide mutations (C38T, C76T and A108C). C38T, resulting in an single amino acid mutation G66D, suggests the existence of a new ASFV strain, which is different from all reported ASFV strains in NCBI GenBank database. These results also suggest that ASFV could have a wide range of hosts or vectors, beyond the well known Suidae family and soft ticks. Our findings pave the way toward further studies of ASFV transmission and development of prevention and control measures.

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Flavonoid Library Screening Reveals Kaempferol as a Potential Antiviral Agent Against African Swine Fever Virus

Frontiers in Microbiology ◽

10.3389/fmicb.2021.736780 ◽

2021 ◽

Vol 12 ◽

Author(s):

Erik Arabyan ◽

Astghik Hakobyan ◽

Tamara Hakobyan ◽

Rafaella Grigoryan ◽

Roza Izmailyan ◽

...

Keyword(s):

African Swine Fever Virus ◽

Screening Method ◽

African Swine Fever ◽

Vero Cells ◽

Fever Virus ◽

Wide Range ◽

Dependent Inhibition ◽

Dose Dependent Inhibition ◽

Dose Dependent

Naturally occurring plant flavonoids are a promising class of antiviral agents to inhibit African swine fever virus (ASFV), which causes highly fatal disease in pigs and is a major threat to the swine industry. Currently known flavonoids with anti-ASFV activity demonstrate a wide range of antiviral mechanisms, which motivates exploration of new antiviral candidates within this class. The objective of this study was to determine whether other flavonoids may significantly inhibit ASFV infection in vitro. We performed a cell-based library screen of 90 flavonoids. Our screening method allowed us to track the development of virus-induced cytopathic effect by MTT in the presence of tested flavonoids. This screening method was shown to be robust for hit identification, with an average Z-factor of 0.683. We identified nine compounds that inhibit ASFV Ba71V strain in Vero cells. Among them, kaempferol was the most potent and exhibited dose-dependent inhibition, which occurred through a virostatic effect. Time-of-addition studies revealed that kaempferol acts on the entry and post-entry stages of the ASFV replication cycle and impairs viral protein and DNA synthesis. It was further identified that kaempferol induces autophagy in ASFV-infected Vero cells, which is related to its antiviral activity and could be partially abrogated by the addition of an autophagy inhibitor. Kaempferol also exhibited dose-dependent inhibition of a highly virulent ASFV Arm/07 isolate in porcine macrophages. Together, these findings support that kaempferol is a promising anti-ASFV agent and has a distinct antiviral mechanism compared to other anti-ASFV flavonoids.

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Effect of inhibitors of the host cell RNA polymerase II on African swine fever virus multiplication

Virology ◽

10.1016/0042-6822(88)90646-0 ◽

1988 ◽

Vol 164 (1) ◽

pp. 280-283 ◽

Cited By ~ 13

Author(s):

José Salas ◽

Maria L. Salas ◽

Eladio Viñuela

Keyword(s):

Rna Polymerase ◽

Host Cell ◽

Rna Polymerase Ii ◽

African Swine Fever Virus ◽

African Swine Fever ◽

Virus Multiplication ◽

Fever Virus ◽

Effect Of Inhibitors

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Talaromyces minioluteus: New Postharvest Fungal Pathogen in Serbia

Plant Disease ◽

10.1094/pdis-08-19-1806-re ◽

2020 ◽

Vol 104 (3) ◽

pp. 656-667 ◽

Cited By ~ 1

Author(s):

Stefan Stošić ◽

Danijela Ristić ◽

Katarina Gašić ◽

Mira Starović ◽

Milica Ljaljević Grbić ◽

...

Keyword(s):

Rna Polymerase Ii ◽

Plant Pathogen ◽

Fruits And Vegetables ◽

First Record ◽

Potato Tubers ◽

Important Species ◽

Onion Bulbs ◽

Wide Range ◽

Different Temperatures ◽

Orange Fruit

Talaromyces minioluteus is one of the important species of genus Talaromyces, which has cosmopolitan distribution and is encountered on a wide range of different habitats. This species has not been considered as an important plant pathogen, even though it has been isolated from various plant hosts. Fruits and vegetables with Penicillium-like mold symptoms were collected from 2015 to 2017 from markets in Serbia. Isolates originating from quince, tomato, and orange fruits, onion bulbs, and potato tubers were identified and characterized on a morphological, physiological, and molecular level. Morphological and physiological examination included observing micromorphology, testing growth on six different media and at five different temperatures, and production of three enzymes. Molecular identification and characterization were performed using four molecular markers: internal transcribed spacer, β-tubulin, calmodulin, and DNA-dependent RNA polymerase II second largest subunit. The results of morphological and molecular analyses were in agreement, and they proved that the obtained isolates are T. minioluteus. In the pathogenicity assay, T. minioluteus was confirmed as a pathogen of all species tested with the exception of potato tubers. This is the first report of T. minioluteus as a postharvest plant pathogen on quince, tomato, and orange fruit and onion bulbs. Also, this is the first record of T. minioluteus in Serbia.

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Meat Exudate for Detection of African Swine Fever Virus Genomic Material and Anti-ASFV Antibodies

Viruses ◽

10.3390/v13091744 ◽

2021 ◽

Vol 13 (9) ◽

pp. 1744

Author(s):

Chukwunonso Onyilagha ◽

Mikyla Nash ◽

Orlando Perez ◽

Melissa Goolia ◽

Alfonso Clavijo ◽

...

Keyword(s):

Nucleic Acids ◽

Whole Blood ◽

African Swine Fever Virus ◽

Clinical Signs ◽

African Swine Fever ◽

Lower Amount ◽

Sample Type ◽

Long Distance ◽

Wide Range ◽

Genomic Material

African swine fever (ASF) is one of the most important viral diseases of pigs caused by the ASF virus (ASFV). The virus is highly stable over a wide range of temperatures and pH and can survive in meat and meat products for several months, leading to long-distance transmission of ASF. Whole blood, serum, and organs from infected pigs are used routinely as approved sample types in the laboratory diagnosis of ASF. However, these sample types may not always be available. Here, we investigated meat exudate as an alternative sample type for the detection of ASFV-specific nucleic acids and antibodies. Pigs were infected with various ASFV strains: the highly virulent ASFV Malawi LIL 18/2 strain, the moderately-virulent ASFV Estonia 2014 strain, or the low-virulent ASFV OURT/88/3 strain. The animals were euthanized on different days post-infection (dpi), and meat exudates were collected and tested for the presence of ASFV-specific nucleic acids and antibodies. Animals infected with the ASFV Malawi LIL 18/2 developed severe clinical signs and succumbed to the infection within seven dpi, while pigs infected with ASFV Estonia 2014 also developed clinical signs but survived longer, with a few animals seroconverting before succumbing to the ASFV infection or being euthanized as they reached humane endpoints. Pigs infected with ASFV OURT/88/3 developed transient fever and seroconverted without mortality. ASFV genomic material was detected in meat exudate from pigs infected with ASFV Malawi LIL 18/2 and ASFV Estonia 2014 at the onset of viremia but at a lower amount when compared to the corresponding whole blood samples. Low levels of ASFV genomic material were detected in the whole blood of ASFV OURT/88/3-infected pigs, and no ASFV genomic material was detected in the meat exudate of these animals. Anti-ASFV antibodies were detected in the serum and meat exudate derived from ASFV OURT/88/3-infected pigs and in some of the samples derived from the ASFV Estonia 2014-infected pigs. These results indicate that ASFV genomic material and anti-ASFV antibodies can be detected in meat exudate, indicating that this sample can be used as an alternative sample type for ASF surveillance when routine sample types are unavailable or are not easily accessible.

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