Classification of multigene families of African swine fever viruses

AbstractAfrican swine fever virus (ASFV) is a large and complex double-stranded DNA virus that poses serious threats to the pig industry. It is well-accepted that the multigene family (MGF) proteins are extensively distributed in ASFVs and are generally classified into five families, including MGF-100, MGF-110, MGF-300, MGF-360 and MGF-505. Most MGF proteins, however, have not been well characterized and classified within each family. To bridge this gap, this study first classified the MGF proteins into 35 groups based on protein sequence homology. A web server for classifying the MGF proteins was then established and available for free at http://www.computationalbiology.cn/MGF/home.html. Results showed that the genetic diversity of the MGF groups varied widely, mainly due to the occurrence of indels. In addition, the MGF proteins were predicted to have large structural and functional diversity, and the MGF proteins of the same MGF family tended to have similar structure, location and function. Evolutionary analysis revealed the dynamic changes of the MGF proteins in the ASFV genomes, and more than half of MGF groups were presented in all ASFV genomes, which indicated the important role of MGF proteins in ASFVs. Overall, it is expected that the work would not only provide a detailed classification for MGF proteins, but also facilitate further research on MGF proteins.

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Classification and characterization of multigene family proteins of African swine fever viruses

Briefings in Bioinformatics ◽

10.1093/bib/bbaa380 ◽

2020 ◽

Author(s):

Zhaozhong Zhu ◽

Huiting Chen ◽

Li Liu ◽

Yang Cao ◽

Taijiao Jiang ◽

...

Keyword(s):

Multigene Family ◽

Copy Number ◽

African Swine Fever Virus ◽

African Swine Fever ◽

Copy Number Variations ◽

Network Clustering ◽

Sequence Motifs ◽

Conserved Sequence ◽

Protein Sequence Homology ◽

And Function

Abstract African swine fever virus (ASFV) poses serious threats to the pig industry. The multigene family (MGF) proteins are extensively distributed in ASFVs and are generally classified into five families, including MGF-100, MGF-110, MGF-300, MGF-360 and MGF-505. Most MGF proteins, however, have not been well characterized and classified within each family. To bridge this gap, this study first classified MGF proteins into 31 groups based on protein sequence homology and network clustering. A web server for classifying MGF proteins was established and kept available for free at http://www.computationalbiology.cn/MGF/home.html. Results showed that MGF groups of the same family were most similar to each other and had conserved sequence motifs; the genetic diversity of MGF groups varied widely, mainly due to the occurrence of indels. In addition, the MGF proteins were predicted to have large structural and functional diversity, and MGF proteins of the same MGF family tended to have similar structure, location and function. Reconstruction of the ancestral states of MGF groups along the ASFV phylogeny showed that most MGF groups experienced either the copy number variations or the gain-or-loss changes, and most of these changes happened within strains of the same genotype. It is found that the copy number decrease and the loss of MGF groups were much larger than the copy number increase and the gain of MGF groups, respectively, suggesting the ASFV tended to lose MGF proteins in the evolution. Overall, the work provides a detailed classification for MGF proteins and would facilitate further research on MGF proteins.

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Deletion of the K145R and DP148R Genes from the Virulent ASFV Georgia 2007/1 Isolate Delays the Onset, but Does Not Reduce Severity, of Clinical Signs in Infected Pigs

Viruses ◽

10.3390/v13081473 ◽

2021 ◽

Vol 13 (8) ◽

pp. 1473

Author(s):

Anusyah Rathakrishnan ◽

Ana L. Reis ◽

Lynnette C. Goatley ◽

Katy Moffat ◽

Linda K. Dixon

Keyword(s):

Post Infection ◽

African Swine Fever Virus ◽

Clinical Signs ◽

African Swine Fever ◽

Wild Type Virus ◽

Genotype I ◽

Host Interactions ◽

Double Stranded Dna ◽

Genotype Ii

African swine fever virus causes a frequently fatal disease of domestic pigs and wild boar that has a high economic impact across 3 continents. The large double-stranded DNA genome codes for approximately 160 proteins. Many of these have unknown functions and this hinders our understanding of the virus and host interactions. The purpose of the study was to evaluate the role of two virus proteins, K145R and DP148R, in virus replication in macrophages and virulence in pigs. To do this, the DP148R gene, alone or in combination with the K145R gene, was deleted from the virulent genotype II Georgia 2007/1 isolate. Neither of these deletions reduced the ability of the viruses to replicate in porcine macrophages compared to the parental wild-type virus. Pigs infected with GeorgiaΔDP148R developed clinical and post-mortem signs and high viremia, typical of acute African swine fever, and were culled on day 6 post-infection. The additional deletion of the K145R gene delayed the onset of clinical signs and viremia in pigs by 3 days, but pigs showed signs of acute African swine fever and were culled on days 10 or 13 post-infection. The results show that the deletion of DP148R did not attenuate the genotype II Georgia 2007/1 isolate, contrary to the results obtained with the genotype I Benin97/1 isolate. Additional deletion of the K145R gene delayed clinical signs, but infected pigs reached the humane endpoint. The deletion of additional genes would be required to attenuate the virus.

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The Role of Interleukine-10 and Interferon-γ as Potential Markers of the Evolution of African Swine Fever Virus Infection in Wild Boar

Pathogens ◽

10.3390/pathogens10060757 ◽

2021 ◽

Vol 10 (6) ◽

pp. 757

Author(s):

Sandra Barroso-Arévalo ◽

Jose A. Barasona ◽

Estefanía Cadenas-Fernández ◽

José M. Sánchez-Vizcaíno

Keyword(s):

Wild Boar ◽

Vaccine Candidate ◽

African Swine Fever Virus ◽

African Swine Fever ◽

Interferon Γ ◽

Fever Virus ◽

Control Group ◽

Challenge Virus ◽

Ifn Γ

African swine fever virus (ASFv) is one of the most challenging pathogens to affect both domestic and wild pigs. The disease has now spread to Europe and Asia, causing great damage to the pig industry. Although no commercial vaccine with which to control the disease is, as yet, available, some potential vaccine candidates have shown good results in terms of protection. However, little is known about the host immune mechanisms underlying that protection, especially in wild boar, which is the main reservoir of the disease in Europe. Here, we study the role played by two cytokines (IL-10 and IFN-γ) in wild boar orally inoculated with the attenuated vaccine candidate Lv17/WB/Rie1 and challenged with a virulent ASFv genotype II isolate. A group of naïve wild boar challenged with the latter isolate was also established as a control group. Our results showed that both cytokines play a key role in protecting the host against the challenge virus. While high levels of IL-10 in serum may trigger an immune system malfunctioning in challenged animals, the provision of stable levels of this cytokine over time may help to control the disease. This, together with high and timely induction of IFN-γ by the vaccine candidate, could help protect animals from fatal outcomes. Further studies should be conducted in order to support these preliminary results and confirm the role of these two cytokines as potential markers of the evolution of ASFV infection.

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Ancestry of the AUTS2 family–A novel group of polycomb-complex proteins involved in human neurological disease

PLoS ONE ◽

10.1371/journal.pone.0232101 ◽

2020 ◽

Vol 15 (12) ◽

pp. e0232101

Author(s):

Robert A. Sellers ◽

David L. Robertson ◽

May Tassabehji

Keyword(s):

Autosomal Dominant ◽

Large Population ◽

Evolutionary Analysis ◽

Genome Data ◽

High Prevalence ◽

And Function ◽

Polycomb Complex ◽

Putative Domain ◽

Human Specific

Autism susceptibility candidate 2 (AUTS2) is a neurodevelopmental regulator associated with an autosomal dominant intellectual disability syndrome, AUTS2 syndrome, and is implicated as an important gene in human-specific evolution. AUTS2 exists as part of a tripartite gene family, the AUTS2 family, which includes two relatively undefined proteins, Fibrosin (FBRS) and Fibrosin-like protein 1 (FBRSL1). Evolutionary ancestors of AUTS2 have not been formally identified outside of the Animalia clade. A Drosophila melanogaster protein, Tay bridge, with a role in neurodevelopment, has been shown to display limited similarity to the C-terminal of AUTS2, suggesting that evolutionary ancestors of the AUTS2 family may exist within other Protostome lineages. Here we present an evolutionary analysis of the AUTS2 family, which highlights ancestral homologs of AUTS2 in multiple Protostome species, implicates AUTS2 as the closest human relative to the progenitor of the AUTS2 family, and demonstrates that Tay bridge is a divergent ortholog of the ancestral AUTS2 progenitor gene. We also define regions of high relative sequence identity, with potential functional significance, shared by the extended AUTS2 protein family. Using structural predictions coupled with sequence conservation and human variant data from 15,708 individuals, a putative domain structure for AUTS2 was produced that can be used to aid interpretation of the consequences of nucleotide variation on protein structure and function in human disease. To assess the role of AUTS2 in human-specific evolution, we recalculated allele frequencies at previously identified human derived sites using large population genome data, and show a high prevalence of ancestral alleles, suggesting that AUTS2 may not be a rapidly evolving gene, as previously thought.

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Role of African swine fever virus (ASFV) proteins EP153R and EP402R in reducing viral persistence and virulence from attenuated BeninΔDP148R

10.1101/2021.04.16.439957 ◽

2021 ◽

Author(s):

Vlad Petrovan ◽

Anusyah Rathakrishnan ◽

Muneeb Islam ◽

Lynnette Goatley ◽

Katy Moffat ◽

...

Keyword(s):

Virus Replication ◽

Vaccine Development ◽

African Swine Fever Virus ◽

Clinical Signs ◽

African Swine Fever ◽

Viral Persistence ◽

Fever Virus ◽

Post Immunization

The limited knowledge on the role of many of the approximately 170 proteins encoded by African swine fever virus restricts progress towards vaccine development. In this study we investigated the effect of deleting combinations of different genes from a previously attenuated virus, BeninΔDP148R on: virus replication in macrophages, virus persistence and clinical signs post immunization, and induction of protection against challenge. Deletion of either EP402R or EP153R genes individually or in combination from BeninΔDP148R did not reduce virus replication in vitro. However, deletion of EP402R dramatically reduced viral persistence in vivo, whilst maintaining high levels of protection against challenge. The additional deletion of EP153R (BeninΔDP148RΔEP153RΔEP402R) further attenuated the virus and no viremia or clinical signs were observed post immunization. This was associated with decreased protection and detection of moderate levels of challenge virus in blood. Interestingly, the deletion of EP153R alone from BeninΔDP148R did not result in further virus attenuation and a slight increase in virus genome copies in blood was observed at different times post immunization when compared with BeninΔDP148R. These results show that EP402R and EP153R have a synergistic role in promoting viremia, however EP153R alone does not seem to have a major impact on virus levels in blood.

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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.

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

Journal of Virology ◽

10.1128/jvi.00212-17 ◽

2017 ◽

Vol 91 (14) ◽

Cited By ~ 50

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.

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Arthropods as potential vectors of African swine fever virus outbreaks on pig farms in the Republic of Korea

10.22541/au.160675931.13136597/v1 ◽

2020 ◽

Author(s):

Hachung Yoon ◽

Seong-Keun Hong ◽

Ilseob Lee ◽

Eune-Seob Lee

Keyword(s):

Genomic Dna ◽

Laboratory Tests ◽

African Swine Fever Virus ◽

African Swine Fever ◽

Chain Reaction ◽

Potential Vector ◽

Pig Farms ◽

Polymerase Chain ◽

The Republic

The seasonality of African swine fever (ASF), with cases concentrated over the summer in Europe, in addition to outbreaks on farms with high levels of biosecurity, suggest that ASF virus (ASFV) may be transmitted by arthropod vectors. In this study, arthropods were collected from Korean pig farms with ASF outbreaks to determine the role of arthropods as a potential vector of ASFV. Arthropods were collected from 14 farms with ASF outbreaks, from September 27 to October 31, 2019. A total of 28,729 arthropods, including 28,508 (99.2%) Diptera, were collected using blacklight traps, insect nets, and yellow sticky strips. All arthropods samples were negative for ASFV genomic DNA according to laboratory tests using real-time polymerase chain reaction. Nevertheless, it is premature to conclude that arthropods do not play any role in ASFV transmission.

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In silicostructural and functional prediction of African swine fever virus protein-B263R reveals features of a TATA-binding protein

PeerJ ◽

10.7717/peerj.4396 ◽

2018 ◽

Vol 6 ◽

pp. e4396 ◽

Cited By ~ 5

Author(s):

Dickson Kinyanyi ◽

George Obiero ◽

George F.O. Obiero ◽

Peris Amwayi ◽

Stephen Mwaniki ◽

...

Keyword(s):

African Swine Fever Virus ◽

Binding Protein ◽

Three Dimensional ◽

African Swine Fever ◽

Tata Binding Protein ◽

Structure And Function ◽

Fever Virus ◽

Dimensional Structure ◽

Three Dimensional Structure ◽

And Function

African swine fever virus (ASFV) is the etiological agent of ASF, a fatal hemorrhagic fever that affects domestic pigs. There is currently no vaccine against ASFV, making it a significant threat to the pork industry. The ASFV genome sequence has been published; however, about half of ASFV open reading frames have not been characterized in terms of their structure and function despite being essential for our understanding of ASFV pathogenicity. The present study reports the three-dimensional structure and function of uncharacterized protein, pB263R (NP_042780.1), an open reading frame found in all ASFV strains. Sequence-based profiling and hidden Markov model search methods were used to identify remote pB263R homologs. Iterative Threading ASSEmbly Refinement (I-TASSER) was used to model the three-dimensional structure of pB263R. The posterior probability of fold family assignment was calculated using TM-fold, and biological function was assigned using TM-site, RaptorXBinding, Gene Ontology, and TM-align. Our results suggests that pB263R has the features of a TATA-binding protein and is thus likely to be involved in viral gene transcription.

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Limbic system hyperactivity and the phenomena of spiritual awakenings. Confronting the supernatural through the neural networks

Humaniora. Czasopismo Internetowe ◽

10.14746/h.2020.1.5 ◽

2020 ◽

Vol 29 (1) ◽

pp. 53-68

Author(s):

Ewelina Nyske

Keyword(s):

Limbic System ◽

Religious Experiences ◽

Spiritual Path ◽

Detailed Classification ◽

Depth Analysis ◽

The Neural Networks ◽

External Stimuli ◽

Spiritual Awakenings

Spiritual awakenings tend to be associated with the religious rapture regardless of the spiritual path one decides to follow and are defined as temporary experiences whose main characteristic is the intensified sense of unity with the sacred. The nature of these particular phenomena gives rise to the need to carry out the in-depth analysis of the human responsiveness pattern in relation to the external stimuli, especially within the context of a religious experience. The limbic system, believed to be the headquarters of human emotions, tends to be easily activated, both verbally and non-verbally, and such activation may influence human behavior to a great extent. The principal objective of this paper is to provide a detailed classification of awakening experiences as well as to focus on the role of the amygdala and hippocampus in the production of particular religious experiences such as spiritual visions, speaking in the tongues or astral projections.

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