Viruses, Immunology & Bioinformatics from Virology.uvic.ca
98.7K views | +6 today
Follow
Viruses, Immunology & Bioinformatics from Virology.uvic.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
Your new post is loading...
Your new post is loading...
Scooped by Cindy
Scoop.it!

A Next-Generation Sequencing Approach Uncovers Viral Transcripts Incorporated in Poxvirus Virions

A Next-Generation Sequencing Approach Uncovers Viral Transcripts Incorporated in Poxvirus Virions | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Transcripts are known to be incorporated in particles of DNA viruses belonging to the families of Herpesviridae and Mimiviridae, but the presence of transcripts in other DNA viruses, such as poxviruses, has not been analyzed yet. Therefore, we first established a next-generation-sequencing (NGS)-based protocol, enabling the unbiased identification of transcripts in virus particles. Subsequently, we applied our protocol to analyze RNA in an emerging zoonotic member of the Poxviridae family, namely Cowpox virus. Our results revealed the incorporation of 19 viral transcripts, while host identifications were restricted to ribosomal and mitochondrial RNA. Most viral transcripts had an unknown and immunomodulatory function, suggesting that transcript incorporation may be beneficial for poxvirus immune evasion. Notably, the most abundant transcript originated from the D5L/I1R gene that encodes a viral inhibitor of the host cytoplasmic DNA sensing machinery.
more...
No comment yet.
Scooped by Cindy
Scoop.it!

Vaccinia virus encodes a novel inhibitor of apoptosis that associates with the apoptosome.

Apoptosis selectively eliminates dangerous cells such as virus-infected cells. Poxviruses express apoptosis antagonists to neutralize this anti-viral host defense. The vaccinia virus (VACV) M1 ankyrin (ANK) protein, a protein with no previously ascribed function, inhibits apoptosis. M1 interacts with the apoptosome and prevents procaspase-9 processing as well as downstream procaspase-3 cleavage in several cell types and under multiple conditions. M1 is the first poxviral protein reported to associate with and prevent the function of the apoptosome, giving a more detailed picture of the threats VACV encounters during infection. Dysregulation of apoptosis is associated with several human diseases. One potential treatment of apoptosis-related diseases is through the use of designed ANK repeat proteins (DARPins), similar to M1, as caspase inhibitors. Thus, the study of the novel anti-apoptosis effects of M1 via apoptosome association will be helpful for understanding how to control apoptosis using either natural or synthetic molecules.
more...
No comment yet.
Scooped by Cindy
Scoop.it!

Poxviruses Utilize Multiple Strategies to Inhibit Apoptosis

Poxviruses Utilize Multiple Strategies to Inhibit Apoptosis | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Cells have multiple means to induce apoptosis in response to viral infection. Poxviruses must prevent activation of cellular apoptosis to ensure successful replication. These viruses devote a substantial portion of their genome to immune evasion. Many of these immune evasion products expressed during infection antagonize cellular apoptotic pathways. Poxvirus products target multiple points in both the extrinsic and intrinsic apoptotic pathways, thereby mitigating apoptosis during infection. Interestingly, recent evidence indicates that poxviruses also hijack cellular means of eliminating apoptotic bodies as a means to spread cell to cell through a process called apoptotic mimicry. Poxviruses are the causative agent of many human and veterinary diseases. Further, there is substantial interest in developing these viruses as vectors for a variety of uses including vaccine delivery and as oncolytic viruses to treat certain human cancers. Therefore, an understanding of the molecular mechanisms through which poxviruses regulate the cellular apoptotic pathways remains a top research priority. In this review, we consider anti-apoptotic strategies of poxviruses focusing on three relevant poxvirus genera: Orthopoxvirus, Molluscipoxvirus, and Leporipoxvirus. All three genera express multiple products to inhibit both extrinsic and intrinsic apoptotic pathways with many of these products required for virulence
more...
No comment yet.
Scooped by Cindy
Scoop.it!

A bioinformatics pipeline to search functional motifs within whole-proteome data: a case study of poxviruses

Proteins harbor domains or short linear motifs, which facilitate their functions and interactions. Finding functional motifs in protein sequences could predict the putative cellular roles or characteristics of hypothetical proteins. In this study, we present Shetti-Motif, which is an interactive tool to (i) map UniProt and PROSITE flat files, (ii) search for multiple pre-defined consensus patterns or experimentally validated functional motifs in large datasets protein sequences (proteome-wide), (iii) search for motifs containing repeated residues (low-complexity regions, e.g., Leu-, SR-, PEST-rich motifs, etc.). As proof of principle, using this comparative proteomics pipeline, eleven proteomes encoded by member of Poxviridae family were searched against about 100 experimentally validated functional motifs. The closely related viruses and viruses infect the same host cells (e.g. vaccinia and variola viruses) show similar motif-containing proteins profile. The motifs encoded by these viruses are correlated, which explains why poxviruses are able to interact with wide range of host cells. In conclusion, this in silico analysis is useful to establish a dataset(s) or potential proteins for further investigation or compare between species.
more...
No comment yet.
Scooped by Cindy
Scoop.it!

Genetic Variability of Myxoma Virus Genomes

IMPORTANCE Myxoma virus (MYXV) is pathogenic for European rabbits and two North American species. Due to sophisticated strategies in immune evasion and oncolysis, MYXV is an important model virus for immunological and pathological research. In its natural hosts, MYXV causes a benign infection, whereas in European rabbits, it causes the lethal disease myxomatosis. Since the introduction of MYXV into Australia and Europe for the biological control of European rabbits in the 1950s, a coevolution of host and pathogen has started, selecting for attenuated virus strains and increased resistance in rabbits. Evolution of viruses is a continuous process and influences the protective potential of vaccines. In our analyses, we sequenced 6 MYXV field, challenge, and vaccine strains. We focused on genes encoding proteins involved in virulence, host range, immunomodulation, and envelope composition. Genes affected most by mutations play a role in immunomodulation. However, attenuation cannot be linked to individual mutations or gene disruptions.
more...
No comment yet.
Scooped by Cindy
Scoop.it!

Recombinant Sheep Pox Virus Proteins Elicit Neutralizing Antibodies

The aim of this work was to evaluate the immunogenicity and neutralizing activity of sheep pox virus (SPPV; genus Capripoxvirus, family Poxviridae) structural proteins as candidate subunit vaccines to control sheep pox disease. SPPV structural proteins were identified by sequence homology with proteins of vaccinia virus (VACV) strain Copenhagen. Four SPPV proteins (SPPV-ORF 060, SPPV-ORF 095, SPPV-ORF 117, and SPPV-ORF 122), orthologs of immunodominant L1, A4, A27, and A33 VACV proteins, respectively, were produced in Escherichia coli. Western blot analysis revealed the antigenic and immunogenic properties of SPPV-060, SPPV-095, SPPV-117 and SPPV-122 proteins when injected with adjuvant into experimental rabbits. Virus-neutralizing activity against SPPV in lamb kidney cell culture was detected for polyclonal antisera raised to SPPV-060, SPPV-117, and SPPV-122 proteins. To our knowledge, this is the first report demonstrating the virus-neutralizing activities of antisera raised to SPPV-060, SPPV-117, and SPPV-122 proteins.
more...
No comment yet.
Scooped by Cindy
Scoop.it!

Domain Organization of Vaccinia Virus Helicase-Primase D5

IMPORTANCE Since the beginning of the 1980s, research on the vaccinia virus replication mechanism has basically stalled due to the absence of structural information. As a result, this important class of pathogens is less well understood than most other viruses. This lack of information concerns in general viruses of the NCLDV clade, which use a superfamily 3 helicase for replication, as do poxviruses. Here we provide for the first time information about the domain structure and DNA-binding activity of D5, the poxvirus helicase-primase. This result not only refines the current model of the poxvirus replication fork but also will lead in the long run to a structural basis for antiviral drug design.
more...
No comment yet.
Scooped by Cindy
Scoop.it!

The vaccinia virus H3 envelope protein, a major target of neutralizing antibodies, exhibits a glycosyltransferase fold and binds UDP-Glucose

The highly conserved H3 poxvirus protein is a major target of the human antibody response against poxviruses and is likely a key contributor to protection against infection. Here, we present the crystal structure of H3 from vaccinia virus at 1.9Å resolution. H3 looks like a glycosyltransferase, a family of enzymes that transfer carbohydrate molecules to a variety of acceptor substrates. Like glycosyltransferases, H3 binds UDP-glucose as shown by saturation transfer difference (STD) NMR spectroscopy and this binding requires Mg2+. Mutating the glycosyltransferase-like metal ion-binding motif in H3 greatly diminished its binding to UDP-glucose. We found by flow cytometry that H3 binds to the surface of human cells, but does not bind well to cells that are deficient in surface glycosaminoglycans. STD NMR experiments using a heparin sulfate decasaccharide confirmed that H3 binds heparin sulfate. We propose that a surface of H3 with an excess of positive charge may be the binding site for heparin. Heparin binding and glycosyltransferase activity may be involved in the function of H3 in the poxvirus lifecycle.
more...
No comment yet.
Scooped by Cindy
Scoop.it!

T Cell Inactivation by Poxviral B22 Family Proteins Increases Viral Virulence

T Cell Inactivation by Poxviral B22 Family Proteins Increases Viral Virulence | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

B22 gene encodes the largest poxvirus protein. Previously unknown in functions, now revealed to take part in T-Cell inactivation to increase viral virulence!

more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Prediction of Steps in the Evolution of Variola Virus Host Range

Prediction of Steps in the Evolution of Variola Virus Host Range | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

Variola virus, the agent of smallpox, has a severely restricted host range (humans) but a devastatingly high mortality rate. Although smallpox has been eradicated by a World Health Organization vaccination program, knowledge of the evolutionary processes by which human super-pathogens such as variola virus arise is important. By analyzing the evolution of variola and other closely related poxviruses at the level of single nucleotide polymorphisms we detected a hotspot of genome variation within the smallpox ortholog of the vaccinia virus O1L gene, which is known to be necessary for efficient replication of vaccinia virus in human cells. These mutations in the variola virus ortholog and the subsequent loss of the functional gene from camelpox virus and taterapox virus, the two closest relatives of variola virus, strongly suggest that changes within this region of the genome may have played a key role in the switch to humans as a host for the ancestral virus and the subsequent host-range restriction that must have occurred to create the phenotype exhibited by smallpox.

more...
No comment yet.
Scooped by Kenzibit
Scoop.it!

Poxvirus Cell Entry: How Many Proteins Does it Take?

For many viruses, one or two proteins enable cell binding, membrane fusion and entry. The large number of proteins employed by poxviruses is unprecedented and may be related to their ability to infect a wide range of cells.
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

A retrospective study of the orthopoxvirus molecular evolution

A retrospective study of the orthopoxvirus molecular evolution | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

The data on the structure of conserved genes of the Old and New World orthopoxviruses and unclassified Yoka poxvirus were used for a Bayesian dating of their independent evolution. This reconstruction estimates the time when an orthopoxvirus ancestor was transferred to the North American continent as approximately 50 thousand years ago (TYA) and allows for relation of this time interval with the global climate changes (with one of the short-term warmings during the Last Ice Age).

more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Biological Characterization and Next-Generation Genome Sequencing of the Unclassified Cotia Virus SPAn232 (Poxviridae)

Cotia virus (COTV) SPAn232 was isolated in 1961 from sentinel mice at Cotia field station, São Paulo, Brazil. Attempts to classify COTV within a recognized genus of the Poxviridae have generated contradictory findings.

more...
No comment yet.
Scooped by Cindy
Scoop.it!

Poxvirus Host Range Genes and Virus–Host Spectrum: A Critical Review

Poxvirus Host Range Genes and Virus–Host Spectrum: A Critical Review | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The Poxviridae family is comprised of double-stranded DNA viruses belonging to nucleocytoplasmic large DNA viruses (NCLDV). Among the NCLDV, poxviruses exhibit the widest known host range, which is likely observed because this viral family has been more heavily investigated. However, relative to each member of the Poxviridae family, the spectrum of the host is variable, where certain viruses can infect a large range of hosts, while others are restricted to only one host species. It has been suggested that the variability in host spectrum among poxviruses is linked with the presence or absence of some host range genes. Would it be possible to extrapolate the restriction of viral replication in a specific cell lineage to an animal, a far more complex organism? In this study, we compare and discuss the relationship between the host range of poxvirus species and the abundance/diversity of host range genes. We analyzed the sequences of 38 previously identified and putative homologs of poxvirus host range genes, and updated these data with deposited sequences of new poxvirus genomes. Overall, the term host range genes might not be the most appropriate for these genes, since no correlation between them and the viruses’ host spectrum was observed, and a change in nomenclature should be considered. Finally, we analyzed the evolutionary history of these genes, and reaffirmed the occurrence of horizontal gene transfer (HGT) for certain elements, as previously suggested. Considering the data presented in this study, it is not possible to associate the diversity of host range factors with the amount of hosts of known poxviruses, and this traditional nomenclature creates misunderstandings.
more...
No comment yet.
Scooped by Cindy
Scoop.it!

Next step in the ongoing arms race between myxoma virus and wild rabbits in Australia is a novel disease phenotype

In host–pathogen arms races, increases in host resistance prompt counteradaptation by pathogens, but the nature of that counteradaptation is seldom directly observed outside of laboratory models. The best-documented field example is the coevolution of myxoma virus (MYXV) in European rabbits. To understand how MYXV in Australia has continued to evolve in wild rabbits under intense selection for genetic resistance to myxomatosis, we compared the phenotypes of the progenitor MYXV and viral isolates from the 1950s and the 1990s in laboratory rabbits with no resistance. Strikingly, and unlike their 1950s counterparts, most virus isolates from the 1990s induced a highly lethal immune collapse syndrome similar to septic shock. Thus, the next step in this canonical case of coevolution after a species jump has been further escalation by the virus in the face of widespread host resistance.
more...
No comment yet.
Scooped by Cindy
Scoop.it!

A virus with a green thumb

A virus with a green thumb | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
I just love it when long standing mysteries in virology are suddenly solved, typically by the use of new technologies. In this story, the long standing mystery was why poxvirus mRNAs have a stretch of poly(A) in their 5′-noncoding regions. The answer is that it allows the ribosome to preferentially translate these viral mRNAs over those of the host
more...
No comment yet.
Scooped by Cindy
Scoop.it!

Emergence of a Viral RNA Polymerase Variant during Gene Copy Number Amplification Promotes Rapid Evolution of Vaccinia Virus

IMPORTANCE Viruses can evolve quickly to defeat host immune functions. For poxviruses, little is known about how multiple adaptive mutations emerge in populations at the same time. In this study, we uncovered a means of vaccinia virus adaptation involving the accumulation of distinct genetic variants within a single population. We identified adaptive point mutations in the viral RNA polymerase gene A24R and, surprisingly, found that one of these mutations activates the nucleic acid sensing factor PKR. We also found that gene copy number variation (CNV) can provide dual benefits to evolving virus populations, including evidence that CNV facilitates the accumulation of a point mutation distant from the expanded locus. Our data suggest that transient CNV can accelerate the fixation of mutations conferring modest benefits, or even fitness trade-offs, and highlight how structural variation might aid poxvirus adaptation through both direct and indirect actions.
more...
No comment yet.
Scooped by Cindy
Scoop.it!

Ectromelia Virus Disease Characterization in the BALB/c Mouse: A Surrogate Model for Assessment of Smallpox Medical Countermeasures

In 2007, the United States– Food and Drug Administration (FDA) issued guidance concerning animal models for testing the efficacy of medical countermeasures against variola virus (VARV), the etiologic agent for smallpox. Ectromelia virus (ECTV) is naturally-occurring and responsible for severe mortality and morbidity as a result of mousepox disease in the murine model, displaying similarities to variola infection in humans. Due to the increased need of acceptable surrogate animal models for poxvirus disease, we have characterized ECTV infection in the BALB/c mouse. Mice were inoculated intranasally with a high lethal dose (125 PFU) of ECTV, resulting in complete mortality 10 days after infection. Decreases in weight and temperature from baseline were observed eight to nine days following infection. Viral titers via quantitative polymerase chain reaction (qPCR) and plaque assay were first observed in the blood at 4.5 days post-infection and in tissue (spleen and liver) at 3.5 days post-infection. Adverse clinical signs of disease were first observed four and five days post-infection, with severe signs occurring on day 7. Pathological changes consistent with ECTV infection were first observed five days after infection. Examination of data obtained from these parameters suggests the ECTV BALB/c model is suitable for potential use in medical countermeasures (MCMs) development and efficacy testing.
more...
No comment yet.
Scooped by Cindy
Scoop.it!

Both CD8+ and CD4+ T-Cells Contribute to Corneal Clouding and Viral Clearance Following Vaccinia Virus Infection in C57BL/6 Mice

Potentially blinding eye infections can occur after vaccination for Smallpox. Very little is known about the pathologic mechanisms that are involved and the information that is available was generated using rabbit models. The lack of immunological reagents for rabbits makes such studies difficult. We have characterized a mouse model of vaccinia virus ocular disease using C57BL/6 mice and strain WR and show that both CD4+ and CD8+ T-cell subsets play a role in the blinding eye disease and controlling virus replication. Based on these results vaccinia virus keratitis is significantly different from Herpes simplex virus keratitis and further studies using this model should generate novel insights into immunopathological responses to viral ocular infection.
more...
No comment yet.
Scooped by Cindy
Scoop.it!

Molluscum Contagiosum Virus Transcriptome in Abortively Infected Cultured Cells and a Human Skin Lesion

IMPORTANCE The inability to propagate molluscum contagiosum virus, which causes benign skin lesions in young children and more extensive infections in immunosuppressed adults, has constrained our understanding of the biology of this human-specific virus. In the present study, we characterized the RNAs synthesized in abortively infected cultured cells and a human skin lesion by next-generation sequencing. These studies provided an initial transcription map of the MOCV genome, suggested temporal regulation of gene expression, and indicated that the in vitro replication block occurs prior to intermediate and late gene expression. RNA-seq and reporter assays, as described here, may help to further evaluate MOCV gene expression and define conditions that could enable MOCV replication in vitro.
more...
No comment yet.
Scooped by Cindy
Scoop.it!

Redundancy complicates the definition of essential genes for vaccinia virus

Redundancy complicates the definition of essential genes for vaccinia virus | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Vaccinia virus (VACV) genes are characterized as either essential or non-essential for growth in culture. It seems intuitively obvious that if a gene can be deleted without imparting a growth defect in vitro it does not have a function related to basic replication or spread. However, this interpretation relies on the untested assumption that there is no redundancy across the genes that have roles in growth in cell culture. First, we provide a comprehensive summary of the literature that describes the essential genes of VACV. Next, we looked for interactions between large blocks of non-essential genes located at the ends of the genome by investigating sets of VACVs with large deletions at the genomic termini. Viruses with deletions at either end of the genome behaved as expected, exhibiting only mild or host-range defects. In contrast, combining deletions at both ends of the genome for the VACV Western Reserve (WR) strain caused a devastating growth defect on all cell lines tested. Unexpectedly, we found that the well-studied VACV growth factor homologue encoded by C11R has a role in growth in vitro that is exposed when 42 genes are absent from the left end of the VACV WR genome. These results demonstrate that some non-essential genes contribute to basic viral growth, but redundancy means these functions are not revealed by single-gene-deletion mutants.
more...
No comment yet.
Scooped by natashai
Scoop.it!

Genomic analysis of vaccinia virus strain TianTan provides new insights into the evolution and evolutionary relationships between Orthopoxviruses

Genomic analysis of vaccinia virus strain TianTan provides new insights into the evolution and evolutionary relationships between Orthopoxviruses | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

Vaccinia virus (VACV) strain TianTan was used for much of China's modern history to vaccinate against smallpox, however the only genome sequence contains errors. We have sequenced additional examples of TianTan to obtain a better picture of this important virus. We detected two different subclones. One (TP03) encodes large deletions in the terminal repeats that extend into both VEGF genes and create a small plaque variant. The second clone (TP05) encodes a nearly intact complement of genes in the terminal repeats, except for an insertion of sequences resembling the telomeric 69 bp repeats. The TP05 genome spans 196,260 bp and encodes 219 genes. The revised sequence documents the integrity of all the genes in the conserved virus core. Phylogenetic methods show that TianTan belongs to a unique clade of VACV, but probably also share a common origin with strains belonging to the Copenhagen/Lister lineage and distinct from the Wyeth/Dryvax lineage.

more...
No comment yet.
Scooped by Chad Smithson
Scoop.it!

Orthopoxvirus variola infection of Cynomys ludovicianus (North American Black tailed prairie dog)

Orthopoxvirus variola infection of Cynomys ludovicianus (North American Black tailed prairie dog) | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

Prairie dogs infected with Orthopoxvirus monkeypox present with a clinical scenario similar to ordinary smallpox, including prodrome, rash, and high mortality. This study examines if Black-tailed prairie dogs can become infected with O. variola and serve as a surrogate model for the study of human smallpox disease.

more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

TWiV 198: Pox has got a squeeze-box, seals are ... - Virology Blog

TWiV 198: Pox has got a squeeze-box, seals are ... - Virology Blog | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Vincent, Alan, Rich, and Kathy review fatal avian influenza virus in harbor seals, and poxvirus deployment of genomic accordions to counter antiviral defenses.
more...
No comment yet.
Scooped by Jeff Habig
Scoop.it!

TWiV 181: ORFan poxviruses and nIRFing prions

TWiV 181: ORFan poxviruses and nIRFing prions | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Vincent, Rich, and Kathy discuss Cotia virus, a new poxvirus, Orf virus infections associated with handling goats and lamb, and the innate immune response to prions.
more...
No comment yet.