Viruses and Bioinformatics from Virology.uvic.ca
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Viruses and Bioinformatics from Virology.uvic.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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Viral pathogen discovery - Current Opinion in Microbiology

Viral pathogen discovery - Current Opinion in Microbiology | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Viral pathogen discovery is of critical importance to clinical microbiology, infectious diseases, and public health. Genomic approaches for pathogen discovery, including consensus polymerase chain reaction (PCR), microarrays, and unbiased next-generation sequencing (NGS), have the capacity to comprehensively identify novel microbes present in clinical samples. Although numerous challenges remain to be addressed, including the bioinformatics analysis and interpretation of large datasets, these technologies have been successful in rapidly identifying emerging outbreak threats, screening vaccines and other biological products for microbial contamination, and discovering novel viruses associated with both acute and chronic illnesses. Downstream studies such as genome assembly, epidemiologic screening, and a culture system or animal model of infection are necessary to establish an association of a candidate pathogen with disease.

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Evidence of the megavirome in humans. [J Clin Virol. 2013] -

We serendipitously detected Mimivirus- and Marseillevirus-like sequences while using a new metagenomic approach targeting bacterial DNA that subsequently led to the isolation of a new member of the family Marseilleviridae, named Senegalvirus, from human stools. This discovery demonstrates the possibility of the presence of giant viruses of amoebae in humans. In addition, we detected sequences related to Megavirales members in several human metagenomes, which adds to previous findings by several groups.

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Malaria: The vector as protector

Malaria: The vector as protector | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Malaria infections are not always lethal. One reason for this may be that transmission from mosquitoes creates malaria parasites that trigger a more protective mammalian immune response.

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Newly discovered virus takes more lives, spreads

Newly discovered virus takes more lives, spreads | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
A new SARS-like virus recently found in humans continues to spread -- with the worldwide total now at 49, the World Health Organization said Wednesday.
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Glycosylations in the Globular Head of the Hemagglutinin Protein Modulate the Virulence and Antigenic Properties of the H1N1 Influenza Viruses

With the global spread of the 2009 pandemic H1N1 (pH1N1) influenza virus, there are increasing worries about evolution through antigenic drift. One way previous seasonal H1N1 and H3N2 influenza strains have evolved over time is by acquiring additional glycosylations in the globular head of their hemagglutinin (HA) proteins; these glycosylations have been believed to shield antigenically relevant regions from antibody immune responses. We added additional HA glycosylation sites to influenza A/Netherlands/602/2009 recombinant (rpH1N1) viruses, reflecting their temporal appearance in previous seasonal H1N1 viruses. Additional glycosylations resulted in substantially attenuated infection in mice and ferrets, whereas deleting HA glycosylation sites from a pre-pandemic virus resulted in increased pathogenicity in mice. We then more directly investigated the interactions of HA glycosylations and antibody responses through mutational analysis. We found that the polyclonal antibody response elicited by wild-type rpH1N1 HA was likely directed against an immunodominant region, which could be shielded by glycosylation at position 144. However, rpH1N1 HA glycosylated at position 144 elicited a broader polyclonal response able to cross-neutralize all wild-type and glycosylation mutant pH1N1 viruses. Moreover, mice infected with a recent seasonal virus in which glycosylation sites were removed elicited antibodies that protected against challenge with the antigenically distant pH1N1 virus. Thus, acquisition of glycosylation sites in the HA of H1N1 human influenza viruses affected not only their pathogenicity and ability to escape from polyclonal antibodies elicited by previous influenza virus strains but also their ability to induce cross-reactive antibodies against drifted antigenic variants

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ScienceDirect.com - Virology - Metagenomic study of the viruses of African straw-coloured fruit bats: Detection of a chiropteran poxvirus and isolation of a novel adenovirus

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Replication modes of Maize streak virus mutants lacking RepA or the RepA–pRBR interaction motif

Replication modes of Maize streak virus mutants lacking RepA or the RepA–pRBR interaction motif | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

The plant-infecting mastreviruses (family Geminiviridae) express two distinct replication-initiator proteins, Rep and RepA. Although RepA is essential for systemic infectivity, little is known about its precise function. We therefore investigated its role in replication using 2D-gel electrophoresis to discriminate the replicative forms of Maize streak virus (MSV) mutants that either fail to express RepA (RepA−), or express RepA that is unable to bind the plant retinoblastoma related protein, pRBR. Whereas amounts of viral DNA were reduced in two pRBR-binding deficient RepA mutants, their repertoires of replicative forms changed only slightly. While a complete lack of RepA expression was also associated with reduced viral DNA titres, the only traces of replicative intermediates of RepA− viruses were those indicative of recombination-dependent replication. We conclude that in MSV, RepA, but not RepA–pRBR binding, is necessary for single-stranded DNA production and efficient rolling circle replication.

  Geminivirus picture courtesy of Russell Kightley Media

Ed Rybicki's insight:

No vested interest.  None at all...B-)

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Evidence of Transstadial and Mechanical Transmission of Lumpy Skin Disease Virus by Amblyomma hebraeum Ticks

Evidence of Transstadial and Mechanical Transmission of Lumpy Skin Disease Virus by Amblyomma hebraeum Ticks | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Lumpy skin disease (LSD) is an economically important disease caused by LSD virus (LSDV), a Capripoxvirus, characterized by fever and circumscribed skin lesions. It is suspected to be transmitted mechanically by biting flies. To assess the vector potential of Amblyomma hebraeum in transmission of LSDV, mechanical/intrastadial and transstadial modes of transmission of the virus by this tick species were investigated.

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Patients leave a microbial mark on hospitals

Patients leave a microbial mark on hospitals | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The microscopic ecosystems in health-care centres mirror those of their patients.
Ed Rybicki's insight:

Do you know what you've left behind?  We can find out...B-)

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Novel Poxvirus in Big Brown Bats, Northwestern United States - Vol. 19 No. 6 - June 2013 - Emerging Infectious Disease journal - CDC

Novel Poxvirus in Big Brown Bats, Northwestern United States - Vol. 19 No. 6 - June 2013 - Emerging Infectious Disease journal - CDC | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
A wildlife hospital and rehabilitation center in northwestern United States received several big brown bats with necrosuppurative osteomyelitis in multiple joints. Wing and joint tissues were positive by PCR for poxvirus.
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What can we predict about viral evolution and emergence? Current Opinion in Virology

Predicting the emergence of infectious diseases has been touted as one of the most important goals of biomedical science, with an array of funding schemes and research projects. However, evolutionary biology generally has a dim view of prediction, and there is a danger that erroneous predictions will mean a misuse of resources and undermine public confidence. Herein, I outline what can be realistically predicted about viral evolution and emergence, argue that any success in predicting what may emerge is likely to be limited, but that forecasting how viruses might evolve and spread following emergence is more tractable. I also emphasize that a properly grounded research program in disease prediction must involve a synthesis of ecological and genetic perspectives

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PLOS Pathogens: Prolonged Influenza Virus Shedding and Emergence of Antiviral Resistance in Immunocompromised Patients and Ferrets

PLOS Pathogens: Prolonged Influenza Virus Shedding and Emergence of Antiviral Resistance in Immunocompromised Patients and Ferrets | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
From molecules to physiology
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New insights into the evolution of Entomopoxvirinae from the complete genome sequences of four entomopoxviruses infecting Adoxophyes honmai, Choristoneura biennis, Choristoneura rosaceana and Mythi...

Poxviruses are nucleocytoplasmic large DNA viruses encompassing two subfamilies, the Chordopoxvirinae and the Entomopoxvirinae, infecting vertebrates and insects, respectively. While chordopoxvirus genomics have been widely studied, only two entomopoxvirus (EPV) genomes have been entirely sequenced. We report the genome sequences of four EPVs of the Betaentomopoxvirus genus infecting the Lepidoptera: Adoxophyes honmai (AHEV), Choristoneura biennis (CBEV), Choristoneura rosaceana (CREV) and Mythimna separata (MySEV). The genomes are 80% AT-rich, are 228-307kbp in length and contain 247-334 ORFs. Most genes are homologous to those of Amsacta moorei entomopoxvirus and encode several protein families repeated in tandem in terminal regions. Some genomes also encode proteins of unknown functions with similarity to other insect viruses. Comparative genomic analyses highlight a high colinearity among the lepidopteran EPV genomes and little gene order conservation with other poxvirus genomes.

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Protection against lethal influenza with a viral mimic

Despite countermeasures against influenza virus that prevent (vaccines) and treat (antivirals) infection, this upper respiratory human pathogen remains a global health burden, causing both seasonal epidemics and occasional pandemics. More potent and safe new vaccine technologies would contribute significantly to the battle against influenza and other respiratory infections. Using plasmid-based reverse genetics techniques, we have developed a single-cycle infectiousInfluenza Virus (sciIV) with immunoprotective potential. In our sciIV approach, the fourth viral segment, which encodes for the receptor-binding and fusion protein hemagglutinin (HA), has been removed. Thus upon infection of normal cells, although no infectious progeny are produced, the expression of other viral proteins occurs and is immunogenic. Consequently, sciIV is protective against influenza homologous and heterologous viral challenges in a mouse model. Vaccination with sciIV protects in a dose- and replication-dependent manner, which is attributed to both humoral responses and T cells. Safety, immunogenicity and protection conferred by sciIV vaccination were also demonstrated in ferrets, where this immunization additionally blocked direct and aerosol transmission events. Altogether, our studies suggest that sciIV may have potential as a broadly protective vaccine against influenza virus.

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As Outbreak Continues, Confusion Reigns Over Virus Patents - ScienceInsider

As Outbreak Continues, Confusion Reigns Over Virus Patents - ScienceInsider | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Are Dutch scientists hampering the fight against a lethal new coronavirus by patenting the virus and making it needlessly difficult for other scientists to study it? Accusations to that effect were flying last week at the World Health Assembly (WHA), the annual meeting of the world's health ministers in Geneva, Switzerland. Margaret Chan, the director-general of the World Health Organization (WHO), used strong words in an apparent attack on virologist Ron Fouchier and his colleagues at Erasmus MC in Rotterdam, the Netherlands.

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Hybrid DNA virus in Chinese patients with seronegative hepatitis discovered by deep sequencing

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A remarkable synergistic effect at the transcriptomic level in peach fruits doubly infected by prunus necrotic ringspot virus and peach latent mosaic viroid

Our results identify a novel synergistic effect of PLMVd and PNRSV on the transcriptome of peach fruits. We demonstrate that mixed infections, which occur frequently in field conditions, result in a more complex transcriptional response than that observed in single infections. Thus, our data demonstrate for the first time that the simultaneous infection of a viroid and a plant virus synergistically affect the host transcriptome in infected peach fruits. These field studies can help to fully understand plant-pathogen interactions and to develop appropriate crop protection strategies.

 
Ed Rybicki's insight:

Who knew such simple things could interact in such a complex manner?  And so MANY plant diseases are caused by more than one agent.  Pity no-one really funds this kind of work much...otherwise I'd still be doing it!

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PLOS ONE: Real Time Classification of Viruses in 12 Dimensions

PLOS ONE: Real Time Classification of Viruses in 12 Dimensions | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Abstract

The International Committee on Taxonomy of Viruses authorizes and organizes the taxonomic classification of viruses. Thus far, the detailed classifications for all viruses are neither complete nor free from dispute. For example, the current missing label rates in GenBank are 12.1% for family label and 30.0% for genus label. Using the proposed Natural Vector representation, all 2,044 single-segment referenced viral genomes in GenBank can be embedded in . Unlike other approaches, this allows us to determine phylogenetic relations for all viruses at any level (e.g., Baltimore class, family, subfamily, genus, and species) in real time. Additionally, the proposed graphical representation for virus phylogeny provides a visualization of the distribution of viruses in . Unlike the commonly used tree visualization methods which suffer from uniqueness and existence problems, our representation always exists and is unique. This approach is successfully used to predict and correct viral classification information, as well as to identify viral origins; e.g. a recent public health threat, the West Nile virus, is closer to the Japanese encephalitis antigenic complex based on our visualization. Based on cross-validation results, the accuracy rates of our predictions are as high as 98.2% for Baltimore class labels, 96.6% for family labels, 99.7% for subfamily labels and 97.2% for genus labels.

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Drug Resistance Confirmed in H7N9 Flu Cases

Drug Resistance Confirmed in H7N9 Flu Cases | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Chinese researchers reported, for the first time, clinical evidence of oseltamivir (Tamiflu) resistance in patients infected with the novel avian H7N9 flu.
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Hunt for broad-spectrum vaccine: PNAG on more microbes than previously thought

Hunt for broad-spectrum vaccine: PNAG on more microbes than previously thought | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Researchers at the Brigham and Women’s Hospital (BWH), Harvard Medical School, have reported that a sugar polymer known as PNAG (or rather beta-1-6-linked poly-N-acetyl glucosamine) is made by more bacterial, fungal and other microbial organisms than previously thought – and the fact that it’s common to several pathogens makes it a promising target for a broad-spectrum vaccine.

 

 

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Emerging tools for synthetic genome design

Emerging tools for synthetic genome design | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Fortunately, our ability to quickly and accurately engineer biological systems that behave predictably has been dramatically expanded by significant advances in DNA-sequencing, DNA-synthesis, and DNA-editing technologies. Here, we review emerging technologies and methodologies in the field of building designed biological systems, and we discuss their future perspectives.

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HIV weak spot found in Scripps-led study

HIV weak spot found in Scripps-led study | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
A weak spot of HIV is far larger once thought, giving more targets for an AIDS vaccine.
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PLOS Neglected Tropical Diseases: Microbial Translocation Is Associated with Extensive Immune Activation in Dengue Virus Infected Patients with Severe Disease

PLOS Neglected Tropical Diseases: Microbial Translocation Is Associated with Extensive Immune Activation in Dengue Virus Infected Patients with Severe Disease | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
PLOS Neglected Tropical Diseases is an open-access journal publishing peer-reviewed research on the world\'s most neglected tropical diseases, such as elephantiasis, river blindness, leprosy, hookworm, schistosomiasis, and African sleeping sickness...
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