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Isolation of a novel herpesvirus from a Pacific white-sided dolphin - Online First - Springer

Isolation of a novel herpesvirus from a Pacific white-sided dolphin - Online First - Springer | Virology and Bioinformatics from Virology.ca | Scoop.it

During establishment of primary cell culture from the kidney of a dead Pacific white-sided dolphin (Lagenorhynchus obliquidens), a cytopathic effect was observed. Polymerase chain reaction with a set of herpesvirus consensus primers yielded a fragment of the expected size. Nucleotide sequencing of the product indicated that the isolated virus was closely related to an alphaherpesvirus detected in a bottlenose dolphin in the United States, but the sequence identity at the protein level was low (86.6 %). Phylogenetic analysis of the encoded sequence confirmed that the new isolate belonged to the subfamily Alphaherpesvirinae and clustered together with other cetacean alphaherpesviruses. The complete gene encoding glycoprotein B (2,757 bp) was amplified from the novel isolate; the encoded protein was compared with the corresponding protein of other herpesviruses, revealing that this virus belongs to the genus Varicellovirus. Taken together, these results suggest that this virus corresponds to a novel herpesvirus capable of infecting Pacific white-sided dolphins.

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Virology and Bioinformatics from Virology.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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It's a group effort - the curators:

It's a group effort - the curators: | Virology and Bioinformatics from Virology.ca | Scoop.it

get in touch if you want to help curate this topic

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Bemol Sido's comment, October 10, 2015 5:28 AM
Thanks. Nice.
Bwana Moses's comment, May 25, 6:13 AM
Great work. Keep it going.
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New Virus Breaks The Rules Of Infection

New Virus Breaks The Rules Of Infection | Virology and Bioinformatics from Virology.ca | Scoop.it
A virus is generally like a little ball with a few genes. Now scientists have found one that's broken up into five little balls — as if it were dismembered.

Via Ian M Mackay, PhD
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Swine flu virus in India 'has become more virulent' since 2009 outbreak

Swine flu virus in India 'has become more virulent' since 2009 outbreak | Virology and Bioinformatics from Virology.ca | Scoop.it
Since December 2014, swine flu has claimed the lives of over 1,300 people in India, making it the worst outbreak of the virus in the country since 2009.
Via Ed Rybicki
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New kind of substances inhibits viruses and bacteria

New kind of substances inhibits viruses and bacteria | Virology and Bioinformatics from Virology.ca | Scoop.it

A new class of substances is effective against both the AIDS pathogen, HIV, and antibiotics-resistant MRSA bacteria. These two pathogensoften occur together. Scientists hope that it may be possible to control them with a single drug in the future. Scientists of the Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) developed so-called dual agents that inhibit the growth of both types of pathogens. They describe their findings in the renowned Journal of Medicinal Chemistry. The HIPS is the Saarbrücken branch of the Helmholtz Centre for Infection Research (HZI), which has its headquarters in Braunschweig. It was founded jointly by the HZI and Saarland University in 2009.

 

The human immunodeficiency virus HIV is one of the most dangerous and widespreadpathogens throughout the world. Some 37 million people are host to the virus and 1.2 million were killed by this disease in 2014 alone. Meanwhile, both the proliferation of the pathogen and the progression of the disease can be halted through a combination therapy, but the viruses show an increasing trend to develop resistance and no longer respond to the medications used against them.

 

The notorious MRSA bacteria, i.e. methicillin-resistant Staphylococcus aureus strains, show similar persistence as many common antibiotics have become ineffective. HIV patients, whose immune systemhas already been weakened by the disease, are often additionally afflicted by MRSA pathogens. These co-infections are very problematic and difficult to treat. "Resistance to the common therapies is quite widespread amongst both the viruses and the MRSA bacteria, which means that the co-infection is very difficult to control," explains HZI scientist Prof Rolf Hartmann, who is the head of the "Drug Design and Optimization" department at the HIPS. "In addition, it is necessary to carefully consider the interactions between the medications given to the patients."


Via Dr. Stefan Gruenwald
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Virus hunters search for the next deadly outbreak

Virus hunters search for the next deadly outbreak | Virology and Bioinformatics from Virology.ca | Scoop.it
Meet the researchers who enter the depths of the earth in search of deadly pathogens with the potential to cause outbreaks.

Via Ian M Mackay, PhD, Ed Rybicki
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Ed Rybicki's curator insight, August 25, 10:41 AM
And here in South Africa, what's more!! Although as a former explorer of bat-infested caves, I think rats may be a better target?
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Non-selective Packaging of Rift Valley Fever Virus Genome Segments

Author Summary The bunyavirus family is one of the largest virus families on Earth, of which several members cause severe disease in humans, animals or plants. Little is known about the mechanisms that facilitate the production of infectious bunyavirus virions, which should contain at least one copy of the small (S), medium (M) and large (L) genome segment. In this study, we investigated the genome packaging process of the Rift Valley fever virus (RVFV) by visualizing individual genome segments inside infected cells and virions. Experiments performed with wild-type virus, two- and four-segmented variants, and a variant with a codon-shuffled M segment showed that the production of infectious virions is a non-selective process and is unlikely to involve the formation of a supramolecular viral RNA complex. These observations have broad implications for understanding the bunyavirus replication cycle and may facilitate the development of new vaccines and the identification of novel antiviral targets.
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So: pretty much random, then? Interesting!
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Exploring the virome of diseased horses

Exploring the virome of diseased horses | Virology and Bioinformatics from Virology.ca | Scoop.it
Metagenomics was used to characterize viral genomes in clinical specimens of horses with various organ-specific diseases of unknown aetiology. A novel parvovirus as well as a previously described hepacivirus closely related to human hepatitis C viru

Via Bradford Condon
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Zika Virus: Two or Three Lineages?

Zika Virus: Two or Three Lineages? | Virology and Bioinformatics from Virology.ca | Scoop.it

Via Ed Rybicki
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Ed Rybicki's curator insight, August 23, 9:54 AM
This is interesting for a number of reasons: one, because it nails down slightly more convincingly where Zika came from; two, because it introduces the concept of a wider range of genotypes than we knew about; three, because vaccines that might be expected to protect against Asian and African 1 types, might conceivably not protect against African II. And given the lesson of dengue types and vaccines and the potential for ADE, that might not be a good thing....
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Fc receptors in antibody-dependent enhancement of viral infections - Taylor - 2015 - Immunological Reviews - Wiley Online Library

Fc receptors in antibody-dependent enhancement of viral infections - Taylor - 2015 - Immunological Reviews - Wiley Online Library | Virology and Bioinformatics from Virology.ca | Scoop.it

Via Gilbert C FAURE, Kenzibit
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Analysis of cis and trans Requirements for DNA Replication at the Right-End Hairpin of the Human Bocavirus 1 Genome

Analysis of cis and trans Requirements for DNA Replication at the Right-End Hairpin of the Human Bocavirus 1 Genome | Virology and Bioinformatics from Virology.ca | Scoop.it
IMPORTANCE Human bocavirus 1 (HBoV1) causes acute respiratory tract infections in young children. The duplex HBoV1 genome replicates in HEK293 cells and produces progeny virions that are infectious in well-differentiated airway epithelial cells. A recombinant AAV2 vector pseudotyped with an HBoV1 capsid has been developed to efficiently deliver the cystic fibrosis transmembrane conductance regulator gene to human airway epithelia. Here, we identified both cis-acting elements and trans-acting proteins that are required for HBoV1 DNA replication at the right-end hairpin in HEK293 cells. We localized the minimal replication origin, which contains both NS1 nicking and binding sites, to a 46-nucleotide sequence in the right-end hairpin. The identification of these essential elements of HBoV1 DNA replication acting both in cis and in trans will provide guidance to develop antiviral strategies targeting viral DNA replication at the right-end hairpin and to design next-generation recombinant HBoV1 vectors, a promising tool for gene therapy of lung diseases.

Ed Rybicki's insight:
Interesting because it throws a little doubt into long-established models of parvovirus replication - because it's an autonomously-replicating virus
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Could SMALLPOX return from the grave?

Could SMALLPOX return from the grave? | Virology and Bioinformatics from Virology.ca | Scoop.it
Scientists are worried that the deadly disease smallpox could return because permafrost is melting close to where hundreds of infected bodies were buried in Siberia, Russia.

Via Ian M Mackay, PhD
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Ed Rybicki's curator insight, August 17, 4:08 AM
Ya. No. I am willing to bet the possibility of there being any viable virus there is so small as to be no chance at all.  But they should test it.
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Distinct Viral Lineages from Fish and Amphibians Reveal the Complex Evolutionary History of Hepadnaviruses

Distinct Viral Lineages from Fish and Amphibians Reveal the Complex Evolutionary History of Hepadnaviruses | Virology and Bioinformatics from Virology.ca | Scoop.it
IMPORTANCE Hepadnaviruses are responsible for significant disease in humans (hepatitis B virus) and have been reported from a diverse range of vertebrates as both exogenous and endogenous viruses. We report the full-length genome of a novel hepadnavirus from a fish and the first hepadnavirus genome from an amphibian. The novel fish hepadnavirus, sampled from bluegills, was more closely related to mammalian hepadnaviruses than to other fish viruses. This phylogenetic pattern reveals that, although hepadnaviruses have likely been associated with vertebrates for hundreds of millions of years, they have also been characterized by species jumping across wide phylogenetic distances.

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PHYPred: a tool for identifying bacteriophage enzymes and hydrolases

Bacteriophages are viruses that attack bacteria and kill them through the lytic replication cycle. Many studies have reported that phages are more specific to bacteria than antibiotics are; thus, phage therapy has many potential applications in human medicine, with the advantage of having few side effects (Keen, 2012). Investigating the mechanisms of bacteria-killing phages will therefore aid in the development of antibacterial drugs. Hydrolases encoded by phages play a key role in the interaction between phages and host bacteria. These enzymes act on the bacterial cell wall to kill the host bacteria and then release progeny phages (Nielsen et al., 1999). Thus, correctly identifying the hydrolases encoded by phages can provide important clues for not only studying the lytic mechanism of the phage-bacteria system but also discovering potential antibacterial drugs. With the accumulation of proteomics data, various machine-learning methods have been applied to predict functional phage proteins. Sequritan et al. designed an artificial neural network (ANN)-based method to predict viral structural proteins using amino acid frequency (Seguritan et al., 2012). Recently, a special type of structural protein, phage virion protein, was identified using primary sequence information (Ding et al., 2014; Feng et al., 2013). However, to our knowledge, no computational method has been developed to predict phage hydrolases. Thus, the aim of this letter is to describe a powerful model for identifying phage hydrolases. We started by discrimi-nating phage enzymes from phage non-enzymes. Once a phage protein is recognized as phage enzyme, the model will determine whether the predicted enzyme is phage hydrolase.

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Researchers Succeed in Growing Norovirus in Culture

Researchers Succeed in Growing Norovirus in Culture | Virology and Bioinformatics from Virology.ca | Scoop.it
Noroviruses are common; they are the primary cause of viral gastroenteritis in people and are infamous for ruining the vacations of cruise-goers. They pres
Via Gilbert C FAURE
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Researchers Discover How Zika Virus Causes Fetal Brain Damage

Researchers Discover How Zika Virus Causes Fetal Brain Damage | Virology and Bioinformatics from Virology.ca | Scoop.it
According to a team of researchers led by Yale University, infection by the Zika virus diverts a key protein necessary for neural cell division in the developing human fetus.

 

Marco Onorati et al. describe the derivation and characterization, including single-cell RNA-seq, of neocortical and spinal cord neuroepithelial stem (NES) cells to model early human neurodevelopment and Zika virus (ZIKV)-related neuropathogenesis. By analyzing human NES cells, organotypic fetal brain slices, and a ZIKV-infected micrencephalic brain, the team shows that ZIKV infects both neocortical and spinal NES cells as well as their fetal homolog, radial glial cells (RGCs), causing disrupted mitoses, supernumerary centrosomes, structural disorganization, and cell death. ZIKV infection of NES cells and RGCs causes centrosomal depletion and mitochondrial sequestration of phospho-TBK1 during mitosis.

 

The scientists also found that nucleoside analogs inhibit ZIKV replication in NES cells, protecting them from ZIKV-induced pTBK1 relocalization and cell death. They established a model system of human neural stem cells to reveal cellular and molecular mechanisms underlying neurodevelopmental defects associated with ZIKV infection and its potential treatment.


Via Dr. Stefan Gruenwald
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Newly discovered multicomponent virus is the first of its kind to infect animals

Newly discovered multicomponent virus is the first of its kind to infect animals | Virology and Bioinformatics from Virology.ca | Scoop.it
A story about Science from Phys.org, as featured in Newsfusion's Science News app.
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Tips for effective use of BLAST and other NCBI tools

The National Center for Biotechnology Information (NCBI) provides one of the most extensive sets of web-based tools for biological research. The tools are indispensable when planning genomics experiments, including for qPCR, NGS, and CRISPR. In this presentation, Dr Matt McNeill takes a practical look at getting started with the wealth of NCBI tools, and shares some relevant tips to help you sift through the tools and options that we regularly use. In particular, he focuses on commonly adjusted parameters that will allow you to more effectively use the powerful Basic Local Alignment Algorithm Tool (BLAST) to identify off-target hybridization/annealing events. Dr McNeill also covers practical examples using NCBI tools to design assays.


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CRISPR inspires new tricks to edit genes

CRISPR inspires new tricks to edit genes | Virology and Bioinformatics from Virology.ca | Scoop.it
CRISPR/Cas9 has been a rockstar gene-editing tool for just four years and it’s already being tweaked to do more things better.
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The Ins and Outs of Multipartite Plant Viruses

The Ins and Outs of Multipartite Plant Viruses | Virology and Bioinformatics from Virology.ca | Scoop.it
Viruses possessing a non-segmented genome require a specific recognition of their nucleic acid to ensure its protection in a capsid. A similar feature exists for viruses having a segmented genome, usually consisting of viral genomic segments joined together into one viral entity. While this appears as a rule for animal viruses, the majority of segmented…
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Smallpox eradication 'giant' Donald Henderson dies at 87 - BBC News

Smallpox eradication 'giant' Donald Henderson dies at 87 - BBC News | Virology and Bioinformatics from Virology.ca | Scoop.it

US doctor Donald Henderson, who led a successful campaign to wipe out #smallpox worldwide, has died at the age of 87.

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ZBP1/DAI is an innate sensor of influenza virus triggering the NLRP3 inflammasome and programmed cell death pathways

ZBP1/DAI is an innate sensor of influenza virus triggering the NLRP3 inflammasome and programmed cell death pathways | Virology and Bioinformatics from Virology.ca | Scoop.it
People infected with influenza get sick not only because of the presence of virus but also because of the inflammatory immune response. Now, Kuriakose et al . report that the protein ZBP1/DAI (Z-DNA binding protein 1/DNA-dependent activator of IFN regulatory factors) senses influenza A virus (IAV) and may contribute to this inflammatory pathogenesis. They found that ZBP1/DAI triggered cell death and inflammatory responses after IAV infection, and that ZBP1/DAI deficiency protected mice from IAV-related mortality. These mice had decreased inflammation and less epithelial damage than control animals. If these findings hold true in humans, ZBP1/DAI may be a host-directed target to decrease the severity of IAV pathogenesis.
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Chimeric RSV virus-like particles confer protection against respiratory syncytial virus infection

Chimeric RSV virus-like particles confer protection against respiratory syncytial virus infection | Virology and Bioinformatics from Virology.ca | Scoop.it
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Statistical relevance—relevant statistics, part II: presenting experimental data

Statistical relevance—relevant statistics, part II: presenting experimental data | Virology and Bioinformatics from Virology.ca | Scoop.it
In the first part of this article series, I discussed general guidelines for analyzing the results of scientific experiments (Klaus, 2015). The next step is the graphical representation of the results. The importance of data presentation should not be underestimated as figures are a key component of both data analysis and publications. Graphics are an important analytical tool as they can help to reveal patterns and illustrate differences. The appropriate plotting of data can also strengthen or even replace more formal statistical procedures, such as hypothesis tests. In the context of scientific publications, figures should guide the reader through the article and provide a clear and precise representation of the experimental results.

In this article, I will focus primarily on key principles and good practices for presenting small‐to‐medium datasets with the aim of comparing results from different experimental groups. As a general rule, authors should show as much of the actual data as possible instead of summarizing datasets via means or variances. Even larger datasets can be displayed efficiently using an appropriate plot; bars and boxes to visualize summary statistics can serve as additional visual guides. To adapt the methods described in this article, readers can download a supplementary “notebook” (see Code EV1) with code to generate the plots in the R language (R Core Team, 2015). Additionally, this web tool (http://embojserver.embl.de) generates the bee swarm plots and dot plots discussed later in the article. Apart from the topics discussed in this article, there are many more aspects that require attention. The “Scientific Figure Design Course” material by the Bioinformatics unit of the Babraham Institute (Babraham Bioinformatics, 2015) and the book by Tufte (1983) are valuable references.

I start with a discussion of displaying small‐scale experimental datasets. Let us assume that we have a fluorescent marker for detecting a recombination event in …
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Viruses 'more dangerous in the morning' - BBC News

Viruses 'more dangerous in the morning' - BBC News | Virology and Bioinformatics from Virology.ca | Scoop.it
Viruses are more dangerous when they infect their victims in the morning, a University of Cambridge study suggests.
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