Viruses, Immunology & Bioinformatics from Virology.uvic.ca
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Viruses, Immunology & Bioinformatics from Virology.uvic.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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Virology Journal | Abstract | Genome characterization of Long Island tick rhabdovirus, a new virus identified in Amblyomma americanum ticks

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Ticks are implicated as hosts to a wide range of animal and human pathogens. The full range of microbes harbored by ticks has not yet been fully explored.
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Mind-controlling virus forces parasitic wasp to put all its eggs in one basket : Not Exactly Rocket Science

Mind-controlling virus forces parasitic wasp to put all its eggs in one basket : Not Exactly Rocket Science | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
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so cool!

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Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea

Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

This special issue ofInternational Journal of Systematic and Evolutionary Microbiology contains both original research and review articles covering the use of genomic sequence data in microbial taxonomy and systematics. It includes contributions on specific taxa as well as outlines of approaches for incorporating genomics into new strain isolation to new taxon description workflows.

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Genomics, Medicine, and Pseudoscience: Internet quack Joe Mercola is worried. Dr. Oz to the rescue!

Genomics, Medicine, and Pseudoscience: Internet quack Joe Mercola is worried. Dr. Oz to the rescue! | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
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Next Generation Sequencing Reveals Regulation of Distinct Aedes microRNAs during Chikungunya Virus Development

Next Generation Sequencing Reveals Regulation of Distinct Aedes microRNAs during Chikungunya Virus Development | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

Small, non-coding, RNAs such as microRNAs (miRNA) of length 18–24 nucleotide are reported in wide range of organisms and known to play a determinative role in regulation of various cellular processes. They have also reported to have regulatory roles during pathogen infection, maturation and transmission. Chikungunya virus is an important alphavirus transmitted through two important vectors, Aedes aegypti and Ae. albopictus. While Ae. aegypti has been the preferred vector for transmission of this virus, recently, Ae. albopictushas gained notoriety for disease transmission. Using Illumina platform, we sequenced the small RNA population an Aedes albopictus cell line infected with chikungunya virus. We studied the expression modulation of miRNAs upon CHIKV infection and found distinct set of miRNAs regulated in Aedes upon CHIKV infection. We further predicted the targets of these miRNAs and performed pathway analysis of these targets. The cellular functional targets of some of these miRNAs overlapped suggesting aggressive participation of the targeted pathways in establishing CHIKV infection.

 

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The Plant Virus and the Bee | Viruses101 | Learn Science at Scitable

The Plant Virus and the Bee | Viruses101 | Learn Science at Scitable | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
A plant virus has made over a billion year evolutionary jump to infect honeybees. Is the plant virus possibly to blame for recent worldwide honeybee population decline?
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Good riddance

Good riddance | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
MALARIA is still a long way from eradication (see article). But dracunculiasis is almost gone. According to a report published on January 16th by the Carter Centre,...
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The dual role of tetraspanin CD63 in HIV-1 replication

Previously, we showed that the tetraspanin membrane protein CD63 mediates both early and post-integration stages of the HIV-1 replication cycle. The temporal roles of CD63 were discerned using monoclonal antibodies and small interfering RNAs (siRNAs) to block CD63 function, and determining which of the sequential steps in HIV-1 replication were disrupted. Inhibition was shown to occur during early infection, suggestive of involvement in virus entry or reverse transcription. In addition, we have shown that treatment with CD63 siRNA post-infection, significantly inhibited virus production in supernatant, suggesting an important role for CD63 in macrophages during HIV-1 replication events occurring after proviral integration, and possibly during egress.
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Bryce Wylde’s Bad Flu Advice « Alternative Medicine « Health « Skeptic North

Bryce Wylde’s Bad Flu Advice « Alternative Medicine « Health « Skeptic North | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
In a recent article for the Globe and Mail, self-styled health-guru Bryce Wylde has stuck his foot in it again.  In an article entitled Eight easy, natural…
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Black Death Left a Mark on Human Genome

Black Death Left a Mark on Human Genome | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

The Black Death didn’t just wipe out millions of Europeans during the 14th century. It left a mark on the human genome, favoring those who carried certain immune system genes, according to a new study. Those changes may help explain why Europeans respond differently from other people to some diseases and have different susceptibilities to autoimmune disorders.

 

Geneticists know that human populations evolve in the face of disease. Certain versions of our genes help us fight infections better than others, and people who carry those genes tend to have more children than those who don’t. So the beneficial genetic versions persist, while other versions tend to disappear as those carrying them die. This weeding-out of all but the best genes is called positive selection. But researchers have trouble pinpointing positively selected genes in humans, as many genes vary from one individual to the next.

 

Enter Mihai Netea, an immunologist at Radboud University Nijmegen Medical Centre in the Netherlands. He realized that in his home country, Romania, the existence of two very distinct ethnic groups provided an opportunity to see the hand of natural selection in the human genome. A thousand years ago, the Rroma people—commonly known as gypsies—migrated into Europe from north India. But they intermarried little with European Romanians and thus have very distinct genetic backgrounds. Yet, by living in the same place, both of these groups experienced the same conditions, including the Black Plague, which did not reach northern India. So the researchers sought genes favored by natural selection by seeking similarities in the Rroma and European Romanians that are not found in North Indians.

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Emergence of a Highly Pathogenic Avian Influenza Virus from a Low Pathogenic Progenitor - Journal of Virology

Avian influenza (AI) viruses of the H7 subtype have the potential to evolve into highly pathogenic (HP) viruses that represent a major economic problem for the poultry industry and a threat to global health. However, the emergence of HPAI viruses from low pathogenic (LPAI) progenitor viruses is currently poorly understood. To investigate the origin and evolution of one of the most important avian influenza epidemics described in Europe, we investigated the evolutionary and spatial dynamics of the entire genome of 109 H7N1 (46 LPAI and 63 HPAI) viruses collected during Italian H7N1 outbreaks between March 1999 and February 2001. Phylogenetic analysis revealed that the LPAI and HPAI epidemics shared a single ancestor, that the HPAI strains evolved from the LPAI viruses in the absence of reassortment, and that there was a parallel emergence of mutations among HPAI and later LPAI lineages. Notably, an ultra-deep sequencing analysis demonstrated that some of the amino acid changes characterizing the HPAI virus cluster were already present with low frequency within several individual viral populations from the beginning of the LPAI H7N1 epidemic. A Bayesian phylogeographic analysis revealed stronger spatial structure during the LPAI outbreak, reflecting the more rapid spread of the virus following the emergence of HPAI. The data generated in this study provide the most complete evolutionary and phylogeographic analysis of epidemiologically intertwined high and low pathogenic viruses undertaken to date, and highlight the importance of implementing prompt eradication measures against LPAI to prevent the appearance of viruses with fitness advantages and unpredictable pathogenic properties.

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Eat your vaccines

Eat your vaccines | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Vaccines have been revolutionary in medicine, but why are they not used in some parts of the world and how can they be improved? ...

Ouch! Wouldn’t it be great if instead of a jab with a needle, you could just eat a vaccine instead? Luckily, researchers at the University of California agree, and their attempts to use algae to produce an edible malaria vaccine is just one example of the many strides forward scientists are taking in vaccine research.

Ed Rybicki's insight:

I love these idealistic but naive statements about how plant-production-of-vaccines-will-let us-get-away-from-needles: very 1990s; a little out of touch with modern realities - unfortunately!

The facts are that any edible (read: oral) vaccine will have to be regulated as tightly as an injectable, in terms of dose and administration.  

Really: giving too little OR too much; giving it too often or not often enough; giving a product that has not been QCed or checked for potency  after storage...is suicide, in the vaccine world.

Even if it IS safe enough to eat.

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Identification, reconstruction and evolutionary history of archaeological Barley Stripe Mosaic Virus

Identification, reconstruction and evolutionary history of archaeological Barley Stripe Mosaic Virus | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The origins of many plant diseases appear to be recent and associated with the rise of domestication, the spread of agriculture or recent global movements of crops. Distinguishing between these possibilities is problematic because of the difficulty of determining rates of molecular evolution over short time frames. Heterochronous approaches using recent and historical samples show that plant viruses exhibit highly variable and often rapid rates of molecular evolution. The accuracy of estimated evolution rates and age of origin can be greatly improved with the inclusion of older molecular data from archaeological material. Here we present the first reconstruction of an archaeological RNA genome, which is of Barley Stripe Mosaic Virus (BSMV) isolated from barley grain ~750 years of age. Phylogenetic analysis of BSMV that includes this genome indicates the divergence of BSMV and its closest relative prior to this time, most likely around 2000 years ago. However, exclusion of the archaeological data results in an apparently much more recent origin of the virus that postdates even the archaeological sample. We conclude that this viral lineage originated in the Near East or North Africa, and spread to North America and East Asia with their hosts along historical trade routes.
Ed Rybicki's insight:

Plant virology rules, OK?!

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Long Distance Signals Protect Brain from Viral Infections

Abstract:

WASHINGTON, DC – February 10, 2014 – The brain contains a defense system that prevents at least two unrelated viruses—and possibly many more—from invading the brain at large. The research is published online ahead of print in the Journal of Virology.
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Scientific method: Statistical errors

Scientific method: Statistical errors | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
P values, the 'gold standard' of statistical validity, are not as reliable as many scientists assume.
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13 people die of flu in two weeks: CDC | Society | FOCUS TAIWAN - CNA ENGLISH NEWS

Taipei, Feb. 11 (CNA) Taiwan reported 256 new flu cases within the last two weeks, including H3N2, H1N1 and type B strains, resulting in 13 fatalities, the Centers for Disease Control (CDC) said Tuesday.
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New application of physics tools used in biology

New application of physics tools used in biology | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

A Lawrence Livermore National Laboratory physicist and his colleagues have found a new application for the tools and mathematics typically used in physics to help solve problems in biology.


Via Integrated DNA Technologies
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Evidence of the causal role of human papillomavirus type 58 in an oropharyngeal carcinoma

Evidence of the causal role of human papillomavirus type 58 in an oropharyngeal carcinoma | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Persistent human papillomavirus infection (HPV) is recognized as an important etiologic factor for a subset of head and neck squamous cell carcinomas (SCC), especially those arising from the oropharynx. Whereas HPV16 accounts for the majority of HPV DNA-positive oropharyngeal SCC, infections with other mucosal high-risk HPV types are quite rare and biological data demonstrating their causal involvement are insufficient. Here we present the first case of an oropharyngeal SCC driven by HPV type 58. A 69-year-old Caucasian woman presented with an enlarged and firm left tonsil. A computed tomography scan showed a left tonsillar mass, extending to the soft palate and the glossotonsillar sulcus. The patient underwent extended radical tonsillectomy and ipsilateral selective neck dissection. Pathology confirmed an infiltrating, poorly differentiated SCC of the left tonsil with node metastasis (pT2N1). Adjuvant external beam radiation therapy (60 Grays (Gy)) was administered. After 1 year of follow-up, the patient is well with no evidence of cancer recurrence. HPV analyses of the tumor tissue by BSGP5+/6+ −PCR/MPG, targeting 51 mucosal HPV types, showed single positivity for HPV type 58. Presence of HPV58 E6*I RNA demonstrated biological activity of the virus in the tumor tissue, and presence of serum antibodies to HPV58 oncoproteins E6 and E7 indicated presence of an HPV58-driven cancer. Overexpression of cellular protein p16INK4a and reduced expression of pRb, two cellular markers for HPV-induced cell transformation, were observed. Exons 4–10 of TP53 showed no mutations or polymorphisms. The presence of HPV58 as single HPV infection in combination with a broad variety of direct and indirect markers of HPV transformation provides comprehensive evidence that this oropharyngeal SCC was driven by HPV58.

 

HPV graphic by Russell Kightley Media

Ed Rybicki's insight:

Can't think how I missed this but here it is.  Firm evidence that it is not just HPVs 16 and 18 involved in human cancers.

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Viruses101 | Learn Science at Scitable

Viruses101 | Learn Science at Scitable | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Viruses 101 will delve into the world of microscopic killers. Each post will explore a new virus ? its components, effects on victims, and its impact on the global community.
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Cholesterol plays a critical role in hantavirus infection

Cholesterol plays a critical role in hantavirus infection | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Viruses mutate fast, which means they can quickly become resistant to anti-viral drugs. But viruses also depend on proteins and nutrients provided by their hosts, and therefore one strategy to identify new anti-viral drugs is to identify and target such host-cell components. A paper published on February ...
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Molecular Structure Reveals How HIV Infects Cells

Molecular Structure Reveals How HIV Infects Cells | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
News Release
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Busting Anti-Vaccine Myths: 100 Sites on the Real Science of Immunization | Online Nurse Practitioner Programs

Busting Anti-Vaccine Myths: 100 Sites on the Real Science of Immunization | Online Nurse Practitioner Programs | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

The concept of immunization has been around for centuries, but the past 100 years has seen more innovation and advancement in the field than ever before. Increasingly effective and widely available vaccines have nearly or completely eradicated smallpox, polio, measles, and other diseases that were once responsible for thousands of deaths annually. There are those who argue that vaccines cause more harm than good, or that vaccines have unacceptable side effects, but scientific studies have proven repeatedly that the benefits of vaccination far outweigh the risks. - See more at: http://onlinenursepractitionerprograms.com/vaccine-immunization/#sthash.DiDvquVT.dpuf

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New Avian Flu Virus Ravages Poultry in Korea

New Avian Flu Virus Ravages Poultry in Korea | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

A dangerous new strain of bird flu that emerged in South Korea on 17 January has spread nationwide despite efforts to clamp down on the virus. Authorities have culled 2.8 million domestic chickens and ducks since the outbreak began, and the strain has also killed dozens of Baikal teal and other migratory birds. As yet, there are no reports of human infections. Scientists are puzzling over where the H5N8 strain, never before seen in a highly pathogenic form, originated. And researchers are scrambling to keep the virus out of the country's premier poultry research center. 

Intensive surveillance of commercial poultry and wild birds had never before detected the H5N8 strain in Korea, says Jae-Hong Kim, a veterinary microbiologist at Seoul National University. Last year, a Chinese group reported having isolated it from apparently healthy ducks at a live poultry market in China. Based on H5N8’s sudden appearance in Korea and the genetic similarity of isolates from poultry and migratory birds, a governmental investigative committee has "tentatively concluded that [the virus] was likely to have been introduced by migratory birds," Kim says.

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Clinical and epidemiological characteristics of a fatal case of avian influenza A H10N8 virus infection

Clinical and epidemiological characteristics of a fatal case of avian influenza A H10N8 virus infection | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Clinical and epidemiological characteristics of a fatal case of avian influenza A H10N8 virus infection: a descriptive study. By - HaiYing Chen MD, Hui Yuan MD, Rongbao Gao MD, Jinxiang Zhang MD, P...
A woman aged 73 years presented with fever and was admitted to hospital on Nov 30, 2013. She developed multiple organ failure and died 9 days after illness onset. A novel reassortant avian influenza A H10N8 virus was isolated from the tracheal aspirate specimen obtained from the patient 7 days after onset of illness. Sequence analyses revealed that all the genes of the virus were of avian origin, with six internal genes from avian influenza A H9N2 viruses. The aminoacid motif GlnSerGly at residues 226—228 of the haemagglutinin protein indicated avian-like receptor binding preference. A mixture of glutamic acid and lysine at residue 627 in PB2 protein—which is associated with mammalian adaptation—was detected in the original tracheal aspirate samples. The virus was sensitive to neuraminidase inhibitors. Sputum and blood cultures and deep sequencing analysis indicated no co-infection with bacteria or fungi. Epidemiological investigation established that the patient had visited a live poultry market 4 days before illness onset. 
Ed Rybicki's insight:

"all the genes of the virus were of avian origin, with six internal genes from avian influenza A H9N2 viruses": so the H9N2 which has been lingering around, not causing much human harm, is now recombining with viruses that have NEVER been implicated in human disease??  As in, H10 and N8??

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Suppression of RNA Silencing by a Plant DNA Virus Satellite

Suppression of RNA Silencing by a Plant DNA Virus Satellite | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

In plants, RNA silencing plays a key role in developmental regulation and antiviral defense. To successfully infect their hosts, plant viruses encode silencing suppressors (VSRs) as counter-defense measures. These VSRs function to disable host antiviral RNA silencing defenses through various mechanisms that are not well understood. Here we report that a host calmodulin-like protein called Nbrgs-CaM, which appears to be an endogenous suppressor of RNA silencing, plays essential roles in suppression of RNA silencing and induction of symptoms by the VSR βC1, the sole protein encoded by a geminivirus-associated DNA satellite. The Nbrgs-CaM was up-regulated by Tomato yellow leaf curl China geminivirus (TYLCCNV)-encoded VSR βC1 upon virus infection or stable expression via a transgene. Further analyses revealed that up-regulation of Nbrgs-CaM by βC1 suppressed RNA silencing likely through repressing the expression of RNA-DEPENDENT RNA POLYMERASE 6(RDR6). We have demonstrated that RDR6-mediated RNA silencing plays an important role in antiviral defense in Nicotiana benthamiana and confers host range restriction against TYLCCNV infection on Arabidopsis thaliana. Our study suggests that exploiting a cellular suppressor can be an efficient mechanism for viruses to counteract host RNA silencing defense response.

 

Ed Rybicki's insight:

Two of my favourite topics: geminiviruses and silencing.  Now the fact that a satellite DNA of a geminivirus is responsible for UPregulation of a NATIVE plant RNA silencer, is just too cunning for words!  And could give a very valuable pointer to just why it is that geminiviruses are associated with DNAbetas.

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