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PLOS Pathogens: A Structure-Guided Mutation in the Major Capsid Protein Retargets BK Polyomavirus

PLOS Pathogens: A Structure-Guided Mutation in the Major Capsid Protein Retargets BK Polyomavirus | Virology and Bioinformatics from Virology.ca | Scoop.it
Abstract

Viruses within a family often vary in their cellular tropism and pathogenicity. In many cases, these variations are due to viruses switching their specificity from one cell surface receptor to another. The structural requirements that underlie such receptor switching are not well understood especially for carbohydrate-binding viruses, as methods capable of structure-specificity studies are only relatively recently being developed for carbohydrates. We have characterized the receptor specificity, structure and infectivity of the human polyomavirus BKPyV, the causative agent of polyomavirus-associated nephropathy, and uncover a molecular switch for binding different carbohydrate receptors. We show that the b-series gangliosides GD3, GD2, GD1b and GT1b all can serve as receptors for BKPyV. The crystal structure of the BKPyV capsid protein VP1 in complex with GD3 reveals contacts with two sialic acid moieties in the receptor, providing a basis for the observed specificity. Comparison with the structure of simian virus 40 (SV40) VP1 bound to ganglioside GM1 identifies the amino acid at position 68 as a determinant of specificity. Mutation of this residue from lysine in BKPyV to serine in SV40 switches the receptor specificity of BKPyV from GD3 to GM1 both in vitro and in cell culture. Our findings highlight the plasticity of viral receptor binding sites and form a template to retarget viruses to different receptors and cell types.

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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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IVA: accurate de novo assembly of RNA virus genomes

Motivation: An accurate genome assembly from short read sequencing data is critical for downstream analysis, for example allowing investigation of variants within a sequenced population. However, assembling sequencing data from virus samples, especially RNA viruses, into a genome sequence is challenging due to the combination of viral population diversity and extremely uneven read depth caused by amplification bias in the inevitable reverse transcription and PCR amplification process of current methods.

Results: We developed IVA (Iterative Virus Assembler), a de novoassembler designed specifically for read pairs sequenced at highly variable depth from RNA virus samples. We tested IVA on datasets from 140 sequenced samples from HIV-1 or Influenza virus infected people and demonstrated that IVA outperforms all other virus de novo assemblers.

Availability: The software runs under Linux, has the GPLv3 licence and is freely available from http://sanger-pathogens.github.io/iva

Contact: iva@sanger.ac.uk

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Battling Infectious Diseases in the 20th Century: The Impact of Vaccines

Battling Infectious Diseases in the 20th Century: The Impact of Vaccines | Virology and Bioinformatics from Virology.ca | Scoop.it
The number of infected people, measured over 70-some years and across all 50 states and the District of Columbia, generally declined after vaccines were introduced.
Chris Upton + helpers's insight:

Vaccines work....

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Is Obesity Contagious? | Viruses101 | Learn Science at Scitable

Is Obesity Contagious? | Viruses101 | Learn Science at Scitable | Virology and Bioinformatics from Virology.ca | Scoop.it
Obesity is a growing problem in the United States. More than a third of all adults in the United States and seventeen percent of children from the ages of two to nineteen are obese according to the Center for Disease Control. A study published in the journal Pediatrics and conducted by two pediatric gastroenterologists from California, led by Dr.
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Phosphatidylserine Vesicles Enable Efficient En Bloc Transmission of Enteroviruses: Cell

Phosphatidylserine Vesicles Enable Efficient En Bloc Transmission of Enteroviruses: Cell | Virology and Bioinformatics from Virology.ca | Scoop.it
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Measles death in Germany prompts calls for mandatory vaccinations

Measles death in Germany prompts calls for mandatory vaccinations | Virology and Bioinformatics from Virology.ca | Scoop.it
Death of 18-month-old boy is the first fatality among 574 reported cases in the country’s worst measles outbreak in more than a decade
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Man's death leads to discovery of new virus in Kansas, CDC reports - CNN.com

The CDC has discovered a new virus, likely spread by tick bites, that may have contributed to a Kansas man's death, the agency said Friday.
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Evolution of Genome Size and Complexity in the Rhabdoviridae

Evolution of Genome Size and Complexity in the  Rhabdoviridae | Virology and Bioinformatics from Virology.ca | Scoop.it
Author Summary Understanding the patterns and mechanisms of genome evolution is one of the most important, yet least understood, aspects of RNA virus biology. The evolutionary challenge faced by RNA viruses is to maximize functional diversity within severe constraints on genome size. Here we show that rhabdoviruses, a family of RNA viruses that infect hosts as diverse as plants, insects and vertebrates, have an unusual capacity for genomic plasticity. By analysing the complete or near-complet
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Bacteriophages, revitalized after 100 years in the shadow of antibiotics

Bacteriophages, revitalized after 100 years in the shadow of antibiotics | Virology and Bioinformatics from Virology.ca | Scoop.it

The year 2015 marks 100 years since Dr. Frederick Twort discovered the “filterable lytic factor”, which was later independently discovered and named “bacteriophage” by Dr. Felix d'Herelle. On this memorable centennial, it is exciting to see a special issue published by Virologica Sinica on Phages and Therapy. In this issue, readers will not only fi nd that bacteriophage research is a booming field but also learn about the diverse applications currently being explored for bacteriophages. The biggest driving force behind these applications is the serious threat of bacterial antibiotic resistance that is emerging in the current era.


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Ed Rybicki's curator insight, February 17, 2:51 AM

Phages: love 'em!

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Interferons and viruses: an evolutionary arms race of molecular interactions: Trends in Immunology

Highlights Pathogen recognition leads to the production of many similar interferons.Interferons signal through the same receptor but can have different effects.Viruses antagonize interferon induction and signaling.Innate immune activators are effective vaccine adjuvants.

 

Over half a century has passed since interferons (IFNs) were discovered and shown to inhibit virus infection in cultured cells. Since then, researchers have steadily brought to light the molecular details of IFN signaling, catalogued their pleiotropic effects on cells, and harnessed their therapeutic potential for a variety of maladies. While advances have been plentiful, several fundamental questions have yet to be answered and much complexity remains to be unraveled. We explore the current knowledge surrounding four main questions: are type I IFN subtypes differentially produced in response to distinct pathogens? How are IFN subtypes distinguished by cells? What are the mechanisms and consequences of viral antagonism? Lastly, how can the IFN response be harnessed to improve vaccine efficacy?

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Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes

Viruses are a significant component of the intestinal microbiota in mammals. In recent years, advances in sequencing technologies and data analysis techniques have enabled detailed metagenomic studies investigating intestinal viromes (collections of bacteriophage and eukaryotic viral nucleic acids) and their potential contributions to the ecology of the microbiota. An important component of virome studies is the isolation and purification of virus-like particles (VLPs) from intestinal contents or feces. Several methods have been applied to isolate VLPs from intestinal samples, yet to our knowledge, the efficiency and reproducibility between methods have not been explored. A rigorous evaluation of methods for VLP purification is critical as many studies begin to move from descriptive analyses of virus diversity to studies striving to quantitatively compare viral abundances across many samples. Therefore, reproducible VLP purification methods which allow for high sample throughput are needed. Here we compared and evaluated four methods for VLP purification using artificial intestinal microbiota samples of known bacterial and viral composition.
Ed Rybicki's insight:

Great paper!  But they really needed to look at Optiprep / iodyxanol as a gradient-forming medium: it is excellent for both rate-zonal and isopycnic gradients, and probably better as a preparative medium because you can go straight to EM or even injection into animals - AND it's much gentler on viruses because you don't get the strong ionic and osmotic effects.

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Biological Warfare: Parasitic Wasp Uses A Virus To Control Its Host - Science Sushi

Biological Warfare: Parasitic Wasp Uses A Virus To Control Its Host - Science Sushi | Virology and Bioinformatics from Virology.ca | Scoop.it
Viral venom? A parasitic wasp uses a unique RNA virus to turn its unwitting host into a bodyguard.
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The Sickeningly Low Vaccination Rates at Silicon Valley Day Cares | WIRED

The Sickeningly Low Vaccination Rates at Silicon Valley Day Cares | WIRED | Virology and Bioinformatics from Virology.ca | Scoop.it
A WIRED investigation shows that some children attending day care facilities affiliated with prominent Silicon Valley companies have not been completely vaccinated against preventable infectious diseases.
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Light scattering to estimate the concentration of virus particles

Most often the determination of the concentration of virus particles is rendered difficult by the availability of proper standards. We have adapted a static light scattering based method for the quantification of virus particles (shown for poliovirus) without the need of virus particle standards. Instead, as standards, well-characterized polymeric nanoparticle solutions are used. The method is applicable for virus particles acting as Rayleigh scatterers, i.e., virus particles with equivalent diameters up to ca. 1/10th of the wavelength of the scattered monochromatic light ($70 nm diameter). Further limitations may arise if the refractive index of the virus is unavailable or cannot be calculated based on its composition, such as in case of enveloped viruses. The method is especially relevant for preparation of virus particle concentration standards and to vaccine formulations based on attenuated or inactivated virus particles where the classical plaque forming assays cannot be applied. The method consists of:

 Measuring the intensity of the light scattered by viruses suspended in an aqueous solution.
 Measuring the intensity of the light scattered by polymeric nanoparticles of known concentration and

comparable size with the investigated virus particle. 

Ed Rybicki's insight:

Good stuff!!  Love methods B-)

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EpiToolKit – A Web-based Workbench for Vaccine Design

Summary: EpiToolKit is a virtual workbench for immunological questions with a focus on vaccine design. It offers an array of immunoinformatics tools covering MHC genotyping, epitope and neo-epitope prediction, epitope selection for vaccine design, and epitope assembly. In its recently re-implemented version 2.0, EpiToolKit provides a range of new functionality and for the first time allows combining tools into complex workflows. For inexperienced users it offers simplified interfaces to guide the users through the analysis of complex immunological data sets.

Availability: http://www.epitoolkit.de

Contact: schubert@informatik.uni-tuebingen.de

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Context similarity scoring improves protein sequence alignments in the midnight zone

Context similarity scoring improves protein sequence alignments in the midnight zone | Virology and Bioinformatics from Virology.ca | Scoop.it
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Amid measles outbreaks, WHO calls for more vaccinations in Europe

Amid measles outbreaks, WHO calls for more vaccinations in Europe | Virology and Bioinformatics from Virology.ca | Scoop.it
UN agency has recorded 22,000 cases of the highly infectious disease since the start of 2014
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Man’s death leads to the discovery of a new virus

Man’s death leads to the discovery of a new virus | Virology and Bioinformatics from Virology.ca | Scoop.it
Scientists have described a previously unknown insect-borne virus, following the death of a man in the Kansas county of Bourbon in the US in mid-2014.

According to the US Centres for Disease Control and Prevention (CDC), the otherwise healthy, 50-year-old man was working outside on his property in mid-2014, when he sustained multiple tick bites, which led to an array of symptoms including fever, fatigue, rash, headaches, nausea and vomiting around two days after. After he was hospitalised, his white blood cell count dipped, his lungs and kidney started failing, and by day 11, suffered a heart attack, and died.

The culprit? Scientists were able to isolate a new virus from a blood sample collected from the patient nine days after he fell ill, and attributed it to the Thogotovirus genus in the virus family Orthomyxoviridae. This family contains six genera - Influenza virus A, Influenza virus B, Influenza virus C, Isavirus, Thogotovirus and Quaranjavirus.

The researchers say there’s a marked difference between the symptoms suffered by this man, and other known Thogotoviruses. As Liz Szabo reports at USA Today, Thogotoviruses usually cause diseases such as meningitis or encephalitis, where the lining of the brain becomes severely inflamed. But they've never seen these viruses destroy white blood cell counts like the Bourbon virus did to this man.

The team discusses this in the current edition of the CDC journal, Emerging Infectious Diseases: "Of the seven symptomatic human infections that have been associated with viruses in the genus Thogotovirus, most case-patients have had neurologic findings (e.g., meningitis, encephalitis) without any described abnormalities in blood counts. Although cerebrospinal fluid was not tested for the patient reported, his clinical signs and symptoms were not suggestive of neurologic infection. Furthermore, the patient did not have any respiratory symptoms that would be expected with other viruses that are known human pathogens in the large family of Orthomyxoviridae, such as influenza virus."

As of this month, this man is the only case of Bourbon virus disease that has been identified, but there are likely more cases that have yet to be diagnosed. “I think we have to assume this has been around for some time, and we haven’t been able to diagnose it,” Dana Hawkinson, an infectious disease specialist who treated the patient at the University of Kansas Medical Centre in Kansas City, told Denise Grady at The New York Times. “We suspect there have been milder cases and people have recovered from them, but we don’t have a lot of information.”

"It will be important to determine how widespread the Bourbon virus is in both ticks, insects, animals and humans and to grasp the spectrum of illness it is capable of causing," Amesh Adalja, senior associate at the Centre for Health Security at the University of Pittsburgh Medical Centre in the US, told USA Today. "The fact that a novel virus was discovered underscores the need for perpetual vigilance, in all locales, with respect to emerging infectious diseases. It is only by leaving no stone unturned when investigating unexplained illnesses that humans can best prepare for microbial threats."

The researchers report that right now, there is no treatment for the disease, no vaccine, and no lab tests to identify it. So those in the US at a high risk of tick bites are advised to wear insect repellents and long-sleeved shirts and pants when outdoors, and to avoid thickly wooded areas as much as possible.
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Virus-cutting enzyme helps bacteria remember a threat

Virus-cutting enzyme helps bacteria remember a threat | Virology and Bioinformatics from Virology.ca | Scoop.it

Bacteria may not have brains, but they do have memories, at least when it comes to viruses that attack them. Many bacteria have a molecular immune system which allows these microbes to capture and retain pieces of viral DNA that they have encountered in the past, in order to recognize and destroy it when it shows up again.


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Influenza Virus Reservoirs and Intermediate Hosts: Dogs, Horses, and New Possibilities for Influenza Virus Exposure of Humans

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Latest updates on today's emerging viruses of pandemic potential

The online version of Microbes and Infection at ScienceDirect.com, the world's leading platform for high quality peer-reviewed full-text journals.

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Ed Rybicki's curator insight, February 20, 7:14 AM

Useful resource, and nice material on Ebola in particular.

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Experience of the Eliava Institute in bacteriophage therapy

Experience of the Eliava Institute in bacteriophage therapy | Virology and Bioinformatics from Virology.ca | Scoop.it

The rapid propagation of multidrug resistant bacterial strains is leading to renewed interest in bacteriophage therapy. With challenges in the treatment of bacterial infections, it is essential for people worldwide to understand how alternative approaches, such as bacteriophages, could be used to combat antibiotic resistant bacteria. The Eliava Institute of Bacteriophages, Microbiology and Virology (Tbilisi, Georgia) is arguably the most famous institution in the world focused on the isolation, study, and selection of phages active against a variety of bacterial pathogens.

 

Figure 1. (A) Felix d'Herelle and George Eliava working at the bacteriophage institute in Tbilisi in the 1930s. (B) The George Eliava Institute of Bacteriophages, Microbiology, and Virology. (Courtesy of the Eliava Institute)

 


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Ed Rybicki's curator insight, February 17, 2:54 AM

Really nice little piece of neglected history.

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Scripps Florida Scientists Announce Anti-HIV Agent So Powerful It Can Work in a Vaccine

Scripps Florida Scientists Announce Anti-HIV Agent So Powerful It Can Work in a Vaccine | Virology and Bioinformatics from Virology.ca | Scoop.it
News Release
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Health experts question lack of crackdown on ‘homeopathic vaccines’

Health experts question lack of crackdown on ‘homeopathic vaccines’ | Virology and Bioinformatics from Virology.ca | Scoop.it
Failure of officials to crack down on promotion of anti-vaccination views by some licensed alternative medicine practitioners being called a dangerous double standard
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Once A Vaccine Skeptic, This Mom Changed Her Mind

Once A Vaccine Skeptic, This Mom Changed Her Mind | Virology and Bioinformatics from Virology.ca | Scoop.it
Juniper Russo wants what is best for her daughter, Vivian, and she sometimes questions mainstream medicine. But after three years of soul-searching, she decided vaccination was best.
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Why aren't there any ebola parties?

Why aren't there any ebola parties? | Virology and Bioinformatics from Virology.ca | Scoop.it
Yesterday, the PBS NewsHour felt compelled to inform its viewers that they should not let their children attend measles parties. Measles parties are relatively new since, until recently, there were...
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