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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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Putative E3 Ubiquitin Ligase of Human Rotavirus Inhibits NF-κB Activation by Using Molecular Mimicry To Target β-TrCP

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Pathogenic Influenza Viruses and Coronaviruses Utilize Similar and Contrasting Approaches To Control Interferon-Stimulated Gene Responses

Pathogenic Influenza Viruses and Coronaviruses Utilize Similar and Contrasting Approaches To Control Interferon-Stimulated Gene Responses | Virology and Bioinformatics from Virology.ca | Scoop.it

IMPORTANCE This work combines systems biology and experimental validation to identify and confirm strategies used by viruses to control the immune response. Using a novel screening approach, specific comparison between highly pathogenic influenza viruses and coronaviruses revealed similarities and differences in strategies to control the interferon and innate immune response. These findings were subsequently confirmed and explored, revealing both a common pathway of antagonism via type I interferon (IFN) delay as well as a novel avenue for control by altered histone modification. Together, the data highlight how comparative systems biology analysis can be combined with experimental validation to derive novel insights into viral pathogenesis.

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Read this before you ever believe another guest on the Dr. Oz Show

A new FTC case reveals the incredible marketing scheme behind the Dr. Oz Show.
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A Scientist in Wonderland: A Memoir of Searching for Truth and Finding Trouble: Amazon.co.uk: Edzard Ernst: 9781845407773: Books

A Scientist in Wonderland: A Memoir of Searching for Truth and Finding Trouble

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Buy A Scientist in Wonderland: A Memoir of Searching for Truth and Finding Trouble by Edzard Ernst (ISBN: 9781845407773) from Amazon's Book Store. Free UK delivery on eligible orders.
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Measles Outbreak at Disneyland | Viruses101 | Learn Science at Scitable

Measles Outbreak at Disneyland | Viruses101 | Learn Science at Scitable | Virology and Bioinformatics from Virology.ca | Scoop.it
A recent measles outbreak has plagued the Disneyland theme park in California. Why the growing anti-vaccination movement is partly to blame.
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The Mermaid's Tale: Your money at work...er, waste: the million genomes project

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Identification of amino acid substitutions supporting antigenic change of A(H1N1)pdm09 viruses.

Importance Influenza A viruses can cause significant morbidity and mortality in humans. Amino acid substitutions in the hemagglutinin protein can result in escape from antibody-mediated neutralization. This allows the virus to re-infect individuals that have acquired immunity to previously circulating strains through infection or vaccination. To date, the vast majority of A(H1N1)pdm09 strains remain antigenically similar to the virus that caused the 2009 influenza pandemic. However, antigenic variants are expected to emerge as a result of increasing population immunity. We show that single amino acid substitutions near the receptor binding site were sufficient to escape from antibodies specific for A(H1N1)pdm09 viruses, but not from antibodies elicited in response to infections with seasonal A(H1N1) and A(H1N1)pdm09 viruses. This study identifies substitutions in A(H1N1)pdm09 viruses that support escape from population immunity, but also suggests that the number of potential escape variants is limited by previous exposure to seasonal A(H1N1) viruses.

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New Tick-Borne 'Bourbon Virus' Is Deadly And Unlike Anything Previously Seen In U.S.

Researchers have identified the cause of a Kansas farmer's mysterious death this summer as Bourbon virus.

Thought to be transmitted by ticks, the virus "was fast-moving and severe, causing lung and kidney failure, and shock," The New Yor...
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Quashing Stubborn Hospital Infections Relies on Genetic Sequencing

Quashing Stubborn Hospital Infections Relies on Genetic Sequencing | Virology and Bioinformatics from Virology.ca | Scoop.it
The technique to stop multidrug-resistant bacteria is spreading after an 80-week test case proved its worth
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Population Structure and Evolution of Rhinoviruses

Population Structure and Evolution of Rhinoviruses | Virology and Bioinformatics from Virology.ca | Scoop.it
Rhinoviruses, formerly known as Human rhinoviruses, are the most common cause of air-borne upper respiratory tract infections in humans. Rhinoviruses belong to the family Picornaviridae and are divided into three species namely, Rhinovirus A, -B and -C, which are antigenically diverse. Genetic recombination is found to be one of the important causes for diversification of Rhinovirus species. Although emerging lineages within Rhinoviruses have been reported, their population structure has not been studied yet. The availability of complete genome sequences facilitates study of population structure, genetic diversity and underlying evolutionary forces, such as mutation, recombination and selection pressure. Analysis of complete genomes of Rhinoviruses using a model-based population genetics approach provided a strong evidence for existence of seven genetically distinct subpopulations. As a result of diversification, Rhinovirus A and -C populations are divided into four and two subpopulations, respectively. Genetically, the Rhinovirus B population was found to be homogeneous. Intra-species recombination was observed to be prominent in Rhinovirus A and -C species. Significant evidence of episodic positive selection was obtained for several sites within coding sequences of structural and non-structural proteins. This corroborates well with known phenotypic properties such as antigenicity of structural proteins. Episodic positive selection appears to be responsible for emergence of new lineages especially in Rhinovirus A. In summary, the Rhinovirus population is an ensemble of seven distinct lineages. In case of Rhinovirus A, intra-species recombination and episodic positive selection contribute to its further diversification. In case of Rhinovirus C, intra- and inter-species recombinations are responsible for observed diversity. Population genetics approach was further useful to analyze phylogenetic tree topologies pertaining to recombinant strains, especially when trees are derived using complete genomes. Understanding of population structure serves as a foundation for designing new vaccines and drugs as well as to explain emergence of drug resistance amongst subpopulations
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Cell Cycle-Independent Phospho-Regulation of Fkh2 during Hyphal Growth Regulates Candida albicans Pathogenesis

Cell Cycle-Independent Phospho-Regulation of Fkh2 during Hyphal Growth Regulates  Candida albicans  Pathogenesis | Virology and Bioinformatics from Virology.ca | Scoop.it
Author Summary The fungus Candida albicans is a commensal in the human microbiota, responsible for superficial infections such as oral and vaginal thrush. However, it can become highly virulent, causing life-threatening systemic candidemia in severely immunocompromised patients, including those taking immunosuppressive drugs for transplantation, sufferers of AIDS and neutropenia, and individuals undergoing chemotherapy or at extremes of age. With a rapidly increasing ageing population worldwide, C. albicans and other fungal pathogens will become more prevalent, demanding a greater understanding of their pathogenesis for the development of effective therapeutics. Fungal pathogenicity requires a coordinated change in the pattern of gene expression orchestrated by a set of transcription factors. Here we have discovered that a transcription factor, Fkh2, is modified by phosphorylation under the control of the kinases Cdc28 and Cbk1 in response to conditions that activate virulence factor expression. Fkh2 is involved in a wide variety of cellular processes including cell proliferation, but this phosphorylation endows it with a specialized function in promoting the expression of genes required for tissue invasion, biofilm formation, and pathogenesis in the host. This study highlights the role of protein phosphorylation in regulating pathogenesis and furthers our understanding of the pathogenic switch in this important opportunistic fungal pathogen.
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KSHV microRNAs repress breakpoint cluster region protein expression, enhance Rac1 activity, and increase in vitro angiogenesis

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The Clinical Significance of Measles: A Review

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Gilbert Faure au nom de l'ASSIM's comment, January 29, 2:35 AM
paper of 2004, still valid
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Why Did Vaccinated People Get Measles at Disneyland? Blame the Unvaccinated | WIRED

Why Did Vaccinated People Get Measles at Disneyland? Blame the Unvaccinated | WIRED | Virology and Bioinformatics from Virology.ca | Scoop.it
The misery of a measles outbreak at the Happiest Place on Earth is an irony even the most jaded epidemiologist could do without, but the 42 measles cases that originated in Disneyland in December hide within them an even scarier number—scary, that is, unless you understand how vaccines work.
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Chimps And Gorillas Desperately Need Ebola Vaccine Too – Virus Has Wiped Out A Third Of Them | IFLScience

Chimps And Gorillas Desperately Need Ebola Vaccine Too – Virus Has Wiped Out A Third Of Them | IFLScience | Virology and Bioinformatics from Virology.ca | Scoop.it
There is a side to the Ebola crisis that, perhaps understandably, has received little media attention: the threat it poses to our nearest cousins, the great apes of Africa. At this moment in time Ebola is the single greatest threat to the survival of gorillas and chimpanzees.
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Disneyland says unvaccinated kids not welcome amid measles outbreak

Disneyland says unvaccinated kids not welcome amid measles outbreak | Virology and Bioinformatics from Virology.ca | Scoop.it
Dozens of California cases prompt warning by park officials; five Disneyland workers have been diagnosed with illness
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Antiviral immunity Dual attack by RIG-I - Nature.com

Antiviral immunity Dual attack by RIG-I
Nature.com
A recent study in Immunity describes a novel antiviral role for the cytosolic sensor RIG-I. Sato et al.

Via Gilbert Faure au nom de l'ASSIM, Kenzibit
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Gilbert Faure au nom de l'ASSIM's curator insight, January 19, 2:13 PM

A recent study in Immunity describes a novel antiviral role for the cytosolic sensor RIG-I. Sato et al. show that RIG-I not only induces an interferon (IFN) response during hepatitis B virus (HBV) infection, but also directly suppresses viral replication by blocking the binding of the HBV polymerase to the pre-genomic RNA (pgRNA) of the virus…

 http://www.scoop.it/t/immunology?q=rig

 

from WIKIPEDIA

RIG-I (retinoic acid-inducible gene 1) is a RIG-I-like receptor dsRNA helicase enzyme that is encoded (in humans) by the DDX58 gene. RIG-I is part of the RIG-I-like receptor family, which also includes MDA5 and LGP2, and functions as a pattern recognition receptor that is a sensor for viruses such as influenza A, Sendai virus, and flavivirus, however RIG-I provides no immunity to DNA viruses or retroviruses. RIG-I typically recognizes short (< 4000nt) 5′ triphosphate uncapped double stranded or single stranded RNA.[1][2][3] RIG-I and MDA5 are involved in activating MAVS and triggering an antiviral response.[4] RIG-I is also able to detect non-self 5′-triphosphorylated dsRNA transcribed from AT-rich dsDNA by DNA-dependent RNA polymerase III (Pol III). For many viruses, effective RIG-I-mediated antiviral responses are dependent on functionally active LGP2.[5]

 







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Why quarantine for measles is critical…and quarantine for Ebola was not

Why quarantine for measles is critical…and quarantine for Ebola was not | Virology and Bioinformatics from Virology.ca | Scoop.it
Measles has come to the happiest place on Earth. As of this writing, a total of 32 cases of measles have been linked to Disneyland visits that took place between December 17th and 20th. About 75% of the cases identified to date were not vaccinated, either because they chose to forgo vaccines or because they…
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The contrasting phylodynamics of human influenza B viruses

A complex interplay of viral, host and ecological factors shape the spatio-temporal incidence and evolution of human influenza viruses. Although considerable attention has been paid to influenza A viruses, a lack of equivalent data means that an integrated evolutionary and epidemiological framework has until now not been available for influenza B viruses, despite their significant disease burden. Through the analysis of over 900 full genomes from an epidemiological collection of more than 26,000 strains from Australia and New Zealand, we reveal fundamental differences in the phylodynamics of the two co-circulating lineages of influenza B virus (Victoria and Yamagata), showing that their individual dynamics are determined by a complex relationship between virus transmission, age of infection and receptor binding preference. In sum, this work identifies new factors that are important determinants of influenza B evolution and epidemiology.

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BMC Bioinformatics | Full text | Metavir 2: new tools for viral metagenome comparison and assembled virome analysis

Metagenomics, based on culture-independent sequencing, is a well-fitted approach to provide insights into the composition, structure and dynamics of environmental viral communities. Following recent advances in sequencing technologies, new challenges arise for existing bioinformatic tools dedicated to viral metagenome (i.e. virome) analysis as (i) the number of viromes is rapidly growing and (ii) large genomic fragments can now be obtained by assembling the huge amount of sequence data generated for each metagenome.
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The Impact of Spatial Structure on Viral Genomic Diversity Generated during Adaptation to Thermal Stress

The Impact of Spatial Structure on Viral Genomic Diversity Generated during Adaptation to Thermal Stress | Virology and Bioinformatics from Virology.ca | Scoop.it
Background

Most clinical and natural microbial communities live and evolve in spatially structured environments. When changes in environmental conditions trigger evolutionary responses, spatial structure can impact the types of adaptive response and the extent to which they spread. In particular, localized competition in a spatial landscape can lead to the emergence of a larger number of different adaptive trajectories than would be found in well-mixed populations. Our goal was to determine how two levels of spatial structure affect genomic diversity in a population and how this diversity is manifested spatially.

Methodology/Principal Findings

We serially transferred bacteriophage populations growing at high temperatures (40°C) on agar plates for 550 generations at two levels of spatial structure. The level of spatial structure was determined by whether the physical locations of the phage subsamples were preserved or disrupted at each passage to fresh bacterial host populations. When spatial structure of the phage populations was preserved, there was significantly greater diversity on a global scale with restricted and patchy distribution. When spatial structure was disrupted with passaging to fresh hosts, beneficial mutants were spread across the entire plate. This resulted in reduced diversity, possibly due to clonal interference as the most fit mutants entered into competition on a global scale. Almost all substitutions present at the end of the adaptation in the populations with disrupted spatial structure were also present in the populations with structure preserved.

Conclusions/Significance

Our results are consistent with the patchy nature of the spread of adaptive mutants in a spatial landscape. Spatial structure enhances diversity and slows fixation of beneficial mutants. This added diversity could be beneficial in fluctuating environments. We also connect observed substitutions and their effects on fitness to aspects of phage biology, and we provide evidence that some substitutions exclude each other.
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HIV Reverse-Transcriptase Drug Resistance Mutations During Early Infection Reveal Greater Transmission Diversity Than in Envelope Sequences

Background. Drug resistance mutations (DRMs) can serve as distinct, nonpolymorphic markers for evaluating diversity of expressed HIV-1. We screened for DRMs during early-acute viremia and examined the diversity in reverse transcriptase (RT) relative to envelope (env) in cases of transmitted drug resistance.

Methods. We evaluated 111 longitudinal plasma samples collected every 2–7 days from 15 individuals who seroconverted for HIV-1 infection in 1994–2000. The samples were screened with sensitive polymerase chain reaction assays for the commonly transmitted M41L and K70R mutations and for K65R, which was undetected by bulk sequencing. Mutation-positive samples were further characterized by clonal sequencing of RT and env V1–V3.

Results. Drug resistance mutations were detected in 4 of 15 seroconverters at 5–50 days of viral nucleic acid expression; most mutations disappeared about the time of seroconversion. Clonal sequencing verified low-level K65R at frequencies of 0.4%–4.9%. In each case, K65R coexisted unlinked with variants carrying 2–5 thymidine analog mutations at frequencies of 1.6%–23.0%. In one seroconverter, variants with M184V and nonnucleoside RT inhibitor mutations were also identified at first RNA expression. Each seroconverter displayed a homogeneous V1–V3 env population.

Conclusions. Reverse-transcriptase DRMs demonstrate that the breadth of variants in transmission may be greater than what is reflected in envelope sequences.
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