Virology and Bioinformatics from Virology.ca
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Harald zur Hausen on human papillomaviruses

Harald zur Hausen on human papillomaviruses | Virology and Bioinformatics from Virology.ca | Scoop.it
I interviewed Harald zur Hausen, MD., recipient of the 2008 Nobel Prize in Physiology or Medicine, at the 2013 meeting of the Society for General Microbiology.

For TWiV by Vincent Racaniello

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Chris Upton + helpers's curator insight, January 22, 2014 12:39 PM

This is about the importance of the HPV vaccine

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.
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HostPhinder: A Phage Host Prediction Tool

The current dramatic increase of antibiotic resistant bacteria has revitalised the interest in bacteriophages as alternative antibacterial treatment. Meanwhile, the development of bioinformatics methods for analysing genomic data places high-throughput approaches for phage characterization within reach. Here, we present HostPhinder, a tool aimed at predicting the bacterial host of phages by examining the phage genome sequence. Using a reference database of 2196 phages with known hosts, HostPhinder predicts the host species of a query phage as the host of the most genomically similar reference phages. As a measure of genomic similarity the number of co-occurring k-mers (DNA sequences of length k) is used. Using an independent evaluation set, HostPhinder was able to correctly predict host genus and species for 81% and 74% of the phages respectively, giving predictions for more phages than BLAST and significantly outperforming BLAST on phages for which both had predictions. HostPhinder predictions on phage draft genomes from the INTESTI phage cocktail corresponded well with the advertised targets of the cocktail. Our study indicates that for most phages genomic similarity correlates well with related bacterial hosts. HostPhinder is available as an interactive web service [1] and as a stand alone download from the Docker registry [2].
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A new (quantitative!) method for comparative phylogeography

A new (quantitative!) method for comparative phylogeography | Virology and Bioinformatics from Virology.ca | Scoop.it
Comparative phylogeographic studies usually involve a) documenting a phylogeographic pattern and b) recognizing that the same pattern is congruent in multiple species. But what if species histories…
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This week in Zika: Haiti hit early, possible monkey hosts, and more

This week in Zika: Haiti hit early, possible monkey hosts, and more | Virology and Bioinformatics from Virology.ca | Scoop.it
A new test for Zika, how Haiti fits into the outbreak timeline, a look at monkeys that can carry the virus, and more in this week’s Zika Watch.
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A single injection of antibodies protected monkeys from HIV for nearly six months

A single injection of antibodies protected monkeys from HIV for nearly six months | Virology and Bioinformatics from Virology.ca | Scoop.it

A new study has shown that a single injection of antibodies that target HIV can protect monkeys from contracting the virus for nearly six months.

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Disease evolution: our long history of fighting viruses

Disease evolution: our long history of fighting viruses | Virology and Bioinformatics from Virology.ca | Scoop.it
e they do not have a responsibility to immunise their children against the standard infections of childh

Via Ian M Mackay, PhD
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Characterization of human and murine T-cell immunoglobulin mucin domain 4 (TIM-4) IgV domain residues critical for Ebola virus entry

IMPORTANCE With more than 28,000 cases and over 11,000 deaths during the largest and most recent Ebola virus (EBOV) outbreak, there has been increased emphasis on the development of therapeutics against filoviruses. Many therapies under investigation target EBOV cell entry. T-cell immunoglobulin mucin domain (TIM) proteins are cell surface factors important for entry of many enveloped viruses, including EBOV. TIM family member, TIM-4, is expressed on macrophages and dendritic cells, which are early cellular targets during EBOV infection. Here, we performed a mutagenesis screen of the IgV domain of murine and human TIM-4 to identify residues that are critical for EBOV entry. Surprisingly, we identified more human TIM-4 IgV domain residues that are required for EBOV entry than murine TIM-4 residues. Defining TIM IgV residues needed for EBOV entry clarifies the virus/receptor interactions and paves the way for the development of novel therapeutics targeting virus binding to this cell surface receptor.
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Rearrangement of influenza virus spliced segments for the development of live attenuated vaccines

IMPORTANCE Vaccination represents our best therapeutic option against influenza viral infections. However, the efficacy of current influenza vaccines is suboptimal, and novel approaches are necessary for the prevention of disease caused by this important human respiratory pathogen. In this work, we describe a novel approach to generate safer and more efficient live attenuated influenza vaccines (LAIV) based on recombinant viruses encoding non-overlapping and independent M1/M2 (Ms) or both M1/M2 and NS1/NEP (Ms/NSs) open reading frames. Viruses containing a modified M segment were highly attenuated in mice, but able to confer, upon a single intranasal immunization, complete protection against a lethal homologous challenge with wild-type virus. Notably, protection efficacy conferred by our split M viruses was better than that obtained with the current temperature sensitive influenza LAIV. Altogether, these results open a new avenue for the development of safer and more protective LAIV based on genome reorganization of spliced viral RNA segments.
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Can we prevent norovirus infections?

Can we prevent norovirus infections? | Virology and Bioinformatics from Virology.ca | Scoop.it
In a new PLOS Collection – The Global Burden of Norovirus & Prospects for Vaccine Development – global norovirus experts fill critical knowledge gaps and provide key information to further development of a much-needed vaccine:
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When a fish virus can lead to government policy changes

When a fish virus can lead to government policy changes | Virology and Bioinformatics from Virology.ca | Scoop.it
Salmon farming company AquaChile reported the detection of a possible ISA virus outbreak in a cage of one of its salmon farming centres located in the Aysen region, in southern Chile.

The salmon farming company indicated that during the regular and routine sampling processes, "there was a finding by a positive reaction to the PCR probe for ISA virus in one of the 20 cages of the Transit Centre 2, of the district 21 B of the Aysen Region", which currently has fish that are about 2 kilograms.

"In compliance with the regulations, the National Fisheries Service (SERNAPESCA) was informed, and the cage re-sampling procedure was implemented to confirm or refute this finding, the results are not yet available," said AquaChile in a statement.

ISA virus causes significant mortalities in Atlantic salmon, especially in the phase in which these fish live in the sea.

This announcement comes at a time when SalmonChile, like other companies, has suffered economic losses because of harmful algal blooms, which are estimated to result in the loss of about 110,000 tonnes of salmon, equivalent to 10-12 per cent of the annual salmon production from Chile.

After the news of the infectious salmon anemia virus detection, AquaChile shares in the Santiago Stock Exchange ended with a loss of 1.66 per cent last Friday after an earlier fall of more than 4 per cent.

Via Ed Rybicki
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Ed Rybicki's curator insight, April 28, 6:10 AM
It's not just people viruses, people...
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TWiEVO 2: Faster than a speeding virus | This Week in Evolution

TWiEVO 2: Faster than a speeding virus | This Week in Evolution | Virology and Bioinformatics from Virology.ca | Scoop.it
Nels and Vincent talk about how a cellular enzyme contributes to the very high mutation rate of human immunodeficiency virus type 1.
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Antigenic Fingerprinting following Primary RSV Infection in Young Children Identifies Novel Antigenic Sites and Reveals Unlinked Evolution of Human Antibody Repertoires to Fusion and Attachment Gly...

Antigenic Fingerprinting following Primary RSV Infection in Young Children Identifies Novel Antigenic Sites and Reveals Unlinked Evolution of Human Antibody Repertoires to Fusion and Attachment Gly... | Virology and Bioinformatics from Virology.ca | Scoop.it
Author Summary Respiratory syncytial virus (RSV) is the major cause of pneumonia and bronchiolitis among infants and children globally.
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Parechovirus hits Australia: New virus can cause brain damage in babies

Parechovirus hits Australia: New virus can cause brain damage in babies | Virology and Bioinformatics from Virology.ca | Scoop.it
A NEW virus which has hospitalised more than 100 Australian babies since 2013 could cause developmental problems and brain damage, an infectious disease expert says.

Via Ian M Mackay, PhD
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OrfM: A fast open reading frame predictor for metagenomic data

Summary: Finding and translating stretches of DNA lacking stop codons is a task common in the analysis of sequence data. However the computational tools for finding open reading frames are sufficiently slow that they are becoming a bottleneck as the volume of sequence data grows. This computational bottleneck is especially problematic in metagenomics when searching unassembled reads, or screening assembled contigs for genes of interest. Here we present OrfM, a tool to rapidly identify open reading frames (ORFs) in sequence data by applying the Aho-Corasick algorithm to find regions uninterrupted by stop codons. Benchmarking revealed that OrfM finds identical ORFs to similar tools (‘GetOrf’ and ‘Translate’) but is five times faster. While OrfM is sequencing platform-agnostic, it is best suited to large, high quality datasets such as those produced by Illumina sequencers.
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Australia to spend over $11mn to eradicate carps by releasing herpes virus into rivers

Australia to spend over $11mn to eradicate carps by releasing herpes virus into rivers | Virology and Bioinformatics from Virology.ca | Scoop.it

Australia will spend more than US$11 million in a bid to exterminate European carp by releasing a virulent strain of herpes into the country’s largest waterway.


Via Ed Rybicki
Chris Upton + helpers's insight:
W
What do they taste like?
 
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Ed Rybicki's curator insight, May 4, 2:57 AM
Because that myxoma virus release worked so well
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Evaluation of Antihemagglutinin and Antineuraminidase Antibodies as Correlates of Protection in an Influenza A/H1N1 Virus Healthy Human Challenge Model

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‘Dirty’ mice better than lab-raised mice for studying human disease

‘Dirty’ mice better than lab-raised mice for studying human disease | Virology and Bioinformatics from Virology.ca | Scoop.it
Dirtier mice may better mimic human immune reactions.
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How to (seriously) read a scientific paper

How to (seriously) read a scientific paper | Virology and Bioinformatics from Virology.ca | Scoop.it
Adam Ruben’s tongue-in-cheek column about the common difficulties and frustrations of reading a scientific paper broadly resonated among Science Careers readers. Many of you have come to us asking for more (and more serious) advice on how to make sense of the scientific literature, so we’ve asked a dozen scientists at different career stages and in a broad range of fields to tell us how they do it. Although it is clear that reading scientific papers becomes easier with experience, the stumbling blocks are real, and it is up to each scientist to identify and apply the techniques that work best for them. The responses have been edited for clarity and brevity.
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DUDes: a top-down taxonomic profiler for metagenomics

Motivation: Species identification and quantification are common tasks in metagenomics and pathogen detection studies. The most recent techniques are built on mapping the sequenced reads against a reference database (e.g. whole genomes, marker genes, proteins) followed by application-dependent analysis steps. Although these methods have been proven to be useful in many scenarios, there is still room for improvement in species and strain level detection, mainly for low abundant organisms.

Results: We propose a new method: DUDes, a reference-based taxonomic profiler that introduces a novel top-down approach to analyze metagenomic Next-generation sequencing (NGS) samples. Rather than predicting an organism presence in the sample based only on relative abundances, DUDes first identifies possible candidates by comparing the strength of the read mapping in each node of the taxonomic tree in an iterative manner. Instead of using the lowest common ancestor we propose a new approach: the deepest uncommon descendent. We showed in experiments that DUDes works for single and multiple organisms and can identify low abundant taxonomic groups with high precision.

Availability and Implementation: DUDes is open source and it is available at http://sf.net/p/dudes
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The global antigenic diversity of swine influenza A viruses

The global antigenic diversity of swine influenza A viruses | Virology and Bioinformatics from Virology.ca | Scoop.it
ritically, the antigenic diversity shapes the risk profile of swine influenza viruses in terms of their epizootic and pandemic potential. Here, using the most comprehensive set of swine influenza virus antigenic data compiled to date, we quantify the antigenic diversity of swine influenza viruses on a multi-continental scale. The substantial antigenic diversity of recently circulating viruses in different parts of the world adds complexity to the risk profiles for the movement of swine and the potential for swine-derived infections in humans.
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VIRALpro: a tool to identify viral capsid and tail sequences

Motivation: Not only sequence data continue to outpace annotation information, but also the problem is further exacerbated when organisms are underrepresented in the annotation databases. This is the case with non-human-pathogenic viruses which occur frequently in metagenomic projects. Thus, there is a need for tools capable of detecting and classifying viral sequences.

Results: We describe VIRALpro a new effective tool for identifying capsid and tail protein sequences, which are the cornerstones toward viral sequence annotation and viral genome classification.

Availability and implementation: The data, software and corresponding web server are available from http://scratch.proteomics.ics.uci.edu as part of the SCRATCH suite.
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Dengue Virus Antibodies Enhance Zika Virus Infection

Dengue Virus Antibodies Enhance Zika Virus Infection | Virology and Bioinformatics from Virology.ca | Scoop.it

We tested the neutralizing and enhancing potential of well-characterized broadly neutralizing human anti-DENV monoclonal antibodies (HMAbs) and human DENV immune sera against ZIKV using neutralization and ADE assays. We show that anti-DENV HMAbs, cross-react, do not neutralize, and greatly enhance ZIKV infection in vitro. DENV immune sera had varying degrees of neutralization against ZIKV and similarly enhanced ZIKV infection. 

Conclusions / Significance 

Our results suggest that pre-existing DENV immunity will enhance ZIKV infection in vivo and may increase disease severity. A clear understanding of the interplay between ZIKV and DENV will be critical in informing public health responses in regions where these viruses co-circulate and will be particularly valuable for ZIKV and DENV vaccine design and implementation strategies.


Zika virus graphic from Russell Kightley Media


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Ed Rybicki's curator insight, April 26, 4:16 AM
This is a big deal: a really big deal.  While people have been speculating around the issue for months now - yes, you, Neil Bodie! - this prepub appears to provide proof that prior immunity to the related dengue virus(es) may enhance Zika virus infection, without neutralising infectivity.  This is termed "antibody-dependent enhancement" (ADE), and is also a major factor in dengue haemorrhagic fever which results from ADE due to reinfection with a different dengue type.
It is also interesting because this is one of the first high-profile uses of the online preprint archive bioRxiv (STUPID name!) for a virology paper - which may open the floodgates, as people see what a good idea it potentially is.
The possibility that ADE exacerbates Zika infection means that the manifestations of Zika may be very different depending upon the seroprevalence of dengue and possibly yellow fever virus antibodies in the target population: where this is very low - as in the USA or Europe - there may be no real problem.  Where the seroprevalences are high - as is the case in Brazil and much of Central America - Zika infections may be much more severe.
We will wait and see.
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Ross River virus and dengue fever increasing in Australia as global temperatures rise

Ross River virus and dengue fever increasing in Australia as global temperatures rise | Virology and Bioinformatics from Virology.ca | Scoop.it
A record number of people were infected with Ross River virus last year in what doctors believe may be a consequence of global warming.

Via Ed Rybicki
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Lab mice have a chill, and that may be messing up study results

Lab mice have a chill, and that may be messing up study results | Virology and Bioinformatics from Virology.ca | Scoop.it
Evidence is mounting that the temperature lab mice are kept in impacts the results of studies on cancer, metabolism, and inflammation.
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Former naturopathic doctor calls for an end to naturopathic pediatrics

Former naturopathic doctor calls for an end to naturopathic pediatrics | Virology and Bioinformatics from Virology.ca | Scoop.it
A couple is on trial for failing to provide the necessaries of life, after treating their son with home remedies and naturopathy. The toddler died of bacterial meningitis. The case caught the eye of former naturopath Britt Marie Hermes - who says governments should block naturopathic pediatrics.
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Viral infection: Zika virus structure, epidemiology and evolution

In another study, Faria et al. used phylogenetic, epidemiological and travel data to investigate the evolution of ZIKV and its introduction to the Americas. Using next-generation sequencing they generated seven complete ZIKV coding sequences from samples that were collected during the outbreak in Brazil, including four self-limited cases, one blood donor, one fatal adult case, and one newborn with microcephaly and congenital malformations. A comparison of these genomes with other available Brazilian strains showed that the isolates differ at several nucleotide sites in the coding region. Furthermore, the authors found that all of the viruses that were sampled in the Americas share a common ancestor with the ZIKV strain that circulated in French Polynesia in 2013 and, using molecular clock analysis, they estimated that a single introduction of ZIKV into the Americas had occurred between May 2013 and December 2013, a time period that coincided with an increase in air travel from ZIKV endemic regions and with reported outbreaks in the Pacific Islands. Finally, they found that viral genomes from Brazil are phylogenetically interspersed with those from other countries in South America and the Caribbean.
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