Virology and Bioinformatics from Virology.ca
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Mutations associated with severity of the pandemic influenza A(H1N1)pdm09 in humans: a systematic review and meta-analysis of epidemiological evidence - Arch Virol. 2014

Abstract

Mutations in the haemagglutinin (HA), non-structural protein 1 (NS1) and polymerase basic protein 2 (PB2) of influenza viruses have been associated with virulence. This study investigated the association between mutations in these genes in influenza A(H1N1)pdm09 virus and the risk of severe or fatal disease. Searches were conducted on the MEDLINE, EMBASE and Web of Science electronic databases and the reference lists of published studies. The PRISMA and STROBE guidelines were followed in assessing the quality of studies and writing-up. Eighteen (18) studies, from all continents, were included in the systematic review (recruiting patients 0 - 77 years old). The mutation D222G was associated with a significant increase in severe disease (pooled RD: 11 %, 95 % CI: 3.0 % - 18.0 %, p = 0.004) and the risk of fatality (RD: 23 %, 95 % CI: 14.0 %-31.0 %, p = < 0.0001). No association was observed between the mutations HA-D222N, D222E, PB2-E627K and NS1-T123V and severe/fatal disease. The results suggest that no virus quasispecies bearing virulence-conferring mutations in the HA, PB2 and NS1 predominated. However issues of sampling bias, and bias due to uncontrolled confounders such as comorbidities, and viral and bacterial coinfection, should be born in mind. Influenza A viruses should continue to be monitored for the occurrence of virulence-conferring mutations in HA, PB2 and NS1. There are suggestions that respiratory virus coinfections also affect virus virulence. Studies investigating the role of genetic mutations on disease outcome should make efforts to also investigate the role of respiratory virus coinfections.

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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.
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Single-stranded DNA phages: from early molecular biology tools to recent revolutions in environmental microbiology

Single-stranded DNA (ssDNA) phages are profoundly different from tailed phages in many aspects including the nature and size of their genome, virion size and morphology, mutation rate, involvement in horizontal gene transfer, infection dynamics and cell lysis mechanisms. Despite the importance of ssDNA phages as molecular biology tools and model systems, the environmental distribution and ecological roles of these phages have been largely unexplored. Viral metagenomics and other culture-independent viral diversity studies have recently challenged the perspective of tailed, double-stranded DNA (dsDNA) phages, dominance by demonstrating the prevalence of ssDNA phages in diverse habitats. However, the differences between ssDNA and dsDNA phages also substantially limit the efficacy of simultaneously assessing the abundance and diversity of these two phage groups. Here we provide an overview of the major differences between ssDNA and tailed dsDNA phages that may influence their effects on bacterial communities. Furthermore, through the analysis of 181 published metaviromes we demonstrate the environmental distribution of ssDNA phages and present an analysis of the methodological biases that distort their study through metagenomics.
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Ebola virus can reside in a survivor's semen up to 12 months

Ebola virus can reside in a survivor's semen up to 12 months | Virology and Bioinformatics from Virology.ca | Scoop.it
A new study carried out in Guinea confirms that the Ebola virus may remain in a survivor's semen up to one year.
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Security spending must cover disease outbreaks

Security spending must cover disease outbreaks | Virology and Bioinformatics from Virology.ca | Scoop.it
Diagnostic tools, medicines and vaccines are in limited supply, non-existent or too costly
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The central roles of two African countries in the evolution and worldwide spread of Zika virus

Abstract: Recent outbreaks of Zika virus (ZIKV) infections in Oceania's islands and the Americas were characterized by high numbers of cases and the spread of the virus to new areas. To better understand the origin of ZIKV, its epidemic history was reviewed. Although the available records and information are limited, two major genetic lineages of ZIKV were identified in previous studies. However, in this study, three lineages were identified based on a phylogenetic analysis of all virus sequences from GenBank, including those of the envelope protein (E) and non-structural protein 5 (NS5) coding regions. The spatial and temporal distributions of the three identified ZIKV lineages and the recombination events and mechanisms underlying their divergence and evolution were further elaborated. The potential migration pathway of ZIKV was also characterized. Our findings revealed the central roles of two African countries, Senegal and Cote d'Ivoire, in ZIKV evolution and genotypic divergence. Furthermore, our results suggested that the outbreaks in Asia and the Pacific islands originated from Africa. The results provide insights into the geographic origins of ZIKV outbreaks and the spread of the virus, and also contribute to a better understanding of ZIKV evolution, which is important for the prevention and control of ZIKV infections.
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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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This week in Zika: An anniversary, how the virus kills brain cells and more

This week in Zika: An anniversary, how the virus kills brain cells and more | Virology and Bioinformatics from Virology.ca | Scoop.it
New weapons in the fight against Zika, how the virus shrinks minibrains, a quick paper-based test for Zika, and more in this week’s Zika Watch.
Kathleen McLeod's insight:
Happy Anniversary?
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A Cure For Chronic Hepatitis B May Be On The Way

A Cure For Chronic Hepatitis B May Be On The Way | Virology and Bioinformatics from Virology.ca | Scoop.it
USC scientists find a connection between a mother's HBV and child's risk of infection, opening the door for a cure.
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Deaths From Hepatitis C Virus Hit All-Time High, CDC Reports

CDC also published a separate study that found more people in the United States now die from hepatitis C than die from HIV or any other infectious disease. The report comes as The American Journal of Managed Care publishes a special issue on policy concerns over patient access to new therapies that cure HCV.
Ed Rybicki's insight:
The other, other, OTHER nastiest flavivirus....
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Assembly of long DNA sequences using a new synthetic Escherichia coli-yeast shuttle vector

Synthetic biology is a newly developed field of research focused on designing and rebuilding novel biomolecular components, circuits, and networks. Synthetic biology can also help understand biological principles and engineer complex artificial metabolic systems. DNA manipulation on a large genome-wide scale is an inevitable challenge, but a necessary tool for synthetic biology. To improve the methods used for the synthesis of long DNA fragments, here we constructed a novel shuttle vector named pGF (plasmid Genome Fast) for DNA assembly in vivo. The BAC plasmid pCC1BAC, which can accommodate large DNA molecules, was chosen as the backbone. The sequence of the yeast artificial chromosome (YAC) regulatory element CEN6-ARS4 was synthesized and inserted into the plasmid to enable it to replicate in yeast. The selection sequence HIS3, obtained by polymerase chain reaction (PCR) from the plasmid pBS313, was inserted for screening. This new synthetic shuttle vector can mediate the transformation-associated recombination (TAR) assembly of large DNA fragments in yeast, and the assembled products can be transformed into Escherichia coli for further amplification. We also conducted in vivo DNA assembly using pGF and yeast homologous recombination and constructed a 31-kb long DNA sequence from the cyanophage PP genome. Our findings show that this novel shuttle vector would be a useful tool for efficient genome-scale DNA reconstruction.
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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


Via Ed Rybicki
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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.