Virology and Bioinformatics from Virology.ca
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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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Cell Reports - Marburgvirus Hijacks Nrf2-Dependent Pathway by Targeting Nrf2-Negative Regulator Keap1

Cell Reports - Marburgvirus Hijacks Nrf2-Dependent Pathway by Targeting Nrf2-Negative Regulator Keap1 | Virology and Bioinformatics from Virology.ca | Scoop.it
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RNAseqViewer: visualization tool for RNA-Seq data

RNAseqViewer: visualization tool for RNA-Seq data | Virology and Bioinformatics from Virology.ca | Scoop.it

Summary: With the advances of RNA sequencing technologies, scientists need new tools to analyze transcriptome data. We introduce RNAseqViewer, a new visualization tool dedicated to RNA-Seq data. The program offers innovative ways to represent transcriptome data for single or multiple samples. It is a handy tool for scientists who use RNA-Seq data to compare multiple transcriptomes, for example, to compare gene expression and alternative splicing of cancer samples or of different development stages.

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TeselaGen Is Building A Platform For Rapid Prototyping in Synthetic Biology | TechCrunch

TeselaGen Is Building A Platform For Rapid Prototyping in Synthetic Biology | TechCrunch | Virology and Bioinformatics from Virology.ca | Scoop.it
As the costs of DNA sequencing and synthesis drop precipitously, a host of computer science-meets-biotech startups are cropping up in Silicon Valley...
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Virology Journal | Abstract | Complete genome analysis of a frog virus 3 (FV3) isolate and sequence comparison with isolates of differing levels of virulence

 

Frog virus 3 (FV3) is the type species of the genus Ranavirus, and in the past few decades, FV3 infections have resulted in considerable morbidity and mortality in a range of wild and cultivated amphibian species in the Americas, Europe, and Asia. The reasons for the pathogenicity of FV3 are not well understood.

 

Findings: We investigated three FV3 isolates designated SSME, wt-FV3, and aza-Cr, and reported that our wt-FV3 and aza-Cr strains showed similar levels of virulence, while SSME was the least virulent in an in vivo study with Lithiobates pipiens tadpoles. Using 454 GS-FLX sequencing technology, we sequenced SSME and compared it to the published wt-FV3 genome. SSME had multiple amino acid deletions in ORFs 49/50L, 65L, 66L, and 87L, which may explain its reduced virulence. We also investigated repeat regions and found that repeat copy number differed between isolates, with only one group of 3 isolates and 1 pair of isolates being identical at all 3 locations.

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TeselaGen Is Building A Platform For Rapid Prototyping in Synthetic Biology - TechCrunch

TeselaGen Is Building A Platform For Rapid Prototyping in Synthetic Biology - TechCrunch | Virology and Bioinformatics from Virology.ca | Scoop.it

TeselaGen has built visual tools that help researchers view and edit sequences, which is somewhat similar to what both Benchling and Genome Compiler do. But they’re also leveraging j5, which is a new software-based tool that automates DNA assembly and design.


Via Marko Dolinar
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The Impact of Missing Vaccines on Africa and Asia - Vaccine Nation : Vaccine Nation

The Impact of Missing Vaccines on Africa and Asia - Vaccine Nation : Vaccine Nation | Virology and Bioinformatics from Virology.ca | Scoop.it

Via Mel Melendrez-Vallard
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The Parable of Google Flu: Traps in Big Data Analysis

In February 2013, Google Flu Trends (GFT) made headlines but not for a reason that Google executives or the creators of the flu tracking system would have hoped. Nature reported that GFT was predicting more than double the proportion of doctor visits for influenza-like illness (ILI) than the Centers for Disease Control and Prevention (CDC), which bases its estimates on surveillance reports from laboratories across the United States (1, 2). This happened despite the fact that GFT was built to predict CDC reports. Given that GFT is often held up as an exemplary use of big data (3, 4), what lessons can we draw from this error?

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Genetic languages guide the design of synthetic biological systems

Genetic languages guide the design of synthetic biological systems | Virology and Bioinformatics from Virology.ca | Scoop.it
(Phys.org) —Researchers at Virginia Tech and the Massachusetts Institute of Technology have used a computer-aided design tool to create genetic languages to guide the design of biological systems.
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Complex Reassortment of Polymerase Genes in Asian Influenza A Virus H7 and H9 Subtypes

The epidemic first caused by a novel H7N9 avian influenza A virus (IAV) has emerged in China recently. Meanwhile, a novel H7N7 IAV with the ability to infect mammals was also found in China. Both IAVs of H7 subtype possess internal genes originating from H9N2. As internal polymerase genes play a key role for interspecies transmission of IAVs, it is important to trace the reassortment history of polymerase genes in the IAVs of H7 and H9 subtypes. Here, by comprehensive phylogenetic analyses of Asian H7 and H9 polymerases, we showed a significant incongruence among the tree topologies of polymerase genes PA, PB1 and PB2, which suggested frequent intra-subtype reassortments in the IAVs of H9N2. Moreover, the PA gene of H1N1pdm09 clustered with that of H9N2 located at the basal position of clade A, including most strains isolated from mammals and the recent novel H7N9 in the phylogenetic tree of PA. This finding indicated that the H1N1pdm09-like PA gene may play an important role in the human H7N9 epidemic. Results also showed that the earlier strains of H7 subtype were divided into several clusters dispersed within the strains of H9N2, implying multiple direct and/or indirect reassortments may occur between H7 and H9 polymerase genes. Furthermore, the most recent reassortments occurred multiply on the polymerase genes of the newly emerging H7N9 isolated from human in South China, evolving E627K mutation in PB2 independently. These results suggest that the reassortment history of polymerase genes in Asian IAVs of H7 and H9 subtypes is complex and timely evolutionary analyses on the novel H7N9 with newly adapted polymerase are necessary for preventing a potential outbreak in South China.

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Sampling Strategies and Biodiversity of Influenza A Subtypes in Wild Birds

Abstract

"Wild aquatic birds are recognized as the natural reservoir of avian influenza A viruses (AIV), but across high and low pathogenic AIV strains, scientists have yet to rigorously identify most competent hosts for the various subtypes. We examined 11,870 GenBank records to provide a baseline inventory and insight into patterns of global AIV subtype diversity and richness. Further, we conducted an extensive literature review and communicated directly with scientists to accumulate data from 50 non-overlapping studies and over 250,000 birds to assess the status of historic sampling effort. We then built virus subtype sample-based accumulation curves to better estimate sample size targets that capture a specific percentage of virus subtype richness at seven sampling locations. Our study identifies a sampling methodology that will detect an estimated 75% of circulating virus subtypes from a targeted bird population and outlines future surveillance and research priorities that are needed to explore the influence of host and virus biodiversity on emergence and transmission."

 

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Interactive visualization and analysis of large-scale sequencing datasets using ZENBU : Nature Biotechnology : Nature Publishing Group

Interactive visualization and analysis of large-scale sequencing datasets using ZENBU : Nature Biotechnology : Nature Publishing Group | Virology and Bioinformatics from Virology.ca | Scoop.it
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iPhylo: Displaying a million DNA barcodes on Google Maps using CouchDB

iPhylo: Displaying a million DNA barcodes on Google Maps using CouchDB | Virology and Bioinformatics from Virology.ca | Scoop.it
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Comparative community burden and severity of seasonal and pandemic influenza: results of the Flu Watch cohort study : The Lancet Respiratory Medicine

BackgroundAssessment of the effect of influenza on populations, including risk of infection, illness if infected, illness severity, and consultation rates, is essential to inform future control and prevention. We aimed to compare the community burden and severity of seasonal and pandemic influenza across different age groups and study years and gain insight into the extent to which traditional surveillance underestimates this burden.MethodsUsing preseason and postseason serology, weekly illness reporting, and RT-PCR identification of influenza from nasal swabs, we tracked the course of seasonal and pandemic influenza over five successive cohorts (England 2006—11; 5448 person-seasons' follow-up). We compared burden and severity of seasonal and pandemic strains. We weighted analyses to the age and regional structure of England to give nationally representative estimates. We compared symptom profiles over the first week of illness for different strains of PCR-confirmed influenza and non-influenza viruses using ordinal logistic regression with symptom severity grade as the outcome variable.FindingsBased on four-fold titre rises in strain-specific serology, on average influenza infected 18% (95% CI 16—22) of unvaccinated people each winter. Of those infected there were 69 respiratory illnesses per 100 person-influenza-seasons compared with 44 per 100 in those not infected with influenza. The age-adjusted attributable rate of illness if infected was 23 illnesses per 100 person-seasons (13—34), suggesting most influenza infections are asymptomatic. 25% (18—35) of all people with serologically confirmed infections had PCR-confirmed disease. 17% (10—26) of people with PCR-confirmed influenza had medically attended illness. These figures did not differ significantly when comparing pandemic with seasonal influenza. Of PCR-confirmed cases, people infected with the 2009 pandemic strain had markedly less severe symptoms than those infected with seasonal H3N2.InterpretationSeasonal influenza and the 2009 pandemic strain were characterised by similar high rates of mainly asymptomatic infection with most symptomatic cases self-managing without medical consultation. In the community the 2009 pandemic strain caused milder symptoms than seasonal H3N2.FundingMedical Research Council and the Wellcome Trust.
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Selfish gene, dead or alive? – David Dobbs & others – Aeon Magazine

Selfish gene, dead or alive? – David Dobbs & others – Aeon Magazine | Virology and Bioinformatics from Virology.ca | Scoop.it
Is it time to kill off the idea of the selfish gene? We asked four experts to respond to our most controversial essay
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A survey of tools for variant analysis of next-generation genome sequencing data

A survey of tools for variant analysis of next-generation genome sequencing data | Virology and Bioinformatics from Virology.ca | Scoop.it

Here, [they] surveyed 205 tools for whole-genome/whole-exome sequencing data analysis supporting five distinct analytical steps: quality assessment, alignment, variant identification, variant annotation and visualization. [They] report an overview of the functionality, features and specific requirements of the individual tools. [They] then selected 32 programs for variant identification, variant annotation and visualization...

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Prediction of Steps in the Evolution of Variola Virus Host Range

Prediction of Steps in the Evolution of Variola Virus Host Range | Virology and Bioinformatics from Virology.ca | Scoop.it

Variola virus, the agent of smallpox, has a severely restricted host range (humans) but a devastatingly high mortality rate. Although smallpox has been eradicated by a World Health Organization vaccination program, knowledge of the evolutionary processes by which human super-pathogens such as variola virus arise is important. By analyzing the evolution of variola and other closely related poxviruses at the level of single nucleotide polymorphisms we detected a hotspot of genome variation within the smallpox ortholog of the vaccinia virus O1L gene, which is known to be necessary for efficient replication of vaccinia virus in human cells. These mutations in the variola virus ortholog and the subsequent loss of the functional gene from camelpox virus and taterapox virus, the two closest relatives of variola virus, strongly suggest that changes within this region of the genome may have played a key role in the switch to humans as a host for the ancestral virus and the subsequent host-range restriction that must have occurred to create the phenotype exhibited by smallpox.

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The Rise and Fall of HIV in High-Prevalence Countries: A Challenge for Mathematical Modeling

The Rise and Fall of HIV in High-Prevalence Countries: A Challenge for Mathematical Modeling | Virology and Bioinformatics from Virology.ca | Scoop.it

Several countries with generalized, high-prevalence HIV epidemics, mostly in sub-Saharan Africa, have experienced rapid declines in transmission. These HIV epidemics, often with rapid onsets, have generally been attributed to a combination of factors related to high-risk sexual behavior. The subsequent declines in these countries began prior to widespread therapy or implementation of any other major biomedical prevention. This change has been construed as evidence of behavior change, often on the basis of mathematical models, but direct evidence for behavior changes that would explain these declines is limited. Here, we look at the structure of current models and argue that the common “fixed risk per sexual contact" assumption favors the conclusion of substantial behavior changes. We argue that this assumption ignores reported non-linearities between exposure and risk. Taking this into account, we propose that some of the decline in HIV transmission may be part of the natural dynamics of the epidemic, and that several factors that have traditionally been ignored by modelers for lack of precise quantitative estimates may well hold the key to understanding epidemiologic trends.

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Past, present and future of influenza viruses

Past, present and future of influenza viruses | Virology and Bioinformatics from Virology.ca | Scoop.it

Influenza viruses are genetically diverse owing to high mutation rates, frequent reassortment among genomic segments and their tendency to jump between hosts. Three studies describe new modelling approaches to analyse and predict influenza virus evolution and also shed light on the origin and spread of currently circulating viruses.

 


Via Ed Rybicki
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Anti-sense RNA and Sensibility

Anti-sense RNA and Sensibility | Virology and Bioinformatics from Virology.ca | Scoop.it

We know antisense RNAs are present in many cells, but how (or if) they function remains a mystery. Can a newly developed method for isolating and characterizing these curious RNAs provide new answers?


Via Integrated DNA Technologies
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The Herpes Virus Fc Receptor gE-gI Mediates Antibody Bipolar Bridging to Clear Viral Antigens from the Cell Surface

The Herpes Virus Fc Receptor gE-gI Mediates Antibody Bipolar Bridging to Clear Viral Antigens from the Cell Surface | Virology and Bioinformatics from Virology.ca | Scoop.it
From molecules to physiology
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Share alike

Share alike | Virology and Bioinformatics from Virology.ca | Scoop.it

Every mountaineer knows the sinking feeling of reaching a peak after a hard climb, only to see the true summit still above. Scientists who take on the tough terrain of open access may have a similar experience. After they reach the notable goal of sharing their research papers, they discover that a higher summit awaits: open data.

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Effects of Introduced and Indigenous Viruses on Native Plants: Exploring Their Disease Causing Potential at the Agro-Ecological Interface

Abstract

"The ever increasing movement of viruses around the world poses a major threat to plants growing in cultivated and natural ecosystems. Both generalist and specialist viruses move via trade in plants and plant products. Their potential to damage cultivated plants is well understood, but little attention has been given to the threat such viruses pose to plant biodiversity. To address this, we studied their impact, and that of indigenous viruses, on native plants from a global biodiversity hot spot in an isolated region where agriculture is very recent (<185 years), making it possible to distinguish between introduced and indigenous viruses readily. To establish their potential to cause severe or mild systemic symptoms in different native plant species, we used introduced generalist and specialist viruses, and indigenous viruses, to inoculate plants of 15 native species belonging to eight families. We also measured resulting losses in biomass and reproductive ability for some host–virus combinations. In addition, we sampled native plants growing over a wide area to increase knowledge of natural infection with introduced viruses. The results suggest that generalist introduced viruses and indigenous viruses from other hosts pose a greater potential threat than introduced specialist viruses to populations of native plants encountered for the first time. Some introduced generalist viruses infected plants in more families than others and so pose a greater potential threat to biodiversity. The indigenous viruses tested were often surprisingly virulent when they infected native plant species they were not adapted to. These results are relevant to managing virus disease in new encounter scenarios at the agro-ecological interface between managed and natural vegetation, and within other disturbed natural vegetation situations. They are also relevant for establishing conservation policies for endangered plant species and avoiding spread of damaging viruses to undisturbed natural vegetation beyond the agro-ecological interface."

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VDU's blog: Influenza in Queensland, Australia: 24-Feb-2014:03-Mar-2014.

VDU's blog: Influenza in Queensland, Australia: 24-Feb-2014:03-Mar-2014. | Virology and Bioinformatics from Virology.ca | Scoop.it
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Fraser Health - Measles Outbreak in Fraser East

Fraser Health - Measles Outbreak in Fraser East | Virology and Bioinformatics from Virology.ca | Scoop.it

he most recent exposure to this highly contagious virus has occurred in a school in Chilliwack in a community with traditionally low immunization rates.  Two confirmed cases of measles have been reported and Fraser Health is following up on dozens of linked suspected cases.

Public Health staff are contacting the affected families directly to offer immunoglobulin or vaccine in order to reduce the chance of the infection developing. Of particular concern is students and families preparing for Spring Break.  Fraser Health is advising individuals who may have been exposed to the virus to refrain from travelling until they have been cleared by Public Health.

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