Virology and Bioinformatics from Virology.ca
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Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History

"The history of click-speaking Khoe-San, and African populations in general, remains poorly understood. We genotyped ∼2.3 million SNPs in 220 southern Africans and found that the Khoe-San diverged from other populations ≥100,000 years ago, but structure within the Khoe-San dated back to about 35,000 years ago. Genetic variation in various sub-Saharan populations did not localize the origin of modern humans to a single geographic region within Africa; instead, it indicated a history of admixture and stratification. We found evidence of adaptation targeting muscle function and immune response, potential adaptive introgression of UV-light protection, and selection predating modern human diversification involving skeletal and neurological development. These new findings illustrate the importance of African genomic diversity in understanding human evolutionary history."

 

Ex Africa, semper aliquid novi...or old, in this case!

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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.
Bwana Moses's comment, May 25, 6:13 AM
Great work. Keep it going.
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Sea Lice Exploded among Wild Young Salmon near BC Fish Farms: Study | The Tyee

Parasites spiked in Broughton area salmon pens, and hit decade high among wild juveniles, says new report.
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Protein cages made in the lab resemble virus particles

Protein cages made in the lab resemble virus particles | Virology and Bioinformatics from Virology.ca | Scoop.it
Viruses store their genetic material inside a protein shell, known as a capsid, which sometimes has an icosahedral shape. Now, in a development that could go viral, chemists have learned how to create protein icosahedra that look just like the ones some viruses use. Potential applications of such caged structures include packaging biomolecules, drugs, and vaccines and delivering displayed antigens capable of eliciting disease-fighting antibodies.

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Ectromelia Virus Disease Characterization in the BALB/c Mouse: A Surrogate Model for Assessment of Smallpox Medical Countermeasures

In 2007, the United States– Food and Drug Administration (FDA) issued guidance concerning animal models for testing the efficacy of medical countermeasures against variola virus (VARV), the etiologic agent for smallpox. Ectromelia virus (ECTV) is naturally-occurring and responsible for severe mortality and morbidity as a result of mousepox disease in the murine model, displaying similarities to variola infection in humans. Due to the increased need of acceptable surrogate animal models for poxvirus disease, we have characterized ECTV infection in the BALB/c mouse. Mice were inoculated intranasally with a high lethal dose (125 PFU) of ECTV, resulting in complete mortality 10 days after infection. Decreases in weight and temperature from baseline were observed eight to nine days following infection. Viral titers via quantitative polymerase chain reaction (qPCR) and plaque assay were first observed in the blood at 4.5 days post-infection and in tissue (spleen and liver) at 3.5 days post-infection. Adverse clinical signs of disease were first observed four and five days post-infection, with severe signs occurring on day 7. Pathological changes consistent with ECTV infection were first observed five days after infection. Examination of data obtained from these parameters suggests the ECTV BALB/c model is suitable for potential use in medical countermeasures (MCMs) development and efficacy testing.
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Smartphone-based rapid fluorescent diagnostic system for H9N2 virus in specific-pathogen-free chickens

Repeated interspecies transmission of H9N2 virus from poultry to humans and human infections transmitted via aerosols highlight the need for a highly sensitive, rapid diagnostic system for the detecti
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How a Guy From A Montana Trailer Park Overturned 150 Years of Biology

How a Guy From A Montana Trailer Park Overturned 150 Years of Biology | Virology and Bioinformatics from Virology.ca | Scoop.it
Biology textbooks tell us that lichens are alliances between two organisms—a fungus and an alga. They are wrong.
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New protein offers hope for HIV cure

New protein offers hope for HIV cure | Virology and Bioinformatics from Virology.ca | Scoop.it
A Queensland scientist develops a protein which switches off HIV infection in cells, potentially paving the way for a cure for the deadly virus.

Via Ian M Mackay, PhD
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Descriptive Statistics of the Genome: Phylogenetic Classification of Viruses | Abstract

The typical process for classifying and submitting a newly sequenced virus to the NCBI database involves two steps. First, a BLAST search is performed to determine likely family candidates. That is followed by checking the candidate families with the pairwise sequence alignment tool for similar species. The submitter's judgment is then used to determine the most likely species classification. The aim of this article is to show that this process can be automated into a fast, accurate, one-step process using the proposed alignment-free method and properly implemented machine learning techniques.

We present a new family of alignment-free vectorizations of the genome, the generalized vector, that maintains the speed of existing alignment-free methods while outperforming all available methods. This new alignment-free vectorization uses the frequency of genomic words (k-mers), as is done in the composition vector, and incorporates descriptive statistics of those k-mers' positional information, as inspired by the natural vector.

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Risk of travelers to Olympics sparking new Zika outbreaks low

Risk of travelers to Olympics sparking new Zika outbreaks low | Virology and Bioinformatics from Virology.ca | Scoop.it
Just four countries — Chad, Djibouti, Eritrea and Yemen — bear a substantial risk of bringing Zika virus home from the Olympics and having it spread, the CDC says.
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Dengue virus has a new distant relative | Queensland Health News

Dengue virus has a new distant relative | Queensland Health News | Virology and Bioinformatics from Virology.ca | Scoop.it
A new strain of dengue virus discovered by Queensland scientists could help researchers evaluate the effectiveness of potential vaccines and treatments for the disease
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Cheap blood test can discriminate between bacterial, viral infections, study finds

Cheap blood test can discriminate between bacterial, viral infections, study finds | Virology and Bioinformatics from Virology.ca | Scoop.it
Researchers at the Stanford University School of Medicine have made an important breakthrough in their ongoing efforts to develop a diagnostic test that can tell health-care providers whether a patient has a bacterial infectio
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Genomoviridae: a new family of widespread single-stranded DNA viruses

Official Full-Text Publication: Genomoviridae: a new family of widespread single-stranded DNA viruses on ResearchGate, the professional network for scientists.

Via Ed Rybicki
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Ed Rybicki's curator insight, July 1, 10:23 AM
Stupid name - but highly interesting viruses B-)
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Mexico: Origins of the 2009 H1N1 influenza pandemic

Mexico: Origins of the 2009 H1N1 influenza pandemic | Virology and Bioinformatics from Virology.ca | Scoop.it
Thanks to Lucie Lecomte for alerting me to this story. Via eLife, an accepted manuscript: Origins of the 2009 H1N1 influenza pandemic in swine in Mexico. The abstract: Asia is considered an important source of influenza A virus (IAV
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Newly discovered virus a prime suspect in often-fatal beak disorder spreading among birds

Newly discovered virus a prime suspect in often-fatal beak disorder spreading among birds | Virology and Bioinformatics from Virology.ca | Scoop.it
Scientists have identified a novel virus -- 'Poecivirus' -- that has been linked to avian keratin disorder (AKD), a disease responsible for debilitating beak overgrowth and whose cause has remained elusive despite more than a decade of research. This new virus is being investigated as a potential cause of AKD and represents a critical step in understanding the emergence of this disease in wild bird populations around the world.
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The Feat of Packaging Eight Unique Genome Segments

The Feat of Packaging Eight Unique Genome Segments | Virology and Bioinformatics from Virology.ca | Scoop.it
Influenza A viruses harbor a segmented RNA genome that is organized into eight distinct viral ribonucleoprotein (vRNP) complexes. Although a segmented genome may be a major advantage to adapt to new host environments, it comes at the cost of a highly sophisticated genome packaging mechanism. Newly synthesized vRNPs conquer the cellular endosomal recycling machinery to…
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Gene editing could destroy herpes viruses living inside you

Gene editing could destroy herpes viruses living inside you | Virology and Bioinformatics from Virology.ca | Scoop.it

The CRISPR technique is a new weapon against dormant herpes viruses in the body, which cause cold sores and can be implicated in blindness and cancer


Herpesvirus graphic from Russell Kightley Media


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Beak and feather disease virus in wild and captive parrots

Psittacine beak and feather disease (PBFD) has emerged in recent years as a major threat to wild parrot populations and is an increasing concern to aviculturists and managers of captive populations. P
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Reversion of Cold-adapted Live Attenuated Influenza Vaccine into a Pathogenic Virus

IMPORTANCE The live attenuated influenza vaccine FluMist® has been proven safe and effective and are widely used in the USA. The phenotype and genotype of the vaccine virus are believed to be very stable and mutants that cause disease in animals or humans have never been reported. By propagating the virus under well-controlled laboratory conditions, we found that the FluMist vaccine backbone could regain virulence to cause severe disease in mice. The identification of the responsible substitutions and elucidation of the underlying mechanisms provide unique insights on the attenuation of influenza virus, which is important to basic research on vaccines, attenuation reversion, and replication. In addition, this study suggests that the safety of LAIVs should be closely monitored after mass vaccination and novel strategies to continue to improve LAIV vaccine safety should be investigated.
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Transcriptome analysis of woodland strawberry response to the infection by Strawberry vein banding virus

Background
Woodland strawberry (Fragaria vesca) infected with Strawberry vein banding virus (SVBV) exhibits chlorotic symptoms along the leaf veins. However, little is known about the molecular mechanism of strawberry disease caused by SVBV.

Methods
We performed the next-generation sequencing (RNA-Seq) study to identify gene expression changes induced by SVBV in woodland strawberry using mock-inoculated plants as a control.

Results
Using RNA-Seq, we have identified 36,850 unigenes, of which 517 were differentially expressed in the virus-infected plants (DEGs). The unigenes were annotated and classified with Gene Ontology (GO), Clusters of Orthologous Group (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. The KEGG pathway analysis of these genes suggested that strawberry disease caused by SVBV may affect multiple processes including pigment metabolism, photosynthesis and plant-pathogen interactions.

Conclusions
Our research provides comprehensive transcriptome information regarding SVBV infection in strawberry.

Ed Rybicki's insight:
Definitely not Zika B-)
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First case of woman-to-man spread of Zika via sex reported

First case of woman-to-man spread of Zika via sex reported | Virology and Bioinformatics from Virology.ca | Scoop.it
The first known case of female-to-male sexual transmission of Zika virus has been reported in New York City.
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Viral pathogenesis: Taking a bite : Nature Reviews Microbiology

Aedes spp. mosquitoes are important vectors of disease as they inject pathogen-containing saliva into a vertebrate host.
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A question off the naturopathic licensing exam (NPLEX) - Naturopathic Diaries

A question off the naturopathic licensing exam (NPLEX) - Naturopathic Diaries | Virology and Bioinformatics from Virology.ca | Scoop.it
Naturopaths often mention that their licensing exam, the NPLEX, is a rigorous test of medical knowledge that ensures standards of care. This point always looks good to the unsuspecting. Consider the following sample from the 2013 official study guide for the NPLEX: … Continue reading →
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6 Ways to Successfully Make Connections (Even if You Hate Networking Events)

6 Ways to Successfully Make Connections (Even if You Hate Networking Events) | Virology and Bioinformatics from Virology.ca | Scoop.it
Enjoy networking at events and online with these apps, tools, and tricks.
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Icarus: visualizer for de novo assembly evaluation

Summary: Data visualization plays an increasingly important role in NGS data analysis. With advances in both sequencing and computational technologies, it has become a new bottleneck in genomics studies. Indeed, evaluation of de novo genome assemblies is one of the areas that can benefit from the visualization. However, even though multiple quality assessment methods are now available, existing visualization tools are hardly suitable for this purpose.

Here we present Icarus – a novel genome visualizer for accurate assessment and analysis of genomic draft assemblies, which is based on the tool QUAST. Icarus can be used in studies where a related reference genome is available, as well as for non-model organisms. The tool is available online and as a standalone application.

Availability: http://quast.sf.net/icarus
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Considerations for the development of Zika virus vaccines

The current Zika virus outbreak has galvanized the public health community, resulting in calls for rapid action from entities including the World Health Organization and the United States government. The response to Zika virus is perhaps the first of its kind, and it has been influenced by the lessons learned from the response to the 2014 Ebola virus outbreak in West Africa. However, Zika virus is not Ebola virus. Prior to 2016, there were only 133 publications on “Zika” in the PubMed database, and a large number of these publications were commentaries or reviews lacking primary research data. In contrast, work had been underway for decades on the development of an Ebola virus vaccine, laying the groundwork for an expedited response in 2014. The broader research community’s extensive experience with dengue virus vaccine development and with the pros and cons of different vaccine platforms has led to speculation that a Zika virus vaccine can be accelerated, potentially with clinical trials initiating by the end of 2016 [1]. However, there are unique attributes of Zika virus, as well as many unanswered questions about the virus, that will need to be considered before a potential vaccine is administered to the public.


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Portable test rapidly detects Zika in saliva for $2

Portable test rapidly detects Zika in saliva for $2 | Virology and Bioinformatics from Virology.ca | Scoop.it
Anxiety over the Zika virus is growing as the Olympic Games in Rio de Janeiro approach. To better diagnose and track the disease, scientists are now reporting in ACS' journal Analytical Chemistry a new $2 test that in the lab can accurately detect low levels of the virus in saliva.
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