Viruses, Immunology & Bioinformatics from Virology.uvic.ca
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Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch

Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

Knowledge of ancient viruses is limited due to their low concentration and poor preservation in ancient specimens. Using a viral particle-associated nucleic acid enrichment approach, we genetically characterized one complete DNA and one partial RNA viral genome from a 700-y-old fecal sample preserved in ice. Using reverse genetics, we reconstituted the DNA virus, which replicated and systemically spread in a model plant species. Under constant freezing conditions, encapsidated viral nucleic acids may therefore be preserved for centuries. Our finding indicates that cryogenically preserved materials can be repositories of ancient viral nucleic acids, which in turn allow molecular genetics to regenerate viruses to study their biology.

 
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Viruses, Immunology & Bioinformatics from Virology.uvic.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: | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

get in touch if you want to help curate this topic

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Bwana Moses's comment, May 25, 2016 6:13 AM
Great work. Keep it going.
Bwana Moses's comment, March 7, 2017 12:46 PM
Thank You.
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The NS Segment of H1N1pdm09 Enhances H5N1 Pathogenicity in a Mouse Model of Influenza Virus Infections

The NS Segment of H1N1pdm09 Enhances H5N1 Pathogenicity in a Mouse Model of Influenza Virus Infections | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
In 2009, the co-circulation of H5N1 and H1N1pdm09 raised concerns that a reassortment event may lead to highly pathogenic influenza strains. H1N1pdm09 and H5N1 are able to infect the same target cells of the lower respiratory tract.
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Baloxavir: A New, Single-Dose Antiviral 

Baloxavir: A New, Single-Dose Antiviral  | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
A 64-year-old otherwise healthy virology professor comes to your office complaining of flu symptoms. She has had fever, cough, and sore throat for the last day or so that she attributes to one of her students. She has been furiously sanitizing her hands and comes to the office wearing a face mask. Being the savvy patient, she brings reverse transcriptase–polymerase chain reaction (RT-PCR) results that confirm she has influenza A virus (as does the student). She is febrile but hemodynamically stable with no signs of lower respiratory tract infection. She asks about available treatment options, explaining that she will be presenting at a conference tomorrow. How would you proceed? In this week’s NEJM, Hayden and colleagues report the results of two double-blind, randomized-controlled trials comparing single-dose baloxavir versus placebo or oseltamivir in patients with uncomplicated influenza in Japan and the United States during the 2015–2017 flu seasons. Baloxavir marboxil (Xofluza) is an important new addition to the armamentarium against flu because it represents a new class of antiviral drugs that target a different process than the other two classes available (amadantanes and neuraminidase inhibitors), and has antiviral activity against strains resistant to those agents. Baloxavir also has the advantage of requiring a single dose, as compared to 5 days of twice daily oseltamivir (Tamiflu). Baloxavir is a cap-dependent endonuclease inhibitor that blocks viral replication by blocking the initiation of mRNA synthesis (read more here). In the phase 3 trial (CAPSTONE-1), the investigators randomized 1436 patients (age range, 12–64 years) with uncomplicated flu to receive a single dose of baloxavir (40 mg), oseltamivir (75 mg twice daily for 5 days), or matching placebos (with those aged 12-19 assigned only to baloxavir or placebo). Uncomplicated flu was defined as fever ≥38.0°C, at least one systemic symptom and one respiratory symptom, and presentation with 48 hours of symptom onset. Pregnant women and those requiring hospitalization were excluded. The primary endpoint was the time until flu symptoms became absent or mild for at least 21.5 hours. The intention-to-treat infected population included only RT-PCR-positive patients. Roughly 85% of patients in the three treatment groups were infected with influenza A (H3N2) and most (77%) were recruited in Japan. The time to alleviation of symptoms was significantly shorter (by 26.5 hours) in the baloxavir group, when compared with the placebo group (median, 53.7 vs. 80.2 hours), and similar to the oseltamivir group (53.5 vs. 53.8 hours). Baloxavir was associated with significantly more rapid decline in potentially infectious viral load as compared to both oseltamivir and placebo. The rate of adverse events was similar in the three groups. Emergence of mutations conferring reduced baloxavir susceptibility occurred in fewer than 10% of baloxavir recipients, which prolonged time to resolution of symptoms by about 13 hours. Per CDC recommendations, only individuals with acute influenza who are at high risk of related complications (e.g., in a chronic care facility, pregnant, age ≥65 years) should receive antiviral treatment. Hence, the results of this trial are not likely to affect current practice or treatment of the professor described above. The importance of this study lies in the demonstration of the safety and efficacy of baloxavir for treatment of uncomplicated acute influenza in otherwise healthy patients. These encouraging results will form the basis for future study of baloxavir in higher risk populations, where its utility and future clinical indications may lie. Browse more From Pages to Practice »  Tenzing T. Lama, MD, MScRes, is a resident physician in the Department of Anesthesiology and Pain Medicine at the University of Washington and a Fellow at the Ethics and Transformative Values Center at the Massachusetts Institute of Technology. He graduated from Harvard Medical School and Oxford.

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The NS Segment of H1N1pdm09 Enhances H5N1 Pathogenicity in a Mouse Model of Influenza Virus Infections

The NS Segment of H1N1pdm09 Enhances H5N1 Pathogenicity in a Mouse Model of Influenza Virus Infections | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
In 2009, the co-circulation of H5N1 and H1N1pdm09 raised concerns that a reassortment event may lead to highly pathogenic influenza strains. H1N1pdm09 and H5N1 are able to infect the same target cells of the lower respiratory tract. To investigate the capacity of the emergence of reassortant viruses, we characterized viruses obtained from the co-infection of cells with H5N1 (A/Turkey/13/2006) and H1N1pdm09 (A/Lyon/969/2009 H1N1). In our analysis, all the screened reassortants possessed the PB2, HA, and NP segments from H5N1 and acquired one or two of the H1N1pdm09 segments. Moreover, the in vivo infections showed that the acquisition of the NS segment from H1N1pdm09 increased the virulence of H5N1 in mice. We conclude, therefore, that reassortment can occur between these two viruses, even if this process has never been detected in nature.
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Mini viral RNAs act as innate immune agonists during influenza virus infection | Nature Microbiology

The molecular processes that determine the outcome of influ- enza virus infection in humans are multifactorial and involve a complex interplay between host, viral and bacterial fac- tors 1 . However, it is generally accepted that a strong innate immune dysregulation known as ‘cytokine storm’ contributes to the pathology of infections with the 1918 H1N1 pandemic or the highly pathogenic avian influenza viruses of the H5N1 subtype 2–4 . The RNA sensor retinoic acid-inducible gene I (RIG-I) plays an important role in sensing viral infection and initiating a signalling cascade that leads to interferon expres- sion 5 . Here, we show that short aberrant RNAs (mini viral RNAs (mvRNAs)), produced by the viral RNA polymerase during the replication of the viral RNA genome, bind to and activate RIG-I and lead to the expression of interferon-β . We find that erroneous polymerase activity, dysregulation of viral RNA replication or the presence of avian-specific amino acids underlie mvRNA generation and cytokine expression in mam- malian cells. By deep sequencing RNA samples from the lungs of ferrets infected with influenza viruses, we show that mvR- NAs are generated during infection in vivo. We propose that mvRNAs act as the main agonists of RIG-I during influenza virus infection.
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Insights into the Human Virome Using CRISPR Spacers from Microbiomes

Insights into the Human Virome Using CRISPR Spacers from Microbiomes | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
CRISPR-Cas systems function by uptake and integration of foreign genetic element sequences into the CRISPR array, which constitutes a genomic archive of iterative vaccination events. Consequently, CRISPR spacers can be investigated to reconstruct interplay between viruses and bacteria, and metagenomic sequencing data can be exploited to provide insights into host-phage interactions within a niche. Here, we show how the CRISPR spacer content of commensal and pathogenic bacteria can be used to determine the evidence of their phage exposure. This framework opens new opportunities for investigating host-virus dynamics in metagenomic data, and highlights the need to dedicate more efforts for virome sampling and sequencing.
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PhyloProfile: dynamic visualization and exploration of multi-layered phylogenetic profiles | Bioinformatics | Oxford Academic

PhyloProfile: dynamic visualization and exploration of multi-layered phylogenetic profiles | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
AbstractSummary. Phylogenetic profiles form the basis for tracing proteins and their functions across species and through time. Novel genome sequences nowadays
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Prot-SpaM: Fast alignment-free phylogeny reconstruction based on whole-proteome sequences

Word-based or `alignment-free' sequence comparison has become an active research area in bioinformatics. While previous word-frequency approaches calculated rough measures of sequence similarity or dissimilarity, some new alignment-free methods are able to accurately estimate phylogenetic distances between genomic sequences. One of these approaches is Filtered Spaced Word Matches. Herein, we extend this approach to estimate evolutionary distances between complete or incomplete proteomes; our implementation of this approach is called Prot-SpaM. We compare the performance of Prot-SpaM to other alignment-free methods on simulated sequences and on various groups of eukaryotic and prokaryotic taxa. Prot-SpaM can be used to calculate high-quality phylogenetic trees for dozens of whole-proteome sequences in a matter of seconds or minutes and often outperforms other alignment-free approaches. The source code of our software is available through Github: https://github.com/jschellh/ProtSpaM
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Research uncovers how the immune system detects DNA damage

Research uncovers how the immune system detects DNA damage | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Our immune system is working every day to protect us from bacteria, viruses, and parasites, but it can also detect when our own cells are damaged.

Via Gilbert C FAURE
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TimeTree :: The Timescale of Life

TimeTree is a public knowledge-base for information on the evolutionary timescale of life. Data from thousands of published studies are assembled into a searchable tree of life scaled to time. Three search modes are possible: Node Time - to find the divergence time of two species or higher taxa Timeline - to drill back through time and find evolutionary branches from the perspective of a single species Timetree - to build a timetree of a group of species or custom list
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Potential impact of introducing a nonavalent HPV vaccination

Objective To test the theoretical utility of incorporating nonavalent vaccination against HPV into a clinical setting. Methods The present retrospective study included data from consecutive patients who underwent HPV‐DNA testing between January 1, 1998, and December 31, 2015. Changes in the prevalence of different HPV types were assessed during three periods (T1, 1998–2003; T2, 2004–2009; and T3, 2010–2015) using XY analysis. Results The study included a total of 13 665 patients. Overall, 1361, 5130, and 7174 patients were included in the T1, T2, and T3 periods, respectively. The quadrivalent vaccine would have potentially protected against HPV in 71.5% (973/1361), 46.5% (2385/5130), and 26.5% (1901/7174) of patients in T1, T2, and T3, respectively (P<0.001 for trend). The nonavalent vaccine could have protected against HPV in 92.5% (1259/1361), 72.3% (3709/5130), and 58.1% (4168/7174) of patients in T1, T2, and T3, respectively (P<0.001 for trend). The proportion of patients with genital dysplasia grade 2+ who did not have infections with HPV genotypes covered by the quadrivalent or nonavalent vaccines increased across the three periods (P<0.001 for trend). For all study periods, the protection provided by the nonavalent vaccine would have been superior to the quadrivalent vaccine (χ2 test P<0.001). Conclusion The introduction of a nonavalent vaccine could improve protection against HPV infections and HPV‐related genital dysplasia.

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Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates

Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
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The Popularity Contest of Human Genes

The Popularity Contest of Human Genes | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

Since 2003, several researchers have noticed that scientists tend to study genes that are already well studied, and the genes that become popular aren’t necessarily the most biologically interesting ones. Even among genes, it seems, the rich get richer. This trend hasn’t changed in the past two decades, according to a new study from Thomas Stoeger from Northwestern University. Through a massive analysis of existing biomedical data, he found that he can predict how intensely a given gene is studied based on a small number of basic biochemical traits. Most of these, he says, reflect how easy a gene was to investigate in the 1980s and 1990s, rather than how important it is.

“People said that knowing all the genes was going to change everything,” says Luis Amaral, who led the new study. But the 16 percent of genes that were known in 1991 still accounted for half of all biomedical papers in 2015. By contrast, more recently discovered genes are more poorly known, and a quarter (27 percent) have never been the focus of a scientific paper. Based on current trends, Stoeger estimates that it would take at least five decades before every gene was characterized at the most basic level, let alone fully understood. “There’s a chance that we are missing out on a lot of interesting biology,” he says.

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Faster, Cheaper, Better: A New Way to Synthesize DNA

In what could address a critical bottleneck in biology research, Berkeley Lab researchers announced they have pioneered a new way to synthesize DNA sequences through a creative use of enzymes that promises to be faster, cheaper, and more accurate.
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Inspired by nature, reaching across disciplines

Inspired by nature, reaching across disciplines | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Inspired by the architectures of different organisms, MIT PhD student Zijay Tang is developing a living material that can sense and filter water contaminants.

Via Gerd Moe-Behrens
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Biology of viral satellites and their role in pathogenesis - ScienceDirect

Biology of viral satellites and their role in pathogenesis - ScienceDirect | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Extraviral components that can influence the accumulation and pathogenesis of their associated helper viruses are known as ‘satellites’. The maintenan…
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MarinStatsLectures

MarinStatsLectures | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Here is your most reliable resource for tutorials in statistics, data science, and working with R prgramming Software created by Mike Marin and his partner in crime Ladan Hamadani . Initially made for Mike's Master's and PhD students at the University of British Columbia (UBC), these tutorials are now made available to everyone.
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Genomes for all

Genomes for all | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The notion that the genetic inheritance of any species can be described as a single sequence has always been a convenient simplification. Most reference genomes are derived from only one or a small number of individuals, and diploid or polyploid species are typically represented as consensus haploid sequences or sequences with reduced heterozygosity produced by inbreeding. For the human genome, the current haploid reference assembly is based on DNA from only ∼50 people, with ∼70% of the sequence coming from just one of those genomes. Thus, it is missing most of the variation that defines the genetic identity of individuals, including variants with clinical relevance and regions of high diversity. In this issue, Garrison et al.1 take an important step toward addressing this deficiency with an approach that represents genetic variation and sequence assembly in a single graph structure. The variation graph (vg) approach promises to transform our ability to account for complex genetic variation across populations.
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scanPAV: a pipeline for extracting presence–absence variations in genome pairs | Bioinformatics | Oxford Academic

scanPAV: a pipeline for extracting presence–absence variations in genome pairs | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
AbstractMotivation. The recent technological advances in genome sequencing techniques have resulted in an exponential increase in the number of sequenced human
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GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens

GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
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Human Monoclonal Antibodies That Neutralize Pandemic GII.4 Noroviruses

Human Monoclonal Antibodies That Neutralize Pandemic GII.4 Noroviruses | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Human noroviruses are responsible for approximately 200,000 deaths worldwide each
year. In 2012, the GII.4 Sydney strain emerged and became the major circulating norovirus
strain associated with human disease.

Via Krishan Maggon , Gilbert C FAURE
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Identification of the Potential Virulence Factors and RNA Silencing Suppressors of Mulberry Mosaic Dwarf-Associated Geminivirus

Identification of the Potential Virulence Factors and RNA Silencing Suppressors of Mulberry Mosaic Dwarf-Associated Geminivirus | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Plant viruses encode virulence factors or RNA silencing suppressors to reprogram plant cellular processes or to fine-tune host RNA silencing-mediated defense responses. In a previous study, Mulberry mosaic dwarf-associated virus (MMDaV), a novel, highly divergent geminivirus, has been identified...
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Rapid and precise alignment of raw reads against redundant databases with KMA | BMC Bioinformatics | Full Text

Rapid and precise alignment of raw reads against redundant databases with KMA | BMC Bioinformatics | Full Text | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
As the cost of sequencing has declined, clinical diagnostics based on next generation sequencing (NGS) have become reality. Diagnostics based on sequencing will require rapid and precise mapping against redundant databases because some of the most important determinants, such as antimicrobial resistance and core genome multilocus sequence typing (MLST) alleles, are highly similar to one another. In order to facilitate this, a novel mapping method, KMA (k-mer alignment), was designed. KMA is able to map raw reads directly against redundant databases, it also scales well for large redundant databases. KMA uses k-mer seeding to speed up mapping and the Needleman-Wunsch algorithm to accurately align extensions from k-mer seeds. Multi-mapping reads are resolved using a novel sorting scheme (ConClave scheme), ensuring an accurate selection of templates. The functionality of KMA was compared with SRST2, MGmapper, BWA-MEM, Bowtie2, Minimap2 and Salmon, using both simulated data and a dataset of Escherichia coli mapped against resistance genes and core genome MLST alleles. KMA outperforms current methods with respect to both accuracy and speed, while using a comparable amount of memory. With KMA, it was possible map raw reads directly against redundant databases with high accuracy, speed and memory efficiency.
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Meet The Forgotten Scientist Who Invented The Measles Vaccine

Meet The Forgotten Scientist Who Invented The Measles Vaccine | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Microbiologist Maurice R. Hilleman, arguably, saved more lives than any other doctor or medical researcher of the 20th century; during his 40-year career, he developed over 40 human and animal vaccines.

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The key to a happy lab life is in the manual

The key to a happy lab life is in the manual | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
I supplemented my lab manual (go.nature.com/2c1dxdt) with a wiki (go.nature.com/2pti9kj), a website of resources for lab members. This included everything from tools for learning the programming languages R and Python and how to do neuroimaging analyses, to tips on keeping up with the research literature (by using RSS feeds and Twitter) and where to find the best bagel in Manhattan (a ten-minute walk from the lab). My goal was that any newly accepted lab member could read the manual and wiki and then strut into the lab knowing what to expect.
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