Viruses and Bioinformatics from Virology.uvic.ca
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France Lost Thousands of Vials Containing the SARS Virus

France Lost Thousands of Vials Containing the SARS Virus | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Somebody's definitely getting fired, after over 2,300 vials containing fragments of the deadly SARS virus went missing from the Pasteur Institute in France earlier this week. Not one or two vials, mind you. Thousands of them.
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Viruses and Bioinformatics from Virology.uvic.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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New video on the NCBI YouTube channel: How You and Your Journal Club Can Contribute Using PubMed Commons

New video on the NCBI YouTube channel: How You and Your Journal Club Can Contribute Using PubMed Commons | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

The newest video on the NCBI YouTube channel discusses how eligible individuals and journal clubs can join PubMed Commons and contribute comments.

PubMed Commons enables members to post comments about publications, which appear directly below abstracts in PubMed.

Subscribe to the NCBI YouTube channel to watch and receive alerts about new videos ranging from quick tips to full presentations.

Cindy's insight:
Did you know NCBI has their own Youtube channel?!
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NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences

NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Comparing sets of sequences is a situation frequently encountered in bioinformatics, examples being comparing an assembly to a reference genome, or two genomes to each other. The purpose of the comparison is usually to find where the two sets differ, e.g. to find where a subsequence is repeated or deleted, or where insertions have been introduced. Such comparisons can be done using whole-genome alignments. Several tools for making such alignments exist, but none of them 1) provides detailed information about the types and locations of all differences between the two sets of sequences, 2) enables visualisation of alignment results at different levels of detail, and 3) carefully takes genomic repeats into consideration. We here present NucDiff, a tool aimed at locating and categorizing differences between two sets of closely related DNA sequences. NucDiff is able to deal with very fragmented genomes, repeated sequences, and various local differences and structural rearrangements. NucDiff determines differences by a rigorous analysis of alignment results obtained by the NUCmer, delta-filter and show-snps programs in the MUMmer sequence alignment package. All differences found are categorized according to a carefully defined classification scheme covering all possible differences between two sequences. Information about the differences is made available as GFF3 files, thus enabling visualisation using genome browsers as well as usage of the results as a component in an analysis pipeline. NucDiff was tested with varying parameters for the alignment step and compared with existing alternatives, called QUAST and dnadiff. We have developed a whole genome alignment difference classification scheme together with the program NucDiff for finding such differences. The proposed classification scheme is comprehensive and can be used by other tools. NucDiff performs comparably to QUAST and dnadiff but gives much more detailed results that can easily be visualized. NucDiff is freely available on
https://github.com/uio-cels/NucDiff

under the MPL license.
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A bioinformatics pipeline to search functional motifs within whole-proteome data: a case study of poxviruses

Proteins harbor domains or short linear motifs, which facilitate their functions and interactions. Finding functional motifs in protein sequences could predict the putative cellular roles or characteristics of hypothetical proteins. In this study, we present Shetti-Motif, which is an interactive tool to (i) map UniProt and PROSITE flat files, (ii) search for multiple pre-defined consensus patterns or experimentally validated functional motifs in large datasets protein sequences (proteome-wide), (iii) search for motifs containing repeated residues (low-complexity regions, e.g., Leu-, SR-, PEST-rich motifs, etc.). As proof of principle, using this comparative proteomics pipeline, eleven proteomes encoded by member of Poxviridae family were searched against about 100 experimentally validated functional motifs. The closely related viruses and viruses infect the same host cells (e.g. vaccinia and variola viruses) show similar motif-containing proteins profile. The motifs encoded by these viruses are correlated, which explains why poxviruses are able to interact with wide range of host cells. In conclusion, this in silico analysis is useful to establish a dataset(s) or potential proteins for further investigation or compare between species.
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Respiratory syncytial virus–Host interaction in the pathogenesis of bronchiolitis and its impact on respiratory morbidity in later life

Respiratory syncytial virus–Host interaction in the pathogenesis of bronchiolitis and its impact on respiratory morbidity in later life | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Respiratory syncytial virus (RSV) is the most common agent of severe airway disease in infants and young children. Large epidemiologic studies have demonstrated a clear relationship between RS

Via Gilbert C FAURE
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Evolution and Vaccination of Influenza Virus

In this study, we present an application paradigm in which an unsupervised machine learning approach is applied to the high-dimensional influenza genetic sequences to investigate whether vaccine is a driving force to the evolution of influenza virus. We first used a visualization approach to visualize the evolutionary paths of vaccine-controlled and non-vaccine-controlled influenza viruses in a low-dimensional space. We then quantified the evolutionary differences between their evolutionary trajectories through the use of within- and between-scatter matrices computation to provide the statistical confidence to support the visualization results. We used the influenza surface Hemagglutinin (HA) gene for this study as the HA gene is the major target of the immune system. The visualization is achieved without using any clustering methods or prior information about the influenza sequences. Our results clearly showed that the evolutionary trajectories between vaccine-controlled and non-vaccine-controlled influenza viruses are different and vaccine as an evolution driving force cannot be completely eliminated.
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Viral infection: Packing to leave

Viral infection: Packing to leave | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
An essential feature of the life cycle of hepatitis B virus (HBV) is the packaging of the viral RNA pre-genome (pgRNA) into virions. It has been hypothesized that pgRNA is specifically packaged into viral nucleocapsids; however, the HBV assembly pathway remains incompletely understood. In a recent study, Patel, White et al. discover that the HBV pgRNA contains specific nucleotide motifs that mediate interactions with the viral capsid protein to drive nucleocapsid assembly.
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Diversity of large DNA viruses of invertebrates

In this review we provide an overview of the diversity of large DNA viruses known to be pathogenic for invertebrates. We present their taxonomical classification and describe the evolutionary relationships among various groups of invertebrate-infecting viruses. We also indicate the relationships of the invertebrate viruses to viruses infecting mammals or other vertebrates. The shared characteristics of the viruses within the various families are described, including the structure of the virus particle, genome properties, and gene expression strategies. Finally, we explain the transmission and mode of infection of the most important viruses in these families and indicate, which orders of invertebrates are susceptible to these pathogens.
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How Canadian researchers reconstituted an extinct poxvirus for $100,000 using mail-order DNA

How Canadian researchers reconstituted an extinct poxvirus for $100,000 using mail-order DNA | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
A study that brought horsepox back to life is triggering a new debate about the risks and power of synthetic biology
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Scientists recreate an extinct virus, a relative of smallpox

Scientists recreate an extinct virus, a relative of smallpox | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
“Demonstrating this can be done — and then writing newspaper articles about it and Science magazine articles — will get the attention of people who might want to use it for the wrong reasons and they might have never known about that,” Lipsitch said.

Via Ian M Mackay, PhD
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Host and viral traits predict zoonotic spillover from mammals

The majority of human emerging infectious diseases are zoonotic, with viruses that originate in wild mammals of particular concern (for example, HIV, Ebola and SARS). Understanding patterns of viral diversity in wildlife and determinants of successful cross-species transmission, or spillover, are therefore key goals for pandemic surveillance programs. However, few analytical tools exist to identify which host species are likely to harbour the next human virus, or which viruses can cross species boundaries. Here we conduct a comprehensive analysis of mammalian host–virus relationships and show that both the total number of viruses that infect a given species and the proportion likely to be zoonotic are predictable. After controlling for research effort, the proportion of zoonotic viruses per species is predicted by phylogenetic relatedness to humans, host taxonomy and human population within a species range—which may reflect human–wildlife contact. We demonstrate that bats harbour a significantly higher proportion of zoonotic viruses than all other mammalian orders. We also identify the taxa and geographic regions with the largest estimated number of ‘missing viruses’ and ‘missing zoonoses’ and therefore of highest value for future surveillance. We then show that phylogenetic host breadth and other viral traits are significant predictors of zoonotic potential, providing a novel framework to assess if a newly discovered mammalian virus could infect people.

Via Ed Rybicki
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ComplexInsight's curator insight, July 7, 5:19 AM
Understanding zoonotic potential will be key to health planning and epidemic prevention in the 21st century.  This paper has key insights such as major hosts (bats) and key geographic zones for observation. If you are involved in health planning or disease modeling - very worthwhile reading.
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Africa health: Rotavirus vaccine could save 500,000 children a year

Africa health: Rotavirus vaccine could save 500,000 children a year | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The Indian vaccine, which protects against gastroenteritis caused by rotavirus, was tested in Niger.

Via Ed Rybicki
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ComplexInsight's curator insight, July 7, 5:20 AM
As if we need a reminder on the importance of vaccinations. 
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Multifunctional cytomegalovirus (CMV)‐specific CD8+ T cells are not restricted by telomere‐related senescence in young or old adults

Multifunctional cytomegalovirus (CMV)‐specific CD8+ T cells are not restricted by telomere‐related senescence in young or old adults | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Antigen‐specific multifunctional T cells that secrete interferon‐γ, interleukin‐2 and tumour necrosis factor‐α simultaneously after activation are important for the control of many infections. It i

Via Gilbert C FAURE
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Molecular Mechanisms of Human Papillomavirus Induced Skin Carcinogenesis

nfection of the cutaneous skin with human papillomaviruses (HPV) of genus betapapillomavirus (βHPV) is associated with the development of premalignant actinic keratoses and squamous cell carcinoma. Due to the higher viral loads of βHPVs in actinic keratoses than in cancerous lesions, it is currently discussed that these viruses play a carcinogenic role in cancer initiation. In vitro assays performed to characterize the cell transforming activities of high-risk HPV types of genus alphapapillomavirus have markedly contributed to the present knowledge on their oncogenic functions. However, these assays failed to detect oncogenic functions of βHPV early proteins. They were not suitable for investigations aiming to study the interactive role of βHPV positive epidermis with mesenchymal cells and the extracellular matrix. This review focuses on βHPV gene functions with special focus on oncogenic mechanisms that may be relevant for skin cancer development.
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CRISPR gene editing controversy - does it cause unexpected mutations?

CRISPR gene editing controversy - does it cause unexpected mutations? | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Just over a month ago, a short paper appeared in Nature Methods saying that the gene editing technique known as CRISPR-Cas9 has a bi
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Rift Valley fever virus NSs protein functions and the similarity to other bunyavirus NSs proteins

Rift Valley fever virus NSs protein functions and the similarity to other bunyavirus NSs proteins | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Rift Valley fever is a mosquito-borne zoonotic disease that affects both ruminants and humans. The nonstructural (NS) protein, which is a major virulence factor for Rift Valley fever virus (RVFV), is encoded on the S-segment. Through the cullin 1-Skp1-Fbox E3 ligase complex, the NSs protein promotes the degradation of at least two host proteins, the TFIIH p62 and the PKR proteins. NSs protein bridges the Fbox protein with subsequent substrates, and facilitates the transfer of ubiquitin. The SAP30-YY1 complex also bridges the NSs protein with chromatin DNA, affecting cohesion and segregation of chromatin DNA as well as the activation of interferon-β promoter. The presence of NSs filaments in the nucleus induces DNA damage responses and causes cell-cycle arrest, p53 activation, and apoptosis. Despite the fact that NSs proteins have poor amino acid similarity among bunyaviruses, the strategy utilized to hijack host cells are similar. This review will provide and summarize an update of recent findings pertaining to the biological functions of the NSs protein of RVFV as well as the differences from those of other bunyaviruses.
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Taming the BEAST - A community teaching material resource for BEAST 2. - PubMed - NCBI

Taming the BEAST - A community teaching material resource for BEAST 2. - PubMed - NCBI | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Syst Biol. 2017 Jun 29. doi: 10.1093/sysbio/syx060. [Epub ahead of print]
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Pathways to zoonotic spillover

Zoonotic spillover, which is the transmission of a pathogen from a vertebrate animal to a human, presents a global public health burden but is a poorly understood phenomenon. Zoonotic spillover requires several factors to align, including the ecological, epidemiological and behavioural determinants of pathogen exposure, and the within-human factors that affect susceptibility to infection. In this Opinion article, we propose a synthetic framework for animal-to-human transmission that integrates the relevant mechanisms. This framework reveals that all zoonotic pathogens must overcome a hierarchical series of barriers to cause spillover infections in humans. Understanding how these barriers are functionally and quantitatively linked, and how they interact in space and time, will substantially improve our ability to predict or prevent spillover events. This work provides a foundation for transdisciplinary investigation of spillover and synthetic theory on zoonotic transmission.
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Viral evolution: Every flu evolves in the same way

Influenza viruses, similarly to other viruses, rapidly acquire de novo mutations when they replicate within their host cells.However, how the emergence of viral variants in the host is reflected at a global scale is still poorly understood. In a new study, Xue et al. used a deep-sequencing approach to analyse longitudinal samples from immunocompromised patients who had long-term influenza infections. The authors found that the same set of mutations had emerged independently in several patients, most commonly in the genes that encode haemagglutinin (HA) and neuraminidase. Furthermore, many of the mutations in HA had also reached high global frequency in the decade following patient infections. This study shows that viral evolution and variation in the host parallel evolution at a global scale. Understanding these dynamics will help to predict the evolution of influenza viruses and the design of more effective vaccines.
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Plasmid mAb Tech Protects against Multiple Influenza Strains

Plasmid mAb Tech Protects against Multiple Influenza Strains | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Using its new technology, Inovio explores the
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Recombinant Influenza Vaccine More Effective Than Standard Inactivated Vaccine

Recombinant Influenza Vaccine More Effective Than Standard Inactivated Vaccine | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
From BioPortfolio: A comparison trial conducted during the 2014–2015 flu season found a difference in efficacy.

Via Ed Rybicki
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16S rRNA indexed primers amplify phylogenic markers for microbiome sequencing analysis

16S rRNA indexed primers amplify phylogenic markers for microbiome sequencing analysis | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

The 16S rRNA gene is frequently used in microbiome studies to identify the subset of microbes present in biological samples. Researchers amplify short hypervariable regions from this gene, tag the amplified products with unique barcodes, perform highly multiplexed sequencing runs, and compare the sequences to the known bacterial genome database. However, primer design for such analyses can be challenging given the massive sequence variability in sampled lifeforms. Read about the development and design of these primers, and how you can obtain your own custom, high fidelity versions of these sequences.


Via Integrated DNA Technologies
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Paul Epping's curator insight, July 8, 3:02 AM

An important step in the fight against resistant bacteria.

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65 Persons Under Surveillance As Lassa Fever Kills Student Nurse In Nigeria

65 Persons Under Surveillance As Lassa Fever Kills Student Nurse In Nigeria | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Speaking with newsmen in Awka, the Director of Public Health, State Ministry of Health, Dr Emmanuel Okafor, said that the deceased (name withheld) was a student in one private nursing school in Nkpor, Idemili North. Okafor said that the lady was admitted at the Chukwuemeka Odumegwu Ojukwu University Teaching Hospital, Awka, on June 11. According to him, she was immediately transferred to the General Hospital, Irua, in Edo for diagnosis where she died on June 17. “She was initially admitted at Amaku in Awka before she was transferred to Irua and was placed on admission there. “She was bleeding from the gums, nostril and vagina and was confirmed Lassa Fever victim in Irua. “The moment it was confirmed that she had Lassa fever, we started contacts tracing. “As of now, we have about 65 we are following up, two of them have developed fever and their samples have been taken to Irua. “We are still tracking others and we have advised them on what to do to ensure they do not transfer it to their loved ones,” he said.


Via Ed Rybicki
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Ed Rybicki's curator insight, June 21, 6:20 AM
Nearly as bad as the Ebola outbreak in Congo - and guess which gets the headlines? Every year, Lassa fever kills people in Nigeria and its neighbours.
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A Random Name Picker for Your Classroom

A Random Name Picker for Your Classroom | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Name Picker Ninja  is free tool for quickly randomly selecting a name from a list. Using Name Picker Ninja is a simple matter of pasting o
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