Viruses, Immunology & Bioinformatics from Virology.uvic.ca
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Reconstruction of 1918-like avian influenza virus stirs concern over gain of function experiments

Reconstruction of 1918-like avian influenza virus stirs concern over gain of function experiments | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The recent publication of new influenza virus gain of function studies from the laboratories of Kawaoka and Perez have unleashed another barrage of criticism.
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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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Meta-transcriptomics and the evolutionary biology of RNA viruses - ScienceDirect

Meta-transcriptomics and the evolutionary biology of RNA viruses - ScienceDirect | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Metagenomics is transforming the study of virus evolution, allowing the full assemblage of virus genomes within a host sample to be determined rapidly…
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BREAKING: CRISPR Could Be Causing Extensive Mutations And Genetic Damage After All

BREAKING: CRISPR Could Be Causing Extensive Mutations And Genetic Damage After All | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
CRISPR has been heralded as one of the most important breakthroughs in modern science, but there could be a hidden and potentially dangerous side effect to the wonders of its genetic editing technology, a new study reveals.
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Parallelization of MAFFT for large-scale multiple sequence alignments | Bioinformatics | Oxford Academic

Parallelization of MAFFT for large-scale multiple sequence alignments | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
AbstractSummary. We report an update for the MAFFT multiple sequence alignment program to enable parallel calculation of large numbers of sequences. The G-INS-
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ClusterScan: simple and generalistic identification of genomic clusters | Bioinformatics | Oxford Academic

ClusterScan: simple and generalistic identification of genomic clusters | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
AbstractSummary. Studies on gene clusters proved to be an excellent source of information to understand genomes evolution and identifying specific metabolic pa
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Kmer-db: instant evolutionary distance estimation | Bioinformatics | Oxford Academic

Kmer-db: instant evolutionary distance estimation | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
AbstractSummary. Kmer-db is a new tool for estimating evolutionary relationship on the basis of k-mers extracted from genomes or sequencing reads. Thanks to an
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Infection of pigs with African swine fever virus via ingestion of stable flies (Stomoxys calcitrans). - PubMed - NCBI

Infection of pigs with African swine fever virus via ingestion of stable flies (Stomoxys calcitrans). - PubMed - NCBI | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Transbound Emerg Dis. 2018 Jun 7. doi: 10.1111/tbed.12918. [Epub ahead of print]
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Cottontail rabbits shed clade 2.3.4.4 H5 highly pathogenic avian influenza A viruses

During 2014-2015, clade 2.3.4.4 H5Nx highly pathogenic (HP) avian influenza A viruses (IAV) were first detected in North America and subsequently caused one of the largest agricultural emergencies in U.S.

HISTORY:
Recent evidence has suggested that cottontail rabbits can shed multiple IAV subtypes. We experimentally infected cottontail rabbits with three HP H5Nx IAVs. All rabbits tested shed virus on at least one day by at least one route. Cottontail rabbits appear to be an exception to the limited capacity for replication that has been previously reported for certain other mammalian species inoculated with clade 2.3.4.4 HP H5Nx avian influenza A viruses.

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Brazil: measles outbreak that infected 500 may devastate indigenous people | World news | The Guardian

Brazil: measles outbreak that infected 500 may devastate indigenous people | World news | The Guardian | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Outbreak could be catastrophic for the Yanomami people living in remote areas who are not protected from the disease
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Multi-antigenic human cytomegalovirus mRNA vaccines that elicit potent humoral and cell-mediated immunity - ScienceDirect

Multi-antigenic human cytomegalovirus mRNA vaccines that elicit potent humoral and cell-mediated immunity - ScienceDirect | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
A cytomegalovirus (CMV) vaccine that is effective at preventing congenital infection and reducing CMV disease in transplant patients remains a high pr…

Via Gilbert C FAURE
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Choice of sequence homologs included in multiple sequence alignments has a dramatic impact on evolutionary conservation analysis

The analysis of sequence conservation patterns has been widely utilized to identify functionally important (catalytic and ligand-binding) protein residues for over a half-century. Despite decades of development, on average state-of-the-art non-template-based functional residue prediction methods must predict ∼25% of a protein’s total residues to correctly identify half of the protein’s functional site residues. The overwhelming proportion of false positives results in reported “F-Scores” of ∼0.3. We investigated the limits of current approaches, focusing on the so-far neglected impact of the specific choice of homologs included in multiple sequence alignments (MSAs).
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Inhibition of Japanese encephalitis virus infection by the host zinc-finger antiviral protein

Inhibition of Japanese encephalitis virus infection by the host zinc-finger antiviral protein | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Author summary In addition to innate and adaptive immunities, many cellular proteins also exert antiviral activity against viral invasion. Human zinc-finger antiviral protein (ZAP) is a cellular restriction factor against many viruses but its role with regard to the flavivirus family is largely...
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Why Your Microbiome Analysis is Wrong

A brief overview of common perils and pitfalls in microbiome analysis
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How safe is the MMR vaccine?

How safe is the MMR vaccine? | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
In the tiny Pacific Nation of Samoa, on Friday 6 July 2018, two babies died shortly after receiving MMR vaccine. How could this happen? Lots of discussion is going around about this tragedy, and even more questions. Here are some responses to the things I have been asked this week summarised under the headings below. About MMR vaccines How safe are MMR vaccines? The risks of measles mumps and rubella People who should forego the MMR vaccine How can vaccination with MMR go wrong? What happened in Samoa? About MMR vaccines MMR vaccines were originally developed in the 1970s to protect against measles, mumps, and rubella, in one convenient jab. However, there is a long history of the development and use of measles-containing these vaccines that extends back to the 1960s. The measles-containing vaccines are called live vaccines. This is because the viruses in the formulation are viable, they can replicate. The viruses need to replicate to get the body to make an immune response that will be protective against disease but they have also been weakened so they are unable to cause disease. These vacciens are extremely effective with measles …
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OpenHelix: List of available tutorials

OpenHelix: List of available tutorials | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
OpenHelix provides on-line and onsite training on bioinformatics and genomics resources. OpenHelix encourages faster and more effective research by enabling the efficient use of publicly available tools to access biological data. OpenHelix tutorial suites on publicly available biomedical resources include an online narrated tutorial as well as PowerPoint slides, handouts and exercises. Customers can effectively and efficiently learn to use a resource and save time and money when teaching others by using the downloadable materials.
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Accurate multiple alignment of distantly related genome sequences using Filtered Spaced Word Matches as anchor points | Bioinformatics | Oxford Academic

Accurate multiple alignment of distantly related genome sequences using Filtered Spaced Word Matches as anchor points | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
AbstractMotivation. Most methods for pairwise and multiple genome alignment use fast local homology search tools to identify anchor points, i.e. high-scoring l
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PARP12 suppresses Zika virus infection through PARP-dependent degradation of NS1 and NS3 viral proteins

PARP12 suppresses Zika virus infection through PARP-dependent degradation of NS1 and NS3 viral proteins | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Type I interferon signaling drives the expression of hundreds of interferon-stimulated genes (ISGs) that are critical for host and cellular defense against viral infection. To identify ISGs that limit Zika virus infection, Li et al . screened CRISPR knockout cell lines and found that loss of PARP12 increased viral replication. Truncation and pharmacological inhibition of PARP12 indicated that antiviral activity required the PARP domain–dependent ADP-ribosylation of required viral proteins, which led to their ubiquitylation and degradation. This work identifies a distinct antiviral mechanism and suggests that PARP agonists may have clinical utility if repurposed as treatments for Zika virus.
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Romania reports African swine fever in farm pigs

Romania reports African swine fever in farm pigs | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Romania reports African swine fever in farm pigs
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Direct cell-to-cell transmission of respiratory viruses: The fast lanes

Direct cell-to-cell transmission of respiratory viruses: The fast lanes | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
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Ask a CDC Scientist: Dr. Terrence Tumpey and the Reconstruction of the 1918 Pandemic Virus | Pandemic Influenza (Flu) | CDC

Ask a CDC Scientist: Dr. Terrence Tumpey and the Reconstruction of the 1918 Pandemic Virus | Pandemic Influenza (Flu) | CDC | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Everything you need to know about the flu illness, including symptoms, treatment and prevention.

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Accurate prediction of orthologs in the presence of divergence after duplication

MOTIVATION:
When gene duplication occurs, one of the copies may become free of selective pressure and evolve at an accelerated pace. This has important consequences on the prediction of orthology relationships, since two orthologous genes separated by divergence after duplication may differ in both sequence and function. In this work, we make the distinction between the primary orthologs, which have not been affected by accelerated mutation rates on their evolutionary path, and the secondary orthologs, which have. Similarity-based prediction methods will tend to miss secondary orthologs, whereas phylogeny-based methods cannot separate primary and secondary orthologs. However, both types of orthology have applications in important areas such as gene function prediction and phylogenetic reconstruction, motivating the need for methods that can distinguish the two types.
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Papua New Guinea is no longer polio-free

Papua New Guinea is no longer polio-free | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
A case of polio in Papua New Guinea caused by circulating type 1 vaccine derived poliovirus has been identified in an under-immunized community.
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Removing contaminants from databases of draft genomes

Removing contaminants from databases of draft genomes | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Metagenomic sequencing of patient samples is a very promising method for the diagnosis of human infections. Sequencing has the ability to capture all the DNA or RNA from pathogenic organisms in a human sample. However, complete and accurate characterization of the sequence, including identification of any pathogens, depends on the availability and quality of genomes for comparison. Thousands of genomes are now available, and as these numbers grow, the power of metagenomic sequencing for diagnosis should increase. However, recent studies have exposed the presence of contamination in published genomes, which when used for diagnosis increases the risk of falsely identifying the wrong pathogen. To address this problem, we have developed a bioinformatics system for eliminating contamination as well as low-complexity genomic sequences in the draft genomes of eukaryotic pathogens. We applied this software to identify and remove human, bacterial, archaeal, and viral sequences present in a comprehensive database of all sequenced eukaryotic pathogen genomes. We also removed low-complexity genomic sequences, another source of false positives. Using this pipeline, we have produced a database of “clean” eukaryotic pathogen genomes for use with bioinformatics classification and analysis tools. We demonstrate that when attempting to find eukaryotic pathogens in metagenomic samples, the new database provides better sensitivity than one using the original genomes while offering a dramatic reduction in false positives.
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