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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The restriction factors of human immunodeficienc... [J Biol Chem. 2012] - PubMed - NCBI

PubMed comprises more than 22 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
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Gain-of-Sensitivity Mutations in a Trim5-Resistant Primary Isolate of Pathogenic SIV Identify Two Independent Conserved Determinants of Trim5α Specificity

Gain-of-Sensitivity Mutations in a Trim5-Resistant Primary Isolate of Pathogenic SIV Identify Two Independent Conserved Determinants of Trim5α Specificity | Virology and Bioinformatics from Virology.ca | Scoop.it
From molecules to physiology
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Ahead of Print - Novel Poxvirus in Big Brown Bats, Northwestern United States - Vol. 19 No. 6 - June 2013 - Emerging Infectious Disease journal - CDC

Ahead of Print - Novel Poxvirus in Big Brown Bats, Northwestern United States - Vol. 19 No. 6 - June 2013 - Emerging Infectious Disease journal - CDC | Virology and Bioinformatics from Virology.ca | Scoop.it
A wildlife hospital and rehabilitation center in northwestern United States received several big brown bats with necrosuppurative osteomyelitis in multiple joints. Wing and joint tissues were positive by PCR for poxvirus.
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UAE is prepared to track and control Sars-like coronavirus - The National

UAE is prepared to track and control Sars-like coronavirus - The National | Virology and Bioinformatics from Virology.ca | Scoop.it
UAE is prepared to track and control Sars-like coronavirus
The National
Dr Al Zarouni said that testing for the virus required a reference virology laboratory, something the UAE has yet to introduce.
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Virology Journal | Abstract | Epidemiological analysis of respiratory viral etiology for influenza-like illness during 2010 in Zhuhai, China

Influenza-like illnesses (ILI), a subset of acute respiratory infections (ARI), are a significant source of morbidity and mortality worldwide.
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Ebola virus does not block apoptotic signaling pathways

Ebola virus does not block apoptotic signaling pathways | Virology and Bioinformatics from Virology.ca | Scoop.it

"Since viruses rely on functional cellular machinery for efficient propagation, apoptosis is an important mechanism to fight viral infections. In this study, we sought to determine the mechanism of cell death caused by Ebola virus (EBOV) infection by assaying for multiple stages of apoptosis and hallmarks of necrosis. Our data indicate that EBOV does not induce apoptosis in infected cells but rather leads to a nonapoptotic form of cell death."

 

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Biophysical Journal - The Ebola Virus Matrix Protein Deeply Penetrates the Plasma Membrane: An Important Step in Viral Egress

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Scientist: Cassava disease spread at alarming rate

Scientist: Cassava disease spread at alarming rate | Virology and Bioinformatics from Virology.ca | Scoop.it

Scientist: Cassava disease spread at alarming rate - A moderate infection with up to 30 percent root damage decreases the market value of cassava tubers drastically, to less than $5 a ton instead of $55, according to a...

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ScienceDirect.com - Vaccine - Understanding the human immune system in the 21st century: The Human Immunology Project Consortium

ScienceDirect.com - Vaccine - Understanding the human immune system in the 21st century: The Human Immunology Project Consortium | Virology and Bioinformatics from Virology.ca | Scoop.it

As much of this work involves deciphering systems level phenomena, HIPC scientists are using sophisticated bioinformatics approaches to define the human transcriptome/proteome.

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PLOS Computational Biology: Estimation of Vaccine Efficacy and Critical Vaccination Coverage in Partially Observed Outbreaks

PLOS Computational Biology: Estimation of Vaccine Efficacy and Critical Vaccination Coverage in Partially Observed Outbreaks | Virology and Bioinformatics from Virology.ca | Scoop.it

Classical approaches to estimate vaccine efficacy are based on the assumption that a person's risk of infection does not depend on the infection status of others. This assumption is untenable for infectious disease data where such dependencies abound. We present a novel approach to estimating vaccine efficacy in a Bayesian framework using disease transmission models.

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BMC Bioinformatics | Abstract | Reconstituting protein interaction networks using parameter-dependent domain-domain interactions

We can describe protein-protein interactions (PPIs) as sets of distinct domain-domain interactions (DDIs) that mediate the physical interactions between proteins.
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PLOS ONE: The Genome Sequence of Lone Star Virus, a Highly Divergent Bunyavirus Found in the Amblyomma americanum Tick

Viruses in the family Bunyaviridae infect a wide range of plant, insect, and animal hosts. Tick-borne bunyaviruses in the Phlebovirus genus, including Severe Fever with Thrombocytopenia Syndrome virus (SFTSV) in China, Heartland virus (HRTV) in the United States, and Bhanja virus in Eurasia and Africa have been associated with acute febrile illness in humans. Here we sought to characterize the growth characteristics and genome of Lone Star virus (LSV), an unclassified bunyavirus originally isolated from the lone star tick Amblyomma americanum. LSV was able to infect both human (HeLa) and monkey (Vero) cells. Cytopathic effects were seen within 72 h in both cell lines; vacuolization was observed in infected Vero, but not HeLa, cells. Viral culture supernatants were examined by unbiased deep sequencing and analysis using an in-house developed rapid computational pipeline for viral discovery, which definitively identified LSV as a phlebovirus. De novo assembly of the full genome revealed that LSV is highly divergent, sharing <61% overall amino acid identity with any other bunyavirus. Despite this sequence diversity, LSV was found by phylogenetic analysis to be part of a well-supported clade that includes members of the Bhanja group viruses, which are most closely related to SFSTV/HRTV. The genome sequencing of LSV is a critical first step in developing diagnostic tools to determine the risk of arbovirus transmission by A. americanum, a tick of growing importance given its expanding geographic range and competence as a disease vector. This study also underscores the power of deep sequencing analysis in rapidly identifying and sequencing the genomes of viruses of potential clinical and public health significance.

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High level of susceptibility to human TRIM5alpha conferred by HIV-2 capsid sequences

HIV-2, which was transmitted to humans from a distant primate species (sooty mangabey), differs remarkably from HIV-1 in its infectivity, transmissibility and pathogenicity.
Ed Rybicki's insight:

Finally, some good news about an HIV - OK, it's HIV-2, but still.

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Immunological assessment of influenza vaccines and immune correlates of protection. Expert Rev Vaccines. 2013

Influenza vaccines remain the primary public health tool in reducing the ever-present burden of influenza and its complications. In seeking more immunogenic, more effective and more broadly cross-protective influenza vaccines, the landscape of influenza vaccines is rapidly expanding, both in near-term advances and next-generation vaccine design. Although the first influenza vaccines were licensed over 60 years ago, the hemagglutination-inhibition antibody titer is currently the only universally accepted immune correlate of protection against influenza. However, hemagglutination-inhibition titers appear to be less effective at predicting protection in populations at high risk for severe influenza disease; older adults, young children and those with certain medical conditions. The lack of knowledge and validated methods to measure alternate immune markers of protection against influenza remain a substantial barrier to the development of more immunogenic, broadly cross-reactive and effective influenza vaccines. Here, the authors review the knowledge of immune effectors of protection against influenza and discuss assessment methods for a broader range of immunological parameters that could be considered in the evaluation of traditional or new-generation influenza vaccines.

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PLOS Pathogens: A Population Genomics Perspective on the Emergence and Adaptation of New Plant Pathogens in Agro-Ecosystems

PLOS Pathogens: A Population Genomics Perspective on the Emergence and Adaptation of New Plant Pathogens in Agro-Ecosystems | Virology and Bioinformatics from Virology.ca | Scoop.it

Plants and pathogens evolve in response to each other. This co-evolutionary arms race is fueled by genetic variation underlying the recognition of pathogen proteins by the host and the defeat of host defenses by the pathogen. Together with new mutations, genetic diversity in populations of both the host and pathogen represent a pool of possible variants to maintain adaptation via natural selection.

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Amid Heightened Concerns, New Name for Novel Coronavirus Emerges

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Ed Rybicki's comment, May 10, 2013 1:05 PM
ABSTRACT!! ANd naming it after the Middle East will go down well...B-)
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Colocalization of Different Influenza Viral RNA Segments in the Cytoplasm before Viral Budding

Colocalization of Different Influenza Viral RNA Segments in the Cytoplasm before Viral Budding | Virology and Bioinformatics from Virology.ca | Scoop.it

Influenza A viruses cause one of the major respiratory infection diseases in humans. The viruses possess a genome consists of eight different RNA segments and the incorporation of all the eight RNA segments is required for the generation of an infectious virus particle. The precise process of how these eight viral RNA segments are co-packaged into progeny virus particles remains undefined due to the limitations of methodology to determine the locations of different vRNA segments in infected cells with single-molecule resolution. In this study, we established an experimental system to examine the localization of different viral RNA segments in an infected cell with high spatial precision. We found that viral RNA belonging to different segments gather together in the cytoplasm which is facilitated by cellular recycling endosomal protein Rab11. Our results supported the idea that eight different viral RNAs likely form a super-complex as they travel to the site for virion incorporation. These findings extend our knowledge on the process of influenza virus genome packaging and suggest a mechanism by which the genome assembly of different viral RNA segments is regulated.

 

Ed Rybicki's insight:

It has always been a bit of a mystery how the 8 different nucleoprotein components of the average influenza A virus come together for assembly - especially, if, as shown here, they assemble and are exported separately from the nucleus.  Yet another example of co-opting of cellular transport and organisation functions for the benefit of a parasite!  Nice use of a sophisticated microscopic technique, too.

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Sickly mosquitoes stymie malaria’s spread

Sickly mosquitoes stymie malaria’s spread | Virology and Bioinformatics from Virology.ca | Scoop.it
Researchers harness bacteria to cripple insects that transmit disease.
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ScienceDirect.com - Virology - Small RNA populations for two unrelated viruses exhibit different biases in strand polarity and proximity to terminal sequences in the insect host Homalodisca vitripe...

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Spatial localization of co-regulated genes exceeds genomic gene clustering in the Saccharomyces cerevisiae genome

Spatial localization of co-regulated genes exceeds genomic gene clustering in the Saccharomyces cerevisiae genome | Virology and Bioinformatics from Virology.ca | Scoop.it

Combining these, we report evidence that co-regulated genes are clustered in space, beyond their observed clustering in the context of gene order along the genome and show this phenomenon is significant for 64 out of 117 transcription factors. Furthermore, we show that those transcription factors with high spatially co-localized targets are expressed higher than those whose targets are not spatially clustered

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The universal epitope of influenza A viral neuraminidase fundamentally contributes to enzyme activity and viral replication...J Biol Chem. 2013

The only universally conserved sequence amongst all influenza A viral neuraminidase is located between amino acids 222-230. However, the potential roles of these amino acids (a.a.) remain largely unknown. Through an array of experimental approaches including mutagenesis, reverse genetics and growth kinetics, we found this sequence could markedly affect viral replication. Additional experiments revealed that enzymes with mutations in this region demonstrated substantially decreased catalytic activity, substrate-binding and thermostability. Consistent with viral replication analyses and enzymatic studies, protein modelling suggests that these amino acids could either directly bind to the substrate or contribute to the formation of the active site in the enzyme. Collectively, these findings reveal the essential role of this unique region in enzyme function and viral growth, which provides the basis for evaluating the validity of this sequence as potential target for antiviral intervention and vaccine development

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When Immunizing, Don’t Accept Alternatives « Canada « Skeptic North

When Immunizing, Don’t Accept Alternatives « Canada « Skeptic North | Virology and Bioinformatics from Virology.ca | Scoop.it
It’s National Immunization Awareness Week in Canada and across the world, and UNICEF is reporting the failure of Canada to achieve the 95% immunization rate…
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BMC Genomics | Abstract | Unscrambling butterfly oogenesis

Butterflies are popular model organisms to study physiological mechanisms underlying
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RegaDB: community-driven data management and analysis for infectious diseases. Bioinformatics. 2013

SUMMARY: RegaDB is a free and open source data management and analysis environment for infectious diseases. RegaDB allows clinicians to store, manage and analyse patient data, including viral genetic sequences. Moreover, RegaDB provides researchers with a mechanism to collect data in a uniform format and offers them a canvas to make newly developed bioinformatics tools available to clinicians and virologists through a user friendly interface.Availability and implementation: Source code, binaries and documentation are available on http://rega.kuleuven.be/cev/regadb. RegaDB is written in the Java programming language, using a web-service-oriented architecture. CONTACT: pieter.libin@rega.kuleuven.be.

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Rising measles outbreaks threaten vaccine-averse

Rising measles outbreaks threaten vaccine-averse | Virology and Bioinformatics from Virology.ca | Scoop.it

Seven confirmed cases of measles in Toronto, Ontario, so far this year, for a total of 12 in Canada to date, are prompting public health officials to remind doctors that the once-common childhood illness risks establishing a foothold again.

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Ed Rybicki's curator insight, May 6, 2013 4:23 PM

And why?  Because risk-averse parents aren't vaccinating their children against the things THEY were vaccinated against, which means we're back in the 1950s again as far as morbidity / mortality figures are concerned.