Virology and Bioi...
Follow
Find
53.8K views | +46 today
 
Scooped by Ken Yaw Agyeman-Badu
onto Virology and Bioinformatics from Virology.ca
Scoop.it!

A DNA virus with the capsid of an RNA virus

A DNA virus with the capsid of an RNA virus | Virology and Bioinformatics from Virology.ca | Scoop.it
A new virus has been discovered that appears to have sequences from both an RNA and a DNA virus.
more...
Ed Rybicki's comment, July 23, 2012 5:01 AM
Ken: this is a rescoop of a paper from April or earlier...?
Ken Yaw Agyeman-Badu's comment, July 23, 2012 5:14 AM
Yes Ed, but I initially thought you could rescoop interesting articles after some time to make sure those who missed it back then see's it this time. Actually my bad and will prevent that next time. Thanks for the alert.

From around the web

Virology and Bioinformatics from Virology.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
Your new post is loading...
Your new post is loading...
Scooped by Chris Upton + helpers
Scoop.it!

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

more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

Omics Find Chinks in Ebola Armor for Vaccine and Drug Development

Omics Find Chinks in Ebola Armor for Vaccine and Drug Development | Virology and Bioinformatics from Virology.ca | Scoop.it

On October 12, the Ebola crisis hit home in a new way, as the first case of person-to-person transmission of the virus was reported in Texas. A nurse who helped treat the Liberian man who died from the virus has tested positive for the disease, despite wearing a gown, gloves, mask, and other protective gear while in contact with the victim.

Ebola (EBOV), a single-stranded RNA filovirus, causes infections characterized by immune suppression and a systemic inflammatory response. This results in impairment of the vascular, coagulation, and immune systems, leading to multiorgan failure and shock (in some ways resembling septic shock).

But while overwhelming challenges in controlling and treating this disease remain, the availability of genomic and proteomic data accumulated and shared by researchers since the virus’ discovery in 1976 has already translated into invaluable knowledge about the deadly RNA virus, pinpointing potential targets for diagnostics, vaccines, and therapeutics.

Ed Rybicki's insight:

Of COURSE 'omics will solve the problem.  It can solve EVERYTHING B-)

more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

Hepatitis A virus and the origins of picornaviruses

Hepatitis A virus and the origins of picornaviruses | Virology and Bioinformatics from Virology.ca | Scoop.it
Hepatitis A virus (HAV) remains enigmatic, despite 1.4 million cases worldwide annually. It differs radically from other picornaviruses, existing in an enveloped form and being unusually stable, both genetically and physically, but has proved difficult to study. Here we report high-resolution X-ray structures for the mature virus and the empty particle. The structures of the two particles are indistinguishable, apart from some disorder on the inside of the empty particle. The full virus contains the small viral protein VP4, whereas the empty particle harbours only the uncleaved precursor, VP0. The smooth particle surface is devoid of depressions that might correspond to receptor-binding sites. Peptide scanning data extend the previously reported VP3 antigenic site, while structure-based predictions suggest further epitopes. HAV contains no pocket factor and can withstand remarkably high temperature and low pH, and empty particles are even more robust than full particles. The virus probably uncoats via a novel mechanism, being assembled differently to other picornaviruses. It utilizes a VP2 /`domain swap/' characteristic of insect picorna-like viruses, and structure-based phylogenetic analysis places HAV between typical picornaviruses and the insect viruses. The enigmatic properties of HAV may reflect its position as a link between /`modern/' picornaviruses and the more /`primitive/' precursor insect viruses; for instance, HAV retains the ability to move from cell-to-cell by transcytosis.
Ed Rybicki's insight:

Cool...B-)

more...
No comment yet.
Scooped by Hannah Davis
Scoop.it!

We Have Nothing: The Human Cost Of Ebola

We Have Nothing: The Human Cost Of Ebola | Virology and Bioinformatics from Virology.ca | Scoop.it
Harrowing personal stories reveal the catastrophic impact of the deadly virus on one of the world's poorest regions.
more...
No comment yet.
Scooped by Hannah Davis
Scoop.it!

Footage From 1976 Documents Discovery of Ebola Virus

Footage From 1976 Documents Discovery of Ebola Virus | Virology and Bioinformatics from Virology.ca | Scoop.it
In 1976, a group of health workers took a pair of film cameras to what was then known as Zaire and documented their discovery of a new, deadly virus. Today we know that virus as Ebola.
more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

On the Quarantine Period for Ebola Virus

On the Quarantine Period for Ebola Virus | Virology and Bioinformatics from Virology.ca | Scoop.it

Background:
21 days has been regarded as the appropriate quarantine period for holding individuals potentially exposed to Ebola Virus (EV) to reduce risk of contagion. There does not appear to be a systematic discussion of the basis for this period.

Methods:
The prior estimates for incubation time to EV were examined, along with data on the first 9 months of the current outbreak. These provided estimates of the distribution of incubation times.

Results:
A 21 day period for quarantine may result in the release of individuals with a 0.2 – 12% risk of release prior to full opportunity for the incubation to proceed. It is suggested that a detailed cost-benefit assessment, including considering full transmission risks, needs to occur in order to determine the appropriate quarantine period for potentially exposed individuals.

Ed Rybicki's insight:

Oops...of course, it was never a figure set in stone - but a 12% risk is significant!

more...
No comment yet.
Scooped by Hannah Davis
Scoop.it!

LRB · Paul Farmer · Diary: Ebola

LRB · Paul Farmer · Diary: Ebola | Virology and Bioinformatics from Virology.ca | Scoop.it
I have just returned from Liberia with a group of physicians and health activists. We are heading back in a few days. The country is in the midst of the largest ever epidemic of Ebola haemorrhagic fever. It’s an acute and brutal affliction. Ebola is a zoonosis – it leaps from animal . . .
more...
No comment yet.
Rescooped by Ken Yaw Agyeman-Badu from Mucosal Immunity
Scoop.it!

A Beneficiary Role for Neuraminidase in Influenza Virus Penetration through the Respiratory Mucus

A Beneficiary Role for Neuraminidase in Influenza Virus Penetration through the Respiratory Mucus | Virology and Bioinformatics from Virology.ca | Scoop.it
by Xiaoyun Yang, Lennert Steukers, Katrien Forier, Ranhua Xiong, Kevin Braeckmans, Kristien Van Reeth, Hans Nauwynck Swine influenza virus (SIV) has a strong tropism for pig respiratory mucosa, which consists of a mucus layer, epithelium, basement...

Via Gilbert Faure au nom de l'ASSIM
more...
No comment yet.
Scooped by Hannah Davis
Scoop.it!

Study suggests 21-day Ebola quarantine period is not enough

Study suggests 21-day Ebola quarantine period is not enough | Virology and Bioinformatics from Virology.ca | Scoop.it
A new study has suggested that the standard 21-day quarantine period that’s currenty being used for cases of Ebola might not be enough.
Hannah Davis's insight:

No need to panic: quarantine period just needs to be extended a bit. The main problem in the current outbreak is not that people aren't being quarantined for long enough, but that they're not being quarantined at all.

more...
No comment yet.
Scooped by natashai
Scoop.it!

How the immune system spots tumors

How the immune system spots tumors | Virology and Bioinformatics from Virology.ca | Scoop.it
The receptor protein Dectin-1 recognizes structures found on cancerous cells, and then triggers an anti-tumor immune response.
more...
No comment yet.
Rescooped by burkesquires from Tools and tips for scientific tinkers and tailors
Scoop.it!

Virus entry at a glance

Virus entry at a glance | Virology and Bioinformatics from Virology.ca | Scoop.it
I'm not normally very keen on infographics - but I like this one:

Source: Yamauchi, Y., and Helenius, A. (2013) Virus entry at a glance. Journal of Cell Science, 126(6): 1289-1295.

Via Mel Melendrez-Vallard
more...
No comment yet.
Scooped by burkesquires
Scoop.it!

A comprehensive collection of systems biology data characterizing the host response to viral infection

A comprehensive collection of systems biology data characterizing the host response to viral infection | Virology and Bioinformatics from Virology.ca | Scoop.it

The Systems Biology for Infectious Diseases Research program was established by the U.S. National Institute of Allergy and Infectious Diseases to investigate host-pathogen interactions at a systems level. This program generated 47 transcriptomic and proteomic datasets from 30 studies that investigate in vivo and in vitro host responses to viral infections. Human pathogens in the Orthomyxoviridae and Coronaviridae families, especially pandemic H1N1 and avian H5N1 influenza A viruses and severe acute respiratory syndrome coronavirus (SARS-CoV), were investigated. Study validation was demonstrated via experimental quality control measures and meta-analysis of independent experiments performed under similar conditions. Primary assay results are archived at the GEO and PeptideAtlas public repositories, while processed statistical results together with standardized metadata are publically available at the Influenza Research Database (www.fludb.org) and the Virus Pathogen Resource (www.viprbrc.org). By comparing data from mutant versus wild-type virus and host strains, RNA versus protein differential expression, and infection with genetically similar strains, these data can be used to further investigate genetic and physiological determinants of host responses to viral infection.

 
more...
No comment yet.
Scooped by Hannah Davis
Scoop.it!

Why Ebola may pose a greater threat in the ICU

Why Ebola may pose a greater threat in the ICU | Virology and Bioinformatics from Virology.ca | Scoop.it
The nature of the Ebola virus makes it a grave threat to those who have the most intimate contact with patients' bodies -- health care workers, family caregivers and grave diggers.
more...
No comment yet.
Scooped by natashai
Scoop.it!

A Loop Region in the N-Terminal Domain of Ebola Virus VP40 Is Important in Viral Assembly, Budding, and Egress

A Loop Region in the N-Terminal Domain of Ebola Virus VP40 Is Important in Viral Assembly, Budding, and Egress | Virology and Bioinformatics from Virology.ca | Scoop.it
Ebola virus (EBOV) causes viral hemorrhagic fever in humans and can have clinical fatality rates of ~60%. The EBOV genome consists of negative sense RNA that encodes seven proteins including viral protein 40 (VP40). VP40 is the major Ebola virus matrix protein and regulates assembly and egress of infectious Ebola virus particles. It is well established that VP40 assembles on the inner leaflet of the plasma membrane of human cells to regulate viral budding where VP40 can produce virus like particles (VLPs) without other Ebola virus proteins present. The mechanistic details, however, of VP40 lipid-interactions and protein-protein interactions that are important for viral release remain to be elucidated. Here, we mutated a loop region in the N-terminal domain of VP40 (Lys127, Thr129, and Asn130) and find that mutations (K127A, T129A, and N130A) in this loop region reduce plasma membrane localization of VP40. Additionally, using total internal reflection fluorescence microscopy and number and brightness analysis we demonstrate these mutations greatly reduce VP40 oligomerization. Lastly, VLP assays demonstrate these mutations significantly reduce VLP release from cells. Taken together, these studies identify an important loop region in VP40 that may be essential to viral egress.
more...
No comment yet.
Rescooped by Bradford Condon from Genomics and metagenomics of microbes
Scoop.it!

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits | Virology and Bioinformatics from Virology.ca | Scoop.it
Approximately 80% of the pan-genome was present in all seven accessions (core), whereas the rest was dispensable and exhibited greater variation than the core genome, perhaps reflecting a role in adaptation to diverse environments.
more...
No comment yet.
Scooped by Ken Yaw Agyeman-Badu
Scoop.it!

This Is What The Ebola Virus Really Looks Like -- And How It Works

This Is What The Ebola Virus Really Looks Like -- And How It Works | Virology and Bioinformatics from Virology.ca | Scoop.it
We're guessing that by now, you're pretty familiar with this little squiggle. But if you want to know what Ebola really looks like -- and how it hijacks cells to wreak havoc inside the human body -- you need a detailed diagram of an Ebola virus parti...
more...
No comment yet.
Scooped by burkesquires
Scoop.it!

Genomic and Functional Characteristics of Human Cytomegalovirus Revealed by Next-Generation Sequencing

Genomic and Functional Characteristics of Human Cytomegalovirus Revealed by Next-Generation Sequencing | Virology and Bioinformatics from Virology.ca | Scoop.it
The complete genome of human cytomegalovirus (HCMV) was elucidated almost 25 years ago using a traditional cloning and Sanger sequencing approach. Analysis of the genetic content of additional laboratory and clinical isolates has lead to a better, albeit still incomplete, definition of the coding potential and diversity of wild-type HCMV strains. The introduction of a new generation of massively parallel sequencing technologies, collectively called next-generation sequencing, has profoundly increased the throughput and resolution of the genomics field. These increased possibilities are already leading to a better understanding of the circulating diversity of HCMV clinical isolates. The higher resolution of next-generation sequencing provides new opportunities in the study of intrahost viral population structures. Furthermore, deep sequencing enables novel diagnostic applications for sensitive drug resistance mutation detection. RNA-seq applications have changed the picture of the HCMV transcriptome, which resulted in proof of a vast amount of splicing events and alternative transcripts. This review discusses the application of next-generation sequencing technologies, which has provided a clearer picture of the intricate nature of the HCMV genome. The continuing development and application of novel sequencing technologies will further augment our understanding of this ubiquitous, but elusive, herpesvirus.
more...
No comment yet.
Scooped by burkesquires
Scoop.it!

Ebola data on DataMarket

Ebola data on DataMarket | Virology and Bioinformatics from Virology.ca | Scoop.it
The outbreak of the Ebola virus disease (EVD) in western Africa that started in March this year is the deadliest outbreak of EVD to date. In August the World Health Organization declared the epidem...
more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

A Beneficiary Role for Neuraminidase in Influenza Virus Penetration through the Respiratory Mucus

A Beneficiary Role for Neuraminidase in Influenza Virus Penetration through the Respiratory Mucus | Virology and Bioinformatics from Virology.ca | Scoop.it

Swine influenza virus (SIV) has a strong tropism for pig respiratory mucosa, which consists of a mucus layer, epithelium, basement membrane and lamina propria. Sialic acids present on the epithelial surface have long been considered to be determinants of influenza virus tropism. However, mucus which is also rich in sialic acids may serve as the first barrier of selection. It was investigated how influenza virus interacts with the mucus to infect epithelial cells. Two techniques were applied to track SIV H1N1 in porcine mucus. The microscopic diffusion of SIV particles in the mucus was analyzed by single particle tracking (SPT), and the macroscopic penetration of SIV through mucus was studied by a virus in-capsule-mucus penetration system, followed by visualizing the translocation of the virions with time by immunofluorescence staining. Furthermore, the effects of neuraminidase on SIV getting through or binding to the mucus were studied by using zanamivir, a neuraminidase inhibitor (NAI), and Arthrobacter ureafaciensneuraminidase. The distribution of the diffusion coefficient shows that 70% of SIV particles were entrapped, while the rest diffused freely in the mucus. Additionally, SIV penetrated the porcine mucus with time, reaching a depth of 65 µm at 30 min post virus addition, 2 fold of that at 2 min. Both the microscopic diffusion and macroscopic penetration were largely diminished by NAI, while were clearly increased by the effect of exogenous neuraminidase. Moreover, the exogenous neuraminidase sufficiently prevented the binding of SIV to mucus which was reversely enhanced by effect of NAI. These findings clearly show that the neuraminidase helps SIV move through the mucus, which is important for the virus to reach and infect epithelial cells and eventually become shed into the lumen of the respiratory tract.

 
Ed Rybicki's insight:

Good stuff!  I especially like their "virus in-capsule-mucus penetration system".  Amazing this hasn't been looked at in this sort of detail previously.

 
more...
No comment yet.
Scooped by natashai
Scoop.it!

Antiviral drug discovery: broad-spectrum drugs from nature - Natural Product Reports (RSC Publishing)

Covering: up to April 2014The development of drugs with broad-spectrum antiviral activities is a long pursued goal in drug discovery. It has been shown that blocking co-opted host-factors abrogates the replication of many viruses, yet the development of such host-targeting drugs has been met with scepticism mainly
more...
No comment yet.
Scooped by Julia Paoli
Scoop.it!

Five Fast Facts About Ebola | Viruses101 | Learn Science at Scitable

Five Fast Facts About Ebola | Viruses101 | Learn Science at Scitable | Virology and Bioinformatics from Virology.ca | Scoop.it
Can cats or dogs become infected with Ebola? Which country has the highest number of Ebola cases? These and other interesting questions about the 2014 Ebola Outbreak are answered.
more...
No comment yet.
Scooped by natashai
Scoop.it!

Live Attenuated and Inactivated Viral Vaccine Formulation and Nasal Delivery: Potential and Challenges

Live Attenuated and Inactivated Viral Vaccine Formulation and Nasal Delivery: Potential and Challenges | Virology and Bioinformatics from Virology.ca | Scoop.it
Vaccines are cost-effective for the prevention of infectious diseases and have significantly reduced mortality and morbidity. Novel approaches are needed to develop safe and effective vaccines against disease. Major challenges in vaccine development include stability in a suitable dosage form, and effective modes of delivery. Many live attenuated vaccines are capable of eliciting both humoral and cell mediated immune responses if physicochemically stable in an appropriate delivery vehicle. Knowing primary stresses that impart instability provide a general rationale for formulation development and mode of delivery. Since most pathogens enter the body through the mucosal route, live-attenuated vaccines have the advantage of mimicking natural immunization via non-invasive delivery. This presentation will examine aspects of formulation design, types of robust dosage forms to consider, effective routes of delivery (invasive and noninvasive), and distinctions between live attenuated or inactivated vaccines.
more...
No comment yet.
Scooped by burkesquires
Scoop.it!

Ebola by the numbers: The size, spread and cost of an outbreak

Ebola by the numbers: The size, spread and cost of an outbreak | Virology and Bioinformatics from Virology.ca | Scoop.it
As the virus continues to rampage in West Africa, Nature’s graphic offers a guide to the figures that matter.
more...
No comment yet.
Rescooped by burkesquires from Bioinformatics
Scoop.it!

Crossroads (iii) – a New Direction for Bioinformatics with Twelve Fundamental Problems « Homolog.us – Bioinformatics

Crossroads (iii) – a New Direction for Bioinformatics with Twelve Fundamental Problems « Homolog.us – Bioinformatics | Virology and Bioinformatics from Virology.ca | Scoop.it

Via Wei Shen
more...
No comment yet.
Scooped by Ben Hetman
Scoop.it!

Computation | Free Full-Text | Incongruencies in Vaccinia Virus Phylogenetic Trees

Over the years, as more complete poxvirus genomes have been sequenced, phylogenetic studies of these viruses have become more prevalent. In general, the results show similar relationships between the poxvirus species; however, some inconsistencies are notable. Previous analyses of the viral genomes contained within the vaccinia virus (VACV)-Dryvax vaccine revealed that their phylogenetic relationships were sometimes clouded by low bootstrapping confidence. To analyze the VACV-Dryvax genomes in detail, a new tool-set was developed and integrated into the Base-By-Base bioinformatics software package. Analyses showed that fewer unique positions were present in each VACV-Dryvax genome than expected. A series of patterns, each containing several single nucleotide polymorphisms (SNPs) were identified that were counter to the results of the phylogenetic analysis. The VACV genomes were found to contain short DNA sequence blocks that matched more distantly related clades. Additionally, similar non-conforming SNP patterns were observed in (1) the variola virus clade; (2) some cowpox clades; and (3) VACV-CVA, the direct ancestor of VACV-MVA. Thus, traces of past recombination events are common in the various orthopoxvirus clades, including those associated with smallpox and cowpox viruses.
more...
No comment yet.
Scooped by burkesquires
Scoop.it!

New Methods in Tissue Engineering: Improved Models for Viral Infection

New insights in the study of virus and host biology in the context of viral infection are made possible by the development of model systems that faithfully recapitulate the in vivo viral life cycle. Standard tissue culture models lack critical emergent properties driven by cellular organization and in vivo–like function, whereas animal models suffer from limited susceptibility to relevant human viruses and make it difficult to perform detailed molecular manipulation and analysis. Tissue engineering techniques may enable virologists to create infection models that combine the facile manipulation and readouts of tissue culture with the virus-relevant complexity of animal models. Here, we review the state of the art in tissue engineering and describe how tissue engineering techniques may alleviate some common shortcomings of existing models of viral infection, with a particular emphasis on hepatotropic viruses. We then discuss possible future applications of tissue engineering to virology, including current challenges and potential solutions.

more...
No comment yet.