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BMC Bioinformatics | Full text | A highly conserved WDYPKCDRA epitope in the RNA directed RNA polymerase of human coronaviruses can be used as epitope-based universal vaccine design

Coronaviruses are the diverse group of RNA virus. From 1960, six strains of human coronaviruses have emerged that includes SARS-CoV and the recent infection by deadly MERS-CoV which is now going to cause another outbreak. Prevention of these viruses is urgent and a universal vaccine for all strain could be a promising solution in this circumstance. In this study we aimed to design an epitope based vaccine against all strain of human coronavirus.
Chris Upton + helpers's insight:

Is SARS really a "human virus"?

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Ed Rybicki's comment, June 11, 3:36 PM
I stopped paying attention at " Coronaviruses are the diverse group of RNA virus" and again at " we aimed to design an epitope based vaccine against all strain...".
Ed Rybicki's comment, June 11, 3:37 PM
PS: and no, Chris, it ain't. Nor's MERS.

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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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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

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Structural insight into cap-snatching and RNA synthesis by influenza polymerase : Nature

Structural insight into cap-snatching and RNA synthesis by influenza polymerase : Nature | Virology and Bioinformatics from Virology.ca | Scoop.it

Influenza virus polymerase uses a capped primer, derived by ‘cap-snatching’ from host pre-messenger RNA, to transcribe its RNA genome into mRNA and a stuttering mechanism to generate the poly(A) tail. By contrast, genome replication is unprimed and generates exact full-length copies of the template. Here we use crystal structures of bat influenza A and human influenza B polymerases (FluA and FluB), bound to the viral RNA promoter, to give mechanistic insight into these distinct processes. In the FluA structure, a loop analogous to the priming loop of flavivirus polymerases suggests that influenza could initiate unprimed template replication by a similar mechanism. Comparing the FluA and FluB structures suggests that cap-snatching involves in siturotation of the PB2 cap-binding domain to direct the capped primer first towards the endonuclease and then into the polymerase active site. The polymerase probably undergoes considerable conformational changes to convert the observed pre-initiation state into the active initiation and elongation states.

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Systematic identification of transcriptional and post-transcriptional regulations in human respiratory epithelial cells during influenza A virus infection - BMC Bioinformatics

Respiratory epithelial cells are the primary target of influenza virus infection in human. However, the molecular mechanisms of airway epithelial cell responses to viral infection are not fully understood. Revealing genome-wide transcriptional and post-transcriptional regulatory relationships can further advance our understanding of this problem, which motivates the development of novel and more efficient computational methods to simultaneously infer the transcriptional and post-transcriptional regulatory networks.
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BMC Research Notes | Abstract | DivA: detection of non-homologous and very divergent regions in protein sequence alignments

Sequence alignments are used to find evidence of homology but sometimes contain regions that are difficult to align which can interfere with the quality of the subsequent analyses. Although it is possible to remove problematic regions manually, this is non-practical in large genome scale studies, and the results suffer from irreproducibility arising from subjectivity. Some automated alignment trimming methods have been developed to remove problematic regions in alignments but these mostly act by removing complete columns or complete sequences from the MSA, discarding a lot of informative sites.
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Scripps Research Institute Scientists Reveal Weak Spots in Ebola’s Defenses

Scripps Research Institute Scientists Reveal Weak Spots in Ebola’s Defenses | Virology and Bioinformatics from Virology.ca | Scoop.it
News Release
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Camels are MERS Reservoirs | The Scientist Magazine®

Camels are MERS Reservoirs | The Scientist Magazine® | Virology and Bioinformatics from Virology.ca | Scoop.it
Researchers have concluded that these animals, known as the “ships of the desert,” can ferry the deadly coronavirus, perhaps infecting people.
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H5N8 Avian Flu Detected in the Netherlands and Britain

H5N8 Avian Flu Detected in the Netherlands and Britain | Virology and Bioinformatics from Virology.ca | Scoop.it
It was not clear if the outbreaks at poultry farms in the two countries were linked, but a British veterinary official said wild birds may have carried the disease.

The authorities ordered the slaughter of 150,000 chickens at the farm. News reports identified the strain as H5N8, which has never been detected in humans, according to the European Center for Disease Control and Prevention in Stockholm, but has been reported in birds in South Korea, China, Japan and, earlier this month, in Germany.

“This highly pathogenic variant of avian influenza is very dangerous for bird life,” the Dutch government said. “The disease can be transmitted from animals to humans.”


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Dogs and wild animals can swap parvovirus

Dogs and wild animals can swap parvovirus | Virology and Bioinformatics from Virology.ca | Scoop.it
When canine parvovirus first emerged in 1978, it started a global pandemic that’s thought to have killed hundreds of thousands of dogs.

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10 Ways Biotechnology Improves Our Lives Beyond GMO Crops

10 Ways Biotechnology Improves Our Lives Beyond GMO Crops | Virology and Bioinformatics from Virology.ca | Scoop.it
Farmers and ranchers are the original environmental stewards. Ever since the earliest days of open range grazing, U.S. Agriculture has been working one on one with our natural resources. There have...
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Cells can fight viruses, even when stimulated to combat bacteria

Cells can fight viruses, even when stimulated to combat bacteria | Virology and Bioinformatics from Virology.ca | Scoop.it
Findings may lead to new ways to treat infectious diseases
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19th-Century Documents Show How Little The Anti-Vaxxers Have Changed

19th-Century Documents Show How Little The Anti-Vaxxers Have Changed | Virology and Bioinformatics from Virology.ca | Scoop.it
More than 150 years ago, the British government made smallpox vaccination compulsory, resulting in a massive political backlash. Opponents used tactics and arguments that are familiar today. If anything, the contemporary anti-vaxxer has regressed even further.
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Genetic Data Clarify Insect Evolution

Genetic Data Clarify Insect Evolution | Virology and Bioinformatics from Virology.ca | Scoop.it
Researchers create a phylogenetic tree of insects by comparing the sequences of 1,478 protein-coding genes among species.

Using an unprecedented quantity of genetic sequence information from insects, researchers have assembled a new phylogenetic tree showing when these invertebrates evolved and how they are related to each other. The tree suggests that insects evolved approximately 479 million years ago, around the time when plants colonized land, and that insects are most closely related to cave-dwelling crustaceans. The new study, published today (November 6) in Science, also confirms some previously suspected family groupings.

 

Ed Rybicki's insight:

This bolsters my contention that it was the coevolution of insects and plants - because what else were insects going to eat? - that has driven much of viral evolution as well.

Because what else was there to infect? Basically, the only terrestrial organisms around some 450 million years ago were primitive green plants, insects, fungi and bacteria. So insects ate plants, fungi infected plants, viruses in insects entered plants and vice-versa; fungi got involved as well, and possibly even bacteria.

I have speculated on the possibilities here (http://www.mcb.uct.ac.za/tutorial/virorig.html), but it is pleasing to see new science that reinforces some of what I have been spreading about for some years now B-)

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Rosetta probe makes history by landing on comet

Rosetta probe makes history by landing on comet | Virology and Bioinformatics from Virology.ca | Scoop.it
Philae spacecraft has transmitted data to Earth, but may not be anchored to comet surface.
Ed Rybicki's insight:

"Darmstadt, the Philae has landed..." B-)

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Antibody landscapes after influenza virus infection or vaccination

We introduce the antibody landscape, a method for the quantitative analysis of antibody-mediated immunity to antigenically variable pathogens, achieved by accounting for antigenic variation among pathogen strains. We generated antibody landscapes to study immune profiles covering 43 years of influenza A/H3N2 virus evolution for 69 individuals monitored for infection over 6 years and for 225 individuals pre- and postvaccination. Upon infection and vaccination, titers increased broadly, including previously encountered viruses far beyond the extent of cross-reactivity observed after a primary infection. We explored implications for vaccination and found that the use of an antigenically advanced virus had the dual benefit of inducing antibodies against both advanced and previous antigenic clusters. These results indicate that preemptive vaccine updates may improve influenza vaccine efficacy in previously exposed individuals.

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Structure of influenza A polymerase bound to the viral RNA promoter : Nature

The influenza virus polymerase transcribes or replicates the segmented RNA genome (viral RNA) into viral messenger RNA or full-length copies. To initiate RNA synthesis, the polymerase binds to the conserved 3′ and 5′ extremities of the viral RNA. Here we present the crystal structure of the heterotrimeric bat influenza A polymerase, comprising subunits PA, PB1 and PB2, bound to its viral RNA promoter. PB1 contains a canonical RNA polymerase fold that is stabilized by large interfaces with PA and PB2. The PA endonuclease and the PB2 cap-binding domain, involved in transcription by cap-snatching, form protrusions facing each other across a solvent channel. The 5′ extremity of the promoter folds into a compact hook that is bound in a pocket formed by PB1 and PA close to the polymerase active site. This structure lays the basis for an atomic-level mechanistic understanding of the many functions of influenza polymerase, and opens new opportunities for anti-influenza drug design.

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Functional Genomics Approach for the Identification of Human Host Factors Supporting Dengue Viral Propagation - Springer

Functional Genomics Approach for the Identification of Human Host Factors Supporting Dengue Viral Propagation - Springer | Virology and Bioinformatics from Virology.ca | Scoop.it

Dengue virus (DENV) is endemic throughout tropical regions of the world and there are no approved treatments or anti-transmission agents currently available. Consequently, there exists an enormous unmet need to treat the human diseases caused by DENV and block viral transmission by the mosquito vector. RNAi screening represents an efficient method to expand the pool of known host factors that could become viable targets for treatments or provide rationale to consider available drugs as anti-DENV treatments. We developed a high-throughput siRNA-based screening protocol that can identify human DENV host factors. The protocol herein describes the materials and the procedures necessary to screen a human cell line in order to identify genes which are either necessary for or restrict DENV propagation at any stage in the viral life cycle.

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A virus that melts sea stars

A virus that melts sea stars | Virology and Bioinformatics from Virology.ca | Scoop.it
Sea star associated densovirus might be the cause of a lethal disease that melts these marine invertebrates into piles of slime and ossicles.
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The threat of zoonotic diseases

While zoonotic EIDs are a major concern globally, their impact in less developed countries is disproportionately high.
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Canada begins domestic trial of experimental Ebola vaccine

Canada begins domestic trial of experimental Ebola vaccine | Virology and Bioinformatics from Virology.ca | Scoop.it
TORONTO (Reuters) - Canada has launched a clinical trial of an experimental Ebola vaccine developed at its national microbiology laboratory and expects to have the results in early 2015, the government said on Friday.

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Dynamics and control of Ebola virus transmission: a mathematical modelling analysis

The number of beds at EVD treatment centres needed to effectively control EVD in Montserrado substantially exceeds the 1700 pledged by the USA to west Africa. Accelerated case ascertainment is needed to maximise effectiveness of expanding the capacity of EVD treatment centres. Distributing protective kits can further augment prevention of EVD, but it is not an adequate stand-alone measure for controlling the outbreak. Our findings highlight the rapidly closing window of opportunity for controlling the outbreak and averting a catastrophic toll of EVD cases and deaths.
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Viral Quasispecies Assembly via Maximal Clique Enumeration

Viral Quasispecies Assembly via Maximal Clique Enumeration | Virology and Bioinformatics from Virology.ca | Scoop.it

Virus populations can display high genetic diversity within individual hosts. The intra-host collection of viral haplotypes, called viral quasispecies, is an important determinant of virulence, pathogenesis, and treatment outcome. We present HaploClique, a computational approach to reconstruct the structure of a viral quasispecies from next-generation sequencing data as obtained from bulk sequencing of mixed virus samples. We develop a statistical model for paired-end reads accounting for mutations, insertions, and deletions. Using an iterative maximal clique enumeration approach, read pairs are assembled into haplotypes of increasing length, eventually enabling global haplotype assembly. The performance of our quasispecies assembly method is assessed on simulated data for varying population characteristics and sequencing technology parameters. Owing to its paired-end handling, HaploClique compares favorably to state-of-the-art haplotype inference methods. It can reconstruct error-free full-length haplotypes from low coverage samples and detect large insertions and deletions at low frequencies. We applied HaploClique to sequencing data derived from a clinical hepatitis C virus population of an infected patient and discovered a novel deletion of length 357±167 bp that was validated by two independent long-read sequencing experiments. HaploClique is available at https://github.com/armintoepfer/haploclique. A summary of this paper appears in the proceedings of the RECOMB 2014 conference, April 2-5.

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HIV Protein Can Guide Viral DNA to Opportune Host DNA Landing Site

HIV Protein Can Guide Viral DNA to Opportune Host DNA Landing Site | Virology and Bioinformatics from Virology.ca | Scoop.it

Just as a spacecraft may settle onto a more or less propitious spot, a scrap of viral DNA may insert itself at different locations in its host’s DNA—and some locations may better serve a retrovirus’ disease-propagating purpose than others. Unlike a spacecraft, however, retroviruses such as HIV lack guidance systems. So, just how does HIV home in on its target? The question has puzzled virologists for over 20 years.

 
Ed Rybicki's insight:

And it even involves South Africa!

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Influenza A virus nucleoprotein selectively decreases neuraminidase gene-segment packaging while enhancing viral fitness and transmissibility

Influenza A virus nucleoprotein selectively decreases neuraminidase gene-segment packaging while enhancing viral fitness and transmissibility | Virology and Bioinformatics from Virology.ca | Scoop.it
Significance

The influenza A virus (IAV) genome consists of eight unique RNA segments, each of which is required for productive infection. IAV is believed to copackage its individual gene segments into virions with nearly perfect efficiency to maximize replicative potential. We contradict this view by demonstrating that decreased gene packaging can be associated with increased in vivo fitness and transmissibility. Incomplete packaging likely is facilitated by the extensive coinfection that we demonstrate in vivo, which promotes complementation and explains the frequent reassortment reported previously. We also reveal roles for the viral nucleoprotein in modulating glycoprotein function and gene packaging during host adaptation. These findings necessitate a major shift in how we think about the infectious and evolutionary potential of IAV populations.

 
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DNA Extraction Kits Contaminated

DNA Extraction Kits Contaminated | Virology and Bioinformatics from Virology.ca | Scoop.it
Sequencing study reveals low levels of microbes in lab reagents that can create big problems for some microbiome studies.


Researchers studying microbiomes can do their best to prevent contamination, but a new study reveals widespread, low-level contamination in DNA extraction kits. Reporting in BMC Biology today (November 11), Alan Walker of the University of Aberdeen in the U.K. and colleagues list dozens of contaminating taxa that can swamp out a sample’s true microbial signal, if starting concentrations are low.

“It’s really important to sequence a negative extraction control,” said Patrick Schloss, a microbiome researcher at the University of Michigan who did not participate in this study. “That’s something people should be doing and are not doing.”

Contamination or signal?

The presence of microbial DNA in laboratory reagents is nothing new. Studies have even found bacterial DNA in ultrapure water, and just a few weeks ago researchers pointed out ubiquitous contamination in next generation sequencing runs. In many cases such extraneous DNA may not be an issue, but for highly sensitive deep sequencing of amplified samples, contaminants can start to compete with signal, as Walker’s team found.

 
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Oops...???

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B Cell Responses to Influenza Infection and Vaccination

B Cell Responses to Influenza Infection and Vaccination | Virology and Bioinformatics from Virology.ca | Scoop.it

Although vaccines against influenza are widely available, control of the disease remains elusive. In part, this is due to the inability of current vaccines to induce durable, broadly protective immune responses. Prevention of influenza depends primarily on effective antibody responses that block virus entry. Following infection, high-affinity IgA antibodies are generated in the respiratory tract that lead to immune exclusion, while IgG prevents systemic spread. These are effective and long-lasting but also exert immune pressure. Mutation of the antigenic determinants of influenza therefore rapidly leads to emergence of novel variants that evade previously generated protective responses. Not only do vaccines suffer from this strain-specific limitation, but also they are suboptimal in their ability to induce durable immunity. However, recent evidence has demonstrated the possibility of inducing broadly cross-reactive antibody responses. Further understanding of the ways in which high-titer, long-lived antibody responses directed against such cross-reactive epitopes can be induced would lead to the development of novel vaccines that may remove the requirement for recurrent vaccination.

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