Viruses and Bioinformatics from Virology.uvic.ca
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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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Use of AAScatterPlot tool for monitoring the evolution of hemagglutinin cleavage site in H9 avian viruses

Given genome sequences, the AAScatterPlot tool compacts into a single plot, information about the hydropathy index, Van der Waals volume, chemical property, and occurrence frequency of amino acid residues. The tool also shows the range of residues that could arise from a single point mutation in the genome, which can then be compared against the observed residues to identify mutation constraints. Through this approach, we found that the 2 nd position towards the N-terminus side of the HA PCS (P2 position) avoided hydrophobic residues, whereas the P3 position avoided hydrophilic residues.


AAScatterPlot is available at https://github.com/WhittakerLab/AAScatterPlot.

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Cross-species jumps may play unexpectedly big role in virus evolution: Comparing host and virus evolutionary trees reveals new insights into emergence of viral diseases

Cross-species jumps may play unexpectedly big role in virus evolution: Comparing host and virus evolutionary trees reveals new insights into emergence of viral diseases | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
On occasion, a virus may jump from one host species to another and adapt to the new host. Such cross-species transmission happens more often than expected, according to new research, and it may play a much bigger role in virus evolution than previously thought.

Via Cindy, Kenzibit
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Emergence of a Viral RNA Polymerase Variant during Gene Copy Number Amplification Promotes Rapid Evolution of Vaccinia Virus

IMPORTANCE Viruses can evolve quickly to defeat host immune functions. For poxviruses, little is known about how multiple adaptive mutations emerge in populations at the same time. In this study, we uncovered a means of vaccinia virus adaptation involving the accumulation of distinct genetic variants within a single population. We identified adaptive point mutations in the viral RNA polymerase gene A24R and, surprisingly, found that one of these mutations activates the nucleic acid sensing factor PKR. We also found that gene copy number variation (CNV) can provide dual benefits to evolving virus populations, including evidence that CNV facilitates the accumulation of a point mutation distant from the expanded locus. Our data suggest that transient CNV can accelerate the fixation of mutations conferring modest benefits, or even fitness trade-offs, and highlight how structural variation might aid poxvirus adaptation through both direct and indirect actions.
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An Evolutionary View of the Arms Race between Protein Kinase R and Large DNA Viruses

To establish productive infections, viruses must counteract numerous cellular defenses that are poised to recognize viruses as nonself and to activate antiviral pathways. The opposing goals of host and viral factors lead to evolutionary arms races that can be illuminated by evolutionary and computational methods and tested in experimental models. Here we illustrate how this perspective has been contributing to our understanding of the interactions of the protein kinase R pathway with large DNA viruses.
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Evolution and molecular epidemiology of classical swine fever virus during a multi-annual outbreak amongst European wild boar

Classical swine fever is a viral disease of pigs that carries tremendous socio-economic impact. In outbreak situations, genetic typing is carried out for the purpose of molecular epidemiology in both domestic pigs and wild boar. These analyses are usually based on harmonized partial sequences. However, for high-resolution analyses towards the understanding of genetic variability and virus evolution, full-genome sequences are more appropriate. In this study, a unique set of representative virus strains was investigated that was collected during an outbreak in French free-ranging wild boar in the Vosges-du-Nord mountains between 2003 and 2007. Comparative sequence and evolutionary analyses of the nearly full-length sequences showed only slow evolution of classical swine fever virus strains over the years and no impact of vaccination on mutation rates. However, substitution rates varied amongst protein genes; furthermore, a spatial and temporal pattern could be observed whereby two separate clusters were formed that coincided with physical barriers.
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Evolution of Newcastle Disease Virus Quasispecies Diversity and Enhanced Virulence after Passage through Chicken Air Sacs

It has been reported that lentogenic Newcastle disease virus (NDV) isolates have the potential to become velogenic after their transmission and circulation in chickens, but the underlying mechanism is unclear. In this study, a highly velogenic NDV variant, JS10-A10, was generated from the duck-origin lentogenic isolate JS10 through 10 consecutive passages in chicken air sacs.
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A phylogenomic data-driven exploration of viral origins and evolution

A phylogenomic data-driven exploration of viral origins and evolution | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

-- What do you think?

 

"Despite the extremely reduced nature of viral proteomes, we established an ancient origin of the “viral supergroup” and the existence of widespread episodes of horizontal transfer of genetic information. ... 


... Phylogenomic analysis uncovered a universal tree of life and revealed that modern viruses reduced from multiple ancient cells that harbored segmented RNA genomes and coexisted with the ancestors of modern cells. The model for the origin and evolution of viruses and cells is backed by strong genomic and structural evidence and can be reconciled with existing models of viral evolution if one considers viruses to have originated from ancient cells and not from modern counterparts." 

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Virophages, polintons, and transpovirons: a complex evolutionary network of diverse selfish genetic elements with different reproduction strategies

Virophages, polintons, and transpovirons: a complex evolutionary network of diverse selfish genetic elements with different reproduction strategies | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

The results of the phylogenomic analysis of the virophages and related genetic elements are compatible with the concept of network-like evolution of the virus world and emphasize multiple evolutionary connections between bona fide viruses and other classes of capsid-less mobile elements.

Altogether, virophages, polintons, a distinct Tetrahymena transposable element Tlr1, transpovirons, adenoviruses, and some bacteriophages form a network of evolutionary relationships that is held together by overlapping sets of shared genes and appears to represent a distinct module in the vast total network of viruses and mobile elements.


Via Chad Smithson, Ed Rybicki
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Ed Rybicki's curator insight, May 24, 2013 9:26 AM

Blow your MINDS, virologists...deep relationships between phages, human viruses, satellite viruses and big DNA viruses - as well as with diverse mobile elements within genomes.

Ignacio López-Goñi's curator insight, May 25, 2013 3:50 AM

Apasionante: el tema se complica! 

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How dairying shaped the human genome

How dairying shaped the human genome | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Genetic mutations enabling adult humans to digest lactose originated in at least three different populations worldwide.


Via Integrated DNA Technologies
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Tracing the genetic pathway from the first Eukaryotes to Homo sapiens

Tracing the genetic pathway from the first Eukaryotes to Homo sapiens | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

www.dhushara.com/book/unraveltree/unravel.htm

 

The Tree of Life, in biological terms, has come to be identified with the evolutionary tree of biological diversity. It is this tree which represents the climax fruitfulness of the biosphere and the genetic foundation of our existence, embracing not just higher Eukaryotes, plants, animals and fungi, but Protista, Eubacteria, and Archaea, the realm, including the extreme heat and salt-loving organisms, which appears to lie almost at the root of life itself.


Via Dr. Stefan Gruenwald
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Virus-like particles speed bacterial evolution : Nature News

Virus-like particles speed bacterial evolution : Nature News | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

"In the ocean, genes can hop between bacteria with unexpected ease, thanks to strange virus-like particles that shuttle genes from one species to another. These particles, called gene-transfer agents (GTAs), insert DNA into bacterial genomes so frequently that gene transfer in the ocean may occur 1,000 to 100 million times more often than previously thought. This suggests that GTAs have had a powerful role in evolution."

 

Yes, I know it's old, but I missed it, and I have a project on oceanic viromics, so...

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Trees of Life: A Visual History of Evolution

Trees of Life: A Visual History of Evolution | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Mapping 450 years of mankind's curiosity about the living world and the relationships between organisms.

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Human Rhinovirus Diversity and Evolution: How Strange the Change from Major to Minor

Rhinoviruses are the most common causes of the common cold. Their many distinct lineages fall into “major” and “minor” groups that use different cell surface receptors to enter host cells. Minor-group rhinoviruses are more immunogenic in laboratory studies, although their patterns of transmission and their cold symptoms are broadly similar to those of the major group. Here we present evolutionary evidence that minor-group viruses are also more immunogenic in humans. A key finding is that rates of amino acid substitutions at exposed sites in the capsid proteins VP2, VP3, and VP1 tend to be elevated in minor-group relative to major-group viruses, while rates at buried sites show no consistent differences. A reanalysis of historical virus watch data also indicates a higher immunogenicity of minor-group viruses, consistent with our findings about evolutionary rates at amino acid positions most directly exposed to immune surveillance. The increased immunogenicity and speed of evolution in minor-group lineages may contribute to the very large numbers of rhinovirus serotypes that coexist while differing in virulence.
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Cross-species jumps may play unexpectedly big role in virus evolution: Comparing host and virus evolutionary trees reveals new insights into emergence of viral diseases

Cross-species jumps may play unexpectedly big role in virus evolution: Comparing host and virus evolutionary trees reveals new insights into emergence of viral diseases | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
On occasion, a virus may jump from one host species to another and adapt to the new host. Such cross-species transmission happens more often than expected, according to new research, and it may play a much bigger role in virus evolution than previously thought.
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Time-Dependent Rate Phenomenon in Viruses

IMPORTANCE This work provides direct evidence that viral evolutionary rate estimates decay with their measurement timescales and that the rate decay speeds do not differ significantly among viruses despite the vast differences in their molecular features. After adjustment for the rate decay dynamics, the division between the rates of double-stranded DNA (dsDNA), single-stranded RNA (ssRNA), and ssDNA/reverse-transcribing viruses could be seen more clearly than before. Our results provide a guideline for further improvement of the molecular clock. As a demonstration of this, we used our model to reestimate the timescales of modern lentiviruses, which were previously thought to be very young, and concluded that they are millions of years old. This result matches the estimate from paleovirological analyses, thus bridging the gap between ancient and extant viral evolutionary studies.
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Viral evolution: One giant leap for Cas-kind

Viral evolution: One giant leap for Cas-kind | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
First reported in 2003, 'giant' viruses are double-stranded DNA viruses that are notable for the presence of several biological features that are usually found in cells rather than viruses, such as an extremely large genome and vulnerability to parasitism by phages ('virophages').
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Virus evolution during chronic hepatitis B virus infection as revealed by ultradeep sequencing data

Recent studies have indicated that virus diversity progressively increases along the course of CHB and that some virus mutations correlate with severe liver conditions such as chronic hepatitis, cirrhosis and hepatocellular carcinoma. Using ultradeep sequencing (UDS) data from an intrafamilial case, we detected such mutations at low frequencies among three immunotolerant patients and at high frequencies in an inactive carrier. Furthermore, our analyses indicated that the HBV population from the seroconverter patient underwent many genetic changes in response to virus clearance. Together, these data indicate a potential use of UDS for developing non-invasive biomarkers for monitoring disease changes over time or in response to specific therapies. In addition, our analyses revealed that virus clearance seemed not to require the virus effective population size to decline
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A new approach to predict evolution of influenza viruses can enhance vaccine efficacy

A new approach to predict evolution of influenza viruses can enhance vaccine efficacy | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
New results from a study performed at the University of Helsinki suggest that genomic information from circulating influenza viruses can help in producing more efficient seasonal vaccines. The researchers were able to develop a simple approach for reliable real-time tracking and prediction of viral evolution based on whole-genome sequences of influenza viruses.
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Evolution and Ecology of Influenza A Viruses.

Wild aquatic bird populations have long been considered the natural reservoir for influenza A viruses with virus transmission from these birds seeding other avian and mammalian hosts. While most evidence still supports this dogma, recent studies in bats have suggested other reservoir species may also exist. Extensive surveillance studies coupled with an enhanced awareness in response to H5N1 and pandemic 2009 H1N1 outbreaks is also revealing a growing list of animals susceptible to infection with influenza A viruses. Although in a relatively stable host-pathogen interaction in aquatic birds, antigenic, and genetic evolution of influenza A viruses often accompanies interspecies transmission as the virus adapts to a new host. The evolutionary changes in the new hosts result from a number of processes including mutation, reassortment, and recombination. Depending on host and virus these changes can be accompanied by disease outbreaks impacting wildlife, veterinary, and public health.

 

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Characterization of HIV-1 gag and nef in Cameroon: further evidence of extreme diversity at the origin of the HIV-1 group M epidemic

Cameroon, in west central Africa, has an extraordinary degree of HIV diversity, presenting a major challenge for the development of an effective HIV vaccine.
Ed Rybicki's insight:

...and it's partially from Cape Town, making it doubly interesting.

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Universal Pacemaker of Genome #Evolution

Universal Pacemaker of Genome #Evolution | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Sagi Snir, Yuri I. Wolf, Eugene V. Koonin

 

A fundamental observation of comparative genomics is that the distribution of evolution rates across the complete sets of orthologous genes in pairs of related genomes remains virtually unchanged throughout the evolution of life, from bacteria to mammals. The most straightforward explanation for the conservation of this distribution appears to be that the relative evolution rates of all genes remain nearly constant, or in other words, that evolutionary rates of different genes are strongly correlated within each evolving genome.

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Rice, MD Anderson scientists probe mystery of operon evolution

Rice, MD Anderson scientists probe mystery of operon evolution | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Solving 1960s genetics mystery could clear obstacles for synthetic biologists


Via Integrated DNA Technologies
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A retrospective study of the orthopoxvirus molecular evolution

A retrospective study of the orthopoxvirus molecular evolution | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

The data on the structure of conserved genes of the Old and New World orthopoxviruses and unclassified Yoka poxvirus were used for a Bayesian dating of their independent evolution. This reconstruction estimates the time when an orthopoxvirus ancestor was transferred to the North American continent as approximately 50 thousand years ago (TYA) and allows for relation of this time interval with the global climate changes (with one of the short-term warmings during the Last Ice Age).

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Phylogeny: Rewriting evolution

Phylogeny: Rewriting evolution | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Tiny molecules called microRNAs are tearing apart traditional ideas about the animal family tree.
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