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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First Case of Deadly Middle Eastern Virus Found in U.S.

First Case of Deadly Middle Eastern Virus Found in U.S. | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The Center for Disease Control has confirmed that a case of the deadly Middle East respiratory syndrome known as MERS has been found in the U.S.
Chris Upton + helpers's insight:

The first thing to worry about is NOT camel to human or human to human.

It's camel to other animals (birds, swine, goats etc)! With an amplification in these animals, the transmission to humans increases, and becomes worrisome.

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New Virus Related To Smallpox Is Found In Republic Of Georgia

New Virus Related To Smallpox Is Found In Republic Of Georgia | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Two men have been infected with a virus newly discovered in dairy cattle, scientists say. The disease causes blisters on the hands and arms, and other symptoms similar to those caused by smallpox.
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Viruses buoy life at hydrothermal vents | Science News

Viruses buoy life at hydrothermal vents | Science News | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Using hijacked genes, deep-sea viruses help sulfur-eating bacteria generate power in the plumes of hydrothermal vents.
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Hybridization Capture Reveals Evolution and Conservation across the Entire Koala Retrovirus Genome

Hybridization Capture Reveals Evolution and Conservation across the Entire Koala Retrovirus Genome | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Abstract

"The koala retrovirus (KoRV) is the only retrovirus known to be in the midst of invading the germ line of its host species. Hybridization capture and next generation sequencing were used on modern and museum DNA samples of koala (Phascolarctos cinereus) to examine ca. 130 years of evolution across the full KoRV genome. Overall, the entire proviral genome appeared to be conserved across time in sequence, protein structure and transcriptional binding sites. A total of 138 polymorphisms were detected, of which 72 were found in more than one individual. At every polymorphic site in the museum koalas, one of the character states matched that of modern KoRV. Among non-synonymous polymorphisms, radical substitutions involving large physiochemical differences between amino acids were elevated in env, potentially reflecting anti-viral immune pressure or avoidance of receptor interference. Polymorphisms were not detected within two functional regions believed to affect infectivity. Host sequences flanking proviral integration sites were also captured; with few proviral loci shared among koalas. Recently described variants of KoRV, designated KoRV-B and KoRV-J, were not detected in museum samples, suggesting that these variants may be of recent origin."

 

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Narcolepsy and pandemic influenza vaccinations

Narcolepsy and pandemic influenza vaccinations | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

The vaccine safety surveillance system effectively detected a very rare adverse event, narcolepsy, in subjects receiving AS03-adjuvanted A(H1N1) pandemic vaccine made using the European inactivation/purification protocol. The reports of increased cases of narcolepsy in non-vaccinated subjects infected with wild A(H1N1) pandemic influenza virus suggest a role for the viral antigen(s) in disease development. However, additional investigations are needed to better understand what factor(s) in wild influenza infection trigger(s) narcolepsy in susceptible hosts. An estimated 31 million doses of European AS03-adjuvanted A(H1N1) pandemic vaccine were used in more than 47 countries. The Canadian AS03-adjuvanted A(H1N1) pandemic vaccine was used with high coverage in Canada where an estimated 12 million doses were administered. As no similar narcolepsy association has been reported to date with the AS03-adjuvanted A(H1N1) pandemic vaccine made using the Canadian inactivation/purification protocol, this suggests that the AS03 adjuvant alone may not be responsible for the narcolepsy association. To date, no narcolepsy association has been reported with the MF59®-adjuvanted A(H1N1) pandemic vaccine. This review article provides a brief background on narcolepsy, outlines the different types of vaccine preparations including the ones for influenza, reviews the accumulated evidence for the safety of adjuvants, and explores the association between autoimmune diseases and natural infections. It concludes by assimilating the historical observations and recent clinical studies to formulate a feasible hypothesis on why vaccine-associated narcolepsy may not be solely linked to the AS03 adjuvant but more likely be linked to how the specific influenza antigen component of the European AS03-adjuvanted pandemic vaccine was prepared. Careful and long-term epidemiological studies of subjects who developed narcolepsy in association with AS03-adjuvanted A(H1N1) pandemic vaccine prepared with the European inactivation/purification protocol are needed.

  


Via Ed Rybicki
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Mutation rate plasticity in rifampicin resistance depends on Escherichia coli cell–cell interactions : Nature Communications : Nature Publishing Group

Abstract" Variation of mutation rate at a particular site in a particular genotype, in other words mutation rate plasticity (MRP), can be caused by stress or ageing. However, mutation rate control by other factors is less well characterized. Here we show that in wild-type Escherichia coli (K-12 and B strains), the mutation rate to rifampicin resistance is plastic and inversely related to population density: lowering density can increase mutation rates at least threefold. This MRP is genetically switchable, dependent on the quorum-sensing gene luxS—specifically its role in the activated methyl cycle—and is socially mediated via cell–cell interactions. Although we identify an inverse association of mutation rate with fitness under some circumstances, we find no functional link with stress-induced mutagenesis. Our experimental manipulation of mutation rates via the social environment raises the possibility that such manipulation occurs in nature and could be exploited medically."

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Infectious diseases: Smallpox watch

Infectious diseases: Smallpox watch | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Frozen mummies and envelopes of scabs could contain remnants of one of history's most prolific killers.

This month, the World Health Assembly — the decision-making body of the World Health Organization (WHO) — will meet in Geneva, Switzerland, and decide when to destroy the only known stocks of smallpox virus, held in deep freezes at highly protected laboratories in the United States and Russia. It is a move that has been delayed since the 1980s, and in all likelihood will be put off yet again. But even if the official stocks of virus are destroyed, the chance remains that other batches of the virus could be hidden in a freezer somewhere — or that the pathogen could re-emerge, zombie-like, from a mummified corpse such as the dead woman found in Queens.


Via Ed Rybicki
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Ed Rybicki's curator insight, April 30, 2014 11:05 AM

The REAL Killer Zombie Virus From Beyond The Grave...B-)  Smallpox!!

See also here: http://rybicki.wordpress.com/2014/05/01/an-actual-killer-virus-that-could-rise-from-the-grave/

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Human cytomegalovirus latent infection alters the expression of cellular and viral microRNA - Gene. 2014

BACKGROUND:

MicroRNAs (miRNAs) play important roles in regulating gene expression of plants, animals and viruses. Comprehensive characterization of host and viral miRNA will help uncover the molecular mechanisms that underlie the progression of human cytomegalovirus (HCMV) latent infection. To investigate the miRNA expression profile of HCMV and host cells during latent infection, we performed deep-sequencing analysis of the small RNAs isolated from HCMV-infected and mock-infected human monocytic leukemia cell line, THP-1.

RESULTS:

We established a HCMV latent infection cell model using the THP-1 cells. High-throughput sequencing technology was used to sequence small RNA libraries of the HCMV-infected and mock-infected THP-1 and to investigate their small RNA transcriptomes. We found eight miRNAs including miR-US25-1, miR-US25-2-5p and miR-UL112 that were expressed by HCMV during latent infection. The expressions of the host miRNAs were also affected by HCMV latent infection. At least 49 cellular miRNAs were differentially expressed: 39 were up-regulated and 10 were down-regulated upon HCMV latent infection. The expression of the human miRNA hsa-miR-124-3p was significantly up-regulated in the HCMV latent infection library. In addition, we found 14 cellular novel miRNAs in the HCMV-infected and mock-infected THP-1 libraries. Functional annotation of the target genes of the differentially expressed miRNAs suggested that the majority of the genes are involved in melanogenesis, pathways in cancer, endocytosis and wnt signaling pathway.

CONCLUSIONS:

The small RNA transcriptomes obtained in this study demonstrate the usefulness of the deep-sequencing combined with bioinformatics approach in understanding of the expression and function of host and viral small RNAs in HCMV latent infection. This approach can also be applied to the study of other kinds of viruses.

 

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Genesis and pathogenesis of the 1918 pandemic H1N1 influenza A virus - PNAS

The origin of the 1918 pandemic influenza A virus (IAV) and the reasons for its unusual severity are two of the foremost biomedical mysteries of the past century. We infer that the virus arose via reassortment between a preexisting human H1 IAV lineage and an avian virus. Phylogenetic, seroarcheological, and epidemiological evidence indicates those born earlier or later than ∼1880–1900 would have had some protection against the 1918 H1N1 virus, whereas many young adults born from ∼1880–1900 may have lacked such protection because of childhood exposure to an antigenically distinct H3N8 virus. Our findings suggest that better understanding of how initial exposure shapes lifetime immunity may enhance the prediction and control of future IAV pandemics and seasonal epidemics.

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The day they discovered the AIDS virus

Thirty years ago, in a hasty and ill-timed press conference, health officials unveiled one of the most important discoveries in medical history.

Via Ed Rybicki
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Ed Rybicki's curator insight, April 24, 2014 2:52 AM

This is a timely and very even-handed recap of the history of the discovery of HIV - which I lived through as a young scientist and supervisor, avidly devouring any and all information we could get on the subject, little realising that South Africa would soon become the world's most infected country.

 

And still it goes on.

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Fast vaccine design and development based on correlates of protection (COPs): Influenza as a trendsetter - Hum Vaccin Immunother. 2014

New and reemerging infectious diseases call for innovative and efficient control strategies of which fast vaccine design and development represent an important element. In emergency situations, when time is limited, identification and use of correlates of protection (COPs) may play a key role as a strategic tool for accelerated vaccine design, testing, and licensure. We propose that general rules for COP-based vaccine design can be extracted from the existing knowledge of protective immune responses against a large spectrum of relevant viral and bacterial pathogens. Herein, we focus on the applicability of this approach by reviewing the established and up-coming COPs for influenza in the context of traditional and a wide array of new vaccine concepts. The lessons learnt from this field may be applied more generally to COP-based accelerated vaccine design for emerging infections

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Should We Destroy Our Last Living Samples of the Virus That Causes Smallpox?

Should We Destroy Our Last Living Samples of the Virus That Causes Smallpox? | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Later this month, the World Health Organization will decide whether or not to get rid of two live virus repositories in the United States and Russia
Kenzibit's insight:

Wonderful read.

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It is Still Not Time to Destroy Small Pox Virus, Researchers Say

It is Still Not Time to Destroy Small Pox Virus, Researchers Say | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
U.S. researchers have urged the World Health Assembly (WHA) to not destroy the last remaining live strains of the Variola virus that causes small pox.
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Bioinformatician's Pocket Reference !!

Bioinformatician's Pocket Reference !! | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
  It is amusing how brain of bioinformaticians work! Learning a new programming language for days feels so much of fun that making 5 minute discussion with neighbours (unless under special cir...
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Killer Pig Virus Wipes Out More Than 10 Percent Of [US] Hogs

Killer Pig Virus Wipes Out More Than 10 Percent Of [US] Hogs | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

The killer stalking U.S. hog farms is known as PEDv, a malady that in less than a year has wiped out more than 10 percent of the nation's pig population and helped send retail pork prices to record highs. The highly contagious Porcine Epidemic Diarrhea virus is puzzling scientists searching for its origins and its cure and leaving farmers devastated in ways that go beyond financial losses.


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Male Scent May Compromise Biomedical Research

Male Scent May Compromise Biomedical Research | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Findings may be having a profound impact on everything from animal behavior experiments to human clinical trials
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Grad Student Advice Series: Approaching Your Advisor About Alternative PhD Careers

This guide explains the 3 steps you need to take to approach your Professor about an important PhD topic: 1) Come up with a plan 2) Open dialogue 3) Execute
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Ed Rybicki's comment, May 1, 2014 8:23 AM
ALWAYS HAVE A PLAN B: I have had two students who had in fact embarked upon Plan B, when Plan A finally worked - 9 months into their projects. They still like me B-)
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Measles outbreak declared in Calgary, Edmonton and central Alberta

Measles outbreak declared in Calgary, Edmonton and central Alberta | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Alberta officially declared a measles outbreak in Calgary, Edmonton and central Alberta on Tuesday.
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Ed Rybicki's comment, May 1, 2014 8:24 AM
Fucking Luddites...
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Bill Gates: We Need Mosquito Week More Than Shark Week

Bill Gates: We Need Mosquito Week More Than Shark Week | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
This week over at my blog, TheGatesNotes, we’re hosting Mosquito Week. It's modeled on Shark Week. But compared to mosquitoes, sharks are wimps.
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Quick mining and visualization of next-generation sequencing data by integrating genomic databases - BMC Genomics

Understanding the relationship between the millions of functional DNA elements and their protein regulators, and how they work in conjunction to manifest diverse phenotypes, is key to advancing our understanding of the mammalian genome.

Via Mel Melendrez-Vallard
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Systems biology and systems genetics—novel innovative approaches to study host–pathogen interactions during influenza infection - Current Opinion in Virology

Systems biology and systems genetics—novel innovative approaches to study host–pathogen interactions during influenza infection - Current Opinion in Virology | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Influenza represents a serious threat to public health with thousands of deaths each year. A deeper understanding of the host–pathogen interactions is urgently needed to evaluate individual and population risks for severe influenza disease and to identify new therapeutic targets. Here, we review recent progress in large scale omics technologies, systems genetics as well as new mathematical and computational developments that are now in place to apply a systems biology approach for a comprehensive description of the multidimensional host response to influenza infection. In addition, we describe how results from experimental animal models can be translated to humans, and we discuss some of the future challenges ahead.

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Your Future Flu Vaccines Could Be Grown Inside a Tobacco Plant

Your Future Flu Vaccines Could Be Grown Inside a Tobacco Plant | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Finally, some good news about tobacco and your health. No, there is no nicotine involved, but there will be lots and lots of virus-like particles. Tobacco plants could be one of the fastest and most effective ways of making the seasonal flu vaccine—much faster than the current method using chicken eggs.

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The immune response and within-host emergence of pandemic influenza virus - Lancet

The immune response and within-host emergence of pandemic influenza virus - Lancet | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Zoonotic influenza viruses that are a few mutations away from pandemic viruses circulate in animals, and can evolve into airborne-transmissible viruses in human beings. Paradoxically, such viruses only occasionally emerge in people; the four influenza pandemics that occurred in the past 100 years were caused by zoonotic viruses that acquired efficient transmissibility. Emergence of a pandemic virus in people can happen when transmissible viruses evolve in individuals with zoonotic influenza and replicate to titres allowing transmission. We postulate that this step in the genesis of a pandemic virus only occasionally occurs in human beings, because the immune response triggered by zoonotic influenza virus also controls transmissible mutants that emerge during infection. Therefore, an impaired immune response might be needed for within-host emergence of a pandemic virus and replication to titres allowing transmission. Immunocompromised individuals—eg, those with comorbidities, of advanced age, or receiving immunosuppressive treatment—could be at increased risk of generating transmissible viruses and initiating chains of human-to-human infection.

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