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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Potent mechanism helps viruses shut down body's defense system against infection

Potent mechanism helps viruses shut down body's defense system against infection | Virology and Bioinformatics from Virology.ca | Scoop.it
Researchers have discovered a powerful mechanism by which viruses such as influenza, West Nile and Dengue evade the body's immune response and infect humans with these potentially deadly diseases.
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Tools for Open Science | OKF Open Science Working Group

In this page are listed a series of tools and services scientists can use to open their science. These are organized in different topics covering different facets of Open Science. Some of these tools are only targeted to certain fields of science, some are more general. Early 2013, the open science community is very active. New initiatives emerge every week and it is hard to be up to date. At the end of the page are links to other webpages tracking the creation and evolution of tools with different emphasis - See more at: http://science.okfn.org/tools-for-open-science/#sthash.G8Lfdz7m.dpuf

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Mel Melendrez-Vallard's curator insight, August 21, 2013 8:06 AM

This is a neat site, also check out the comments from others at the bottom they list more resources

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Pink Eye Tied to Poor Infection Control in Clinics

Pink Eye Tied to Poor Infection Control in Clinics | Virology and Bioinformatics from Virology.ca | Scoop.it
Six unrelated outbreaks of epidemic keratoconjunctivitis linked to human adenovirus underscore the importance of infection control measures in ophthalmology, according to the CDC.
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PLOS Pathogens: Bed Bugs and Infectious Disease: A Case for the Arboviruses

PLOS Pathogens: Bed Bugs and Infectious Disease: A Case for the Arboviruses | Virology and Bioinformatics from Virology.ca | Scoop.it

Bed bug infestations (Cimicidae; Cimex lectularius) have been increasing worldwide over the last few decades [1], [2]. Several factors have been posited to explain this resurgence, including widespread insecticide resistance, human population growth, and increased international travel [1]. Clinically, reactions to bed bug bites vary from unapparent, to small (<5 mm) maculopapular lesions, to large wheals (2–6 cm); other reactions include bullous rashes, dermatitis, and asthma [1], [3]. However, in the developed world the psychological, social, and economic impacts of bed bugs may be the most troubling aspects of the resurgence [2]. While the bed bug invasion cuts across economic lines, those with sufficient resources are able to clear the infestations, while those without may have to live with their bed bugs into the foreseeable future [2], [4].

Bloodfeeding arthropods such as mosquitoes, ticks, fleas, kissing bugs, biting flies, and lice serve as biological vectors for human pathogens. Thus, it seems natural that bed bugs would also transmit infectious agents. However, more than 100 years of searching has produced little evidence to support this assumption. Comprehensive reviews examining bed bugs' ability to vector a wide range of high-profile human pathogens, such as HIV, MRSA, and hepatitis B, C, and E viruses, among others, have recently been published [1], [3]. Such experiments have so far failed to provide any convincing evidence of bed bugs in the transmission of these agents and thus will not be discussed here. Surprisingly, previous attempts to link bed bugs with disease transmission have largely omitted those viral pathogens known to have transmission cycles involving insect vectors. Thus, the purpose of this review is to refocus the attention of the research community on those pathogens most likely to be vectored by bed bug species given the appropriate ecological circumstances, and away from human pathogens with no previous history of transmission by insect vectors.

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Structural Rearrangement of Ebola Virus VP40 Begets Multiple Functions in the Virus Life Cycle

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Mel Melendrez-Vallard's comment, August 16, 2013 1:57 PM
Unfortunately this article is behind a paywall...for those that want to learn about the work, the group made a youtube video about the work: http://www.youtube.com/watch?v=HTNeq6_mXGs
Kenzibit's comment, August 20, 2013 3:06 PM
Thanks for this Mel
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A baculovirus-mediated strategy for full-length plant virus coat protein expression and purification

A baculovirus-mediated strategy for full-length plant virus coat protein expression and purification | Virology and Bioinformatics from Virology.ca | Scoop.it
Background

Garlic production is severely affected by virus infection, causing a decrease in productivity and quality. There are no virus-free cultivars and garlic-infecting viruses are difficult to purify, which make specific antibody production very laborious. Since high quality antisera against plant viruses are important tools for serological detection, we have developed a method to express and purify full-length plant virus coat proteins using baculovirus expression system and insects as bioreactors.

Conclusions

The expression of a plant virus full-length coat protein fused to the baculovirus Polyhedrin in recombinant baculovirus-infected insects was shown to produce high amounts of the recombinant protein which was easily purified and efficiently used to generate specific antibodies. Therefore, this strategy can potentially be used for the development of plant virus diagnostic kits for those viruses that are difficult to purify, are present in low titers or are present in mix infection in their plant hosts.

 

Baculovirus image from own collection

Ed Rybicki's insight:

I love the way plant virology / biotechnology now makes use of the whole spectrum of mol biol: this paper uses cDNA clones of an RNA plant virus, via E coli, to make recombinant baculoviruses, to express a fusion protein in insect cells - to make sera for detection of the plant virus by ELISA and other serological assays.

I'm biased because my lab uses ALL of these techniques (and I would have made the protein via agroinfiltration in plants), but this sort of science has really come of age.  One that I have lived through, incidentally, as cloning was VERY young when I started out - and ELISA had only just been invented.

I also know Renato quite well - so parabens, meu amigo!

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New device can extract human DNA with full genetic data in minutes

New device can extract human DNA with full genetic data in minutes | Virology and Bioinformatics from Virology.ca | Scoop.it

Take a swab of saliva from your mouth and within minutes your DNA could be ready for analysis and genome sequencing with the help of a new device.

 

University of Washington engineers and NanoFacture, a Bellevue, Wash., company, have created a device that can extract human DNA from fluid samples in a simpler, more efficient and environmentally friendly way than conventional methods.

 

The device will give hospitals and research labs a much easier way to separate DNA from human fluid samples, which will help with genome sequencing, disease diagnosis and forensic investigations.

 

“It’s very complex to extract DNA,” said Jae-Hyun Chung, a UW associate professor of mechanical engineering who led the research. “When you think of the current procedure, the equivalent is like collecting human hairs using a construction crane.”

 

This technology aims to clear those hurdles. The small, box-shaped kit now is ready for manufacturing, then eventual distribution to hospitals and clinics. NanoFacture, a UW spinout company, signed a contract with Korean manufacturer KNR Systems last month at aceremony in Olympia, Wash.

 

The UW, led by Chung, spearheaded the research and invention of the technology, and still manages the intellectual property. Separating DNA from bodily fluids is a cumbersome process that’s become a bottleneck as scientists make advances in genome sequencing, particularly for disease prevention and treatment. The market for DNA preparation alone is about $3 billion each year.

 

Conventional methods use a centrifuge to spin and separate DNA molecules or strain them from a fluid sample with a micro-filter, but these processes take 20 to 30 minutes to complete and can require excessive toxic chemicals.

 

UW engineers designed microscopic probes that dip into a fluid sample – saliva, sputum or blood – and apply an electric field within the liquid. That draws particles to concentrate around the surface of the tiny probe. Larger particles hit the tip and swerve away, but DNA-sized molecules stick to the probe and are trapped on the surface. It takes two or three minutes to separate and purify DNA using this technology.


Via Dr. Stefan Gruenwald, sonia ramos, Loiret David
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Biosciencia's curator insight, May 15, 2013 7:25 AM

The device will give hospitals and research labs a much easier way to separate DNA from human fluid samples, which will help with genome sequencing, disease diagnosis and forensic investigations.

Linda Coburn's comment, May 15, 2013 11:28 AM
It bothers me that an American university which receives American tax dollars for funding has decided to contract with a Korean company to manufacture this amazing device. We will never solve our economic woes if we don't bring mfg back to the US.
Center for Accessible Living NKY's curator insight, May 15, 2013 5:29 PM

This should make obtaining genetic diagnosis much easier and faster.

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The hidden threat that could prevent Polio’s global eradication

The hidden threat that could prevent Polio’s global eradication | Virology and Bioinformatics from Virology.ca | Scoop.it
Polio could soon be wiped out—but only if scientists can track down the last carriers
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Identification of new cattle virus will help rule out mad cow disease :: UC Davis News & Information

Identification of new cattle virus will help rule out mad cow disease :: UC Davis News & Information | Virology and Bioinformatics from Virology.ca | Scoop.it
A new cow virus that causes neurologic symptoms reminiscent of mad cow disease has been identified and its genome sequenced by a team of researchers including scientists at the University of (RT @LairmoreDVMDean: New cattle astrovirus discovered :#UCDavisVetMed...
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TWiV 245: Writing Principles of Virology

TWiV 245: Writing Principles of Virology | Virology and Bioinformatics from Virology.ca | Scoop.it
The authors of the popular textbook Principles of Virology discuss how the book was conceived and written.
Ed Rybicki's insight:

Seeing as Vincent probably won't blow HIS trumpet...B-)

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MicroRNA-based strategy to mitigate the risk of gain-of-function influenza studies - Nature Biotechnology

Recent gain-of-function studies in influenza A virus H5N1 strains revealed that as few as three-amino-acid changes in the hemagglutinin protein confer the capacity for viral transmission between ferrets1, 2. As transmission between ferrets is considered a surrogate indicator of transmissibility between humans, these studies raised concerns about the risks of gain-of-function influenza A virus research. Here we present an approach to strengthen the biosafety of gain-of-function influenza experiments. We exploit species-specific endogenous small RNAs to restrict influenza A virus tropism. In particular, we found that the microRNA miR-192 was expressed in primary human respiratory tract epithelial cells as well as in mouse lungs but absent from the ferret respiratory tract. Incorporation of miR-192 target sites into influenza A virus did not prevent influenza replication and transmissibility in ferrets, but did attenuate influenza pathogenicity in mice. This molecular biocontainment approach should be applicable beyond influenza A virus to minimize the risk of experiments involving other pathogenic viruses.

  
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Host genetic determinants of influenza pathogenicity

Despite effective vaccines, influenza remains a major global health threat due to the morbidity and mortality caused by seasonal epidemics, as well as the 2009 pandemic. Also of profound concern are the rare but potentially catastrophic transmissions of avian influenza to humans, highlighted by a recent H7N9 influenza outbreak. Murine and human studies reveal that the clinical course of influenza is the result of a combination of both host and viral genetic determinants. While viral pathogenicity has long been the subject of intensive efforts, research to elucidate host genetic determinants, particularly human, is now in the ascendant, and the goal of this review is to highlight these recent insights

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BMC Bioinformatics | 4273pi: Bioinformatics education on low cost ARM hardware

BMC Bioinformatics | 4273pi: Bioinformatics education on low cost ARM hardware | Virology and Bioinformatics from Virology.ca | Scoop.it

An open access, open learning method for teaching bioinformatics uses the Raspberry Pi computer and a custom operating system to teach early-career researchers key skills in systems administration and computational biology at low cost.

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Ed Rybicki's comment, August 18, 2013 9:09 AM
My son has adapted a Raspberry Pi as a media server, attached to our home network. Right now the heaviest users are my wife, who has watched the whole of "The Sarah Connor Chronicles" on her iPad from the comfort of her bed, and my daughter, who is into "Breaking Bad". I'm sure you can ALSO use one for bioinformatics, though...B-)
Ed Rybicki's comment, August 18, 2013 9:33 AM
But I have also shared this article with our Computational Biology Group and our Open UCT initiative, who are always looking for good Open SOurce products - thanks!
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Full Genome of H7N9 Flu Virus Derived by Direct Sequencing

Full Genome of H7N9 Flu Virus Derived by Direct Sequencing | Virology and Bioinformatics from Virology.ca | Scoop.it

Recently, a novel influenza A (H7N9) virus infected humans in China (1,2), leading to great concerns about its threat to public health (3). However, almost all the current genomes of the novel subtype H7N9 virus have been sequenced after culture in embryonated chicken eggs or mammalian cells. Switching the evolutionary selection pressure from in vivo human respiratory tract to embryonated chicken eggs might introduce mutations into the final genome sequences during culture (4). We report determination of the full genome of the influenza A (H7N9) virus derived directly by deep sequencing, without virus culture, from a sputum specimen of an infected human. Deep sequencing provides a direct way to evaluate the genome characteristics and potential virulence and transmissibility of the novel influenza A (H7N9) virus.


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Ed Rybicki's curator insight, August 18, 2013 9:03 AM

This is the second paper I have seen recently to make the point that the virus derived from the "wild" is not necessarily the same as the one that is adapted to grow in chicken eggs - unsurprisingly, one might say, but it is still a valid point that culture selects the virus best suited to grow in it.

I would be very interested to see an analysis of what the HA sequence looks like in a range of isolates sequenced this way.

Paul Britton's comment, August 19, 2013 5:55 AM
Hi Ed, This is potentially true for other if not all avaian viruses. There is the possibility that particular minor genomes presnt in the "wild type" population may be preferentially selected by passage in eggs.
Ed Rybicki's comment, August 20, 2013 3:49 AM
Which just reinforces my desire to see what wild-type populations REALLY look like!
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Homeopathy First Aid Kits

Homeopathy First Aid Kits | Virology and Bioinformatics from Virology.ca | Scoop.it
I don’t know how I missed them, but somehow homeopathic first aid kits had not registered on my radar. They’re readily available. Even Amazon.com sells them, for $54.99. They contain 18 vials of ti...
Chris Upton + helpers's insight:

more like:  homeopathetic!!

Yes, I'm a homeopathophobe!!

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Ed Rybicki's comment, August 20, 2013 4:10 AM
Homeopathic bandages? Homeopathic splints?? The mind boggles.
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College Of Practical Homeopathy – (Cph)

Learn to be a Homeopath – Not just about Homeopathy

Today, we have all been indoctrinated to believe in the germ theory of disease. This ‘theory’ is that disease is the direct consequence of germs or viruses that pass from one host to another and that ‘Healing’ requires some powerful external intervention by experts. It also implies that illness is not our responsibility but something that happens to us.


Chris Upton + helpers's insight:

I guess all the microbiologists can go home now....   everything is cured...

 

I THINK NOT!!!!!!!!!

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Researchers Scramble to Understand Camel Connection to MERS

The discovery that a dangerous new virus that surfaced in the Middle East last year may be lurking in camels has reenergized the hunt for its source. There had been little progress in finding the origins of the Middle East respiratory syndrome (MERS) coronavirus, which has sickened 94 people and killed 46. But after last week's report in The Lancet Infectious Diseases, "everybody's scrambling to figure out what we know about camels," says Anthony Mounts, the point person for MERS at the World Health Organization (WHO) in Geneva, Switzerland.

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Full Genome of Influenza A (H7N9) Virus Derived by Direct Sequencing without Culture - EID

An epidemic caused by influenza A (H7N9) virus was recently reported in China. Deep sequencing revealed the full genome of the virus obtained directly from a patient’s sputum without virus culture. The full genome showed substantial sequence heterogeneity and large differences compared with that from embryonated chicken eggs

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Age-Specific Mortality During the 1918 Influenza Pandemic: Unravelling the Mystery of High Young Adult Mortality - PLOS ONE

Age-Specific Mortality During the 1918 Influenza Pandemic: Unravelling the Mystery of High Young Adult Mortality - PLOS ONE | Virology and Bioinformatics from Virology.ca | Scoop.it

The worldwide spread of a novel influenza A (H1N1) virus in 2009 showed that influenza remains a significant health threat, even for individuals in the prime of life. This paper focuses on the unusually high young adult mortality observed during the Spanish flu pandemic of 1918. Using historical records from Canada and the U.S., we report a peak of mortality at the exact age of 28 during the pandemic and argue that this increased mortality resulted from an early life exposure to influenza during the previous Russian flu pandemic of 1889–90. We posit that in specific instances, development of immunological memory to an influenza virus strain in early life may lead to a dysregulated immune response to antigenically novel strains encountered in later life, thereby increasing the risk of death. Exposure during critical periods of development could also create holes in the T cell repertoire and impair fetal maturation in general, thereby increasing mortality from infectious diseases later in life. Knowledge of the age-pattern of susceptibility to mortality from influenza could improve crisis management during future influenza pandemics.

 
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Ed Rybicki's curator insight, August 16, 2013 6:26 AM

This is the second purported explanation I have seen for this phenomenon: the first was that people older than 28 were PROTECTED more, due to prior exposure, and that if this were not the case, the mortality curve would have just kept rising.

Just as happened - at a far lower mortality incidence - for the recent H1N1 pandemic, incidentally.

Mel Melendrez-Vallard's comment, August 16, 2013 10:34 AM
Right, makes sense. 2 sides of the coin here for sure. This article seems to imply timing of exposure in terms of 'age' as well given the evolution of the virus and how it antigenically changed from the 1889 virus that the 28 yr olds were purportedly exposed to as babies. This same virus from 1889 on an adult, given adult development and immune response could've elicited protection from 1918 flu to an extent while negatively impacting their children/babies which would've been exposed at the same time. Both would've 'survived' to experience the 1918 flu but the babies which are now ~28 would be at a disadvantage because when they got the 1889 virus their bodies were perhaps not developed enough to sustain protective immunity or the virus perhaps? food for thought, it was a nice article.
Patti Hamilton's curator insight, August 18, 2013 9:10 PM

Wow, this is an interesting story.  Check it out.

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First direct evidence of HPV-related tonsillar cancer on the rise in Canada

First direct evidence of HPV-related tonsillar cancer on the rise in Canada | Virology and Bioinformatics from Virology.ca | Scoop.it

American and European research shows an alarming increase in the rate of tonsillar cancer related to the human papilloma virus (HPV), a sexually transmitted virus. Experts suggest a similar trend has emerged in Canada, but it had yet to be confirmed through scientific analysis. In a new study published in Current Oncology, a group of researchers from Lawson Health Research Institute and Western University have produced evidence confirming this epidemic.

Orophararyngeal cancer impacts part of the throat, including the tonsils and the base of the tongue. Historically, these types of throat cancers were caused by smoking and alcohol use, but recent studies show that HPV is now a major cause. When an individual contracts HPV, the virus's DNA can infiltrate healthy cells and induce cancer years later.


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Modified-virus treatment causes hope for leukemia cure - Ottawa - CBC News

Modified-virus treatment causes hope for leukemia cure - Ottawa - CBC News | Virology and Bioinformatics from Virology.ca | Scoop.it
Researchers at the Ottawa Hospital Research Institute say they've been able to use a virus-like particle to kill human blood cancer cells and cure mice of leukemia.
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Peptide Aptamers That Bind to Geminivirus Replication Proteins Confer a Resistance Phenotype to Tomato Yellow Leaf Curl Virus and Tomato Mottle Virus Infection in Tomato

Peptide Aptamers That Bind to Geminivirus Replication Proteins Confer a Resistance Phenotype to Tomato Yellow Leaf Curl Virus and Tomato Mottle Virus Infection in Tomato | Virology and Bioinformatics from Virology.ca | Scoop.it

Geminiviruses constitute a large family of single-stranded DNA viruses that cause serious losses in important crops worldwide. They often exist in disease complexes and have high recombination and mutation rates, allowing them to adapt rapidly to new hosts and environments. Thus, an effective resistance strategy must be general in character and able to target multiple viruses. The geminivirus replication protein (Rep) is a good target for broad-based disease control because it is highly conserved and required for viral replication. In an earlier study, we identified a set of peptide aptamers that bind to Rep and reduce viral replication in cultured plant cells. In this study, we selected 16 of the peptide aptamers for further analysis in yeast two-hybrid assays. These experiments showed that all 16 peptide aptamers interact with all or most of the Rep proteins from 9 viruses representing the three major Geminiviridae genera and identified two peptide aptamers (A22 and A64) that interact strongly with different regions in the Rep N-terminus. Transgenic tomato lines expressing A22 or A64 and inoculated with Tomato yellow leaf curl virus or Tomato mottle virus were delayed for viral DNA accumulation and often contained lower levels of viral DNA. Strikingly, the effect on symptoms was stronger, with many of the plants showing no symptoms or strongly attenuated symptoms. Together, these results established the efficacy of using Rep-binding peptide aptamers to develop crops that are resistant to diverse geminiviruses.

 Geminivirus graphic courtesy of Russell Kightley Media
Ed Rybicki's insight:

...and peptide aptamers binding to the Rep proteins are a novel way of combatting their replication - and probably quite broad-spectrum, too, given the reasonably highly conserved sequence of Rep, and especially the active sites.  Given that Rep has a variety of functions, based on its concentration and aggregation state, messing with its binding to Rb analogues, other Reps, ss- and dsDNA is a useful thing to do.

Still prefer dominant-negative mutant Reps, though...B-)

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The antigenic architecture of the hemagglutinin ... [Mol Immunol. 2013]

Human infection with the highly pathogenic avian influenza A virus H5N1 is associated with a high mortality and morbidity. H5N1 continues to transmit from poultry to the human population, raising serious concerns about its pandemic potential. Current influenza H5N1 vaccines are based upon the elicitation of a neutralizing antibody (Ab) response against the major epitope regions of the viral surface glycoprotein, hemagglutinin (HA). However, antigenic drift mutations in immune-dominant regions on the HA structure allow the virus to escape Ab neutralization. Epitope mapping using neutralizing monoclonal antibodies (mAb) helps define mechanisms of antigenic drift, neutralizing escape and can facilitate pre-pandemic vaccine design. This review explores the current knowledge base of the antigenic sites of the H5N1 HA molecule. The relationship between the epitope architecture of the H5N1 HA, antigenic evolution of the different H5N1 lineages and the antigenic complexity of the H5N1 virus lineages that constitute potential pandemic strains are discussed in detail

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New strategy to disarm the dengue virus brings new hope for a universal dengue vaccine

New strategy to disarm the dengue virus brings new hope for a universal dengue vaccine | Virology and Bioinformatics from Virology.ca | Scoop.it
A new strategy that cripples the ability of the dengue virus to escape the host immune system has been discovered.
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Transmission of influenza A/H5N1 viruses in mammals

Highly pathogenic avian H5N1 influenza A viruses occasionally infect humans and cause severe respiratory disease and fatalities. Currently, these viruses are not efficiently transmitted from person to person, although limited human-to-human transmission may have occurred. Nevertheless, further adaptation of avian H5N1 influenza A viruses to humans and/or reassortment with human influenza A viruses may result in aerosol transmissible viruses with pandemic potential. Although the full range of factors that modulate the transmission and replication of influenza A viruses in humans are not yet known, we are beginning to understand some of the molecular changes that may allow H5N1 influenza A viruses to transmit via aerosols or respiratory droplets among mammals. A better understanding of the biological basis and genetic determinants that confer transmissibility to H5N1 influenza A viruses in mammals is important to enhance our pandemic preparedness.

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