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PostPosted: Mon Apr 16, 2012 5:53 pm 
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Recent studies on H5N1 transmission in ferrets have identified a series of associated key changes in H5 and PB2, including some that were found in multiple studies.

Of concern is A/duck/Egypt/10185SS/2010, which has H5 N158D and N224K on an H5 clade 2.2.1 G genetic background, which also had S133del and T155I, which is in all human H5N1 public sequences since 2009.

Moreover, clade 2.2.1 G has PB2 E627K.

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PostPosted: Mon Apr 16, 2012 6:00 pm 
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Dangerous flu mutations revealed

04 Apr 2012 | 10:45 BST | Posted by Brian Owens | Category: Biology & Biotechnology, Health and medicine, Lab life



MEDICAL RF.COM/SPL

Posted on behalf of Ed Yong.

Two scientists recently hit the headlines when they created mutant strains of H5N1 influenza, which can spread between mammals (see ‘Fears grow over lab-bred flu‘). But although Ron Fouchier of Erasmus Medical Center in Rotterdam, the Netherlands, spoke publicly to explain and defend the work, Yoshihiro Kawaoka, of the School of Veterinary Medicine at the University of Wisconsin–Madison, has been far quieter, deliberately saying nothing to the press.

That has now changed. At a Royal Society meeting in London about H5N1 research yesterday, the thus-far silent scientist spoke openly about his results after the National Science Advisory Board for Biosecurity (NSABB), an independent advisory group to the US government, unanimously voted last week that Kawaoka’s paper should be published in full. Nature intends to “proceed with publication as soon as possible”.

His experiments began when he tweaked the H5N1 virus to reproduce in a ferret’s airways. He introduced random alterations into its haemagglutinin (HA) protein, which it uses to stick to host cells. From the resulting library of mutants, he isolated viruses with two mutations in HA — N224K and Q226L — that could stick to receptors in human tracheal cells. That is something H5N1 viruses cannot usually do.

Kawaoka then combined this mutated HA-encoding gene with other genes from the H1N1 virus behind the 2009 pandemic, mirroring the natural process through which wild viruses swap genes. This chimeric virus still would not go airborne.

However, Kawaoka noticed that one of the ferrets he infected had especially high levels of virus in its nose. These viruses had picked up a third HA mutation — N158D — and could now spread between neighbouring ferrets. Kawaoka found that two of six healthy animals picked up infections from neighbours they had no contact with. Along the way, the virus acquired a fourth mutation — T318I.

With all four mutations, the virus spread even more easily. Kawaoka exposed six more uninfected ferrets to sick peers in adjacent cages. Within a week, he had found signs of the virus in all of them.

However, this mutant virus didn’t kill any of the animals, and spread more slowly than the 2009 pandemic H1N1 strain. It was also vulnerable to our current antivirals and vaccines. Fouchier’s virus shares the same inefficient spread and non-lethal character, although at the time of the conference, he was still unable to share any details.

One of Kawaoka’s four critical mutations, T318I, is found on the stalk of the mushroom-shaped HA protein, and probably helps to stabilize it. The other three are found in the head. N224K and Q226L probably affect its ability to stick to human cells. The fourth mutation, N158D, abolishes a ‘glycosylation site’ — a part of the protein’s head where a carbohydrate molecule can be fused. It is unclear how this affects the protein.

Three of these mutations are new, at least in public databases. N158D is the only one of the four mutations that has been documented in wild birds. It was found in several samples collected from Egypt in recent years, and seems to be common among viruses that jumped into humans. This mutation is clearly one to study and watch. It also illustrates some of the benefits of this controversial work. Data about N158D were already in published flu sequences but Kawaoka says, “Unless you knew what to look for, you wouldn’t have found it.”

Here is a Storify giving a real-time account of how the meeting unfolded. And read more about the research and the controversy surrounding it in Nature‘s mutant flu special.

http://blogs.nature.com/news/2012/04/da ... ealed.html

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PostPosted: Mon Apr 16, 2012 6:10 pm 
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niman wrote:
Dangerous flu mutations revealed

04 Apr 2012 | 10:45 BST | Posted by Brian Owens | Category: Biology & Biotechnology, Health and medicine, Lab life

Three of these mutations are new, at least in public databases. N158D is the only one of the four mutations that has been documented in wild birds. It was found in several samples collected from Egypt in recent years, and seems to be common among viruses that jumped into humans. This mutation is clearly one to study and watch. It also illustrates some of the benefits of this controversial work. Data about N158D were already in published flu sequences but Kawaoka says, “Unless you knew what to look for, you wouldn’t have found it.”

http://blogs.nature.com/news/2012/04/da ... ealed.html

The above statements are false. Q226L has not been reported in H5N1. It was of interest because of its presence in earlier pandemics (1957 and 1968), which involved H2 and H3.

However, the other three have all been found in H5N1. As noted above, N158D is widespread in clade 2.2 H5N1, which currently is dominant in Egypt.

However, N224K is in a duck sequence, A/duck/Egypt/10185SS/2010, which has N158D, which is widespread in Egypt and abolishes the gylcosylation site.

N224K is also in a duck sequence in Vietnam, A/MuscovyDk/Vietnam/NCVD-11/2007, which also has a change at position 158 (N158S), which also abolishes the glycosylation site.

T318I is also found in wild birds (both H5N1 and H5N2 - but the H5 in the H5N2 is high path)
A/mallard/Xuyi/10/2005 (A/H5N2)
A/spotbill duck/Xuyi/18/2005 (A/H5N2)
A/duck/Guangxi/53/2002 (A/H5N1)

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PostPosted: Mon Apr 16, 2012 6:22 pm 
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T318I
C991T
EPI182377 A/mallard/Xuyi/10/2005 (A/H5N2) segment 4 (HA) 27.0 8.000149e+00 14/14 (100%)
EPI182375 A/spotbill duck/Xuyi/18/2005 (A/H5N2) segment 4 (HA) 27.0 8.000149e+00 14/14 (100%)
EPI21072 A/duck/Guangxi/53/2002 (A/H5N1) segment 4 (HA) 27.0 8.000149e+00 14/14 (100%)

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PostPosted: Mon Apr 16, 2012 6:24 pm 
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N224K
C705A
EPI167553 A/Muscovy duck/Vietnam/NCVD-11/2007 (A/H5N1) segment 4 (HA) 27.0 8.000149e+00 14/14 (100%)

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PostPosted: Mon Apr 16, 2012 6:25 pm 
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N224K
C705G
EPI340168 A/duck/Egypt/10185SS/2010 (A/H5N1) segment 4 (HA) 27.0 8.000149e+00 14/14 (100%)

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PostPosted: Tue Apr 17, 2012 5:50 am 
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Commentary

http://www.recombinomics.com/News/04171 ... on_WB.html

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PostPosted: Tue Apr 17, 2012 8:50 am 
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Commentary

http://www.recombinomics.com/News/04171 ... Egypt.html

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PostPosted: Wed May 16, 2012 9:47 am 
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A242S pedigree

EPI245992 A/duck/Egypt/0982-NLQP/2009 (A/H5N1) segment 4 (HA) 27.0 8.182327e+00 14/14 (100%)
EPI245983 A/duck/Egypt/08355S-NLQP/2008 (A/H5N1) segment 4 (HA) 27.0 8.182327e+00 14/14 (100%)
EPI245981 A/chicken/Egypt/0883-NLQP/2008 (A/H5N1) segment 4 (HA) 27.0 8.182327e+00 14/14 (100%)
EPI127756 A/duck/Egypt/9399NAMRU3-CLEVB202/2007 (A/H5N1) segment 4 (HA) 27.0 8.182327e+00 14/14 (100%)

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PostPosted: Wed May 16, 2012 12:35 pm 
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http://www.abc2news.com/dpp/news/health ... z1ur3X9Z4p


Posted: 05/14/2012

•Libby Lewis, CNN Radio
A science journal is poised to publish a study that some experts believe could give a recipe to bioterrorists.
The study is from an experiment by a Dutch scientist who engineered the avian flu virus to make it more deadly to mammals by making it spread through the air.

That experiment was funded by the U.S. government, and it has sparked a passionate debate among scientists. Part of that debate is over where this research could lead, and whether it is worth it.

The National Institutes of Health and some scientists say it is worth it. They say it could ultimately protect mankind by trying to anticipate how the virus could mutate to one that causes a pandemic -- like the one in the film "Contagion."

Dr. Anthony Fauci heads the NIH agency that funds infectious diseases research. It funded the controversial Dutch experiment.

"We need as scientists and health officials to stay one step ahead of the virus as it mutates and changes its capability," Fauci told CNN Radio recently. "To anticipate that would be important to determine whether the countermeasures we have available, such as antivirals and vaccines, would actually be effective against such a virus that changed in such a way."

But a number of scientists are stepping forward to say it is not worth it -- and that this research could actually bring us closer to that nightmare.

How? By making a lethal virus that spreads like seasonal flu.

"We are playing with fire," says Dr. Thomas Inglesby and his colleagues at the Center for Biosecurity at the University of Pittsburgh Medical Center.

If this engineered virus were to escape the laboratory, by accident or by evil, "it could endanger the lives of hundreds of millions of persons," Inglesby says.

The journal Science is now reviewing the manuscript by Dutch scientist Ron Fouchier, a virologist at the Erasmus Medical Center in the Netherlands.

In December, the National Scientific Advisory Board for Biosecurity warned against publishing Fouchier's study and a similar study from Wisconsin. The Wisconsin study was based on a similar experiment but used a less lethal strain of the virus.

In March, that same advisory board looked at revised versions and said the Wisconsin study was safe to publish. But some on the panel broke ranks on publishing Fouchier's work. Twelve said yes; six said no.

Michael Osterholm, an infectious diseases expert at the University of Minnesota, was one of the six "no" votes on the board. In a letter to NIH after the vote, Osterholm described the studies as "nearly a complete cookbook" for those who would do harm.

The journal Nature just published the Wisconsin study. The journal Science is expected to publish Ron Fouchier's study within weeks.

Here's what you need to know about the avian flu research:

Is the engineered avian flu virus as easily spread between people, as well as animals?

It's not certain. But evidence shows it's likely to spread the same way between people as it does between the ferrets that Fouchier used in his experiment.

Why did the government fund this research if it's so risky?

They wanted to know why avian flu spreads so fast among birds but not among people. People only catch bird flu if in they're in close contact with infected birds.

Here, the government funded two studies, one led by Fouchier and the other by Wisconsin flu researcher Yoshi Kawaoka. Both used genetic engineering to explore which mutations might turn an avian flu into one that could spread easily between people.

The NIH says these experiments show that it's possible for the bird flu virus to evolve to a highly transmissible killer virus like the one in "Contagion."

"These studies raised the red flag," said Robert Webster, a virologist and flu researcher at St. Jude Children's Research Hospital. "The cat's out of the bag."

Well, now what?

These experiments lay a path to a whole new area of genetic engineering in flu research.

The government and supporters of the controversial experiments say more research will lead to a better understanding of the genetic mutations that could lead to a viral pandemic.

But other scientists say this is the wrong road to take.

Sir Richard Roberts, a molecular biologist who's won the Nobel Prize, spoke out at a recent National Academies workshop on the bird flu experiments.

"Someone is trying to make the most dangerous virus we can think of," Roberts said. "I don't understand how one can justify that, unless there is no other way of getting the data that you're interested in.

"And the way you get data is surveillance, and to see what is going on in nature, and to respond to it accordingly. And you go out of your way to find a universal vaccine. I would much sooner see money spent on that than on creating the most dangerous virus imaginable. I find it indefensible."

Roger Brent, a biologist at the Fred Hutchinson Cancer Research Center in Seattle, said he believes these experiments create more danger than benefit.

Brent told CNN that in order to be valuable -- that is, to reliably show the ways that bird flu could evolve to infect humans -- these experiments would require more experiments that could generate recipes for more, and different, man-made viruses -- all of them dangerous.

"Scientists must ask: Do we really want to do these experiments?" Brent said. "If we're generating knowledge that we feel dodgy about, do we really want to generate 20 or 100 additional (engineered viruses) that create something that most people would believe to be bad?"

Is the government going to fund more of this research?

Possibly. The controversy over the Fouchier experiment led to a temporary "voluntary moratorium" by flu researchers on genetic engineering.

It also prompted the U.S. government to begin crafting a policy on how to deal with "dual use" research like this that can lead to harm, as well as good.

At a recent hearing on the bird flu virus research, Sen. Joe Lierberman, I-Connecticut, asked Fauci whether he thought there were any experiments that should not be done.

Yes, Fauci replied, but he said he thought that would be rare.

Supporters of the Fouchier experiment say the results make the case for more support and funding.

At the National Academies workshop, one journalist said he had talked to a number of scientists who questioned the value of these experiments and where they could lead.

Flu researcher Robert Webster replied by saying the experiments brought bird flu back into the research conversation.

"Concern for bird flu had dropped. Really, H5N1 had disappeared from the radar screen. This shows it can occur. So we have to maintain pandemic preparedness."



Read more: http://www.abc2news.com/dpp/news/health ... z1v3FVR6ea

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