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"There is a concern the virus may be airborne...."
Calm down.
"When it comes to viruses, it is always difficult to predict what they can or cannot do. It is instructive, however, to see what viruses have done in the past, and use that information to guide our thinking. Therefore we can ask: has any human virus ever changed its mode of transmission? The answer is no. We have been studying viruses for over 100 years, and we’ve never seen a human virus change the way it is transmitted."
http://www.virology.ws/2014/09...

Probably the biggest concern is the possibility of a mutation occurring that would allow the virus to go airborne.

Except that in 100 years of studying viruses, we have never seen one change the way its transmitted.

Furthermore HIV is similar to Ebola and it has never become airborne. Even in the laboratory conditions when they tried to make it airborne it lost its lethality. For a virus to gain a function it usually loses a function too. In the last 100 years no known virus has gone from being contact transmission (including droplets - still fluids just traveling a short distance through the air) to "airborne" transmission via aerosols (dry virus floating in the air).

http://www.virology.ws/2014/09...

As far as I understand the influenza genome, it has 8 chunks of genes, roughly the equivalent of a chromosome, not 8 genes. But perhaps I misunderstood that? And each of those chunks has estimated (based on base pairs) 8 to 14 genes. So in total we are in the range of 100 +/- I had guessed. But that might be wrong :) It seems regarding viruses we did not do much genome mapping. .

You are correct that it has 8 "chunks" that are essentially the equivalent of a chromosome. How ever each chunk/chromosome only encodes a single gene. Three of those genes can express 2 different proteins, either through alternatively splicing or frameshifting resulting in a total of 11 possible protein sequences expressed from the entire influenza genome. 100 genes is big for viruses, usually those are large, complex viruses like the herpesviruses which have all kinds of special viral proteins that are designed to subvert the host immune system. Here is a good illustration of the influenza genome: http://www.virology.ws/2009/05...

The most researched and very primitive tobacco mosaic virus. It produces roughly 160 different amino acids. OTOH, the hull around the RNA strand is constructed from a single repeating peptide. I would assume that that peptide is constructed from those amino acids, but that sounds unlikely. So: how many genes do you need to produce 160 different amino acids? I thought 160 genes, but perhaps a gene can code several amino acids in a row, without stop markers and without causing them to 'stick together'.

Amino acids are just the individual components that are linked together to form peptides/proteins, there are only 20 possible amino acids in eukaryotes. The Tobacco Mosaic virus capsid protein is indeed 160 amino acids in length, but there are still only 20 amino acids used to make that protein, some are used more than twice. Here is the actual amino acid sequence of the protein, each letter represents a single amino acid, so you can see that some are used more than once: http://www.uniprot.org/uniprot...

Regarding modeling: depends what you want to model, chemical interactions, likely challenging. High level production and accumulation and assembly of proteins? Not so challenging.

Modeling protein structures is hard, look at the "Folding at Home" project, they've got petaflops of computational power cranking away on modeling a handful of structures. And that's just individual 3-D structures, to ask how changing a single amino acid in a protein would influence the structure and then how that new structure would interact with the 20,000+ other proteins is impossible right now. I wish it were, it would make my job a hell of lot easier.

Just look at the oceans!. If mammals only host ~3e5 unknown viruses, that's nothing.

Why not just try to sequence enough geness, to have it multiplied with a DIY PCM machine, and create the super deadly flu,

For one, the flu has already been sequenced, so doing it again wouldn't be useful.

Second, the flu genome is RNA, and around 14,000 bases long which is beyond what many PCR thermocyclers can do reliably, even with the best enzymes available. In other words, you would need better molecular biology techniques to get it to work well. Even more so, older DNA sequencers topped out at reading ~800 bases so you'd have to do a ton of sequencing in order to make sure you got your flu genome right after making your desired changes to it.

Third, if you want to create the virus and make it useful you need to transfect it into something, as the flu can't replicate without a host. Hence if it is "super deadly" you need to be able to get it into a host without killing yourself - and on top of that you need to get it to a host that can transmit it to other living people since corpses don't tend to sneeze much.

Is Dr. Orient wrong? Is there evidence that immunized workers are less likely to transmit the virus.

'Flu is transmitted (among other routes) by airborne water droplets. It also causes the sufferer to cough and sneeze (thus spraying such droplets).

It's hardly conclusive, but based on those facts I find it a little hard to believe that the vaccine (which will prevent the coughing and sneezing) has no effect on transmission...

Unless you can explain how the vaccinating the nurse will keep the flu infected patient from coughing and sneezing, those droplets will keep transmitting the virus. The vaccine only protects the person who received it. They can still transmit it, for instance, they pick up the food tray that an infected patient used and take it to the commissary. While there, they see and old friend and shake their hand. Voila, even though vaccinated and protected, they have now spread the virus (assuming the old friend was not).

Is Dr. Orient wrong? Is there evidence that immunized workers are less likely to transmit the virus.

'Flu is transmitted (among other routes) by airborne water droplets. It also causes the sufferer to cough and sneeze (thus spraying such droplets).

It's hardly conclusive, but based on those facts I find it a little hard to believe that the vaccine (which will prevent the coughing and sneezing) has no effect on transmission...

Some types of viruses, like AIDS and flu, mutate more rapidly because of their mechanism of making DNA from RNA which is error-prone. http://www.virology.ws/2009/05/10/the-error-prone-ways-of-rna-synthesis/ Other viruses are more stable may benefit from the idea in TFA. However, to me it seems dangerous to engineer viruses just reduce the number of required booster shots.

The smartest saying related to things like this I ever heard was "Trust science, not scientists."

http://www.virology.ws/2011/09/27/trust-science-not-scientists/

"Just no. That's totally wrong. Are you deliberately misunderstanding? A mutation found to allow binding of human tissue was developed, but not by infecting ferrets."

Except that YOU are wrong. Right here (the same link provided by someone else above), paragraph 5.

That very clearly says that they created a new H5N1 strain with the H5 HA protein, which increased transmissibility. And (as I cite references for in another post below), it was precisely "To determine whether H5N1 viruses could be transmitted between humans..." [paragraph 4 of that same link].

Further as this article, and others, point out, the virus was deliberately selected for transmissibility by infecting a sequence of ferrets.

So you are just wrong, man. Nice job of speculation, but you need to get your facts straight.

there was no "new strain of the virus", .... here you go, mandatory link to non-brain-damaged content ... http://www.virology.ws/2011/12/06/ferreting-out-influenza-h5n1/

From your link: "A laboratory in the Netherlands has identified a lethal influenza H5N1 virus strain that is transmitted among ferrets."

The whole argument from your link about it not being as lethal as H5N1 is pure speculation - as he admits, we don't know transmissibility of the strain in humans, because we won't do that experiment. His basic argument is the virulence of the virus in humans is reduced by having the virus be transmitted through non-human hosts. This is not necessarily true - it depends on what species the virus is moving between. If a virus makes the leap from something further from humans (eg fish) to something closer to humans (eg pigs) then it becomes more dangerous to us. His argument may be correct in the case where you have an organism adapted very well to humans and you expose it to non-human transmission selective pressures, then it will probably evolve and become less adapted to humans. But this is not always the situation.

He also says:

Nature is far better at producing viruses that can kill – to think that we can duplicate the enormous diversity and selection pressures that occur in the wild is a severe case of scientific hubris.

Maybe he is right (at the moment) about manually targetted changes - but we are only going to get better at this over time. He has also ignored the practice of laboratory evolution (or synthetic evolution), where nature is used in the lab to evolve or enhance certain characteristics of organisms. For a far-out plan, some rogue biologists could expose humans, see which ones are infected and die first, and then infect others with flu samples taken from those bodies. After repeating for some generations, this selective pressure may well produce a highly lethal and highly transmissible variant.

there was another thread about this same subject a few weeks ago, and there was no "new strain of the virus", just a virus sharing one of the proteins that help the virii attach to cells

while we have lots of resistant bacterias living in our hospitals (and by our mean "all the hospitals in the world"), we're getting hype over this ... not sure any more it's hysterics or histrionics ... maybe Netherlands needs pretexts to wipe out chicken farms somewhere ...

here you go, mandatory link to non-brain-damaged content ... http://www.virology.ws/2011/12/06/ferreting-out-influenza-h5n1/

Scientists appear to be responsible for the hype surrounding this experiment. Fouchier called it ‘one of the most dangerous viruses you can make’. Paul Keim, chair of NSABB, ‘can’t think of another pathogenic organism that is as scary as this one’, and Richard Ebright, a molecular biologist at Rutgers University says the experiment should not have been done. Martin Enserink writing in ScienceInsider says that the virus could change world history, and similar proclamations of doom can be found in the popular press.

Passage of viruses in a different host is one strategy for reducing the virulence in humans. This concept is explained in this passage from Principles of Virology:

Less virulent (attenuated) viruses can be selected by growth in cells other than those of the normal host, or by propagation at nonphysiological temperatures. Mutants able to propagate better under these selective conditions arise during viral replication. When such mutants are isolated, purified, and subsequently tested for pathogenicity in appropriate models, some may be less pathogenic than their parent.

The possibility that passage of the H5N1 virus in ferrets will attenuate its virulence in humans has been ignored.

getting tired of this ...

Did ya know that DNA does not a virus make?

Are you sure about that...?

Though not necessarily in a form capable of enjoying, or even being conscious of, that fact.(It sounds like her present state isn't all that high on the consciousness scale either, unfortunately.)