Robert Webster on H5N1 evolution, vaccines 12-11-06

[JetStuuby]

Re: Robert Webster on H5N1 evolution, vaccines 12-11-06

I think that it IS normal , old, 'plain jane' darwinian evolution that is driving the selection of which elements of a gene are recombined to form new strains.

Gene your earlier references to Occam's Razor are probably right, the simplest solution works, but it seems to me that RECOMBINATION is the simplest solution.

a) RECOMBINATION is not random and that matches with the fact that certain segments of isolates haven't changed for decades, so this seems to destroy the "sloppy copy" assumption. Logic prevails.

b) RECOMBINATION clearly demonstrates how different sized areas of recombination could be interpreted as "drift" and "shift" - so now we have one theory in stead of two. Logic prevails.

c) Just my guess but i would say that evolution is what selects the areas that are recombined at the genetic level with in the cell. Seems logical, something has to cause one segment over another to be selected and it sure isn't 'God' doing it. Logic prevails.

I agree Gene, Occam's Razor is at work and it points to recombination.

It might be hard to accept a new truth when you have held onto a theory for many years, but that is what science is all about

Jet

 

[sharon sanders]

Re: Robert Webster on H5N1 evolution, vaccines 12-11-06

I am glad that we are having this debate. Please stay civil and use "clean language".

Obviously there are economic forces that are motivating the advocacy of certain theories. This is understood. It, however, does not lessen the potential validity of these theories.

Gene is a prominent researcher and very well qualified to debate the various processes at work here. Welcome and thank you for participating.

 

[AlaskaDenise]

Re: Robert Webster on H5N1 evolution, vaccines 12-11-06

.....1.2 billion USD has been awarded by the US government to fund both pandemic vaccine development AND the infrastructure to manufacture seasonal and pandemic vaccines. We need both......

So how many vaccine plants have been built or are under construction? When will the US have the capacity to manufacture vaccines for an acceptably high population? In 2 years, 5 years, 10 years?

Some people within the science policy field, think plants shouldn't be built unless high profits for big pharma can be assured. I public health policy should not be subject to the dictates of shareholders.

Regarding influenza replication.....given the role of the "tail" in RNA replication, there appears to be some kind of "programmed intelligence" taking place in the process. Whether it be recombinaton or some combination of theories, it may not be entirely random.

see http://jvi.asm.org/cgi/content/abstract/74/11/5053

.

 

[Laidback Al]

Re: Robert Webster on H5N1 evolution, vaccines 12-11-06

Hi Gene ?

Welcome to Flutrackers. Dredging up an old thread is perfectly acceptable, especially when it stimulates discussion.

So let me see if I understand your point. For you, the mechanism by which the variants arise is not as important as understanding that at some point the ?fittest? strain will overwhelm and dominate other current strains when (if) it becomes easily transmissible among human hosts.

So, how can we address AlaskaDenise?s concern about preparing and stockpiling a vaccine ahead of time. Is it possible "to scale up production in new cell-based substrates using seasonal flu vaccine as the model" as you recommend to produce the quantities of vaccine that would be needed worldwide in the event of a pandemic? Is this feasible without knowing which of the strain will win out as the ?fittest? for human to human transmission?

 

[gsgs]

Re: Robert Webster on H5N1 evolution, vaccines 12-11-06

we observe some few recombination events of long subsegments
being exchanged. E.g. Canadian swine etc.
It is claimed that single nucleotide-changes also often
happen by recombination, but then why don't we observe
more recombinations of short segments,
2-10 neighbor changes being preserved.
Is it the copy-choice mechanism ? (I didn't examine this)


what's with synonymous vs. nonsynonymous mutations ?
70% of observed mutations are synonymous, 3rd base,
while statistically
we would expect only 11%. So selection deletes most
nonsyn. but few syn.
Still the syn. ones are not entirely random. Do they effect the
3d-structure or is it explained by the change of probabilities for
future nonsyn. mutations ?

 

[4-ABBA]

Re: Robert Webster on H5N1 evolution, vaccines 12-11-06

Is it possible "to scale up production in new cell-based substrates using seasonal flu vaccine as the model" as you recommend to produce the quantities of vaccine that would be needed worldwide in the event of a pandemic? Is this feasible without knowing which of the strain will win out as the ?fittest? for human to human transmission?

There may be several distinct clades that end up as "fit" when pandemic arrives. How, therefore, would this affect scaling up cell-based production?

 

[GenePalmer]

Re: Robert Webster on H5N1 evolution, vaccines 12-11-06

Hi Gene ?

So let me see if I understand your point. For you, the mechanism by which the variants arise is not as important as understanding that at some point the ?fittest? strain will overwhelm and dominate other current strains when (if) it becomes easily transmissible among human hosts.

Well, no. Understanding the mechanism could be key to developing a
strategy to model what changes might be expected to confer a more
effeicient transmission phenotype to the virus. I'm not ruling out the
contribution recomination might be playing in generating new strains.

I would happily entertain both mechanisms as alternative hypotheses.
More likely than not both play a role in this respect. Why would anyone
care if I was "married" to one over the other. My vested interest in
is understanding how we might use the emerging data to more effectively
design vaccines against this wily beast. I suspect that many others have
been doing exactly what I've been doing; poring over sequences from
clade 1 viruses aligned with clade 2 and Fujian-like viruses hoping to see
a pattern.

If mergence of a pandemic strain is solely a function of recombination
any hope of developing predictive models of which amino acid substitution
in HA1 becomes hopeless, since the entire biosphere of influenza can
participate as donors of novel recombinations. The high fidelity observed
over much of this target antigen notwithstanding, it is the small clusters
of substitutions that result in both antigenic drift and immune escape.

If, on the otherhand, you can model tracked changes to their binding
affinity to alpha 2-6-linked sialic acid, demonstrate that subtle changes
in the multibasic cleavage site confer better intiation of infection, map
single amino acid substitutions in M2 when virus is grown under MAb
selective pressure, and track which changes in the polymerase confer
a more robust virus, you can learn things that might help toward better
vaccine development and antiviral drugs.

So, how can we address AlaskaDenise?s concern about preparing and stockpiling a vaccine ahead of time. Is it possible "to scale up production in new cell-based substrates using seasonal flu vaccine as the model" as you recommend to produce the quantities of vaccine that would be needed worldwide in the event of a pandemic? Is this feasible without knowing which of the strain will win out as the ?fittest? for human to human transmission?

As many of you know DARPA has initiated a competitive grant program
for rapid development of pharmaceuticals that take a given sequence
from paper to clinic in 12 weeks.
see: http://www.darpa.mil/dso/solicitations/amppip.pdf

Thanks for all your comments. It's been fun.
Gene

 

[wetDirt]

Re: Robert Webster on H5N1 evolution, vaccines 12-11-06

As many of you know DARPA has initiated a competitive grant program
for rapid development of pharmaceuticals that take a given sequence
from paper to clinic in 12 weeks.
see: http://www.darpa.mil/dso/solicitations/amppip.pdf

Thanks for all your comments. It's been fun.
Gene

Well, now, that's interesting. It is well-suited to military use, but precarious for civilian. It implies that there is no time allocated for any proof testing before deployment. The military is willing to take that risk, but would the general population? Perhaps, if the CFR was high enough.

 

[Mingus]

Re: Robert Webster on H5N1 evolution, vaccines 12-11-06

If in the event H5N1 ever becomes efficient at human-to-human transmission,
an effective vaccine would be indispensible. Choosing the right one is the
trick.

~gene

also

"It's (H5N1) continuing to evolve and there are multiple lineages of this virus still out there. What cross-protection is there between these clades (strains) and sub-clades?"

Webster said several H5N1 strains had become widespread and different enough to cause unease among experts, and no one would dare assume that any one vaccine would be able to protect against other H5N1 strains

Why not produce a multi-clades vaccine the same way we now produce a trivalent vaccine(tree different strain) for annual flu ??

This is not the first time I propose this idea, i just don't understand why I never heard this idea from somewhere else

 

[Mingus]

Re: Robert Webster on H5N1 evolution, vaccines 12-11-06

Funny debate about what driving the evolution...

Reality is often more in gray tone than just white & black.
Differents mechanisms plays here in a complex interaction.

I would like to add my welcome to GenePalmer & ask him what he think of the multi-clades vaccine idea acording to his experience.
There is an old thread about that here from last summer...
http://www.flutrackers.com/forum/showthread.php?t=7736
You can skip the software explanation & do directly to the multi-clades hypothesys.

Thanks if you answer

 

[Anne]

Re: Robert Webster on H5N1 evolution, vaccines 12-11-06

yes, it's a good idea, but perhaps there is a problem with the dose, in vaccin.
And why not produce a vaccin against the internals proteins, or M2 ( pro ion channel )
I ve read that this proteins mutates not much.

 

[Niko]

Re: Robert Webster on H5N1 evolution, vaccines 12-11-06

The DARPA proposal mentioned in previous posts
View attachment DARPA .pdf
"The vision of the Accelerated Manufacturing of Pharmaceuticals (AMP) program is to create an extremely rapid, flexible and cost-effective manufacturing system capable of producing three million doses of GMP-quality vaccines or monoclonal antibodies within 12 weeks."

Later in the document it indicates a 42 month timeframe (page 3).


3 million doses for a population of 300 million - within a 12 week timeframe from delivery of a target antigen or genetic sequence. This may be a significant proposal for use by the military, but I question the benefit of such a program for the general population in the near term (see chart on page 4). Let's all hope that a pandemic doesn't happen (at least in the next 42-48 months). The rest of the world...well, you're on your own.
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[Niko]

Re: Robert Webster on H5N1 evolution, vaccines 12-11-06

also



Why not produce a multi-clades vaccine the same way we now produce a trivalent vaccine(tree different strain) for annual flu ??

This is not the first time I propose this idea, i just don't understand why I never heard this idea from somewhere else

I thought the issue with a trivalent vaccine for H5N1 was the large doses necessary for sufficient antibody response based upon trail vaccine now stockpiled (and outdated). If memory is correct - 90 mcg X two doses??? Do you propose that smaller quantities of different clades being used to brew a vaccine? Has this been tried/tested?

 

[Mingus]

Re: Robert Webster on H5N1 evolution, vaccines 12-11-06

yes, it's a good idea, but perhaps there is a problem with the dose, in vaccin.
And why not produce a vaccin against the internals proteins, or M2 ( pro ion channel )
I ve read that this proteins mutates not much.

My guess wich is to be proven or disproven is that less than a tree fold dose will be required due to the cross-protective reaction.

As for the Matrix protein vaccine, I would'nt count on it.
Due to the high promess it make ( universal vaccine )
many scientific team have been sponsored on that.
But since the last ten year, I heard about that many time but never saw any conclusive results.
The problem is that even if you trigger a immune reaction agaist the M protein,
that protein is lock inside the virus in place where our antibody have no access.
The surface proteins, that are in close contact with our body ARE the NA & HA proteins, that's why they change so much
because they are under the selective pressure of our immune system (antibody).
If the M protein was in contact with our immune system, it would mutate a lot too...
I have no hope for an universal Mgene vax.

 

[gsgs]

Re: Robert Webster on H5N1 evolution, vaccines 12-11-06

maybe better 3 monovalent doses than one trivalent.
It's more flexible.
You would stockpile the vaccine now, but only take it,
when panflu started.

Actually prepandemic vaccine costs $20-$75 per dose,
with many doses and valences required and limited capacities
it would probably rise

 

[sharon sanders]

Re: Robert Webster on H5N1 evolution, vaccines 12-11-06

Respiratory and systemic humoral and cellular immune responses of pigs to a heterosubtypic influenza A virus infection

</NOBR><NOBR>Paul P. Heinen<SUP>1</SUP></NOBR>, <NOBR>Els A. de Boer-Luijtze<SUP>1</SUP></NOBR> and <NOBR>Andre T. J. Bianchi<SUP>1</SUP></NOBR>


[SIZE=-1]Department of Mammalian Virology, Institute for Animal Science and Health (ID-Lelystad BV), PO Box 65, 8200 AB Lelystad, The Netherlands<SUP>1</SUP> [/SIZE]

[SIZE=-1]Author for correspondence: Paul Heinen. Fax +31 320 238668. e-mail p.p.heinen@id.wag-ur.nl<SCRIPT type=text/javascript><!-- var u = "p.p.heinen", d = "id.wag-ur.nl"; document.getElementById("em0").innerHTML = '<a href="mailto:' + u + '@' + d + '">' + u + '@' + d + '<\/a>'//--></SCRIPT> [/SIZE]
<!-- null -->
<TABLE cellSpacing=0 cellPadding=0 width="100%" bgColor=#e1e1e1><TBODY><TR><TD vAlign=center align=left width="5%" bgColor=#ffffff>

</TD><TH vAlign=center align=left width="95%">[SIZE=+2]Abstract [/SIZE]</TH></TR></TBODY></TABLE><TABLE cellPadding=5 align=right border=1><TBODY><TR><TH align=left>[SIZE=-1]TOP

Abstract
Introduction
Methods
Results
Discussion
References
[/SIZE]</TH></TR></TBODY></TABLE>
The level of heterosubtypic immunity (Het-I) and the immune<SUP> </SUP>mechanisms stimulated by a heterosubtypic influenza virus infection<SUP> </SUP>were investigated in pigs. Pigs are natural hosts for influenza<SUP> </SUP>virus and, like humans, they host both subtypes H1N1 and H3N2.<SUP> </SUP>Marked Het-I was observed when pigs were infected with H1N1<SUP> </SUP>and subsequently challenged with H3N2. After challenge with<SUP> </SUP>H3N2, pigs infected earlier with H1N1 did not develop fever<SUP> </SUP>and showed reduced virus excretion compared with non-immune<SUP> </SUP>control pigs. In addition, virus transmission to unchallenged<SUP> </SUP>group-mates could be shown by virus isolation in the non-immune<SUP> </SUP>control group but not in the group infected previously with<SUP> </SUP>H1N1. Pigs infected previously with homologous H3N2 virus were<SUP> </SUP>protected completely. After challenge with H3N2, pigs infected<SUP> </SUP>previously with H1N1 showed a considerable increase in serum<SUP> </SUP>IgG titre to the conserved extracellular domain of M2 but not<SUP> </SUP>to the conserved nucleoprotein. These results suggest that antibodies<SUP> </SUP>against external conserved epitopes can have an important role<SUP> </SUP>in broad-spectrum immunity. After primary infection with both<SUP> </SUP>H1N1 and H3N2, a long-lived increase was observed in the percentage<SUP> </SUP>of CD8<SUP>+</SUP> T cells in the lungs and in the lymphoproliferation<SUP> </SUP>response in the blood. Upon challenge with H3N2, pigs infected<SUP> </SUP>previously with H1N1 again showed an increase in the percentage<SUP> </SUP>of CD8<SUP>+</SUP> T cells in the lungs, whereas pigs infected previously<SUP> </SUP>with H3N2 did not, suggesting that CD8<SUP>+</SUP> T cells also have a<SUP> </SUP>role in Het-I. To confer broad-spectrum immunity, future vaccines<SUP> </SUP>should induce antibodies and CD8<SUP>+</SUP> T cells against conserved<SUP> </SUP>antigens.....

http://www.flutrackers.com/forum/showthread.php?t=13584&highlight=cross


Comments?

 

[GenePalmer]

Re: Robert Webster on H5N1 evolution, vaccines 12-11-06

Well, now, that's interesting. It is well-suited to military use, but precarious for civilian. It implies that there is no time allocated for any proof testing before deployment. The military is willing to take that risk, but would the general population? Perhaps, if the CFR was high enough.

wetDirt, you have a knack for pejorative. As a potential recipient I am
loathe to bite the hand that feeds. These grants are exploratory.
We are a non-profit incubator of technology. Therefore, neither
institution is aiming for clinical trials or FDA approval.

Meanwhile, to address other valid points made in this thread, some big
pharma players are moving ahead to clinical trials with vaccine candidates.
GSK announced a split virus vaccine that protects at 1/4 the usual dose
of seasonal trivalent vaccine when given with their proprietary adjuvant.

Treanor's group showed protection with baculovirus-expressed H5 HA,
but had to deliver 90 mcg in two doses to hit the mark. Sanofi-Pastuer
has had success scaling up a human-derived cell line for pandemic
vaccine production. The idea being properly glycosylated HA may be
essential to induce neutralizing antibody. Medimmune, Wyeth, and
Novartis (acquiring Chiron recently) are all heavy hitters developing
cell-based platforms.

The concept of a multi-clade vaccine is attractive in theory, but
extremely expensive in pratice. The reason it works for seasonal
trivalent vaccine production is because those viruses grow so well
in embryonated hens eggs. To be cost effective pharma wants to
produce a vaccine that costs about a buck a dose to manufacture.
Each new strain added to the mix dilutes out the others.

When you consider the investment made in Sinovac to produce
H5N1 vaccine in China it works out to closer to $75/dose. Multiply
that by the minimum population that would need to be vaccinated
to provide herd protection and I get something like 22 billion USD.
Sinovac makes a split virus vaccine based on A/Vietnam/1194/04;
a single strain. If costs double for each strain you add... well,
who can afford to foot this bill?

 

[sharon sanders]

Re: Robert Webster on H5N1 evolution, vaccines 12-11-06

Just a note to everyone: We have many scientists participating here and sometimes the environment can become pejorative. Please respect the differing views and competing interests.

Thanks.

:tiphat:

 

[wetDirt]

Re: Robert Webster on H5N1 evolution, vaccines 12-11-06

wetDirt, you have a knack for pejorative. As a potential recipient I am loathe to bite the hand that feeds. These grants are exploratory. We are a non-profit incubator of technology. Therefore, neither institution is aiming for clinical trials or FDA approval.

I'm sorry, I wasn't trying to knock the idea, and didn't intend to come across that way. I've competed for SBIR work before, so I have an idea how the DARPA grant process works. What I was trying to point out was that the successful product would essentially be for military use only, under circumstances that would make clinical trials moot, probably.

But as a bystander, I note that it's unlikely that the described process would be used to develop a civilian pandemic vaccine. And being a civilian, it's a little disappointing to realize how big the hurdles are for a fast-track vaccine. And your explanation of the costs involved for a polyvalent vaccine just make it that much worse. Add to that Mingus's explanation of why a M subunit vaccine is unlikely to work, and my vaccine hopes for the general population are about squashed flat. There, I've done it again.

 

[AlaskaDenise]

Re: Robert Webster on H5N1 evolution, vaccines 12-11-06

I get something like 22 billion USD.
..... If costs double for each strain you add... well,
who can afford to foot this bill?

Current cost of Iraq war = $506 billion USD and climbing by $8 billion/month.

.