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Old 07-13-2013, 03:20 PM   #26
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and another method :

make filamentous swine viruses spherical by just adding
a few mutations :


Triple reassortant swine(1998) strains were observed to be mostly filamentous

mutations at 30, 142, 207, and 209. (7) made it spherical
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3507794/

pH1N1 containing substitutions at positions 30, 207 and 209 exhibited a switch to filamentous morphology,



i wonder, whether with this knowledge, given triple reassortant swine, could they have made a pandemic
from it just with these sphericalizing mutations ?

hopefully this won't work with H5N1 or H7N9 ...
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Old 07-15-2013, 12:41 PM   #27
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Feb.2006 Biowar for Dummies

http://mikefalick.blogs.com/my_blog/...s_the_sca.html
Brent guesses he would need a couple million dollars to whip up a batch of smallpox from scratch
An advanced grad student could do it,”

smallpox is 200000 basepairs, flu < 14000
Biotech's growth curves leave Moore's Law in the dust.
home. According to his calculations, if the current pace of biotech proceeds for another decade,
cooking up a lethal bug will be as easy and cheap as building a Web site.

-------------------------------------
http://www.ebay.com/itm/APPLIED-BIOS...e#ht_555wt_647

still $5000
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Old 07-19-2013, 06:52 AM   #28
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http://oba.od.nih.gov/biosecurity/me...0-%20Final.pdf

The Board was asked to advise on two papers in the process of being published, one in Science
by Tumpey, et al., titled Characterization of the Reconstructed 1918 Spanish Influenza Pandemic Virus
and one in Nature by Taubenberger, titled Characterization of the 1918 Influenza Virus Polymerase
Genes.

The Board unanimously concluded that the public health benefits of these two
publications far outweighed the risks or potential risks of misuse by persons with malevolent
intent. The Board recommended that the papers be published.

The Board also recommended the development of additional Federal biosafety guidelines and a
Federal regulatory framework for controlling access to the 1918 virus.
Subsequent to these discussions, the virus was added to the Select Agent list. Lastly, the Board recommended development of a comprehensive communication plan for public dissemination of this
type of information.

Dr. Keim stated that a working group survey of the American Society for Microbiology (ASM)
indicated that only a very small number of submitted articles raise security concerns.

Dr. Keim stated that it’s important to consider not only what is communicated, but also the way
in which information is communicated.

One of the proposed tools would be a framework for assessing the risks and benefits of
communicating dual use research products

Working Group Progress Report: International Collaboration
David R. Franz, Ph.D., D.V.M., Chair
He said there is currently a lack of international consensus on the level
of risk posed by the dual use life sciences

The public session was recessed. The Board then met in a closed session

----------------------------------------------------------------------------------------------------------------------------

[where is the report from the risk-assessment group ? I can't find it.

They do not say, _why_
" The Board unanimously concluded that the public health benefits of these two
publications far outweighed the risks or potential risks of misuse by persons with malevolent
intent."

was there an expert group involved to assess the risks ? What were the arguments ?
I find it amazing that this central question is not mentioned in that report.
What is it, that NSABB is good for, if not the weighting of risks and benefits ?
Were they weighted at all ? By whom ? Is it secret ? ]

================================================== ====================

http://oba.od.nih.gov/oba/biosecurit...11-16-2012.pdf

Over the course of its
deliberations, the Board has developed a framework for assessing the benefits and risks of
conducting work with DURC potential as well as the risks and benefits of communicating the
important results of DURC, and an overview of this framework can be found in Appendix B.5

5 NSABB, “Points to Consider in Assessing the Risks and Benefits of Communicating Research
Information with Dual Use Potential,” in
Responsible Communication of Life Sciences Research with Dual Use Potential,
http://oba.od.nih.gov/biosecurity/pd..._Potential.pdf
developed as part of the NSABB’s 2007 report

[how can such a general tool, established 4 years before the specific discussion
arose be much helpful in assessing the H5N1 risks ?
You will have to read the available papers and discuss the methods, where it is going,
estimate the probabilities. There is no way around this. And this can't be done
in a general way before the problem arises. This all looks like an attempt to divert
from the issue at question by institutionalizing the discussion itself and replacing the essential
risk discussion by that instituionalizing general discussion }
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Old 07-19-2013, 07:42 AM   #29
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"immediate risk" is one of their key-points.
They don't care much about a slow scientific process that gains knowledge
in multiple small steps about how to generate a high-virulence pandemic virus.
But that's, how it usually goes.

> As a general principle, the NSABB strongly supports the unrestricted communication
> of research information unless that information could be directly misused to pose a
> significant and immediate risk to public health and safety
http://oba.od.nih.gov/oba/biosecurit...12_Meeting.pdf

http://www.nih.gov/about/director/03...mendations.pdf
*The data are not immediately enabling.
The Board emphasized that if additional
information were included that would enable the construction of an H5N1 virus that was both
highly pathogenic and transmissible between mammals through the air, then the information in
the manuscripts would have more implications for misuse and would require additional
consideration regarding communication
[why "immediate" is so important, evades me. Whether we will get these virulent pandemics
in 2 or 10 or 50 years , mankind is doomed anyway and the anticipation has immediate
consequences. ]
*These data may benefit public health and surveillance efforts.
enhanced surveillance of viruses in birds and humans and other mammals (e.g., possible
reassortment viruses in pigs)
improved risk assessment of circulating strains.
[ok. But experience shows that this cannot help to prevent pandemics. Even if we detect them early
or before they jump to humans. There will likely be lots of other occasions]
*Global cooperation is essential for pandemic influenza preparedness
the risks associated with not sharing the information, (international accusations of withholding)
[NSABB was charged to decide pros and cons, not these other international organizations.
NSABB somehow anticipates that they want the data to be published and take the risks.
So, does NSABB think "they" are more competent to judge this ?]
*The research was conducted under appropriate conditions
studies were conducted under rigorous biosafety conditions
[not relevant. Future research using these data may have weaker conditions. I.e. in countries
with other biosafety conditions]
*there is an urgent need for effective United States and international policies for the oversight
and communication of dual use research of concern
*There is a critical need for a mechanism for disseminating sensitive scientific information.
[these are no arguments wrt. the risk assessment]

In contrast, a minority of members of NSABB concluded that:
* The data in the newly‐revised Fouchier manuscript are immediately and directly enabling.
Kawaoka : less virulent strains
*While the data in the two manuscripts may benefit public health and surveillance efforts,
these data may not be directly relevant or immediately helpful to the current public health or
surveillance infrastructure.

------------------------------------------------------------------------------------------------------
nothing about the details of the mutations, passaging strategy, reassortments
and what can be reasonably expected in the future and the chances
that "they" might succeed.
Nothing about the strategies, what they would do then, whether the "success"
should be communicated and the potential killer strains should be published.
(before others find them )

this is silly
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Old 07-19-2013, 10:53 AM   #30
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from the _Boston lab document on NSABB's webpage ä

all humans older than 2–3 years have
immunity to both H1N1 and H3N2 viruses (Murphy 2008).

blood transfusions or blood products from convalescent patients were of benefit in
decreasing risk of death in patients (Luke, Kilbane et al. 2006).

There are experimental data from the
early 1970s that looked at infections in human volunteers after exposing them to a related H1N1
strain of influenza virus (Carrat, Vergu et al. 2008)

In these volunteers, doses ranging from ten
thousand to one million CCID50 result in approximately 80% to 95% infection probability

In other experiments (Alford, Kasel et al. 1966), the low-dose inhalational data reveal that roughly
50% of unprotected humans were infected after inhaling doses of 1–5 CCID50 Thus the human
infectious dose is presumed to be low for 1918 H1N1V.

During the period 2000-2010, there were 7 incidents reported in government and academic
laboratories as noted in the Biosafety Review (Appendix D). These included a centrifuge leak and
other incidents leading to potential exposures of several different strains of influenza virus. There
were no influenza virus infections reported and no deaths from these incidents.
From a review of the published literature, there are at least 3 laboratory-acquired infections
reported for influenza viruses (Wentworth, McGregor et al. 1997; Harding 2006). Of these,
symptomatic influenza infections were reported in two laboratory workers who were involved in
taking nasal swabs from laboratory pigs infected with a swine influenza virus. The influenza
viruses isolated from the laboratory workers were antigenically identical to the inoculum swine
influenza virus used in the experiments. Partial gene sequencing of the viruses isolated from
humans indicated that they were direct descendants of the inoculum swine virus; they were 99.7%
identical with regard to the hemagglutinin genes.

----------------------------------------------------------------------
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Old 07-20-2013, 11:19 AM   #31
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Influenza viruses: breaking all the rules.
Taubenberger JK, Morens DM.
SourceViral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases.
ABSTRACT Influenza A viruses (IAV) are significant pathogens able to repeatedly switch hosts to infect multiple avian and mammalian species, including humans. The unpredictability of IAV evolution and interspecies movement creates continual public health challenges, such as the emergence of the 2009 pandemic H1N1 virus from swine, as well as pandemic threats from the ongoing H5N1 and the recent H7N9 epizootics. In the last decade there has been increased concern about the "dual use" nature of microbiology, and a set of guidelines covering "dual use research of concern" includes seven categories of potentially problematic scientific experiments. In this Perspective, we consider how in nature IAV continually undergo "dual use experiments" as a matter of evolution and selection, and we conclude that studying these properties of IAV is critical for mitigating and preventing future epidemics and pandemics.
------------------------------------------------------------
recent pubmed articles that are useful for pandemic virus creation research:
73437 influenza articles in total , 2013.07.20
---------------------------------------------------------------
The homologous tripartite viral RNA polymerase of A/swine/Korea/CT1204/2009(H1N2)
influenza virus synergistically drives efficient replication and promotes respiratory-droplet
transmission in ferrets.
----------------------------------------------------------------------
The short stalk length of HPAI H5N1 influenza neuraminidase limits transmission of
pandemic H1N1 virus in ferrets.
-----------------------------------------------------------------------------
Mammalian adaptation in the PB2 gene of avian H5N1 influenza virus.
-------------------------------------------------------------------------------
Influenza: Pathways to human adaptation.
-----------------------------------------------------------------------------
Genetic changes that accompanied shifts of low pathogenic avian influenza viruses
toward higher pathogenicity in poultry.
---------------------------------------------------------------------------------
Endothelial activation and dysfunction in the pathogenesis of influenza A virus infection.
-----------------------------------------------------------------------------
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Old 07-21-2013, 11:10 AM   #32
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http://www.sciencemag.org/content/ea...cience.1240532
The viruses isolated from birds were nonpathogenic in chickens, ducks, and mice;
however, the viruses isolated from humans caused up to 30% body weight loss in mice.
Most importantly, one virus isolated from humans was highly transmissible in ferrets by
respiratory droplets.

Three human viruses (SH/1, SH/2, and AH/1)


they can stop it in nature by closing wet markets
but how to stop its "evolution" in labs ?

----------------------------------------------------------------------------
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3393695/ , July 2012
1-line-summary: virulent mouse-adapted H9N2 (147L,627K in PB2) ,
3-line summary: 8 lung passages in mice resulted in mutations M147L(1),V250G,
E627K,L226Q(4),R210K(7) and a lethal virus of increased transmissibility.
Using the virus A/chicken/Shandong/16/05(H9N2) [that virus is not at genbank]
....
[so, what did the H7N9 passaging experiments in mice and ferrets yield ?
isn't it likely that they did try it, when they even tried it with H9N2 in 2012,
when there was no immediate threat to humans yet ?
should the mutations be published, so it could help evildoers to create a pandemic
with reverse genetics using them ?]
--------------------------------------------------------------------------------
remember Fouchier about passaging in 2011:
http://blogs.scientificamerican.com/...rst-announced/
...And that was when “someone finally convinced me to do something really, really stupid,”
Fouchier recounted. They put the mutated H5N1 into the nose of one ferret, then took a sample
of nasal fluid from that ferret and put it in the nose of another. After 10 ferrets, the virus began
spreading from ferret to ferret via the air just about as easily as a seasonal flu virus.
In all that ferret hopping, the virus gained only five new genetic substitutions ....
------------------------------------------------------------------------------------
[why might it have been "really,really stupid" ? It finally gave them the 5 mutations
and yielded the result. The reason can only be the anticipated gof-critical debate.
But that also means, that there is much behind the curtains, that is not being talked
about in public. Or just experiments that are not being done in NIH-granted studies.
(but probably elewhere, and they have little reason to publish the results,
considering the negative impact, see e.g. the Chen study, May,Hobson comments
You see that the current international system is highly inappropriate to deal with
these problems. It encourages secret gof-research in unknown low-security labs
(3rd world ?)
------------------------------------------------------------------------------
Führen die Geheimdienste ein Eigenleben in Deutschland? : Kanzleramt gerät in Erklärungsnot
n-tv.de NACHRICHTEN - ‎vor 4 Minuten‎

--------------------------------------------------------------------------------------
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Old 07-25-2013, 11:41 AM   #33
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there is frequent likely contamination in Chinese labs

we had several examples
most recent: (the last one was uploaded to genbank just today)

(all these are probably contaminated from the 1977-Colorado virus,
they have too few mutations for natural evolution)



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  14 >GU086137,A/swine/Guangdong/423/2006,2006//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,14-OCT-2009,Department of Veterinary Prevention           .............A......T.....C...........G.....G..............        5      5 ,      5      5      14:>GU086137,A/swine/Guangdong/423/2006,2006//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,14-OCT-2009,Department of Veterinary Prevention           
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  16 >GU086153,A/swine/Guangdong/968/2006,2006//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,14-OCT-2009,Department of Veterinary Prevention           ..AC.TA..A..........T......................................        6      6 ,      6      6      16:>GU086153,A/swine/Guangdong/968/2006,2006//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,14-OCT-2009,Department of Veterinary Prevention           

   1 >U07146,A/swine/Ange-Gardien/150/1990,1990//,H3N2,Canada,2NA,Swine,4,.43A.,.433_72.,,                                                       .....................A.........A..TC...........C...........        5      5 ,      5      5       1:>U07146,A/swine/Ange-Gardien/150/1990,1990//,H3N2,Canada,2NA,Swine,4,.43A.,.433_72.,,                                                       
   5 >FJ830855,A/swine/Guangdong/01/1998,1998//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,14-MAR-2009,Department of Life Scienceœ Sun Yet-san        ............C........A.....G....G....G...........C.........        6      6 ,      6      6       5:>FJ830855,A/swine/Guangdong/01/1998,1998//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,14-MAR-2009,Department of Life Scienceœ Sun Yet-san        
  19 >DQ021911,A/swine/Heilongjiang/74/2000,2000//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,29-APR-2005,National Key Laboratory of Biotechnologyœ   --...............C...A.T.....................G....AG-------       15     15 ,      6      6      19:>DQ021911,A/swine/Heilongjiang/74/2000,2000//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,29-APR-2005,National Key Laboratory of Biotechnologyœ   
  10 >GQ422436,A/swine/Guangdong/111/2002,2002//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,29-JUL-2009,Sun Yat-Sen Universityœ Life Science          .....................A.....................................        1      1 ,      1      1      10:>GQ422436,A/swine/Guangdong/111/2002,2002//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,29-JUL-2009,Sun Yat-Sen Universityœ Life Science          
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  13 >GU086129,A/swine/Guangdong/223/2006,2006//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,14-OCT-2009,Department of Veterinary Prevention           ..................AG.A...................G.................        4      4 ,      4      4      13:>GU086129,A/swine/Guangdong/223/2006,2006//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,14-OCT-2009,Department of Veterinary Prevention           
  18 >EU273774,A/swine/Heilongjiang/1/05,2005//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,11-NOV-2007,National Key Laboratory of Veterinary          --......G............A...........G..A...........G...-------       14     14 ,      5      5      18:>EU273774,A/swine/Heilongjiang/1/05,2005//,H3N2,China,:ES,Swine,4,.43A.,.433_72.,11-NOV-2007,National Key Laboratory of Veterinary          
   4 >JN105973,A/swine/Fujian/F2/2007,2007/10/05,H3N2,China,:ES,Swine,4,.43A.,.433_72.,08-JUN-2011,Fujian Academy of Agriculture Sciencesœ       TT...................A............................AGAGATAAT       12     12 ,     12     12       4:>JN105973,A/swine/Fujian/F2/2007,2007/10/05,H3N2,China,:ES,Swine,4,.43A.,.433_72.,08-JUN-2011,Fujian Academy of Agriculture Sciencesœ       
  20 >JX138525,A/swine/Hunan/3/2008,2008/07/,H3N2,China,:ES,Swine,4,.43A.,.433_72.,07-JUN-2012,Dabeinong Research Center for Veterinary          .......A.............AA...................C................        4      4 ,      4      4      20:>JX138525,A/swine/Hunan/3/2008,2008/07/,H3N2,China,:ES,Swine,4,.43A.,.433_72.,07-JUN-2012,Dabeinong Research Center for Veterinary          
  21 >A/swine/HuNan/01/2008(H3N2)                                                                                                                --.....A.............A.......CA.........A...........-------       14     14 ,      5      5      21:>A/swine/HuNan/01/2008(H3N2)                                                                                                                
                                                                                                                                                                                                             
---Index-----------------------------------------------------------------------------------------------------------------------------------------CCCTTCGGTTTTTGTTCTCAGGGCGATACTGGAACTGAATGATCTAAGATGAGTTATTA 
-codon-position----------------------------------------------------------------------------------------------------------------------------------2   2 2222  11  21211 211 2 22221212121  2 122211 2 1212 12 
                                                                                                                                                 00000000000000000000000000001111111111111111111111111111111 
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                                                                                                                                                 90361827211710400243227531396472483464675700733774678912345
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Old 07-26-2013, 02:49 PM   #34
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http://jvi.asm.org/content/86/17/9211.full

> Therefore, at least in the context of
> the other seven 1918 genes, a low-pathogenicity avian HA could
> elicit responses similar to the 1918 HA protein.

to which then we had no immunity

again another idea how to create a bad pandemic


... which NSABB did not consider or discuss

--------------------------------------------------------------
comparison with nuclear research:
http://www.brad.ac.uk/bioethics/medi...SciencesWP.pdf
------------------------------------------------------------
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Old 09-02-2013, 02:43 PM   #35
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http://www.ncbi.nlm.nih.gov/pubmed/23990570
...The H7N9 virus could replicate in the upper and lower respiratory tract, heart, liver,
and olfactory bulb of ferrets. It is worth noting that the H7N9 virus exhibited low level
of transmission between ferrets via respiratory droplets. There were four mutations
in the virus isolated from the contact ferret which were D678Y in PB2, R157 K
in HA(H3 numbering), I109T in NP, and T10I in NA. These data provide useful
information for a possible method on how to create a severe influenza pandemic.
Further research is needed to determine whether these mutations will also
increase transmissibility in humans.
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Old 09-03-2013, 01:34 PM   #36
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here is some old discussion and opinions from PROmed

http://forum.prisonplanet.com/index....142366.10;wap2

at that time reverse genetics was quite new and "not a piece of cake"



Taubenberger,Tumpey,Ebright,Holmes,Gerberding,Fauc i,
Hatch Rosenberg,Tucker,Campbell,Kennedy,
Oxford,Kawaoka,Mulcahy,Garcia Sastre,Wimmer,Kaplan,
Alibek=Alibekov,

those who are involved in the research, who benefit from it
financially or in their career are for it.
It's a clear pattern. Coincidence ?

and , btw., NSABB is operated by NIH
webpage : oba.od.nih.gov/


it's also my lifelong experience, once people move out of University
and get a job, they no longer say what they really think.
But rather what they anticipate is best for their job,career.
There goes trust...

===========================================
http://dujs.dartmouth.edu/applied_sc...modern-warfare
================================================
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Old 09-11-2013, 03:21 PM   #37
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here is a philosophical paper about the 2011f H5N1 debate
with many interesting references :
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3766690/
(published now, but apparently written in early 2012,
so nothing about H7N9 and the subsequent reassortment papers in 2013 )

with a surprise to me, how after 11 pages of analysis without clear direction,
presenting arguments of both parties, he suddenly came to that clear conclusion
on page 12 towards publishing.
Based mainly on the bad communication of NSABB's risk assessment.

> Here, with the assessment carried out in the discussion of this analysis,
> the recommendation is clear: Given an epistemological assessment in
> relation to a moral assessment where facts, predictions, and moral
> standards are taken into account, neither Fouchier nor Kawaoka can
> be characterized as irrational in deciding to continue their research
> endeavor or in deciding to publish their research in full detail. In this case,
> there is moral warrant in place reasonably to permit genetic alteration
> of the H5N1 strain of avian influenza for the purposes presented in the
> research protocol.

because Fouchier and Kawaoka were not shown as irrational,
they should not be hindered in their research and publishing it.
That's the logic of the philosopher.
Nowhere in that article did I find any mention that Fouchier and Kawaoka
(and the other quoted flu-researchers like Palese,Taubenberger,Racaniello)
could be biased, since they benefit from that research by funding.
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Old 09-12-2013, 07:37 AM   #38
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former Microsoft chief technolgy officer
patentholder - (evil copyright guy)
multi-interests (including cooking)
no blog or forum on his webpage
http://en.wikipedia.org/wiki/Nathan_Myhrvold

about bioterrorism
http://papers.ssrn.com/sol3/papers.c...2&download=yes
33 pages, mostly text,opinion, no science, no reviews
Influenza seems not to be so high on his list of dangers
------------------------------------------------------------------

http://emergency.cdc.gov/agent/agentlist.asp
influenza not listed as bioterrorism agent ;-)
-----------------------------------------------------------------------------------------
CIDRAP: Think tank sees big risks in flu gain-of-function research
http://www.cidrap.umn.edu/news-persp...ction-research
The Center for Arms Control and Non-Proliferation, Lynn C. Klotz, estimates the
gof lab escape risk at 180-1100 deaths per lab per year
Center for Arms Control report: The Human Fatality Burden of Gain of Function Flu Research: A Risk Assessment
http://armscontrolcenter.org/The_Hum...h_v8-29-13.pdf
16 pages
----------------------------------------------------------------------------------------
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Old 09-17-2013, 07:31 PM   #39
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Influenza is just not a good agent for bioterrorism despite all the whining about dual use.

There is partial immunity & we are much better at treating the secondary infections.
I am pretty sure that even if we released the 1918 virus now we would do much, much better if only because we have antibiotics.
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Old 09-19-2013, 11:03 AM   #40
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maybe, maybe not. This is unclear.
They had the antibodies in USA 1929, Liverpool 1951
still they got it badly.
Why lost it virulence in 1921-1928 ?
maybe immunity, but maybe it just mutated.

And remember the recent Taubenberger experiments in mice,
They gave it another H1, avian, quite different, no immunity,
and there was almost no change in replication and virulence

and the elderly were spared in 1918, why ? Could we expect
the same thing today ?

It's risky.

it may become a "good" bioweapon soon - we are making
progress.
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Old 09-19-2013, 12:26 PM   #41
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Quote:
Originally Posted by Kassy View Post
Influenza is just not a good agent for bioterrorism despite all the whining about dual use.

There is partial immunity & we are much better at treating the secondary infections.
I am pretty sure that even if we released the 1918 virus now we would do much, much better if only because we have antibiotics.
I view it sort of like a dirty bomb. At the end of the day, it might not cause a huge number of excess deaths but the chaos created would be crippling for the economy. Look at what SARS did.
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Old 09-21-2013, 09:18 AM   #42
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that would be nice.
People would awake.
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Old 09-21-2013, 10:51 AM   #43
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http://www.ncbi.nlm.nih.gov/pubmed/24044207
[Reverse genetics platform construction of influenza pandemic virus strain].
[Article in Chinese]
CONCLUSION: The pandemic virus reverse genetics platform of A/California/07/2009 (H1N1)
were built. Based on this platform, rescued virus hold the similarity of antigenicity and growth
ability with wild type virus.

--------------------------

soon it will be common knowledge how to make influenza
viruses from sequences
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Old 10-24-2013, 11:22 PM   #44
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http://nypost.com/2013/10/23/scienti...ant-bird-flu/?
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Old 11-10-2013, 03:51 AM   #45
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new article by Wain-Hobson:
http://onlinelibrary.wiley.com/doi/1....201303475/pdf

Pandemic influenza viruses: time to recognize our inability to predict the unpredictable and stop
dangerous gain-of-function experiments

ahh, he quotes that silly Rumsfeld quote about "known knowns"
(gs: give us probability estimates !)

I'm not sure what Wain-Hobson wants.
He wants them to stop gof experiments because he is afraid the virus might escape
their labs ?! But these are high-security labs . others will be doing the experiments
in lower security labs.
Wain-Hobson's headline from March 2013: H5N1 viral-engineering dangers will not go away.

So, by stopping the experiments we will only get a delay.
A delay in which the lab-terrorists may close the gap
A delay in which we just stop.
Stop worrying.
Stop prepping.


I've been looking at the NSABB protocols and I tend to agree,
that they are biased, spreading propaganda.
How useful the experiments and the research is,
how the risk is overblown.
The typical strategy is to concentrate on newspaper headlines and
then to picture out what factors they didn't consider.
But we have no risk assessment about the possibilities and
probabilities of what bio-engineering might achieve in the next
years and decades.
How many really dangerous flu-viruses are there in the giant search-space
of 4^13000 nucleotides and what strategies may find them ?
Usually we start from known viruses and apply mutations and reassortments,
it's still a lot of possibilities and testing. Once we get that automized
and computerized, it will likely outperform nature (IMO)


Wain-Hobson doesn't reply to my emails nor does Peter Hale,
who had organized that letter to Obama with the signatories,
most from FVR, foundation for vaccine reasearch.
Their webpage is still not up.
http://www.vaccinefoundation.org/
"our website is in development. It will be
fully operational by fall 2013"
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Old 12-22-2013, 01:37 AM   #46
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56 signatures, 50 professors

http://www.independent.co.uk/news/sc...s-9018666.html

The point is not how useful this is for vaccine research or antivirals.
The point is not how likely these muations may happen in nature.
The point is not the danger of an escape from Erasmus labs.
The point is, that these viruses can be successfully manipulated
now in the lab and that lots of others will be trying to do this in future
and that we have no regulations to control this and no plans and no
international consensus on how to react and contain it and prepare.

--------edit--------------
see also: http://www.nature.com/news/scientist...europe-1.14429
---------edit-------------
I found the letter here: http://news.sciencemag.org/sites/def...0Barroso_0.pdf
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Old 02-10-2014, 02:25 PM   #47
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http://optionsviii.controlinfluenza....nce-materials/

The Pros and Cons of Influenza Gain of Function Studies
CapeTown,Sep.2013 Sat.Sep.7.2013 , 8:00-11:30 Panelists include:
Yoshihiro Kawaoka, University of Wisconsin Madison,
Charles Russell, St. Jude Children’s Research Hospital, Memphis,
Adolfo Garcia-Sastre, Mount Sinai School of Medicine, New York,
Michael Osterholm, Center for Infectious Disease Research and
Marc Lipsitch, Harvard University, Cambridge, Massachusetts,
Jesse Bloom, Fred Hutchinson Cancer Research Center, Seattle,

video:
http://ncwebcasting.mediasite.com/me...39a1117179541d
http://ncwebcasting.mediasite.com/me...39a1117179541d
Cox at ~1:00 influenza risk assessment tool (works without expert
probability estimates, avoids to estimate pandemic likelyhood, only impact)
Garcia-Sastre at
Kawaoka at 1:54 - 2:07
Lipsitch at 2:08-2:36
Simonsen at 2:36-2:40
Garcia-Sastre at 2:40-2:44
Russell at 2:44-2:53
Osterholm at 2:54-2:57
Kawaoka at 2:57-3:01
3:09 chances
...questions
3:17 end


Workshop 4C: Transmission and Infection Control
Meeting Room 2.60 (Level Two)
Chairs: Randy Albrecht, Icahn School of Medicine at Mount Sinai, Department of
Microbiology, New York, New York, United States of America
Sun-Woo Yoon, St. Jude Children’s Research Hospital, Memphis,
Tennessee, United States of America
Friday 28 Oral Presentations:
O-864 Biosafety and biosecurity in a biocontainment laboratory working with
highly pathogenic avian influenza (HPAI). Lisa Kercher
O-865 Utilizing endogenous microRNA to confer molecular biocontainment to
gain-of-function influenza viruses: towards risk mitigation. Randy Albrecht
O-866 Limited airborne transmission of influenza A/H7N9 virus between
ferrets. Eefje Schrauwen
O-867 Transmission bottlenecks in the ferret model differ between respiratory
droplet and contact transmission routes. Wendy Barclay
O-868 Efficacy of surgical face masks in reducing influenza virus dissemination
in human exhaled breath. Nancy Leung
O-869 Household transmission of influenza in Nicaragua. Aubree Gordon


H7N9-NS segment codes for a truncated NS1 protein that lacks a putative PDZ binding motif,
seroprevalence for H3N2v at 1:02,slide95
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Old 04-24-2014, 02:15 PM   #48
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another great idea for a manmade pandemic


The Yanagi group in Japan managed to segment the naturally nonsegmented measles virus into three segments and the recovered viruses were viable in vitro. This was possible in the lab because the molecular biology of replication is well characterised and that measles virus is polyploid allowing the engineering of a tri-segmented genome that can replicate and be packaged into virions. I speculate that this hasn't commonly occurred in nature because measles and paramyxoviruses notoriously do not undergo recombination. However, the biological and evolutionary consequences of giving measles virus a tri-segmented have not really been explored but would shed light on this process. This question can - and should - be addressed experimentally!
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Old 05-21-2014, 01:15 PM   #49
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what I learned through the years of searching for expert estimates is, that they
usually are biased, they don't say what they really think but rather what they
anticipate is best for their career, their work.
Or what they expect their employer wants to hear from them.
Or what increases their book sellings . Or ...
It's really hard to find someone who has no horse in the science business
but still the expertise to analize and judge.
And who is willing to honestly say what he/she thinks.

What makes me believe this ? Expert opinions "strangely" correlate with
what is best for them. Flu researchers, who can do them, are pro these experiments
non-flu researchers or flu-researchers who are not doing these experiments are contra.

People who made an opinion or wrote books rarely change their opinion
when new aspects or data come up.

Experts put "propaganda" pieces into newspaper articles or papers where they
sum up the pros of their agenda but don't really address the cons.

When a new aspect appears which challenges my previous opinion or estimate,
then I would be especially eager and interested to examine it - not so the experts,
they would try to ignore it.

Lipsitch e.g. replied to tweets until the "other, 3rd world labs" point came up ...

Racaniello enjoys to pick newspaper headlines, but not critical controversial arguments.
Osterholm was just too extreme with his H5N1 in 2006, (I missed SARS)
the "just in time problem" and such.

Alcabes just argues historically, ignoring that things have changed recently.
monotreme just pushes his anti-China agenda, yes.

Fauci coauthored Taubenberger, see his bias wrt. the 1918-publishing in the
NSABB-transcripts

FVR doesn't reply to emails, don't update their webpage. They "communicate"
by mass-letters.

no forums, no real internet discussion as I used to see in Usenet-times
(on things much less important)


--------------------------------------------------------------------------------

now, reading the paper at (6 pages , .pdf)

http://www.plosmedicine.org/article/...l.pmed.1001646
Citation: Lipsitch M, Galvani AP (2014) Ethical Alternatives to Experiments with Novel
Potential Pandemic Pathogens. PLoS Med 11(5): e1001646. doi:10.1371/journal.pmed.1001646

and especially the last paragraph gives me the impression/suspicion that the main motivation
of the authors could be the fear that more from the somehow fixed influenza grant budget
goes to GOF-research (which they are not doing/ can't do) and thus leaves fewer grants
for the alternative research that they are doing.

The concern about global public health may only be a welcome opportunity to make their claims.

That doesn't mean that their risk-benefit analysis is wrong or that I think
there is no concern about these gof-experiments.

Just that the players are maybe biased, (as usual ...).


--------------------------------

in fact, I'm pretty much concerned, as you can see from reading
the previous posts in this thread.
But not so much about escapes from the USA-granted labs
more about escapes from 2nd,3rd world labs or even unauthorized
labs or terrorist labs or qualified "rogue-state" labs like Russia
in the 70s or such.
And about gof-research in general, even on low-path flu.
What we learn about how to create a low-path influenza pandemic
like 2009, may be used to create a high-path pandemic also.

The recent experience and especially H7N9 taught us, that
virulence is often just dependent on one single mutation
and much easier "achieved" than transmission efficiency.


What I am really missing is the research on how to make influenza less
virulent. How to "replace" (potentially) virulent strains by milder ones
through immunity to an antigenically similar, but better transmissable virus.

This isn't even discussed, I never saw it. Strange.
Maybe not much money could be earned with that approach.

===========================================

Mike Coston has many further links on this issue.

he is very busy updating his blog since 2006 or earlier
and _not_ slowing down as the forums, including CE-->TBM, did since 2007 with
public interest in birdflu waning, so it's maybe even better
and more informative now than most forums



http://networkedblogs.com/X4qKA

http://afludiary.blogspot.de/2013/09...ch-argues.html

http://afludiary.blogspot.de/search?...&max-results=6

http://afludiary.blogspot.de/2014/05...-concerns.html
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Old 06-12-2014, 11:48 AM   #50
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http://www.theguardian.com/science/2...rus?CMP=twt_gu

Kawaoka: wild flu has potential to adapt to humans and cause a pandemic
May : The work they are doing is absolutely crazy. The whole thing is exceedingly dangerous
protect people, but instead puts the global population in more danger.
Lipsitch: This is a risky activity, even in the safest labs
Wain-Hobson: It's madness, folly. It shows profound lack of respect for the collective decision-making
process
NIH peer review: the research was scientifically meritorious
Heilman: appropriate biosafety
gsgs: so much arguing - but no mention of the m.E. biggest threat:
increase of knowledge for and encouragement of evildoers to create
bad viruses (in unsafe labs)
----------------------edit-----------------
Kolter: Kawaoka and his team are driven by ambition and not truly acting in the
human population’s best interest.
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