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PostPosted: Tue Jan 17, 2012 8:19 pm 
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http://www.recombinomics.com/News/01171 ... _H1N1.html

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PostPosted: Wed Jan 25, 2012 2:48 pm 
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Nature(2012)doi:10.1038/nature10884Published online 25 January 2012



Yoshihiro Kawaoka explains that research on transmissible avian flu viruses needs to continue if pandemics are to be prevented.




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Highly pathogenic avian H5N1 influenza viruses first proved lethal in humans in 1997 in Hong Kong. Since 2003, 578 confirmed infections have resulted in 340 deaths (go.nature.com/epb7ts). Now widespread in parts of southeast Asia and the Middle East, H5N1 viruses have killed or led to the culling of hundreds of millions of birds.

To date, H5N1 viruses have not been transmitted between humans. Some experts have argued that it is impossible. But given the potential consequences of a global outbreak, it is crucial to know whether these viruses can ever become transmissible. Work by my group (accepted by Nature) and an independent study (accepted by Science) led by Ron Fouchier of the Erasmus Medical Center in Rotterdam, the Netherlands, suggest that H5N1 viruses have the potential to spread between mammals. As the risks of such research and its publication are debated by the community, I argue that we should pursue transmission studies of highly pathogenic avian influenza viruses with urgency.

To determine whether H5N1 viruses could be transmitted between humans, my team generated viruses that combined the H5 haemagglutinin (HA) gene with the remaining genes from a pandemic 2009 H1N1 influenza virus. Avian H5N1 and human pandemic 2009 viruses readily exchange genes in experimental settings, and those from a human virus may facilitate replication in mammals. Indeed, we identified a mutant H5 HA/2009 virus that spread between infected and uninfected ferrets (used as models to study the transmission of influenza in mammals) in separate cages via respiratory droplets in the air. Thus viruses possessing an H5 HA protein can transmit between mammals.

Our results also show that not all transmissible H5 HA-possessing viruses are lethal. In ferrets, our mutant H5 HA/2009 virus was no more pathogenic than the pandemic 2009 virus — it did not kill any of the infected animals. And, importantly, current vaccines and antiviral compounds are effective against it.



NIBSC/SPL


H5N1 avian influenza virus particles.

Fouchier and his team also generated a transmissible H5 HA-possessing virus — meaning that two independent studies have demonstrated the potential for transmissibility of H5 HA-possessing viruses between ferrets. Their mutant H5 HA virus, generated in the genetic background of an H5N1 virus, did kill infected ferrets.

Some people have argued that the risks of such studies — misuse and accidental release, for example — outweigh the benefits. I counter that H5N1 viruses circulating in nature already pose a threat, because influenza viruses mutate constantly and can cause pandemics with great losses of life. Within the past century, 'Spanish' influenza, which stemmed from a virus of avian origin, killed between 20 million and 50 million people. Because H5N1 mutations that confer transmissibility in mammals may emerge in nature, I believe that it would be irresponsible not to study the underlying mechanisms.

The new work has implications for pandemic preparedness. There is an urgent need to expand development, production and distribution of vaccines against H5 viruses, and to stockpile antiviral compounds. Both studies identify specific mutations in HA that confer transmissibility in ferrets to H5 HA-possessing viruses. A subset of these mutations has been detected in H5N1 viruses circulating in certain countries. It is therefore imperative that these viruses are monitored closely so that eradication efforts and countermeasures (such as vaccine-strain selection) can be focused on them, should they acquire transmissibility.

Consequently, I believe that the benefits of these studies — the knowledge that H5 HA-possessing viruses pose a risk and the ability to monitor them and develop countermeasures — outweigh the risks. High biosafety and security standards can be met. Our experiments were carried out in a high-containment facility by a small group of highly trained individuals who operate under strict procedures to prevent the accidental release of viruses.

However, the US National Science Advisory Board for Biosecurity (NSABB) has recommended that details of both studies (including the mutations that confer transmissibility) should be restricted, and released only to select individuals on a 'need-to-know' basis. I acknowledge the advisory role of the NSABB, but I do not concur with its decision.

The primary justification for the NSABB's recommendation is that publication of our data “could enable replication of the experiments by those who would seek to do harm” (go.nature.com/nywkdy). But redacting our papers will not eliminate that possibility — there is already enough information publicly available to allow someone to make a transmissible H5 HA-possessing virus.

The mechanism that the US government proposes for releasing data would also be unwieldy. Thousands of applications to access the research are likely to be filed, and potential background checks would create a huge administrative burden. We cannot afford to lose time if we are to combat emerging pandemic threats. Even if an efficient process can be established, it would be difficult to enforce continued confidentiality in the scientific community.

By contrast, wide data dissemination will attract researchers from other areas to contribute to the field. This is crucial, because new ideas are needed to answer some of the most urgent questions. For example, the specific mutations that we identified suggest that influenza transmission is more complex than anticipated and involves not only the receptor-binding properties of HA, but other biological and physical properties.

The redaction of our manuscript, intended to contain risk, will make it harder for legitimate scientists to get this information while failing to provide a barrier to those who would do harm. To find better solutions to dual-use concerns, the international community should convene to discuss how to minimize risk while supporting scientific discovery. Flu investigators (including me) have agreed to a 60-day moratorium on avian flu transmission research (go.nature.com/ttivj5) because of the current controversy. But our work remains urgent — we cannot give up.

http://www.nature.com/nature/journal/va ... 10884.html

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PostPosted: Wed Jan 25, 2012 5:04 pm 
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http://www.recombinomics.com/News/01251 ... Egypt.html

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PostPosted: Tue May 01, 2012 6:19 pm 
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niman wrote:
The recently released (by St Jude at Genbank) avian H5N1 sequences from Egypt include extensive recombination with seasonal H1N1 and as well as reassortment with pandemic H1N1 recombined with seasonal H3N2.

The sequences have been confirmed by independent sequencing in Egypt.

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PostPosted: Fri May 04, 2012 2:46 am 
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First 62 positions update
G15A T19C C27T A36G A60C
EPI369061 A/swine/Illinois/A00857304b/2012 (A/H3N2) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI369053 A/swine/Illinois/A00857304a/2012 (A/H3N2) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI369042 A/swine/Illinois/A00857138b/2011 (A/H3N2) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI369034 A/swine/Illinois/A00857138a/2011 (A/H3N2) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI369019 A/swine/Illinois/A00857300/2011 (A/H3N2) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI352553 A/chicken/Egypt/Q1185/2010 (A/H5N1) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI352552 A/chicken/Egypt/Q1182/2010 (A/H5N1) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI351659 A/swine/Iowa/A01202659/2011 (A/H3N2) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI351650 A/swine/Iowa/A01202640/2011 (A/H3N2) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI345358 A/Indiana/10/2011 (A/H3N2) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI345155 A/shorebird/Delaware Bay/133/2002 (A/H9N1) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI344402 A/Indiana/08/2011 (A/H3N2) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI344394 A/Indiana/10/2011 (A/H3N2) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI343744 A/laughing gull/Delaware Bay/5/2003 (A/H9N1) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI343728 A/shorebird/Delaware Bay/246/2003 (A/H9N5) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI343720 A/shorebird/Delaware Bay/283/2003 (A/H9N1) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI342606 A/swine/NY/A01104005/2011 (A/H3N2) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI340981 A/Indiana/10/2011 (A/H3N2) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI335626 A/Indiana/08/2011 (A/H3N2) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI335615 A/Pennsylvania/11/2011 (A/H3N2) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI335607 A/Pennsylvania/09/2011 (A/H3N2) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI333194 A/Indiana/08/2011 (A/H3N2) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI331985 A/blue-winged teal/Guatemala/CIP049-04/2010 (A/H8N4) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI331961 A/blue-winged teal/Guatemala/CIP049-12/2010 (A/H5N4) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI331953 A/blue-winged teal/Guatemala/CIP049-13/2010 (A/H5N4) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI328175 A/mallard/California/9573/2008 (A/H4N6) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI321807 A/swine/Hubei/05/2009 (A/H1N2) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI321799 A/swine/Hubei/04/2009 (A/H1N2) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI292381 A/northern shoveler/California/44287-162/2007 (A/H10N7) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI286470 A/sanderling/Delaware/654/2002 (A/H6N4) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI286469 A/ruddy turnstone/Delaware/892/2002 (A/H6N4) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI286466 A/ruddy turnstone/Delaware/1234/2002 (A/H2N9) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI286463 A/ruddy turnstone/New Jersey/954/2002 (A/H2N9) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI286457 A/sanderling/Delaware/882/2002 (A/H2N1) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI272300 A/blue-winged teal/Guatemala/CIP049-01/2008 (A/H7N9) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI238580 A/mallard/Minnesota/334/1999 (A/H6N5) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI238552 A/mallard/Minnesota/253/1999 (A/H6N5) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI238527 A/mallard/Minnesota/195/1999 (A/H4N6) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI238519 A/mallard/Minnesota/192/1999 (A/H4N6) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI236788 A/mallard/Maryland/302/2001 (A/H5N2) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI236780 A/mallard/Maryland/252/2001 (A/H5N2) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI236363 A/ruddy turnstone/New Jersey/690/2002 (A/H2N9) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI236350 A/ruddy turnstone/New Jersey/1780/2002 (A/H2N9) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI236326 A/ruddy turnstone/Delaware/726/2002 (A/H2N1) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI236309 A/ruddy turnstone/Delaware/413/2002 (A/H2N1) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI236281 A/ruddy turnstone/Delaware/1543/2002 (A/H2N9) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI236271 A/ruddy turnstone/Delaware/1488/2002 (A/H2N9) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI236264 A/ruddy turnstone/Delaware/1190/2002 (A/H2N9) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI236117 A/mallard/Maryland/792/2002 (A/H5N2) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI236109 A/mallard/Maryland/789/2002 (A/H5N2) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI236101 A/mallard/Maryland/786/2002 (A/H5N2) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI169671 A/ruddy turnstone/NJ/631/2002 (A/H11N1) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI166060 A/swine/Shanghai/1/2007 (A/H1N2) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI162432 A/mallard/MD/790/2002 (A/H5N2) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI158462 A/mallard/MN/280/99 (A/H3N5) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI88349 A/shorebird/DE/261/2003 (A/H9N5) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI88340 A/shorebird/DE/231/2003 (A/H9N4) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI86529 A/laughing gull/DE/5/2003 (A/H9N1) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI50019 A/blue-winged teal/Ohio/31/1999 (A/H3N2) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)
EPI46723 A/mallard/Maryland/789/2002 (A/H5N2) segment 1 (PB2) 115.6 2.109268e-25 62/62 (100%)

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PostPosted: Sun May 06, 2012 12:49 pm 
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it's H5N1 but has old H1N1 (634-1579) and mexflu (310-449,1580-2057) PB2
in it. And >3 breakpoints.
And the old H1N1 is from 2005

doesn't seem reasonable

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PostPosted: Sun May 06, 2012 1:10 pm 
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gsgs wrote:
it's H5N1 but has old H1N1 (634-1579) and mexflu (310-449,1580-2057) PB2
in it. And >3 breakpoints.
And the old H1N1 is from 2005

doesn't seem reasonable

yada yada.

Egypt has resequenced and confirmed St Jude data.

You fail to understand recombination (with MULTIPLE breakpoints as seen in H3N2 in Korea or swine in Canada) or animal reservoirs. Korea also had "old" H3 sequences and was confirmed by US CDC and Japan NIID who obtained EXACT matches with resequencing.

You continue to IGNORE REAL data and claim that the data is false because it doesn't matched your unsupportable model of random mutation and "lab error".

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PostPosted: Sun May 06, 2012 1:24 pm 
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gsgs wrote:
it's H5N1 but has old H1N1 (634-1579) and mexflu (310-449,1580-2057) PB2
in it. And >3 breakpoints.
And the old H1N1 is from 2005

doesn't seem reasonable

Reality check. The PB1 sequences of Q1011 and Q1185 are IDENTICAL (as are the H5 sequences). The PB1 sequences have H1N1pdm09 at both ends.

Q1011 PB2 also has H1N1pdm09 sequneces at both ends. Q1185 PB2 has clade 2.2.1 F alternating with seasonal H1N1 and also has identity with H3N2v at 5' end (first 62 base pairs are IDENTICAL).

Q1182 has the same 62 BP identity at 5' end followed by low path avian, which is also at 3' end. Backbone is H1N1pdm09 with alternating seasonal H1N1 interspeced with seasonal H3N2. Most changes are 3rd codon position and synonymous. The carboxly half of PB2 is IDENTICAL to H1N1pdm09 at protein level (all nucleotide changes are silent).

It is your continued denial of reality which is not reasonable.

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PostPosted: Mon May 07, 2012 11:06 am 
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just a few such examples out of thousands.
And also a very few where a segment is preserved for 5 years.

And now we have both in one ?!?

And not only this one, also in your Canadian swine, Korea H3N2
and others.

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PostPosted: Mon May 07, 2012 12:57 pm 
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gsgs wrote:
just a few such examples out of thousands.
And also a very few where a segment is preserved for 5 years.

And now we have both in one ?!?

And not only this one, also in your Canadian swine, Korea H3N2
and others.

Please. You are as lost as ever. For this series there are FIVE examples in 2 genes which support each other and internally consistant. You STILL can't analyze data, and just post nonsense on what you think (while MISREPRESENTING data).

the Egyptian sequences are from 2010 collections (as is OBVIOUS by the dates in the names - A/chicken/Egypt/Q1011/2010, A/chicken/Egypt/Q1182/2010, A/chicken/Egypt/Q1185/2010) and H1N1pdm09 sequences are from 2009.

Like the Korean sequences they are internally consistant, involve multiple collections from same area in same time frame, and are independently confirmed years later.

You can't address the REAL DATA. Instead you just do hand waving demonstrating your inability to respond with anything but your standard mantras.

This (obviously) isn't your area of expertise and your babble is as old and incoherent as ever.

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