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PostPosted: Tue Mar 16, 2010 3:40 pm 
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novascotia35 wrote:
I assume you are right that this is E627K, but that is partially because of your remarkable track record. Are there any other PB2 changes that it could be from the description?

I looked around for a confirmation of E627K and haven't found one yet, but I really can't see any other change getting into the mainstream media. I believe that only E627K has been cited as causing increased virulence, which is based on studies in mice going back to E627K in some of the severe/fatal cases from the 1997 H5N1 outbreak in Hong Kong.

Moreover, E627K was predicted last May

http://www.recombinomics.com/News/05120 ... sonal.html

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Last edited by niman on Tue Mar 16, 2010 6:58 pm, edited 1 time in total.

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PostPosted: Tue Mar 16, 2010 3:57 pm 
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My own $0.02, which may or may not have any validity. I always thought that the presence of E627K by itself wouldn't lead to increased virulence since it moves most of the virus into the upper respiratory tract. However, learning of the RBD changes in Ukraine, etc., I became concerned of the presence of these two polymorphisms together.

My rationale is as follows:

  • E627 wild type grows best at a higher temperature, leading the virus deeper into the respiratory tract. This leads to the higher levels of viral pneumonia we have seen.
  • The RBD changes (D225G, D225N) allow the virus to attack the lungs more directly, but transmission isn't necessarily as efficient as it could be.
  • E627K allows the virus to grow better at a lower temperature, allowing the virus to move into the upper respiratory tract where it will transmit more efficiently.
  • E627K plus RBD changes allow for increased viral load, more efficient transmission, plus the ability to attack the lower respiratory tract.

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PostPosted: Tue Mar 16, 2010 4:05 pm 
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Niman,

If K627 becomes fixed in pH1N1, from what I can find out, this be the first time both the SR polymorphisms (PB2 R590 & S591) and K627 are in play together, can you confirm this? What are your thoughts on the possible consequences of this combination?

Regarding H5N1, I thought K627 is still rather rare? I thought that K627 becoming more common and obviously fixed in H5N1 is one of the major concerns with H5N1.

Thanks.


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PostPosted: Tue Mar 16, 2010 4:07 pm 
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wotan wrote:
My own $0.02, which may or may not have any validity. I always thought that the presence of E627K by itself wouldn't lead to increased virulence since it moves most of the virus into the upper respiratory tract. However, learning of the RBD changes in Ukraine, etc., I became concerned of the presence of these two polymorphisms together.

My rationale is as follows:

  • E627 wild type grows best at a higher temperature, leading the virus deeper into the respiratory tract. This leads to the higher levels of viral pneumonia we have seen.
  • The RBD changes (D225G, D225N) allow the virus to attack the lungs more directly, but transmission isn't necessarily as efficient as it could be.
  • E627K allows the virus to grow better at a lower temperature, allowing the virus to move into the upper respiratory tract where it will transmit more efficiently.
  • E627K plus RBD changes allow for increased viral load, more efficient transmission, plus the ability to attack the lower respiratory tract.

I agree that E627K has a much higher potential for causing more severe and fatal disease becasue it makes for virus, and that virus tends to be somewhat heterogeneous. That is why D225G is frequently found as a mixture with D225N or wild type. The virus really has multiple options and more virus generally means more problems.

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PostPosted: Tue Mar 16, 2010 4:10 pm 
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spentitall wrote:
Niman,

If K627 becomes fixed in pH1N1, from what I can find out, this be the first time both the SR polymorphisms (PB2 R590 & S591) and K627 are in play together, can you confirm this? What are your thoughts on the possible consequences of this combination?

Regarding H5N1, I thought K627 is still rather rare? I thought that K627 becoming more common and obviously fixed in H5N1 is one of the major concerns with H5N1.

Thanks.

E627K is fixed in H5N1 clade 2.2 (Qinghai strain). Most other H5N1 with E627K are from patients or other mammals.

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PostPosted: Tue Mar 16, 2010 6:41 pm 
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Researchers from India's National Institute of Virology (NIV) yesterday announced that they detected a small mutation in pandemic H1N1 virus in samples from three patients, fueling speculation that it may be the same change that surfaced in two Dutch patients last fall.

Experts say if the two mutations are the same it doesn't appear to have much clinical significance, though the development is worth monitoring, because the change could theoretically enhance viral replication and virulence.

Indian researchers said the throat swab samples from the patients show a small mutation in the polymerase 2 (PB2), gene, the Times of India reported today. Dr A.C. Mishra, the NIV's director, said the virus was not resistant to oseltamivir (Tamiflu).

Dr Michael Shaw, associate director of the US Center for Disease Control and Prevention (CDC) Laboratory Science Influenza Division, told CIDRAP News that he doesn't have any more details on the Indian findings aside from the Times of India story. However, he said the researchers' description sounds like the E627K mutation that was first reported by a group from the Netherlands at the end of September.

The Dutch researchers found the E627K mutation in the basic polymerase 2 (PB2) protein in samples from two patients who had links to an island in northern Holland. They described their findings in a Sep 28 report on ProMed mail, an Internet-based reporting system of the International Society for Infectious Diseases. One of the patients, an adult, had a mild infection, and the other, a girl, recovered after a week of treatment with oseltamivir.

The E627K mutation in PB2 had previously been linked to increased replication and possible virulence changes in other influenza A viruses. Though the mutation has been rarely seen in avian-derived viruses, it had been associated with fatal H5N1 cases and H7N7 infections in humans, the researchers said in their ProMed mail report.

They added that the clinical and epidemiological significance of the mutation is unclear and that experimental infection of ferrets with the H1N1 virus containing the mutation did not suggest increased shedding, virulence, or transmissibility.

Shaw said nothing stood out about the Dutch patients—the mutation didn't appear to give the virus a transmission advantage. If the mutation described by the Indian researchers turns out to be the E627K in PB2 mutation, "it's an interesting observation, but probably irrelevant clinically," he said.

Virologists expect to see such mutations and remain on the lookout for clusters of such cases, Shaw said. Scientists are concerned about the mutation, because it could allow the virus to better adjust to host body temperature. However, he added that reports of two or three patients at a time, such as the Indian and Dutch reports, aren't worrisome.

Mishra told the Times of India that, although the mutation they found has been linked to increased replication and virulence changes in other influenza A viruses, they did not detect any increased virulence or replication in the isolates they studied. "The mutation is not very significant in that sense," he said.

Dr Siddharth Dalvi, a consulting microbiologist and immunologist, told the Times that protein made by the PB2 gene doesn't directly play a role in immune response, so point mutations may have little clinical impact. However, he added that the mutation could theoretically change replication.

http://www.cidrap.umn.edu/cidrap/conten ... on-jw.html

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PostPosted: Tue Mar 16, 2010 6:46 pm 
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niman wrote:
Though the mutation has been rarely seen in avian-derived viruses, it had been associated with fatal H5N1 cases and H7N7 infections in humans, the researchers said in their ProMed mail report.


http://www.cidrap.umn.edu/cidrap/conten ... on-jw.html

The above is incorrect. E627K is in virtually all cade 2.2 (Qinghai strain) H5N1, which is virtually all H5N1 west of China. It is transported and transmitted by wild migratory birds.

This has been well known since 2005

http://www.recombinomics.com/News/07070 ... nghai.html

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Last edited by niman on Tue Mar 16, 2010 6:49 pm, edited 1 time in total.

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PostPosted: Tue Mar 16, 2010 6:48 pm 
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E627K in pandemic H1N1 sets the stage for significant changes.

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PostPosted: Tue Mar 16, 2010 7:13 pm 
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niman wrote:
They added that the clinical and epidemiological significance of the mutation is unclear and that experimental infection of ferrets with the H1N1 virus containing the mutation did not suggest increased shedding, virulence, or transmissibility.

Shaw said nothing stood out about the Dutch patients—the mutation didn't appear to give the virus a transmission advantage. If the mutation described by the Indian researchers turns out to be the E627K in PB2 mutation, "it's an interesting observation, but probably irrelevant clinically," he said.


http://www.cidrap.umn.edu/cidrap/conten ... on-jw.html

Once again the CDC is hanging its hat on NEGATIVE experimental data. Ferrets infected with H1N1 with D225G also did not appear unusual. However, in 1918/1919 two of five fatal HUMAN cases had D225G and in Ukraine 27/37 fatal HUMAN lung samples had D225G/N. Once again the CDC is using negative animal data to say to not believe your lyin' eyes with regard to dead H1N1 patients in 1918/1919 or 2009/2010.

Speaking of clusters, E627K is in ALL human seasonal flu since 1918.

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PostPosted: Tue Mar 16, 2010 8:10 pm 
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CIDRAP version

links at bottom to the Times of India and to a 9/09 ProMed item

http://www.cidrap.umn.edu//cidrap/conte ... on-jw.html

Pandemic H1N1 mutation in India resembles Dutch findings

Lisa Schnirring * Staff Writer

Mar 16, 2010 (CIDRAP News) – Researchers from India's National Institute of Virology (NIV) yesterday announced that they detected a small mutation in pandemic H1N1 virus in samples from three patients, fueling speculation that it may be the same change that surfaced in two Dutch patients last fall.

Experts say if the two mutations are the same it doesn't appear to have much clinical significance, though the development is worth monitoring, because the change could theoretically enhance viral replication and virulence.

Indian researchers said the throat swab samples from the patients show a small mutation in the polymerase 2 (PB2), gene, the Times of India reported today. Dr A.C. Mishra, the NIV's director, said the virus was not resistant to oseltamivir (Tamiflu).

Dr Michael Shaw, associate director of the US Center for Disease Control and Prevention (CDC) Laboratory Science Influenza Division, told CIDRAP News that he doesn't have any more details on the Indian findings aside from the Times of India story. However, he said the researchers' description sounds like the E627K mutation that was first reported by a group from the Netherlands at the end of September.

continues ....


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