Nature - HA mutations responsible for the binding of H5N1 A viruses

[Mingus]

Re: Nature - HA mutations responsible for the binding of H5N1 A viruses

I did'nt check, they have writen this in the Nature article.

Have you check also in the H5 numbering ( 182 & 192 ) ?

Sorry i did a mistake before i edit the present post it is 192

 

[HenryN]

Re: Nature - HA mutations responsible for the binding of H5N1 A viruses

Which Iraq sequence do you mean? I checked A/human/Iraq/207-NAMRU3/2006(H5N1) HA which has S186 and Q196.

The sequences with the changes are being withheld by WHO in their private database at Los Alamos (but the S186 that is in the public sequence matches human H3N2 from Hong Kong - the start of the 1968 pandemic).

 

[HenryN]

Re: Nature - HA mutations responsible for the binding of H5N1 A viruses

Commentary at

http://www.recombinomics.com/News/11160601/H5N1_Human_Acquisitions.html

 

[MHSC]

Re: Nature - HA mutations responsible for the binding of H5N1 A viruses

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Additional H5N1 Acquisitions of Human RBD Polymorphisms
Recombinomics Commentary
November 15, 2006

two of these changes, lysine at position 182 and arginine at position 192, were present in the HA's of clade-2 H5N1 viruses isolated from two individuals in Azerbaijan and one individual in Iraq,clade

The above comments from today's Nature paper describe patients infected with the Qinghai strain of H5N1. The paper identified acquisitions in human H5N1 isolates that enhanced binding to human receptors, either individually or in combination.

The above comment is somewhat ambiguous. It is not clear if all three patients had both receptor bind domain (RBD) changes described above, or both changes were found among the three patients. The statement cannot be independently confirmed, because the sequences from these patients are still being hoarded by WHO, and have not been made public.

The hoarding of the sequences by WHO, weakens their complaints about China not sharing samples or sequences, when WHO and consultants at St Jude, Hong Kong University, and Weybridge are hoarding thousands of H5N1 sequence collected this year, including human cases as indicated above.

The hoarding labs have failed to understand how these changes are acquired and continue to call them random mutations. The changes at position 182, described above corresponds to position 186 in the H3 numbering system. The change of asparagine to lysine, N186K, creates a match with position 186 in the human influenza B. This match is not mentioned in the Nature paper.

Moreover, the public sequences from the index case in Iraq, also has a change at this position. This change, N186S, is found in the 1986 human pandemic sequence from Hong Kong, which also points toward its role in binding to human receptors. The S at position 186 is also found in H3N8 sequences from dogs and horse, again pointing toward a role in recognizing mammalian receptors.

These changes in Qinghai isolates are important, because another mammalian polymorphism, PB2 E627K, has become fixed in the Qinghai strain. This change is found in all human flu isolates and the change creates higher polymerase activity at lower temperatures (34 C).

The Nature paper also found S227N one of the patients in Vietnam, and receptor binding by S227N was enhanced by Q196R. S227N has also been found in two of the human isolates from Turkey, as well as one from Egypt, which are more examples of changes in the receptor binding domain in Qinghai isolates that have E627K.

Thus, the number of changes in the receptor binding domain, or regions adjacent to the receptor binding domain. The recent fatal case in Egypt, had M230I, which creates a change that matches all three human strains currently in circulation, H3N2 and H1N1 serotypes in Influenza A, as well as Influenza B.

The co-circulation of N186K, Q196R, S227N, and M230I in Qinghai strains which also have PB2 E627K remains a cause for concern, as WHO continues to hoard H5N1 sequences and continues to isolate H5N1 in chicken eggs, selecting against H5N1 isolates with the acquisition of these mammalian polymorphisms (the second sequence submitted to Genbank from the patient in Thailand has lost N186K).

Media sources

Phylogenetic Trees

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[Ganseerpel]

Re: Nature - HA mutations responsible for the binding of H5N1 A viruses

In VN 1194 (GenBank) I get the following numbering:

starting at pos 160 up to pos 239 (h5 numbering) example: A/Vietnam/1194/2004

H5: 179 (=H3: 183) | H5:N182K (=H3: N186K)|H5: E186 (=H3: E190)| H5: Q192R (=H3 Q196R)| H3: Q226 (=H5: Q222)H HPSDAAEQTR LYQNPTTYIS VGTSTLNQRL VPKIATRSKV NGQSGRMEFF WTILKPNDAI <?xml:namespace prefix = o ns = "urn:schemas-microsoft-comhttp://www.flutrackers.com/forum/ /><o:p></o:p>[/FONT][/COLOR]</U>[/B]
*
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[HenryN]

Re: Nature - HA mutations responsible for the binding of H5N1 A viruses

In VN 1194 (GenBank) I get the following numbering:

starting at pos 160 up to pos 239 (h5 numbering) example: A/Vietnam/1194/2004

H5: 179 (=H3: 183) | H5:N182K (=H3: N186K)|H5: E186 (=H3: E190)| H5: Q192R (=H3 Q196R)| H3: Q226 (=H5: Q222)H HPSDAAEQTR LYQNPTTYIS VGTSTLNQRL VPKIATRSKV NGQSGRMEFF WTILKPNDAI [FONT=[/IMG]IKRSYNNTNQ]<font color=" /><?xml:namespace prefix = o ns = "urn:schemas-microsoft-comhttp://www.flutrackers.com/forum/ /><o:p></o:p>[/FONT][/FONT][/U][/B]
*
[B]<font color=" /><o:p></o:p>[/B][/quote]</U>[/COLOR][/COLOR]
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[COLOR=maroon][COLOR=black][FONT=Courier New][U]Yes, that is correct. If you add 4 to the positions in the Nature paper, you will get the H3 number (S223N in Nature is S227N in H3 numbering.
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[gsgs]

Re: Nature - HA mutations responsible for the binding of H5N1 A viruses

so WHO, the Japanese researchers, probably also Osterhaus,Palese
and the 16 WHO-reference laboratories all knew about these
mutations since spring but didn't say anything about it all the time ?

Nor do they admit or comment about this policy in public.

Is this current policy of WHO and the world's leading researchers
and experts and officials to keep such information secret ?

Are there clear directives whether and when evidence for the
start of a pandemic will be made public or which people
will be told about it and when ?

Or are these directives, if they exist, secret as well ?

Has someone asked these questions to WHO and associated
laboratories or is the whole subject somehow taboo and
journalists shall not report about it ?

I have seen nothing about this subject so far, except
from niman.
Isn't this an important issue, which should be discussed now ?
Yes, they were hording sequences all the time since years
and this was discussed and critisized earlier this year
and it is improving. But those important informations are also
kept secret and I think it's a new development and I'm not happy
about it.

 

[gsgs]

Re: Nature - HA mutations responsible for the binding of H5N1 A viruses

it needn't be done in the USA. Other countries are less restrictive.

Such research have strong security issues & are strongly monitored by nationals security services.

See the FAS (federation of american scientist) pedagogic module about thoses dual-uses research. They are affiliated with the americans intelligence networks.

Their key example, the mouse pox virus case study. outch.

http://www.fas.org/biosecurity/education/dualuse/index.html

That must be why they did artificials reassortant with old human virus by reverse genetics in this study, they probably know from the CDC reassortment study that such reassortment virus replicate poorly and thus reducing the experiment danger.

 

[AlaskaDenise]

Re: Nature - HA mutations responsible for the binding of H5N1 A viruses

Did someone see the use they did with ??



migh be this the active ingredient of elderberry ?

By binding to human receptor they prevent the virus attatchment...maybe

I found that in a lot of reading last winter. It appeared to be used solely as a stain. I wonder if they're aware of it's antiviral properties?

.

 

[HenryN]

Re: Nature - HA mutations responsible for the binding of H5N1 A viruses

Commentary at

http://www.recombinomics.com/News/11190601/H5N1_RBD_Middle_East.htmlhttp://www.recombinomics.com/News/11180602/H5N1_RBD_Negatives.html

 

[wetDirt]

Re: Nature - HA mutations responsible for the binding of H5N1 A viruses

So, does this mean the hidden Indonesian reservoir could still be in the chickens, but in a virus strain that does not culture in eggs? If they ran the chicken tests in MDCK cells, would they get a different picture?

 

[AlaskaDenise]

Re: Nature - HA mutations responsible for the binding of H5N1 A viruses

Commentary at

http://www.recombinomics.com/News/11180602/H5N1_RBD_Negatives.html

False Negatives for H5N1 Receptor Binding Domain Changes?
Recombinomics Commentary
November 18, 2006

A/Vietnam/30262III/04 and A/Vietnam/3028II/04 contained a heterogeneous mixture of HAs on sequence analysis, prompting us to plaque-purify the viruses in Madin?Darby canine kidney (MDCK) cells to obtain viral clones with distinct HA sequences

Moreover, two of these changes, lysine at position 182 and arginine at position 192, were present in the HAs of clade-2 H5N1 viruses isolated from two individuals in Azerbaijan and one individual in Iraq, but not in any of the more than 600 avian isolates examined.

The above comments, describing isolates that had several of the changes that increased receptor binding, suggest that false negatives may mask the prevalence of such changes in avian populations.

The receptor changes were identified by isolating the H5N1 on mammalian cells, which select for H5N1 with mammalian receptor specificity. It is known that growth of flu in chicken eggs can lead to the loss of mammalian specific sequences, which may account for the failure to detect these changes in avian isolates.

The history of S227N positive H5N1 isolates is instructive. S227N was first identified in two human H5N1 isolates, A/Hong Kong/212/03 and A/Hong Kong/213/03, from a father and son who had traveled to Fujian province in 2003. The H5N1 was isolated on MDCK mammalian cells, as described above for the human Vietnam isolates.

The increased affinity of these two isolates for mammalian receptors led to a warning in October, 2005 that donor sequences for the formation of S227N were present in H9N2 isolates in the Middle East. In January, 2006, the first confirmed human Qinghai case was announced, and the isolate, A/Turkey/12/2006, was positive for S227N. However, the isolate from his sister, A/Turkey/15/2006 was negative for S227N, although another human isolate from Turkey, A/Turkey/65596/2006, was also positive for S227N, while a fourth isolate, A/Turkey651242//2006 was also negative.

The data for the three clones from A/Vietnam/3028II/04 provide an explanation for the detection of S227N in two of the four isolates from Turkey. Even though the isolates from Vietnam were grown on mammalian MDCK cells, only clone 3 had S227N, as well as Q196R. Neither polymorphism was in clone 1 or clone 2, although both had position 138 polymorphisms (A138A and A138T, respectively). Clone 2 also had N248S. Thus, S227N was only found in one of three clones from the same patient, even though all isolates were obtained using the same mammalian cell line in the same lab.

This variation using MDCK cells raises the string possibility that other changes that increase affinity for mammalian receptors and decrease affinity for avian receptors. might be lost during isolation, especially if the isolation is in chicken eggs.

Difference were also seen in sequences from the patient in Thailand, A/Thailand/1-KAN-1/04. The original sequence had both G143R and N186K. However, that sequence was replaced with a sequence that had only G143R. G143R is present in H5N1 avian sequences. N186K is only in human isolates, including influenza B.

These data suggest that the failure to find some of the receptor binding domain changes in avian isolates, may be linked to the use of chicken eggs to isolate the virus. The receptor binding changes described in humans in Vietnam, Thailand, Hong Kong, Turkey, Egypt, Azerbaijan, and Iraq have not been described in human H5N1 from Indonesia, but Hong Kong and the CDC labs use chicken eggs to isolate the human H5N1 from Indonesia, which may select against the changes that increase affinity for mammalian receptors.

Isolation of both human and avian H5N1 on mammalian cells may be useful.

.

 

[HenryN]

Re: Nature - HA mutations responsible for the binding of H5N1 A viruses

So, does this mean the hidden Indonesian reservoir could still be in the chickens, but in a virus strain that does not culture in eggs? If they ran the chicken tests in MDCK cells, would they get a different picture?

Yes. in Indonesia, they are flying blind.

 

[HenryN]

Re: Nature - HA mutations responsible for the binding of H5N1 A viruses

Commentary at

http://www.recombinomics.com/News/11180602/H5N1_RBD_Negatives.html

 

[MHSC]

Re: Nature - HA mutations responsible for the binding of H5N1 A viruses

Qinghai H5N1 Receptor Binding Domain Changes In Middle East
Recombinomics Commentary
November 19, 2006

Moreover, two of these changes, lysine at position 182 and arginine at position 192, were present in the HAs of clade-2 H5N1 viruses isolated from two individuals in Azerbaijan and one individual in Iraq, but not in any of the more than 600 avian isolates examined.

The above comments indicate that two of the changes that increase receptor binding are found in additional human H5N1 Qinghai isolates in the Middle East, The changes above, which correspond to positions 186 and196 in the H3 numbering, are in addition to S227N and M230I, which have also been detected in Qinghai isolates in Turkey and/or Egypt.

Previously, attention had been focused on positions 226 and 228 which had become Q226S and G228L in human H3N2. However, Q226 and G228 were in initial H2N2 human isolates in 1957 at the beginning of that pandemic, and Q226 and G228 are in current influenza B, and they are in virtually all influenza B sequences, which include isolates from 1940 through 2006. Moreover, the recent H5N1 from Egypt has M230I, which is in all three current serotypes, H3N2, H1N1 and influenza B. M230I in influenza B creates a five amino acid stretch of identity between H5N1 and influenza B (QSGRI). Moreover, influenza B has N186K, which as indicated above is also in Qinghai isolates in Azerbaijan and Iraq.

Although the Azerbaijan and Iraq sequences described above are being hoarded in the WHO database, and are not public, the only public human H5N1 sequence from Iraq also has a change at position 186 except the change is from N to S (N186S). This change is also found in the initial H3N2 isolates associated with the beginning of the 1968 pandemic. Moreover, it is also H3N8 sequences from dogs and horses. The dog H3N8 is easily transmitted from dog to dog, highlighting its presence in additional mammalian species. It has also been found in a recently released 1997 H5N1 isolate from Hubei, A/chicken/Hubei/wi/1997.

The presence of Q196R in the Middle East is also a concern, because it synergizes with S227N, which has been detected in human H5N1 in Turkey and Egypt. Thus, in addition to the mammalian polymorphisms, PB2 E627K, the Qinghai isolates in the region have N186K, N186S, Q196R, S227N, and M230I. These polymorphisms are either linked to increases in affinity for human receptors, or have been found in human isolates, suggesting various combinations can lead to more efficient human to humans transmission. Since all are on the Qinghai strain, recombination between these sequences, can be expected, as has been seen previous in H5N1 HA cleavage site as well as the receptor binding domain.

These co-circulating polymorphisms in Qinghai isolates in the Middle East. create additional concerns.

Media sources

Phylogenetic Trees

 

[vinny]

Re: Nature - HA mutations responsible for the binding of H5N1 A viruses

dr niman first of all hi,i just wanted to say thanks for explaining things to us and for all your time and help.what i wanted to ask was if its ok is there any more news on whats happening and is the virus getting closer to becoming H2H,on the other site(ce),not sure if youve seen it they are running a poll over when they think it will happen and most votes go for march next year,do you think it will be this long away yourself.??

 

[sharon sanders]

Re: Nature - HA mutations responsible for the binding of H5N1 A viruses

Welcome Vinny.

 

[HenryN]

Re: Nature - HA mutations responsible for the binding of H5N1 A viruses

dr niman first of all hi,i just wanted to say thanks for explaining things to us and for all your time and help.what i wanted to ask was if its ok is there any more news on whats happening and is the virus getting closer to becoming H2H,on the other site(ce),not sure if youve seen it they are running a poll over when they think it will happen and most votes go for march next year,do you think it will be this long away yourself.??

Nailing a pandemic down to a given day or month isn't very realistic, and those polls really have zero validity or reliability.

However, the receptor binding domain changes are accumulating rapidly, and birds are flying into the area, so I expect more to come this season, and the more to come will be this winter, not next spring.

 

[vinny]

Re: Nature - HA mutations responsible for the binding of H5N1 A viruses

hi florida thanks for the welcome,its very kind of you.

 

[vinny]

Re: Nature - HA mutations responsible for the binding of H5N1 A viruses

thank you dr niman for answering my question.can i ask one more question please,when you said in your reply, more to come this winter do you mean the human pandemic.??