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Tracking the next pandemic: Avian Flu Talk

New Suspect H5N1 Bird Flu Cluster in Bandung Indon - Event Date: May 29 2006
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    Posted: May 29 2006 at 6:23pm
Recombinomics Commentary
May 29, 2006

The patient, according to him, has been given by medical treatment and was done by the inspection of blood, the throat and other. The sample of the patient's inspection will be sent to Jakarta, on Monday (29/5) and when positive results, will be given by medical treatment in the first stage. "Hopefully, his condition continued to improve.

Moreover tomorrow him, on Friday (26/5), his brother-in-law who worked as the driver in a company, has wrought again as usual. However, on Saturday (27/5), his brother-in-law again was hot and breathless. Finally my brother-in-law was brought to the community health centre. "But from puskemas even was reconciled to RSHS Bandung," he revealed.

It was further that LK explained, his brother's family and himself did not maintain the poultry, like the chicken or birds. However the neighbour in his house environment, indeed many that maintained the chicken. Moreover, in his area also had the poultry farm. Nevertheless, had not spread the news had the chicken that died.

But on Saturday, last May 27 had the chicken inspection from the Livestock Breeding Service. These chickens were gathered from each RT. results of the inspection, he said had eight positive chickens was affected by bird flu and was destroyed

The above translation describes a new suspect H5N1 bird flu family cluster in Bandung in West Java.  The new cluster is near the fatal familial cluster that was just confirmed by WHO.  The new WHO website shows the earlier confirmed H5N1 positive cases in West Java, which has had 13 cases of which 10 were fatal..

H5N1 isolated from these patients has a novel cleavage site, as do most of the isolates from Jakarta and Tangerang.

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These new cases cover large geographical regions in Indonesia and involve at least two different versions of H5N1.  The cases in West Java have a novel cleavage site RESRRKKR, which has not been reported in poultry, raising concerns of Mammalian reservoir.  In contrast the large cluster in Sumatra appears to be related to the wild type H5N1 cleavage site sound in birds in Indonesia, RERRRKKR, which has bee found throughout Asia.
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Originally posted by PonyGirl PonyGirl wrote:

These new cases cover large geographical regions in Indonesia and involve at least two different versions of H5N1.  The cases in West Java have a novel cleavage site RESRRKKR, which has not been reported in poultry, raising concerns of Mammalian reservoir.  In contrast the large cluster in Sumatra appears to be related to the wild type H5N1 cleavage site sound in birds in Indonesia, RERRRKKR, which has bee found throughout Asia.

Would someone explain to me what a cleavage site is?
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Post Options Post Options   Thanks (0) Thanks(0)   Quote Guests Quote  Post ReplyReply Direct Link To This Post Posted: May 29 2006 at 6:59pm
its part of the H as in H5N1 its hemagglutinin
 
The hemagglutinin gene plays a key role in defining virulence in avian influenza
 
thats where it sticks to your throat or lung molecules and infects you
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Points: 265 		Post Options Post Options   Thanks (0) Thanks(0)   Quote Linda Quote  Post ReplyReply Direct Link To This Post Posted: May 29 2006 at 7:00pm
the media link doesn't work.....link please
Insanity is making the same mistakes and expecting different results....therefore...Those who don't learn from history are bound to go insane.
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Figure 1. Ribbon representation of the hemagglutinin HA0 trimer from the 1918 influenza virus. Each monomer possesses two important sites: 1) the 'Receptor binding site' (blue shade) for virus attachment to the host lung epithelial cells via sialic acid containing host cell receptors. 2) the 'Cleavage site' where for full infectivity, the single chain (HA0) is cut into two chains (HA1 colored red and HA2 colored green). At the N-terminal end of the HA2 chain is the fusion peptide which is critical for subsequent membrane fusion events that lead to infection. The 1918 HA monomer also possesses 2 basic patches (orange shade) which may have contributed to the increased infectivity observed during the pandemic.

In 1918, a Great Flu Pandemic swept the

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Post Options Post Options   Thanks (0) Thanks(0)   Quote Guests Quote  Post ReplyReply Direct Link To This Post Posted: May 29 2006 at 7:10pm
http://*************/forum/showthread.php?t=6591

This is the media link from Dr. Niman's article.

Interesting - I posted the link directly from Dr.Niman's source; I pasted it correctly here, but when I opened it to check, it brought me back to the Avian Flu Forum. Question: My error posting? or censorship? Albert, do you have the answer?
    
http://*************/forum/showthread.php?t=6591

here is the link to be cut and pasted; maybe this will get through.

Nope, it got changed too; I feel like Alice. This is getting curiouser and curiouser. Anyone know how or why this happens?
    
Okay, last shot. The missing link, (the asterisks) refer to AFT. Fill in the blanks with 3 w's at the beginning and a com at the end and you will have the media link for Dr. Niman's post.   
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Post Options Post Options   Thanks (0) Thanks(0)   Quote Guests Quote  Post ReplyReply Direct Link To This Post Posted: May 29 2006 at 7:21pm
I give up. This is creepy, no it is downright scary. I had referred to a site about BF and the name I put was changed to AFT. This must be an automatic program; it was too quick to have been somebody changing it.

If we can't even get correct info here, research information, follow sources, where does that leave us? I had had trust in this site and those running it. What gives? Please convince me I am having hallucinations!
    
I checked and the other two links in PonyGirl's post from Dr. Niman worked; they referred back to his Recombinomics Site. I guess that one is permitted . . why not others? Aren't we here to share and help each other get through this looming catastrophe? By "each other" I mean all those prepping and those we hope to convince to prep, not just those who post on this site. After all, I have seen many of the names who frequent AFT on other forums too, what's the problem? I really want to know. Please help!! someone??
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The thing is that a link that pots back to Dr. Nimans site still doesn't give us info on where his info is coming from. I have not found any other source that says the cleavage site has changed. 
Insanity is making the same mistakes and expecting different results....therefore...Those who don't learn from history are bound to go insane.
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Originally posted by Kilt Kilt wrote:

its part of the H as in H5N1 its hemagglutinin
 
The hemagglutinin gene plays a key role in defining virulence in avian influenza
 
thats where it sticks to your throat or lung molecules and infects you


I thought the cleavage site was the receptor for the cell...like a lock and key and that right now it had a key to lock into the lower lung but if it changed it could lock into the upper respiratory tract making it easier to pass H2H...is this correct?
Insanity is making the same mistakes and expecting different results....therefore...Those who don't learn from history are bound to go insane.
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Rutsuyasun - The problem is fixed. 
 
Thanks.
 
Smile
 
 
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the lower lung tissue is like that of a chicken especially in children
 
its not too but a leap to adapt to human upper lung tissie and throat tissue
 
we are very close to a pandemic
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Post Options Post Options   Thanks (0) Thanks(0)   Quote Guests Quote  Post ReplyReply Direct Link To This Post Posted: May 29 2006 at 9:38pm
Many viruses have membrane glycoproteins that are activated at cleavage sites containing multiple arginine and lysine residues by cellular proteases so far not identified. The proteases responsible for cleavage of the hemagglutinin of fowl plague virus, a prototype of these glycoproteins, has now been isolated from Madin-Darby bovine kidney cells. The enzyme has a mol. wt of 85,000, a pH optimum ranging from 6.5 to 7.5, is calcium dependent and recognizes the consensus sequence R-X-K/R-R at the cleavage site of the hemagglutinin. Using a specific antiserum it has been identified as furin, a subtilisin-like eukaryotic protease. The fowl plague virus hemagglutinin was also cleaved after coexpression with human furin from cDNA by vaccinia virus vectors. Peptidyl chloroalkylketones containing the R-X-K/R-R motif specifically bind to the catalytic site of furin and are therefore potent inhibitors of hemagglutinin cleavage and fusion activity.
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Post Options Post Options   Thanks (0) Thanks(0)   Quote Guests Quote  Post ReplyReply Direct Link To This Post Posted: May 30 2006 at 12:08pm
Originally posted by Linda Linda wrote:

The thing is that a link that pots back to Dr. Nimans site still doesn't give us info on where his info is coming from. I have not found any other source that says the cleavage site has changed. 

    

This is the original source for Dr. Niman's info. (toggletext-ed from Indonesian:)
www.pikiran-rakyat.com/cetak/...06/29/0202.htm

The above link was cited by the forum that "trackers" the progress of the "flu" (when I put their name in it gets changed to AFT) at the following link:

http://*************/forum/showthread.php?t=6591
(substitute the correct forum name for the above asterisks and it should take you there. I am trying to get around this glitch that keeps replacing what I type with AFT or asterisks)

I hope this works this time; Albert said the problem was fixed.
    
    
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Post Options Post Options   Thanks (0) Thanks(0)   Quote Guests Quote  Post ReplyReply Direct Link To This Post Posted: May 30 2006 at 12:10pm
Originally posted by Albert Albert wrote:

Rutsuyasun - The problem is fixed. 

 

Thanks.



I'm afraid not, Albert. See the last post I made at approx. 3:04pm EDT.
Again the forum that should be referenced here was changed to AFT and in the link it was repaced by asterisks !!?? Can you help?
    
    
    
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I would say this is all conjecture until the sequences are released.
 
Commentary
 
H5N1 Sequence Analysis of North Sumatra Cluster

Recombinomics Commentary
May 25, 2006

The CDC head said the genetic sequencing of viruses from the cluster so far has yielded four main findings:

The isolates are all "virtually identical," implying a single source.

They are susceptible to the antiviral drug Tamiflu (oseltamivir).

"There is no evidence of motif changes in the particular areas of the genes that are responsible for how the virus binds to the respiratory tract of people."

The isolates are very similar to viruses previously collected from poultry in the region.

The above comments from the CDC are similar to comments from Hong Kong.  Both groups receive human samples from Indonesia as indicated in the WHO update.  However, as with the earlier WHO updates, more information is available from what is not said in the reports. 

Since only part of human sequence has been made public (HA and NA from the first confirmed case in July of 2005), more sequence interpretations come from short and well parsed comments, such as those above.

The first two confirmed cases in Indonesia were associated with short descriptions which contained subtle differences. 

The released sequence from the first case in 2005 (suburb of Jakarta) has a novel cleavage site (RESRRKKR), which is why it was not called “virtually identical” but was said to have ”high homology” with poultry sequences, which have the more common cleavage site (RERRRKKR). 

The second sequence in 2005 (Jakarta) was called “essentially the same” as poultry (as opposed to essentially the same as the first human sequence), indicating it had the RERRRKKR cleavage site.  Thus, there were two sequences in human cases in the Jakarta area. 

A subsequent report (Jhetta did not find info reporting RESRRKKR in Sumatra cluster here... help me out) indicated all human sequences from the area had RESRRKKR which did not match any known poultry source, which created a problem since all WHO updates indicated the human cases were linked to H5N1 in poultry. 

The only animal in the Jakarta area with a sequence with RESRRKKR was not a bird, but a cat, raising serious questions about origins and transmission, since many of the patients in the area were from familial clusters with 5-10 day gaps, indicating human-to-human transmission (H2H).  These clusters included both of the above sequences, indicating both cleavage sites were linked to H2H, but only one was linked to poultry.

The comments above indicating that the sequences from the Sumatra cluster were “virtually identical” to each other and “very similar” to poultry isolated previously from the area indicates a poultry source infected the index case, but the subsequent infections were from the index case or other family members and the normal incubation time of 2-5 days suggests that there were multiple transmissions within the family that were not linked to the index case.

The cleavage site would be the common poultry sequence of RERRRKKR, but the failure to mention amantadine sensitivity suggests the cluster sequences were amantadine resistant, as has been seen previously in poultry isolates from Indonesia.

Thus, the only antiviral mentioned was Tamiflu susceptibility, and the United States is shipping Tamiflu to “Asia”.  However. local media reports indicate that the patients in the cluster were treated with 3 X 75 mg Tamiflu, and all but one died, even though the later cases seem to have been hospitalized shortly after developing symptoms.  The exact times are not clear because the onset dates for all relatives other than the last fatality, who refused Tamiflu treatment, were not included in the WHO update.

The “resistance” to the Tamiflu treatment may have been due to another change, which is not related to the receptor binding domain, which the above comments indicate the human isolates match an avian motif. 
 
That change, which has been seen in H5N1 human cases in Asia as well as dog and wild and domestic cat sequences in Thailand, is PB2 E627K, which may be why the cluster sequences are “virtually identical” to each other, but “very similar” to the poultry sequences, which have not been reported to have PB2 E627K. 

The only bird H5N1 sequences with E627K are the Qinghai strain, which is quite distinct from Indonesian bird or human HA and NA sequences (no other human genes have been released from Indonesia)..

The accuracy of the above analysis can be easily determined by simply releasing the full Indonesian sequences, which have been sequestered at the private WHO database at Los Alamos since August of 2005.

Media Link

Map


PB2 amino acid at position 627 affects replicative efficiency of Hong Kong H5N1 influenza A viruses in mice.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15016548

Shinya K, Hamm S, Hatta M, Ito H, Ito T, Kawaoka Y.

Department of Pathobiological Sciences, University of Wisconsin, Madison, WI 53706, USA.

A single amino acid substitution, from glutamic acid to lysine at position 627 of the PB2 protein, converts a nonlethal H5N1 influenza A virus isolated from a human to a lethal virus in mice. In contrast to the nonlethal virus, which replicates only in respiratory organs, the lethal isolate replicates in a variety of organs, producing systemic infection.
 
Despite a clear difference in virulence and organ tropism between the two viruses, it remains unknown whether the dissimilarity is a result of differences in cell tropism or the reduced replicative ability of the nonlethal virus in mouse cells in general. To determine how this single amino acid change affects virulence and organ tropism in mice, we investigated the growth kinetics of the two H5N1 viruses both in vitro and in vivo. The identity of the PB2 amino acid at position 627 did not appreciably affect viral replicative efficiency in chicken embryo fibroblasts and a quail cell line; however, viruses with lysine at this position instead of glutamic acid grew better in the different mouse cells tested. When the effect of this substitution was investigated in mice, all of the test viruses showed the same cell tropism, but infection by viruses containing lysine at position 627 spread more rapidly than those viruses containing glutamic acid at this position.
 
Further analysis showed a difference in local immune responses: neutrophil infiltration in lungs infected with viruses containing lysine at position 627 persisted longer than that associated with viruses lacking a glutamic acid substitution.
 
Our data indicate that the amino acid at position 627 of the PB2 protein determines the efficiency of viral replication in mouse (not avian) cells, but not tropism among cells in different mouse organs. The presence of lysine leads to more aggressive viral replication, overwhelming the host's defense mechanisms and resulting in high mortality rates in mice.

PMID: 15016548 [PubMed - indexed for MEDLINE]"
 
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