From Flu Wiki 2

Forum: Retracted Sequences

16 June 2006

Monotreme – at 22:12

To continue discussion of retracted sequences and separate from polymerase accuracy.


A group of H5N1 sequences have been removed from GenBank. These sequences were deposited by a Chinese group and relate to isolates from pigs. Removing sequences from GenBank is extremely rare, as anyone with slightest experience with GenBank can confirm. I would suggest that given concerns about mammalian reservoirs, the role of bad vaccines in generating the particularly nasty form of H5N1 currently circulating, the fact that Chinese citizens are being infected with H5N1 with no obvious source, any retraction of H5N1 sequences from China is significant and should be investigated. At the very least, it would be worth asking the scientists involved why they took the highly unusual step of retracting the sequences.


Note, I am traveling for the next 10 days and have very limited access to the internet. “Quietness” on my part should not be construed as agreement with Dr. Niman or anyone else.

DemFromCTat 22:17

I would never take “quietness” on your part as agreeing with me. ;-)

Monotreme – at 22:23

DemFromCT, you’re not the one making that claim ;-) And you know me better than most.

Grace RN – at 22:28

Monotreme-when were they deposited and when removed? Were they deposited/removed by the same person(s)?

DemFromCTat 22:32

Before we get into a Niman-Monotreme argument, let’s just consider the absence or retraction of sequences a question to be asked in and of itself, independent of whether it is germaine to a different point niman was making on a different thread. This is not an invitation to rehash that.

Hurricane Alley RN – at 22:32

Monotreme - at 22:23

Have a nice trip and don’t loose any tail feathers in the process. Another way of saying this - Get your butt back here in one piece. gina

De jure – at 22:46

Monotreme, hopefully your trip won’t take you near China? We can’t afford to have you disappear!

Many Cats – at 22:49

Or come down with anything. :)

Leo7 – at 23:00

Monotreme:

Goes without saying some of us have other jobs and can’t instantly rebute a challenge. I’m in complete agreement with you, and I find the statement that sequences are deposited and often get removed or changed at whim, incredible. That cetainly doesn’t seem to support the concept of a scientific data source, and does not establish a sense of trust or reliability in the scientists that post, use, or remove them. Changes removed according to the Genebank policy are absoulutely acceptable, otherwise no. This isn’t the scientific process taught at even the most basic level and the removal didn’t follow policy (at least the way it looks now). A physician conducting clinical research can’t white out data to correct an error on a form. They must strike through it, but allowing it to remain legible, write error, date, time and initial it before inserting correct data. These steps ensure quality and validity. If this is the data a vaccine is based on it will be flawed before it ever reaches a single human. I agree a query should be considered.

beehiver – at 23:17

Could somebody please direct me to a place where I can get up to speed on what has transpired regarding retracted sequences? Thanks.

DemFromCTat 23:24

that would be here (Monotreme – at 01:08) and here (part 2).

Monotreme – at 23:31

Thanks all for good thoughts.

DemFromCT provided appropriate links. The sequences were removed 6 weeks after they were deposited (yesterday) by the people who submitted them, Chinese researchers. The reason given was that the sequences could not be confirmed.

beehiver – at 23:50

Yikes, quite a bit of reading, so I will jump in to say thanks DemFromCT for your reply. The forum gets so busy it’s hard to keep up!

Hurricane Alley RN – at 23:54

Monotreme,

See what happens when you open up a can of worms or was it just coincidence?

They did all that work just to have to pull it. Shame on you.};) gina

Tom DVM – at 23:55

Monotreme. Having interacted with professionals most of my life, it’s pretty obvious to me how this debate is going to turn out.

You have already shown that you are way out ahead of the pack.

Just make the data dance…you can do it…once again what is coming up on these types of threads does not make common sense and you will explain exactly why…after some time for analysis and reflection…

…Wish I could help but this stuff makes no sense to me…to study it more would make my head hurt and remind me and give me nightmares about being back in university. Thanks

Tom DVM – at 23:57

Thans Gina…and speaking about the worms of weybridge, did you notice who signed the document with Dr. Capalari on the News Thread today…congratulations again!!

17 June 2006

Still Open - Tall in MS – at 01:00

Bump - so that ‘Closed BroncoBill’ won’t own the ‘Last 50′ list

I’m-workin’-on-it – at 08:27

bump

anonymous – at 10:11

so, has someone asked the genbank people or the original submitters ?

Monotreme – at 11:34

Thanks Hurricane Alley RN and Tom DVM.

I don’t think NCBI staff (genbank people) would provide any more information than they have already. They respect confidentiality. The people to ask would be the original submitters. I would argue that asking them why they pulled very important H5N1 sequences from GenBank should be a very high priority. If they refuse to explain, I would assume the worst.

Dude – at 13:02

I remember that China kept promissing repeatedly to share all of their sequences with the world. It looks like not only do they prevaricate, they also retract. So what are the range of “reasons” for their behavior. It could be sloppy research…maybe..just does not resonate. It could be economic…if they have the killer sequence early enough, they can be the ones first to market with a vaccine and make a hugh profit. It may be biological war…they don’t want us to figure out what has been done. It may be accidental release…they don’t want us to figure out what has been done. It could be publication/resume building…that would be no sicker than what some others are doing (later crimes agains humanity trials on that issue). It could be the tread started by Monotreme…it hit to close to revealing one of the things they don’t want us to know. In any logic tree I could build I come out with Greed, War, Incompetience, and unprofessionalism. I don’t like any of these conclusions.

anonymous – at 13:04

the worst would be that you’ll turn them into worms or monsters ?

De jure – at 13:06

Rather it looks like some monsters are trying to leave the rest of us for the worms….

Grace RN – at 13:09

Dude at 1302-re: China-my bet’s on the economic angle-with the only vaccine in town, they get the $$ and the power too….

crfullmoon – at 15:39

Monotreme, safe travels to you! (I buy the thread members a round of rootbeer)

18 June 2006

Monotreme – at 00:28

Dude – at 13:02

In any logic tree I could build I come out with Greed, War, Incompetence, and unprofessionalism. I don’t like any of these conclusions.

I agree.

crfullmoon

Thanks. The root beer hit the spot.

De jure – at 09:23

bump.

Monotreme – at 23:45

I just realized I don’t have a link to any of the retracted sequences. Here’s the link to A/swine/Anhui/2004. Other sequences isolated from pigs were retracted - all by Sun,L., Liu,B.H., Zhang,G.H., Huang,Y., Wang,G.H., Xiao,H.X.,Yang,L.M., Wang,Z.F., Huang,W., Zhu,Q.Y., Li,T.X., Liu,J.H., Gao,G.F. and Liu,W.J. of the The Center for Molecular Virology and the Center for Molecular Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, China.

The reason given for the retraction was:

This record was removed at the submitter’s request because the sequence cannot be confirmed.

Again, I will point out that this is extremely unusual. It’s the first time I have ever heard of it happening after many years of depositing and utilizing sequences at GenBank.

19 June 2006

Many Cats – at 00:00

If “the sequence cannot be confirmed” then how much of the H5N1 data may not be real? how much of what we think we know may be based on erroneous data? How does that affect what is versus what was. This could turn much of the speculation regarding sequence conservation into question. As I said, best to monitir reports from MaMa et al. The body count is not easily retracted.

Tom DVM – at 01:01

Monotreme. What is your opinion as to why these sequences were removed form the website?

niman – at 05:09

The sequences (40 H5N1 of them from 5 swine isolates) were pulled by the owner. Occasionally, sequences are released prematurely - i.e. they are deposited but to be released on publication. These sequnces have not been published.

The sequences were NOT unusual. They were all similar to 24 swine sequences that are H5N1 from China and have not been pulled. The sequences were also internally consistant (isolates 1 and 2 were closest to each orther as were 4 and 5 to each other).

The sequences can still be accessed. Pulling then pretty much eliminates publications by others and creates several tin foil thread on Flu Wiki.

anon_22 – at 06:23

Not having data for the frequency of sequences being pulled is cause for concern.

niman – at 06:33

Why, these are unpublished and the number of sequences at GenBank or on hard hard drives has always been high,

For H5N1 it is higher however because H5N1 has migrated to many new locations. Ian Bown alone has listed [[http://www.recombinomics.com/phylo/Brown_Italy_1.html|73 from 2006}}, but only ONE is public at GenBank,

De jure – at 09:09

Niman at 05:09: “Occasionally, sequences are released prematurely - i.e. they are deposited but to be released on publication. These sequnces have not been published.” Dr. Niman, how many are we talking about? What is your definition of “occasionally”? Is there an agreement, written or otherwise with GenBank, that GenBank will keep the sequences separate and unaccessible until the sequences are published? Does anyone know?

niman – at 09:14

The vast majority of sequences at GenBank are deposited pending publication. These are the conditions of deposit.

niman – at 09:16

To identify sequences deposited pending publication, just compare deposit date and date on characterization sheet when the sequences first come out.

Monotreme – at 12:46

Tom DVM,

I think the sequences were pulled because of the implications of the HA gene in two of the isolates being identical - across 2 years. The clear implication for every flu scientist except Dr. Niman is that there is something wrong. There may be a trivial explanation such as mislabeling or lab contamination. If these trivial explanations are not correct then a lab escapee is the most likely explanation, IMO.

Dr. Niman,

As far this being a tinfoil thread, could you please provide a link to your commentary on the origins of WSN/33 in pigs?

TreasureIslandGalat 12:59

Not to be a simpleton in this argument, but could the posting have literally just been an error? I mean, most likely these guys use Admin Assistants to do the majority of their filing, paperwork, communications, etc.

The sequence file is probably named very similarly to other swine sequences. Possibly the person posting up the file to the GenBank merely selected the wrong sequence. Literally posting an old sequence up instead of a newer file. The posting date would look new but the data was old.

Littel things like that happen so often. Maybe someone just noticed it when they went doing a littel research. Possibly they were aware of what the data *should* have said and so alerted the necessary persons to “pull it” until the proper file could be uploaded.

I am always catching database snaffoos and badly uploaded files at work. It happens.

Monotreme – at 12:59

Some clarification, as there appear to be deliberate attempts at obfuscation, sad to say.

It is possible to deposit sequences in GenBank with a hold on public release of the sequences. This is becoming increasingly less common, but it does occur. There is a published protocol for acheive this. This is not what happened in the case of the Chinese pig isolates. The sequences had been released for 6 weeks before they were retracted. So, we are expected to believe that the sequences were public for 6 weeks before the H5N1 experts who released them realized their mistake? Or did they deposit them in some sort of trance and coincidentally come out of the trance when it was suggested that one of the sequences might suggest a lab escapee? Really!

I feel the need to repeat the following:

The reason given for the retraction was: This record was removed at the submitter’s request because the sequence cannot be confirmed.

Again, I will point out that this is extremely unusual. It’s the first time I have ever heard of it happening after many years of depositing and utilizing sequences at GenBank.

anon_22′s point about how often this occurs out of the millions of sequences at GenBank is well-taken.

TreasureIslandGalat 13:00

I also catch my consistent inability to properly type the word “little”! haha

Monotreme – at 13:04

Some interesting links from Recombinomics

Flu Bioterrorism?

Have Bioterrorists Infected Swine in Korea with Human WSN/33?

WSN/33 Chronology


Dr. Niman, have you had a change in heart regarding this issue? If so, what prompted it?

TreasureIslandGalat 13:06

Monotreme,

Did they retract the listing right after you announced that it was identical to an earlier release? -or did the retraction occur prior to you pointing that out? -taking into account the time change, is it verifiable based on any date/time pulled listing on GenBank?

Monotreme – at 13:07

TreasureIslandGal, there is a protocol for correcting sequences. This was not followed. Instead, a batch of sequences were retracted. Very different and highly unusual procedure.

Monotreme – at 13:10

TreasureIslandGal, there was a gap of about a day from when I did my first BLAST to confirm Dr. Niman’s finding and when I tried to look for the record again in response to a comment from anon_22. My post and the retraction occurred in between these two events. I don’t know for sure exactly when each one occurred. One thing is for sure, the retraction definitely occured after Dr. Niman called attention to the identity of the two sequences.

FrenchieGirlat 13:15

Monotreme — at 13:10 - I quote from Dr. Niman’s own comments on the way things happened, if the “sequence” (no pun intended) of posts is enlightening:

niman – at 12:30
Just to clarify the relationship of this thread to the pulled sequences, this thread was started on June 14, at 22:09.

I posted the 1707 bp of the pulled H5N1 swine sequence on Jun 14, at 15:54, which was over 6 hours BEFORE this thread was started. At that time I had to use a file with the sequences because the sequences had been pulled from GenBank BEFORE my post and BEFORE ths thread was started. I hadn’t looked at the sequences for several weeks (the recombinomics commentaries were in March), so I don’t know the exact date, but it was aat least six hours prior to the start of this thread.

My post on June 14 post at 15:54 is on the thread linked below\\\

thread

Unquote

ANON-YYZ – at 13:18

Monotreme – at 13:04

Tin foil? No.

I can think of four (4) possibilities:

1. Assessments are correct

2. Incorrect assessments caused by bad logic

3. Incorrect assessments caused by bad data

4. You believe what you want to believe

Any other explanations?

niman – at 13:23

TreasureIslandGal,

The sequences were pulled BEFORE Monotreme started his thread. He says it was mid-June, but I haven’t seen any evidence on that. I analyzed the sequences when they first came out at the beginning of May, so I hadn’t looked at the sequences for about a month. I can say they were public for a week or two. When I looked on June 14th, they were not available from the NIH H5N1 page.

I am not sure when they were pulled. Monotrome seemed to think the pulling was related to his thread, but that DEFINITELY was not the case, since I had gone to the NIH page to double check the sequence I posted. The sequence I used on the 14th was from a file I had created in May, when the sequences were where they were initially.

There were two premises that are incorrect. In early 2005 I gave another example of a swine gene that was EXACTLY the same 5 years later and I have provided MANY examples in the Canadian sequences where long stretches were EXACT matches with sequneces from TWO isolates from 1977.

These examples were used to avoid the nonsense about the wrong sequences being uploaded, or PCR errors, or other dataless hand waving.

Yet the hand waving continues, with or without tin foil hats.

NS1 – at 20:15

Niman,

Thanks for being patient with us. We don’t have the resources or the insight to find the identities with the ease that you do.

Would you mind formatting a message, say with 10 identities, showing the lineages.

Feel free to use the pull swine sequences as one of them.

Describe the two sequences by name, describe the length of the identity and the start nucleotide / protein.

Show some longer and some single polymorphisms.

If you’d like me to format them for you, feel free to email me the results of your search.

niman – at 20:51

Montrome, I really don’t have time to play your tinfoil games. You have acknowledged that the exampels of large sections of identity were present in the examples I gave. They have been written up in recombinomics commnetaries some time ago and each one throws the “random mutation” nonsense into the garbage can. I haven’t seen a reasonable explanation for any, other the frantic handwaving.

A brief review:

An M gene from a 1998 H9N2 swine that is exactly the same as an H9N2 2003 chicken, I believe Hong Kong did the Hong Kong swine sequence and St Jude did the Korean chicken.

The H5 in the 2003 swine is a exact match of the H5 in 2001 swine (both H5N1). The sequences were by two groups in China.

Large portions of a 1997 H1N1 swine sequence from Tennesssee match 2003 and 2004 isolates from Canadian swine (H1N1 and H1N2). The Tennessee sequence was by St Jude and the swine was by Wisconsin. For PA there were 6 differents swine sequences that had staggered matches with 1977 across the gene. For PB2 the identity was with another 1977 swine and was with 5 different Canadian sequences. The same two groups did the sequencing a decade apart.

Any one of the 13 examples above destroys the “random mutation” nonsense. Within these sequences are more EXACT matches with a 1998 sequences from North Carolina and a 2002 sequence from Korea.

The sequence involve 5 different labs and 4 different genes and 12 isolates from two different species.

The lab error or tin foil nonsense are not reasonable responses.

If you have any reasonal explanation, please post. If not, why not start a tin foil thread with an appropriate title.

Tom DVM – at 21:10

Dr. Niman. I can accept the fact that there is a possibility that you are right and the rest of the scientific world is wrong.

But then your credibility falters because you don’t seem to be able to explain your theory to anyone convincingly and secondly, you can’t make your point without insulting others who are interested enough to interact with you and ask you questions.

It seems to me that they are doing you a favour and not visa versa.

20 June 2006

Leo7 – at 00:02

Dr. Niman

Tin foil comments are poking fun at ourselves. Didn’t you see the movie Signs? Lighten up.

NS1 – at 00:24

niman – at 20:51

Can you take those examples and tag them like I mentioned in the 20:15 post? The addition of the labs to each strain was a brilliant insight to reduce our concern on lab contamination.

If you were to rework that post, add the length of each identity and the start position for each identity per strain, then we’d have our questions answered well, even the one at 21:10 from TomDVM.

If you’ll put it in a spreadsheet or write a commentary using your standard format or email the free format info, I’ll be glad to restructure it, send it to you for pre-publication review and then put it on a forum thread and into the Wiki proper so everyone can see the sensibility of what you mean by recombination.

If you do show this info, you’ll even be address Taubenberger’s comments about influenza recombination being unimportant for any pandemic.

Then perhaps, we can get his eyes on the recombination possibility too.

Monotreme – at 00:58

Time scale of events as I remember them.

As you will see, I gave full credit to Dr. Niman for identifying the identity between the sequences. As far as when the sequence was retracted, this is not indicated on the record. I know it had to be after my first BLAST on June 14 and before the late evening of June 15. I can’t be any more precise. Dr. Niman is claiming that the sequence had already been retracted before his post on June 14. Yet I was able to seen both sequences on June 14 after his post. I can’t explain this discrepancy. The record doesn’t specify when the sequence was retracted. Perhaps there were several stages of retraction and I could get it to it from a BLAST but Dr. Niman could not get not get to it by whatever method he was using, I don’t know. Perhaps an enquiry at NCBI could clarify the retraction process.


14 June 2006 Monotreme – at 22:09 Lab Generated H5N1 - An Unpleasant Thought

I am very reluctant to post this, but feel I have no choice.

I have been trying to reconcile Dr. Niman’s theories of recombination with conventional wisdom regarding influenza mutation rates for some time, with no luck. This came to a head today when I BLASTed the sequence he provided at 15:54 on the H5N1 Scientific Forecast 2006 thread. As he claims, this HA sequence is identical between different pig isolates sequenced 2 years apart. To Dr. Niman, this implies a super error free replication of H5N1 nucleotides. This contradicts many published calculated mutation rates for influenza. See here, for example.

I do not believe any virus is capable of error free replication through 2 years of animal-to-animal passage. Yet, Dr. Niman’s report of 100% match between HA sequences isolated 2 years apart is absolutely accurate. Assuming the sequences are correctly labeled, I can think of only one explanation - a virus that had been frozen in the lab, which would stop the clock on mutation, escaped or was released from a laboratory.

One possibility is that various strains of H5N1 were manipulated in a laboratory to make a vaccine. I prefer this explanation to darker possibilities, which I have always rejected in the past.

If anyone can think of a more likely explanation for the available data, please post here. I want to be wrong.

btw, the H1N1 virus that circulates to this day is thought by many virologists to have escaped from a Chinese lab in 1978. It was identical to a virus that not been seen since the 1950s. The assumption was that it had been frozen all of that time until it was thawed for work in a laboratory.

Monotreme – at 01:04

Dr. Niman, the focus of this thread is the retraction of the sequences, not the accuracy of the polymerase complex. I will address your comment about the other identity sequences on the accuracy of flu polymerases thread. I don’t doubt the identities you report, just your interpretation. I will need some time to extract the relevant information.

As regards tinfoil, please respond to my post at 13:04. I genuinely want to know the answer. I think it is germane to the topic of this thread.

Monotreme – at 01:12

Tom DVM, thanks. You and I agree on most things, but not everything, but we are able to have spirited but civil discussions. Same goes for DemFromCT and anon_22.

Leo7, thanks to you also. One person’s conspiracy theory is someone else’s reasonable hypothesis. In the end, only the facts count.

My goals for this thread is to call attention to the retraction of important H5N1 sequences, point out how unusual this is, and try to stimulate an investigation of the reason for the retraction. I don’t think this is unreasonable - given the stakes.

NS1 – at 07:48

Monotreme – at 13:04

I wondered, because of the tone, of some odd change of heart. But the more I thought about it, I felt that it was just a change of focus. He may think that you’ve missed all of his other matches?

niman – at 08:17

Monotreme, I went to the NIH page listing H5N1 isolates. All 8 of the H5N1 swine isoaltes were listed (3 that have been there for awhile - maybe a year) and the 5 new ones available on May 1. On May 2 all 8 isolates could be accessed and 8 all isolates had 8 gene segments. When I used this access page on June 14, the 5 recent isolates no long had links to the 8 gene segments. Thus, all 40 sequences had been pulled from the 5 new isolates. This has happened previous on sequences that were released prematurely. They were listed on the H5N1 page, but only the names could be seen. The sequence itself was not linked. In those instances, the names also disappeared, so there was no evidence that the sequences were at GenBank. In some instances, those earlier sequences have yet to reappear. In other instances, the bname reappeared with links to the sequence.

I think the time limit is 1 year (sequences deposited but held for publication have to be released within 1 year of depost). I have seen sequence first appear 364 days after deposit date.

The NIH H5N1 page is here and links are as they were on June 14 (three older sets of swine sequences can be accessed, while 5 recent sets of 40 gene segments cannot be accessed. On May 2 and for 1–2 weeks following, all 64 gene segments were accessible from the H5N1 page.

NS1 – at 08:22

Niman,

Did you see anything else suspect or unusual about those sequences, homologies with vaccine strains, etc? Is there anything that might have caused them to retract that might be out of the ordinary?

niman – at 08:24

As an addition piece of information, sequences that appear in public searchable database generally first appear on the NIH page listing the deposits. Initially, the links to the sequences are not there. That is followed by links to the sequences, but the sequences themselves are not yet in the database. That is followed by the sequences in the database. The names without links are usually present for 1–2 days, but I have seen names listed for many days or weeks without links, as is the case for the retracted sequences at this time.

The sequences available, but not in the database can be from 1-several days.

niman – at 08:33

The was nothing usual with the swine sequences. Guangdong 1 and 2 were close to each other. Guandong 4 and 5 were close to each other. Anhui PA gene had regions of homolgy with Korean and tree sparrow sequences. I believe all 40 pulled sequences can still be accessed using the accession numbers. All of the pulled isoaltes were closest to the two Fujian swine H5N1 sequences, which have been available for quite some time (and are still available).

niman – at 08:33

The first sentence above should start with:

There was nothing unusual with the swine sequences……

NS1 – at 08:35

Niman,

So do you think that there was anything that the submitters had to hide or might want to shelter from prying eyes?

niman – at 09:05

I believe the sequences can still be accessed. The retraction merely prevents publication of the data by others. By pulling all forty sequences, the entire submission is not usuable in publications. The three other sets of sequences remain and most of the pulled sequences are closely related to the Fijian H5N1 swine sequences (from 2001 and 2003), and as has been mentioned, the H5 sequences of one of the pulled sequence is an EXACT match of the public sequence.

The idea that the sequences represnt something that submitter’s want to hide has no basis in fact.

That idea is a tin foil fairy tale (wasting everyone’s time other than those who read these threads for comic relief).

niman – at 09:08

The H5 in A/swine/Fujian/F1/2001(H5N1) is exactly the same as A/swine/Guangdong/2/2003(H5N1). The Fujian sequence has not been pulled.

anonymous – at 09:16

when the reason for the withholding of the numerous other sequences is just protection of originality as has been reported, couldn’t they just use the same method, submitting them and then pulling them ? Apparantly it is supposed to work with the Chinese sequences here.

niman – at 09:32

The sequences are still accessible. Anhui sequence is here.

Why would anyone want to submit and withdraw sequences? The sequencer can withdaw sequences without showing the world the data.

The premise of this thread is so bizzare it is unclear what misconception lead to the start of the thread or the questions, but they are clearly NOT based on reality.

It is just one wacko question leading to a wacko answer, leading to another wacko question.

Unfortunately, most reading the thread don’t realize how absurd the questions are, so the answers lead to more absurd questions.

Monotreme – at 09:41

Here is the Sequence Revision Revision history for DQ419819.1

This record was removed at the submitter’s request because the sequence cannot be confirmed. GI Version Update Date Status 89114152 1 May 1 2006 12:09 AM Suppressed

  Accession was first seen at NCBI on May 1 2006 12:09 AM

This file does not state when the sequence was retracted, so we must still try to reconstruct this. I will restate my chronology: I could see A/swine/Guangdong/2/2003 via BLAST on June 14 2006, before my post. I could not see it via BLAST late on June 15, after my post, hence my concern. The only way to find the sequences now is if you already have the accession numbers. Searches on the isolate names will yield nothing.

There are many links to GenBank sequences throughout NCBI. It’s certainly possible that the retraction process took a day or two to complete. If so, then the link via BLAST could have been removed after the link from the H5N1 isolates page which would explain the discrepancy. The only way to resolve this would be an inquiry of NCBI. Again, I don’t think it’s unreasonable to ask for clarification of what happened with this sequence. Information from NCBI and the submitters is preferable to anyone’s speculation.

niman – at 09:41

Here is the URL for another “pulled” sequence

http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?list_uids=89114159

Just change the number at the end of the URL (going up or down 1 and you will get another sequence). I assume you can get ALL 40 pulled sequences. Each page is EXACTLY the same as the original submitted page, except now there is a disclaimer at the top of each page.

Both the proetin and nucleotide sequences are listed on each “pulled page”.

To hide the data, the sequencer merely keeps it on his hard drive. He doesn’t submit the data to a public database and then ask them to remove it (but it really hasn’t been removed, because as shown by the links above, the data are still there and can be copied and pasted, just like the original page.

niman – at 09:48

Montreme,

I still don’t follow the reasoning. The data was pulled BEFORE you started the June 14 thread.

The pulled data is still available.

All 40 sequences were available May 1 and then pulled before June 14. I am not sure if you have your times correct because before I made my June 14th post I did do BLAST and the only EXACT was the 2001 sequence. The 2003 Guangdong sequence was no longer in the NIH database, which was balsted with the NIH BLAST progam which searched the GenBank database.

Monotreme – at 09:51

Dr. NIman, I can only assume you are not reading my posts carefully; I provided the link to this file some time ago. For example, look at my post at at 23:45 from June 18.

It’s not clear to me that the submitters are allowed by NCBI to completely erase any trace that a record had been available. Again, inquiry at NCBI would be useful. The impression I get is that the submitters have done as much as they can do prevent others from looking at the sequences. Most importantly, they have prevented BLAST searches from revealing the identity between the 2 HA isolates.

As I have said many times, I think the submitters made some sort of error with the sequences and now want to pull them back. The nature of the error is unknown by you or me. I repeat, it would be worth asking them for their reasons. This is preferable to speculation by you or me.

Hurricane Alley RN – at 10:02

Monotreme - @ 09:51

 You can ask the submitters why, but can you expect to get the truth or an answer at all? gina
Monotreme – at 10:02

Dr. Niman, if you did a BLAST on June 14 and could not find the 2 sequences, then I am at a loss. I used the sequence you provided on June 14 for my BLAST. I do not know how to explain this discrepancy. Again, an inquiry at NCBI would be helpful.

I would appreciate if anyone would send an email to NCBI asking them when the DQ419819.1 record was pulled and how long it took for all links to this sequence to removed from all NCBI databases, especially BLAST. I would do this myself but would like to maintain anonymity.

Monotreme – at 10:04

Hurricane Alley RN, you’re right that if something embarassing happened, they may not be willing to fess up. However, I still think it would be worth asking. Even a refusal to answer may be informative.

Monotreme – at 10:12

Dr. Niman, you still have not addressed my post at 13:04. In it, I list several links to your commentaries suggesting the possibility that flu viruses could be used for bioterrorism. Further, you suggested that Bioterrorists may infected pigs in Korea with a laboratory strain of influenza. I actually had these commentaries of yours in mind when I posted my concerns of laboratory escapees. Hence , I remain quite puzzled by your tinfoil comments. Please explain.

Here are Dr. Niman’s commentary on the use of laboratory strains of flu by bioterrorists to infect pigs:

Flu Bioterrorism? Have Bioterrorists Infected Swine in Korea with Human WSN/33? WSN/33 Chronology

niman – at 10:30

Monotreme, You are correct assuming that I don’t read most of the posts on this thread (or most threads at this site). I did not read the tin foil thread that you started on June 14 until I received about a half dozen e-mails from others who thought your posts had some significance and needed to be addressed. As expected, the thread has created a significant waste of time, and now you want to start more tin foil nonsense.

The WSN/33 sequence are still at GenBank in swine isolates from Korea. There is no question that those wequence originated from the 1933 lab isolate. The origin of those sequences are still at issue. WHO spent over a year investigating and the investigation involved all of the major labs doing flu sequences (St Jude, Hong Kong, Wisconsin, Weybridge, and Tokyo). The H9N2 were never identified and the origin of the WSN/33 sequences was not determined.

WHO maintained that they were lab contaminants from Sang Seo’s lab. I saw the published sequences as well as sequences from additional swine from 2005 (the sequences at GenBank are from 2003) and those sequences looked quite real. They were not exact matches and were evolving. E-mails from Sang Seo ceased last year, so I really have no more to add than was described in the commentaries. There is no doubt that the WSN/33 came from a lab. The identity of the lab remains unclear. However, if it were an accidental or deliberate release, the terror aspect is minimal, because the source two years after the fact remains unknown.

This was covered in news at Nature and Science and the origin of the WSN/33 or H9N2 sequences remain unclear, but H9N2 was clearly related to South Korean isoaltes and WSN/33 was clearly evolving from WSN/33 (which can be found in labs worldwide).

Hurricane Alley RN – at 10:30

Monotreme @ 10:04

I’m like to be lazy on occasion. Do you have the e-mail address at hand or do I need to go search? gina

niman – at 10:32

Back to the original premis of this and earlier threads, here is the 2003 H5 sequence that is an exact match of the 2001 H5 sequence

http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?list_uids=89114156

I have seen no indication that all 40 “pulled sequences” cannot be accessed at this time.

niman – at 10:34

Correction, the above link is Guangdong 5. This is Guangdong 2, which matches 2001.

http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?list_uids=89114152

Hurricane Alley RN – at 11:07

Thank you Henry. I must admit I was concerned when the first link sequence didn’t match. Of course, that was before I had realized you had changed the link. I will leave this alone. gina

Monotreme – at 11:58

Hurricane Alley RN,

Here are 2 email addresses for GenBank:

gb-sub@ncbi.nlm.nih.gov

and

update@ncbi.nlm.nih.gov

I’m not sure, which, if either, will get you a response because there is no mention on the GenBank website of a prortocol for retraction of a sequence, but these 2 email addresses might be a good place to start.

I’m very curious to hear what the response will be.

Monotreme – at 12:10

So, Dr. Niman, let me get this straight. You think the swine sequence from Korea is evidence of a lab escapee. Further, you suggested that this might represent a bioterrorist attack.

I suggest a different swine sequence indicates a possible lab escapee, and I’m a conspiracy theorist? Interesting logic.

For the record, I do not think it is necessary to invoke a deliberate release of modified H5N1 strain to account for a lab escapee. It is quite possible that researchers were experimenting with various strains of H5N1 in an attempt to understand virulence and/or to develop a vaccine strain. As part of these experiments they may have infected animals to test for virulence or in challenge experiments. Some of these animals may have escaped from their holding areas. I do not understand why this hypothesis requires tinfoil.

Dude – at 12:11

Is it a coincidence then that unfolding events in Hong Kong are pointing to 70 cases of pneumonia like symptoms and a check of the temperature of all people arriving from southern China? I don’t wish to imply a tinfoil hat jumping to conclusions point. The data will prove the data in time. I say this only to preface a question: IF a H-H flu were now to emerge and it is based on one or more of the pulled strains, does this give the Chinese some market advantage in the production of a vaccine that they would not have if the sequences were still in the data base?

niman – at 13:12

Monotreme, The WSN/33 sequences are in swine isolates at GenBank. They are not there via a “natural process”. The sequences are either a lab contaminant of a release from a lab (accidental or deliberate). That is what the commentaries said and I don’t know of anyone who disagrees. The sequences did not involve H5N1.

In China there was no evidence of anything unusual in the H5N1 swine sequences. The pulled sequencs were from Guangdong and Anhui, which are not geographically close.

Only one of the forty sequences was an exact match.

De jure – at 16:10

Is anyone aware of whether there are universal safety protocols for biohazard materials? Are some countries more careful (careless?) than others in handling lab materials? Are there any stats on lab accidents per country? I always thought CDC labs in the U.S. were pretty careful, but I’ve read where accidents (human exposure) have happened. I guess routine, repititious experiments get a little boring, even in level 4 units. Are there stats kept on accidents?

NS1 – at 16:21

People are people and people make mistakes even under the best of training, recursion and equipment. All labs have reported and unreported mishaps.

Monotreme – at 21:27

NS1 is entirely correct. There have been a number of breeches of safety protocols. For example, there were laboratory infections of personnel with SARS in China and Taiwan. An American company sending out routine flu positive controls inadvertently sent out a pandemic strain to hundreds of labs.

Mistakes do happen. Laboratory escapees are not in the least bit far-fetched.

As to whether any of the Chinese sequences suggest unusual origins, that depends on a number of issues. The first is whether there was labeling error or contamination. The second is whether you subscribe to Dr. Niman’s views regarding the accuracy of flu polymerases. If you do, then there is nothing to be alarmed about. If you don’t, then one should be asking very hard questions of the submitters.

Monotreme – at 21:31

Dude, I don’t think the Chinese would benefit in any way from a deliberate release of H5N1. Even if they think they have a good vaccine, once a flu virus is out, it will mutate in unpredicable ways (with apologies for disagreeing with Dr. Niman on this issue ;-) )

That being said, who knows how strategic planners in the PRC think. Herman Kahn, American, thought all-out nuclear war was winnable - and he guided US nuclear weapons strategy.

Hurricane Alley RN – at 22:18

Monotreme, Sent out a couple of e-mails. The first link was a dud, but the second one went through without a glich. Now for the waiting game. I hope someone answers, for I would like to see this issue resolved.

I honestly smell something bad in the air and it’s not China. I had a nightmare last night involving North Korea. Yes, they shot off their missle, but everyone thought it was a dud because it didn’t explode. It was full of lab mutated Avian virus. I told you it was a nightmare. Let’s just hope it stays a dream. gina

21 June 2006

Monotreme – at 10:21

Thanks Hurricane Alley RN.

niman – at 18:14

Beijing pulled the H5N1 swine sequences, and now they tried to pull a NEJM article on the first H5N1 case in 2003:

“At least one scientist e-mailed the journal Wednesday morning, asking that the report be withdrawn. With the article already in print, journal editors were waiting to see whether the authors would now retract the paper.

“We can’t speculate” what the problem was, said journal spokeswoman Karen Pedersen.”

niman – at 18:16

The New England Journal report raises the possibility that the two dangerous viruses emerged simultaneously.

The patient, a 24-year-old man with pneumonia and respiratory distress, died four days after he was hospitalized in 2003, they reported. The main outbreak of SARS, occurred earlier that year and sporadic cases were still happening. Doctors initially diagnosed that as his cause of death. But tests failed to find the SARS virus.

Further tests of the man’s lung tissue yielded fragments of a flu virus, the Chinese scientists reported. Genetic sequencing revealed it to be a mixed virus, with genes similar to two distinct types of bird flu seen in northern and southern China.

“It suggests to me that H5N1 infections were occurring in China probably not recognized or not detected maybe in the background of the SARS epidemic,” Treanor said. “I don’t know how you could interpret it any other way.”

NS1 – at 19:07

Henry,

Please start a new thread with this dual emergence idea, so we can have a look at it separately.

Monotreme – at 19:21

NS1, I’m glad Dr. Niman posted this on this thread. It may not be related to the retracted sequences, but there are clearly strange things happening in Beijing.

Tom DVM – at 19:26

Hi everyone. I understood that initially, they thought SARS was the beginning of the H5N1 pandemic…so I assume they were looking for influenza viruses in testing. The identification of SARS and the corona virus connection did not occur in China so they would have been looking for influenza for months before the real cause was discovered.

Hurricane Alley RN – at 20:17

Monotreme, Keep an eye on you e-mail. I have been having some network problems soooo, I sent something to your e-mail. I tried to post it here, but their was magic in my network. It disappeared. gina

Hi Tom!

22 June 2006

Monotreme – at 03:57

Hurricane Alley RN, I don’t have access to my email right now. Please try to post anything you found out from NCBI here again.

Thanks.

Monotreme – at 04:12

From Bird flu may have been mistaken for SARS -doctors

In the case of the Chinese man, tests of his tissue were positive for influenza virus and genetic sequencing later showed it to be H5N1 avian influenza.

It genetically resembled samples of viruses taken from Chinese chickens in various provinces in 2004, the letter says. Parts of the virus also resembled Japanese samples.

The eight researchers who signed the letter include Dr. Wu-Chun Cao of the State Key Laboratory of Pathogens and Biosecurity, Dr. Qing-Yu Zhu of the State Key Laboratory of the Beijing Institute of Microbiology and Epidemiology, and Dr. Wei Wang of the 309th Hospital of the People’s Liberation Army.

They said the virus infecting the man had mixed lineages and that their findings were important for developing an eventual bird flu vaccine. “The genetic distance between the isolate reported and the strain currently proposed for vaccine development implies that viruses from different regions may need to be considered in the development of an effective vaccine against influenza A virus,” they wrote.


Most journals require that sequences associated with a paper be deposited in GenBank and be released to the public at or before publication. The information in the text is already out there. What about the sequences? Is this another attempt to pull H5N1 sequences from China?

niman – at 08:10

I can’t find the sequences yet at GenBank, but here is the HA phylogenetic tree.

Hurricane Alley RN – at 09:25

Monotreme - E-mail received from NCBI.

Dear Colleague,

DQ419819 was suppressed on 5/31/06 at the submitter’s request because the sequence cannot be confirmed.

If NCBI suppresses the sequences and remove them from the public view, then they will no longer be included in NCBI’s BLAST databases, indexed in Entrez, or distributed as part of a GenBank release. However, they may remain in other third party databases, and will still be retrievable in Entrez by accession and gi number based queries.l

For BLAST database update, you can view this document at: ftp://ftp.nchi.nih.gov/blast/db/blastdb.html

It takes about two months for every new GenBank release. This, the DQ419819.1 record will be removed from the BLAST database with the new GenBank release.

Best regards.

Hanguan Liu, M.D., Ph.D. NCBI User Services

__________________________________________________________

Hope this helps.

__________________________________________________________

Mods., Please forgive if I did something incorrect for I really am a computer morron. gina

niman – at 09:47

The above reply from NCBI confirms that the sequence was suppressed two weeks prior to the thread that began June 14 and noted the retraction.

Thus, the sequence was available for the month of May and now can only be accessed indirectly (but all 40 H5N1 Chinese swine sequences can still be accessed and the 24 other H5N1 swine sequences that have been accessible for some time are not affected).

Hurricane Alley RN – at 10:24

Henry, You and Monotreme are sweethearts. Both of you can be stubborn, but that is fine by me. Checks and balances are a good idea considering the amount of secrecy that is going on. Gina

Monotreme – at 12:24

Thanks Hurricane Alley RN. The response explains conflicting accounts of when the sequence ceased being available. Since I accessed it from a BLAST search it was still available to me when I did my search in June. It does like the suppression preceded either Dr. Niman’s or my thread.

However, it was public for 4 weeks before suppression. The reason for the suppression of these sequences and the attempts at suppression of the New England Journal of Medicine article remain causes for concern ;-)

Hurricane Alley RN – at 12:46

Monotreme, Could any of this suppressed information have anyting to do with the human case of BF in China in 2003 that was neatly conceled? gina

Tom DVM – at 12:59

Monotreme. Something doesn’t make sense here. There has to be an understandable explanation.

I have noticed a recent repeated pattern of China trying to control the movement of scientific data.

They have to be protecting something that we don’t know about yet.

anonymous – at 13:04

I have noticed a recent repeated pattern of China trying to control the movement of scientific data


how ? where ?

Monotreme – at 13:06

Hurricane Alley RN, it’s possible. That idea certainly occured to me. It’s impossible to know without seeing the sequences from the human 2003 case. I actually think we may see that sequence. Here’s why. Most journals require any sequences referred to in a paper be deposited in GenBank. If the sequence has been deposited but is on hold pending publication, NCBI rules require making the sequence public upon publication of the article. So, assuming the article is published, the sequences will have to be released at that point, whether the submitters want to or not. At least that’s my understanding. I think this is why the Chinese scientists are trying so hard to suppress the publication of their article even thought the contents of the article have already been released to the press.

Tom DVM, I agree. There is something rotten in China (apologies to Denmark, and Shakespeare).

Tom DVM – at 13:30

anonymous. Good question. Actually, that’s what I do. I watch for changing patterns in nature. It is a bad habit that comes from twenty years of trying to anticipate the next disease my farmers would be confronting.

The problem is that I don’t keep records of the contents of the patterns.

However, two components have been Chinese Officials (non-government) being evasive about a Foot and Mouth outbreak that has been ongoing for more than a decade, has done serious damage to the world’s livestock and currently is causing a similar problem in Vietnam to the one caused by H5N1, of course when China didn’t have any H5N1 cases…Vietnam being a border country to China…they have my sympathies.

Similar comments have been made about Streptococcus suis, a pig bacteria that jumped to humans…

…but they are being most evasive about H5N1 and every authority in the world knows it and are collectively turning their heads…

…something is up in China, we just don’t know what it is yet but we will in time.

Hurricane Alley RN – at 14:48
Dude – at 15:06

Monotreme, if you have accesses to this forum you can use the mailbox I setup for you. It is just singtomeohmuse.com/webmail then the username/password I provided. Got to keep you in touch… Questions dude@singtomeohmuse.com

NS1 – at 19:26

Monotreme,

I’m hoping to see more on the dual infection soon. Those sequences, even the SARS, may give us some new leads.

Niman,

You studied SARS with the HK lab right? Do you think we’ll see anything interesting if they publish the SARS sequence.

I know that you don’t usually comment on the pressures that drive the sequence changes, but you may want to comment on the elegance or inelegance of co-emergence or parallel emergence of two HP pathogens and how they might affect one another in a single host.

Does your rules-based polymorphism approach allow for cross-species pressures, competition for resources, competition for real estate, cooperation . . .

All of these, of course, without any genetic exchange or acquisition.

anon_22 – at 23:54

Without knowing specifics, I would suggest that you guys are seriously underestimating the ability of clueless politicians in every country to make decisions entirely against science and often against the interests of the people and even themselves. Witness the ineptitude of the CDC etc. The rest of it is just a matter of degree.

When politics or bureaucratic convenience is allowed to override science, countries as a whole lose out on their ability to progress. IMHO.

23 June 2006

bird-dog – at 01:49

bump

anonymous – at 03:19

I won’t call that “ability” ;-)

mmmelody47 – at 06:38

Tom DVM – at 13:30 - “…something is up in China, we just don’t know what it is yet but we will in time.”

Aside from the evident lack of basic freedoms and openness….the 2008 Summer Games in Beijing and the $1.6 billion (US) budgeted for Olympic facilities (and the resulting return on investment) may certainly play a roll in “something is up in China…..”

The implications could be catastrophic.

NS1 – at 06:58

mmmelody47,

Though the Olympics add pressure to the leadership, we’ve always seen a hegemony of medical and research information behind the Great Wall.

mmmelody47 – at 08:31

NS1 – at 06:58 - is there truly enough separation between the Oligarchy and medical research that the latter has the necessary autonomy to act and report as we hope?

niman – at 17:23

Looks like the e-mail withdrawing the NEJM story was a fake. I woneder about teh withdrawl of the H5N1 swine sequnces:

A researcher who reported that a Chinese man may have died from avian influenza before anyone else in China was known to have the disease denied on Friday he tried to have the report retracted, according to the U.S. journal that published the report.

Dr. Wu Chun Cao of the State Key Laboratory of Pathogens and Biosecurity in Beijing told The New England Journal of Medicine that e-mails bearing his name sent to the journal this week were not written or sent by him.

NS1 – at 18:45

mmmelody47 – at 08:31

is there truly enough separation between the Oligarchy and medical research that the latter has the necessary autonomy to act and report as we hope?

Not likely.

Refer to Niman’s post at 17:23?

In the Western world, we impose the same types of information management techniques. We just dress them in more polite terms.

24 June 2006

Monotreme – at 10:25

This story is stranger than a soap opera. I have never heard of anyone retracting their sequences - a month after they made public at that. I have never heard of fake emails being used to block publication of an article. When relying on emails, both GenBank and most journals require that you provide a valid email at the time of submission. If someone just started to send of flurry of emails from Dr.Cao@yahoo.com requesting a paper be retracted, I would hope that the NEJM would try to verify the email address before issuing a press release on the subject. I would expect that the NEJM would not have gone out on a limb unless the requests for retraction came from the submitters email. If so, this would require some hacking or a higher level of authorization within the submitters institution or the Chinese government itself.

It would be useful to know what email address was used to request the retraction of the paper.

Monotreme – at 10:29

Dude, thanks, but I’m not “on” much these days. I should have access to my email soon.

Leo7 – at 12:09

Monotreme:

What a ride, and a great debate. While nothing about those sequences or the request to pull the NEJM article makes sense, I give you the full credit of exposure.

LMWatBullRunat 12:28

The following is PURE SPECULATION.

My suspicion is that the sequence retraction and the deliberate ‘outing’ of Chinese government policy being to attempt deliberate deception of the rest of the world with respect to the nature and extent of h5n1 infections in China, have a common link.

One possibility is that China, having concealed H5N1 infections in livestock and poultry, is now seeing increased human infections and human to human H5N1 infections. The sequence data, may, for some reason, allow researchers to prove that China has been doing this, or the politicos are afriad that they will, and thus ordered the retraction of the data.

THe reason the Chinese govt would be attempting to cover this up is that something BAD is happening. The reason that the scientists published their letter in the NEJM is to try to warn the rest of the world that something BAD is happening.

What that bad thing is, if it even exists, cannot be determined, but one might think it relates to H5N1.

Now, this is all speculation, and the reality is probably different, but when doing intel and threat analysis, I was taught to always look for common events to explain disparate but chronologically and geographically related actions.

anonymous – at 12:36

then, why submitting a long prepared letter with phylogenetic tree to NEJM, istead of just saying: “something bad is happening” ?

LMWatBullRunat 12:47

because a phylogenetic tree diagram is mostly mumbo-jumbo to the political officer who originally OK’d the release, and the political officer who OK’d it has probably been shot. It took a while for the implication of the letter to get to a high enough level and understood. Pity, really.

If those 8 scientists had simply tried to send a letter saying “Hey, world, there is a pandemic brewing here in China, and we thought y’all ought to know about it” there would have been 8 fewer scientists in CHina and no letter published at all. That letter was a very clever and ballsy effort, IMO, and it almost worked. As it is, unless there is immense pressure put on CHina to come clean, and to not mistreat the scientists, they’ll bury the issue and the scientists, and claim it was all an unfortunate misunderstanding and that they have absolutely no culpability in the pandemic that’s ravaging the world. Just joss.

niman – at 13:07

If the paper isn’t retracted, the sequences have to be submitted to Genbank, which is a publication requirement.

LMWatBullRunat 13:14

Dr. Niman, my guess is that hell will freeze over before those sequences are submitted. My guess also is that those 8 Chinese scientists are hip deep in a large world of hurt right now, and I doubt one person in a thousand will ever know a thing about it. THere may or may not actually be a reason for China’s actions in this case, nor is China the only government that does such things. Watergate comes to mind.

That said, given China’s disrespect for human rights generally, I don’t think they’ll blink at violating the publication rules. Or did I completely miss your point?

anonymous – at 13:34

and why _8_ scientists ? If there is insider-information, then one scientist would be more likely to know it. And there are better ways to communicate something than a letter to NEJM. And why not sending it anonymously ? Have you searched for an encrypted message in that letter ?

Nightowl – at 13:49

I also believe the Chinese scientists have been courageous, and the sequences issue and the NEJM issue are linked. A couple of the scientists who submitted the retracted sequences also are authors on the NEJM letter.

I hope the journalists, Helen Branswell (Canadian Press) or Donald G. McNeil, Jr. (NY Times), will give the folks at GenBank a call. By now, GenBank people have to be wondering if they received a legitimate request from the Chinese scientists.

Further, WHO did an interesting thing and put up their official request to the Chinese government (regarding the NEJM info) on the new WHO China website. They should also look into the GenBank sequence issue and post an official request regarding that as well. It will be interesting to see what WHO posts about the Chinese government response. This all is even more amazing given that the new WHO Collaborating Centre on Emerging Infectious Diseases was established this month in Guangdong Province.

New WHO in China Website

Leo7 – at 16:47

This is pure speculation as well:

Perhaps the dissident group Falun Dafa sent the e-mail to the journal and GenBank trying to draw attention to something, maybe widespread flu? The woman heckler at Bush and the Chinese President’s news op was from this group, and she was protesting taking of human organs from jailed dissidents while they were alive. Link here: http://tinyurl.com/ks2kb

Monotreme – at 22:16

The sequences related to the NEJM article may have already been deposited in GenBank, if, like most journals, the NEJM requires publication of all sequences related to an article. If so, then it is my understanding that no-one can stop the release of the sequences once the article is officially published. Does anyone know when that will be?

Nightowl – at 22:32

Link to NEJM article

niman – at 22:39

Yes, sequences are deposited prior to submission of the manuscript. They should appear at GenBank anywhere from 1 day to 1 month after publication (and they will appear at Los Alamos in the same time frame. Sometimes it helps to let NCBI or Los Alamos know taht the paper has been published, even if it is ahead of the press. I was looking for the Accession numabers in the apper, but couldn’t find them.

The number of sequences from China is considerably higher than the number that some poster here imagine, including human sequences rom 2005 and 2006 (and the 2003 human sequences from Hong Kong sans Fujian Povince, which were in February 2003, considerably earlier than the sequences at issue at NEJM - the 2003 sequences have S227N.

Monotreme – at 23:11

Thanks Leo7.

Thanks Nightowl for the link.

Does anyone know for sure if NEJM requires deposit of sequences? The absence of accession numbers is somewhat worrying. It might be worth sending NEJM an email to find out as the paper is already published. An email to NCBI alerting them to the NEJM article and asking them if they have any sequences related to it that will be released would be worthwhile.

Dr. Niman, there are many isolates from birds deposited from China. However, the number from mammals has just been reduced greatly by the retraction of many of the recent swine sequences. How many sequences from isolates from humans in China have been published?

And if there is nothing unusual about those sequences, why haven’t they been published?

Leo7 – at 23:17

Monotreme:

Aren’t those the sequences in the NEJM article. Look at the supplements in the article.

niman – at 23:54

I believe there are 4 human (6 if you count the two fromHong Kong residents infected in China) and 3 swine isolates and many bird. The human H5N1 look quite a bit like the bird and none of the sequences, including the 5 swine withdrawn sequences have anything that looks unusal to anyone who has spent any time looking at pandemic flu sequences.

China actually is the only country with swine sequences and has more human sequences than any country other than Vietman and Thailand (and now Turkey has tied China by releasing 4 sequences). Hong Kong has 18 human from 1997, but China considers Hong Kong as China so if Hong Kong is added, China leads in all categories, except birds, which are highest from Vietnam and Thaland. Indonesia may be ahead of China in the boird actegory also, unless Hong Kong is added to the China total. China/Hong Kong combined would lead in all areas.

I think many assumptions of posters to this thread are in need of a realty check.

25 June 2006

Monotreme – at 00:19

Leo7, I looked at the Supplement and did not see any sequences. What I saw was diagram relating the sequences from A/Beijing/01/2003 to other strains, not the sequences themselves.

btw, if anyone does write the NEJM or NCBI, the strain that we are interested in getting sequence information from is A/Beijing/01/2003.

Monotreme – at 00:26

Just to be clear, Mainland China has not released any sequences from any H5N1 isolates from humans. All the human isolates related to China were released from Hong Kong. Dr. Niman, are you seriously going to argue that the degree of openess or scientific standards in Mainland China are the same as in Hong Kong? Mainland China never acknowledged the cases of the family from Hong Kong that likely got H5N1 while visiting Fujian province. Mainalnd China closed down Guan Yi’s lab on the Mainland and have actively tried to stop his work, as you well know. I don’t understand the 180 degree change in your attitude toward Mainland China. You used to be very strong in your condemnation of their secretiveness. What happened?

Tom DVM – at 01:16

If it walks like a duck, and quacks like a duck and swims like a duck it is not a rhinocerus.

China is never going to change for one good reason…it works for them. Money talks, China knows it, the WHO knows it and the rest of the world knows it.

They have spread a Foot and Mouth epidemic around the world…have not controlled it in their own country…and now it is recirculating through Vietnam, their unfortunate neighbour. The official word from the Chinese Government is Foot and Mouth outbreak…What Foot and Mouth outbreak?

Guandong is the world greatest petri dish for culturing emerging diseases for a reason (last decade THAT WE KNOW OF SARS, strept. suis and H5N1). They have the highest concentration of people mixed with the highest concentration of a wide variety of animals…and a Government that could care less…

…under the watchful eye of our gaurd dog the WHO Which is old, lost its eyesight and its teeth…and now appears to have lost its bark as well… I hear nothing, I see nothing, therefore I make it look good.

Monotreme – at 01:26

Tom DVM, I could be wrong in my interpretation, but I get a feeling of desperation on the part of the Chinese government. Although their natural instinct is always to censor bad news, they are now using very heavy-handed tactics. I can almost smell the fear.

What scares me is: what do they know that makes them so scared?

Closed and Continued - Bronco Bill – at 01:29

Closed due to length. Conversation is continued here.

Tom DVM – at 01:32

In my opinion, there is only one thing they could be concerned about at this point. I don’t think the 2008 Olympics is it… they have bull-****** themselves out of worse trouble before and many times since Tianamen Square…

…I think they are afraid of panic…internal strife…revolution.

I think it was Randolph M. Kruger on Effect Measure who said…if each Chinese citizen throws one stone at the head office of the Communist Party of China, what happens?

Avian influenza is the quickest route to anarchy…The Chinese Government isn’t stupid…they read the same tea leaves that we do plus they have all of the inside information supplied by their colleagues the WHO…we know what’s up and they know what’s up…and they know that things are past the tipping point…there is no going back.

in my opinion and for what its worth.

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