Indonesia does the right thing

Yes, Revere, good proposal!
This rule should be taken up in every official set of ethical regulations concerning publication of medical studies.

I believe virtually all peer reviewed journals have that rule for all sequences.

The only exception that I can recall is the human H5N1 sequences from Beijing in 2003 published in NEJM.

The Indonesian sequences were not released because they were not published. Usually sequences are deposited and receive an accession number, but the sequences are not released until the paper is published.

Niman just posted that he can't see the son to father sequences referenced previously. They're not all there.

Is it possible that HK has not released all the information because it released everything for H5N1 but not for some other influenza influencing factor, be it H5N1.1 or something else?

At FluTracker.com, Niman on Sat morning posted his observation that it's possible that one of the entities HK is not being fully disclosive.

Without that dual infection Niman references, we are again back at square 2, instead of square 1, and this time, it may be a greater challenge as the response might be, "I released what I was told to release."

I'll be an optimist and wait a day or two.

Anyone know more about this?

Henry: I don't know all the journals, but I know this is not something that is usually part of the peer review process. I know many journals have no pollicy at all. You might check the Instructions for Authors on the main ones that publish these articles and see which ones have this stipulation. I am currently on the road and on dial up and even getting my email is painfully slow. Let us know what you find.

This is very good news. I wonder what did the trick? It seemed to me that the people with an interest in withholding data had more power than the ones with an interest in releasing it.

revere. I don't know what is and what isn't spelled out in instrauctions to authors, but the genral requirement of a peer reviewed paper is that it contain enough detail to allow the reader to verify or independently generate the data that support the paper's conclusions.

Therefore, papers that discuss new sequences would have to make those sequences publicly available.

This is the procedure followed by all major labs that sequence. As I mentioned earlier, the sequneces sequestered have not been published. Sequneces frequently are placed on hold until publication.

I frequently e-mail GenBank and Los Alamos to tell them a sequences has been published, including those published ahead of the press. I have never had GenBank or Los Alamos say that the sequences won't be released until some future date, because it is well know that once a sequence is published it has to be released.

I think you and many reporters are operating under misconceptions. Most of the media talked about GenBank releases of the Indonesian sequences, but there was little doubt that the WHO sequneces would be released by Los Alamos, not GenBank, which is exactly what happened. Similarly, the withheld sequences have not been published. The only acception that I know about is the H5N1 Beijing sequence, which is the exception that proves the rule.

Henry: I think you are under some misconceptions about peer review. I do quite a lot of it myself, being on the editorial boards of two journals and I'm also Editor in Chief of a peer reviewed journal. Reviewers are highly variable in the time and care they take, one of the banes of being a journal editor. You certainly cannot count on them to catch whether sequences are publicly available or not, if that is the only safety net. Even laboratory Methods sections are notorious for having insufficient information to allow replication, a major issue today in scientific publication. The question whether there are papers published without publicly available sequences is an empirical one. It may be true that no paper ever gets reviewed without the sequences being public, but I rather doubt it.

revere, If you have any examples of publications that cite unpublished sequences that would be useful. As I said, the major labs release sequences upon publication. That is standard practice.

I stand by my misconseption statements. Publications do not cite withheld sequences. It has been that way for several decades.

You have already said this isn't your area. Significant sequencing began in the late 70's early 80's. These rules have been in place for some time. The sequencers know the rules. They submit the sequences before they submit the papers. They just place holds on the sequences until they are published.

There is no need to re-invent the wheel.

So revere, why does your proposal only apply to influenza only? What about something like HIV/AIDS and other diseases that kill millions?

Journals generally require that sequence data presented in a paper be published in a public database, not necessarily GenBank, and that the accession numbers be referenced in the paper. The authors are only required to provide the accession numbers by the proof stage.

Typically GB releases the sequence data immediately, or the authors can stipulate that a date for release. Usually what happens is that the sequence data are released upon publication and this happened automatically. However, GB has slowed down somewhat recently due to the huge amounts of submissions they now receive. So in some cases I have been caught out with a published paper but no publicly available sequences. So I email GB tell them the paper citation and they release the sequences.

But there are still some papers that do not references any sequences, this seems to happen in the human papers, not just the NEJM one that Niman mentioned but also a Lancet paper.

Now something different. "Niman on Sat morning posted his observation that it's possible that one of the entities HK is not being fully disclosive." Why is it that the people on this and other sites, particularly Niman, jump to the worst conclusions? Perhaps some data are missing because things take time and it is the weekend and HK is in a different time zone!

Regardless, the father/son sequences are there, so how about stopping the complaining already?

And I really think it is high time that Niman stopped mouthing off about things he has no clue about. "The Indonesian sequences were not released because they were not published" is a load of bull. The sequences weren't released because the Indonesian government wouldn't allow it.

Tell me Niman what is your source for that observation? Have you asked the people involved or did you just think it up?

Even now after the sequences are released all you can do is complain and blame. It has been apparent to me for sometime that the main reason you have been pushing this is for publicity, perfect for a company start up!

People always question my posts by asking why I am so rude to Niman. Well the answer is that he just talks to much and I think that he is a charlatan. For 3 years talking but nothing published. There is plenty of dat out there already, not just on inlfuenza but many other viruses for which he could demonstrate his methodology (see more below if you can be bothered). Also, Niman never quotes scientific papers, and this is a serious failing in a scientist. What he actually does is when a new paper comes out, he will authoritatively start using similar languange (sometimes verbatim) and just work it into his commentaries. If this was journalism fine but for science you should cite your sources.

Then there is the dumbass statements about which he has no clue, the example given about about sequence release. Everything he says about others is negative and designed to boost himself.

Please listen to me people, as someone who is an evolutionary biologist and works on infectious diseases. HENRY NIMAN IS MISLEADING YOU!! He is alarmist and much of what he writes is incorrect, misguided or unproven.

See the post http://www.recombinomics.com/News/08050602/H5N1_Indonesia_E627K.html.

Niman raises concern that there are no close avian matches to the Indonesian human sequences and also that the have the dreaded PB2 627 mutation. There have been no avian sequences from Indonesia since mid-2005 as reported in Nature, so it is not surprising that there are no close matches. More data is needed. As for the PB2 mutation, it has been present in at least one human case from all regions and has also been found to not correlate with disease outcome for human cases in Vietnam (see de Jong et al in NEJM).

So without the full background data it is very easy to be alarmist and scare the crap out of people. But is it really useful and what is the purpose of doing this?

Enough I suppose, but Niman has been passing himself off as a flu and evolutionary expert for far too long and peole keep buying it which is a damn shame.

The below comes from an earlier post, but it is relevant to my Niman rant.

It is impossible to ascertain what Niman is talking about as he has never presented a methodology. Detecting recombination on a small scale is problematic and would probably require a new approach/methodology. As far as I can tell from his website, Niman does not mention any methodology, just listing nucleotide differences. But just the presence of a nucleotide change does not provide any information regarding whether it arose through mutation or recombination.

So yes, Niman makes his contentions in public but there is no way to assess his theory as there is no data available.

Influenza is a negative stranded RNA virus with no proof reading mechanism when copying of genetic material during virus replication. This means that influenza has a high mutation rate, even among viruses.

Also, the segmented nature of the influenza genome makes it less likely that recombination would occur. Not that it is impossible, just that it has not been frequently identified. This is mostly due to the problems with the methodology for detecting recombination.

Then there is the issure of quasi-species that Niman has never addressed. Imagine that a drop of influenza virus contains 1 million virus particles. Because of the high mutation rate, theoretically, each vurus particle could be genetically distinct, even if by just a single nucleotide. Therefore, what we see as a point mutation could in fact be a change in the proportion of virus particles with that particular nucleotide as it adapts to its host.

So as I said you would need a new method. If Niman has a new method, then great, I would love to be proved wrong as it would be a great help to my work, and truly revolutionary. But there is absolutely nothing about a methodology on his website, the best you get is an statement that "influenza evolves through recombination" which has never been shown in the literature.

This leads me to conclude that he is full of hot air and using this issue purely for publicity.

Niman, when have you sequenced or submitted something to GenBank? Get off that high horse and stop the posing.

Henry: My proposal was not to have it publicly available on publication, but on submission of the ms. When the paper on the Nigerian sequences was published a few weeks ago I checked the sequences and they were not available until a couple of days after publcation.

Anon2: I won't get involved in the recombination argument. It isn't of particular interest to me and won't be until one side or the other makes a useful prediction.

It is not just an argument about recombination. It goes to the creditibility of those people that dictate the tone of these discussion forums, and I think you should be interested in it. What is the use of unnecessarily alarming people?

Also, why should the proposal be limited to influenza? Why not everything else?

Acutally, I am also amazed by how little you knew about situations you felt free to blab on about.

For all those posts blaming the WHO, scientist, government, and it came down to the Indonesian governments permission for realease. So where is the apology to those people you unfairly ripped on?

And you had no idea that there had been no avian viruses sequenced! But you are qualified to go on about these things.

Now you won't "chide" the government anymore (so very big of you by the way, I am sure they are releived to be spared the chiding of the mighty revere!) but for flu scientists the onslaught continues.

I repeat, there is more than one disease out there causing death, why restrict your approbrium to flu?

anon2: LOL. Thanks for the great advice. I guess you don't really read this blog, because if you did you'd find I cut quite a lot of slack for WHO (and took a lot of crap from your mirror images on the anti-WHO side) and for scientists. I just ran out of patience with them. The issue, as I've pointed out, is the isolates, not the sequences. Regarding my "approbrium" (sic), I also have been quite strong on copyright and patenting issues. I am Open Access, Open Source and anti-patenting all the way. The issue before us is the flu sequences. I don't approve of withholding any scientific data except for reasons of confidentiality. I say that as someone who actually collects scientific deata, analyzes it and writes about it. What exactly is your point? That I didn't include HIV? I'm glad to, not because you think so but because I don't like keeping useful data private. But I was talking about something else, not what you wanted me to talk about.

I'll also give you some advice. Starting a blog is very easy. Go over to Blogger.com and click the button, Create a Blog. Then you can say whatever you want and maybe someone will read it if it's worthwhile. It only takes about 30 seconds. Go ahead. We'll wait.

If the theory is true that recombination is a major force in viral alteration, could the quirks that make H5N1 wildly pathogenic also make their way into existing H2H flu strains?

This is more worrisome to me that H5N1 itself, because I suspect that a huge number of factors in a flu virus allow it to be effectively contagious, and that it could take a lot of evolving before there is an H5N1 strain with this ability. There seem to be a zillion flu strains (the other 10+ H's) that never turn up in humans.

If a common mechanism allows H5N1's particular pieces of poison to recombine into, say, the H3N1 California that rampaged this past winter, this is a bigger threat than H5N1 evolution.

Can y'all please have a polite conversation about this?

Just to set the record straight on the missing sequence from the father, I simply stated that the data present in Jakarta was not present in the three isolates from the father of the nephew in the Karo cluster.

This sequence was initially described in a Recombinomics commentary

http://www.recombinomics.com/News/06250602/H5N1_Instability_Karo.html

and was the subject of at least two presentations in Jakarta. The sharing of one of the polymorphisms by the father and son was cited as the first genetic evidence of H2H and was the subject of a larger number of wire reports.

I had taken the position that the father was actually infected with a second H5N1's because of the large number of chanes in the father relative to the other members of the Karo cluster.

However, the above statements could not be properly confirmed without the full sequence. Friday the sequences were released at Los Alamos and the sequence presented in Jakarta was missing. The CDC had two isolates from the father and Hong Kong had another, yet each HA sequence differed from the consensus by a single nucleotide, which is in line with the number of differences reported for other family members.

I noted on the flutrackers message board that there was no public HA uence with the 9 changes.

http://www.flutrackers.com/forum/showpost.php?p=23918&postcount=131

I did not comment on the significance of the absence of the reported sequence.

anon_22 follows me around and posts misrepresentations, which I don't think are useful for intelligent discussions. After banning me on fluwiki she held a public lynching

http://www.fluwikie2.com/pmwiki.php?n=Forum.TheHenryNimanControversy

She now seems to want to extend the attacks here.

Henry: Thank you for the clarification. Note that anon2 and anon22 are different people. Anon22 is not following you around. Anon2 is someone else (I know this to be true).

Most journals do require that GenBank accessions be provided before papers are accepted. The NEJM does not explicitly require this in their instructions to authors. Even so, I agree with Dr. Niman that abscence of a publicly available sequence for the 2002 Chinese sequence is odd. Perhaps an email to the editors would be helpful.

Dr. Niman, I don't think Anon2 is anon_22.

On the missing H5N1 sequences from China, I did contact GenBank and they did indicate they had no record of a submission of the 2003 isolate from a fatal case in Beijing.

This paper is unusual in that there was no sequence submitted. I don't think that a requirement of release of a sequence prior to publication (or at least acceptance) would be very workable.

Many sequencers are reluctant to make sequences publuc prior to publication. That is why almost 100 sets of sequences of H5N1 in Europe are held a Weybridge.

Requiring release prior to acceptance would probably not be very workable. Some sequencers do reelase sequences prior to acceptance, but making that a hard rule would probably slow submissions of manusrcipts or redirect submissions to journals that did not have such a rule.

Now that all 8 gene segments of human isoaltes in Indonesia have been released, the failure to match avian sequences is quite glaring. These sequences have a number of polymorphisms that are in all or most of the human sequences on the lower branch of the HA phylogenetic tree (in green)

http://www.recombinomics.com/phylo/Indo_Karo_HA1.html

In addition to the novel cleavage site RESRRKKR, these isolates have a large number of polymorphisms on HA and the other 7 gene segments that are not found in other Indonesian H5N1's (or other public H5N1's at Genbank or Los Alamos) even though the genetic background of these sequences is clearly Indonesian.

Many of these polymorphisms are frequently found in mammalian isolates, including humans, swine, dogs, and horses - some are listed in the flutrackers discussion

http://www.flutrackers.com/forum/showthread.php?t=8856

These data suggest that there is an alternate source of the H5N1 found in humans in Indonesia. Although Australian has received 91 recent avian H5N1 samples and will likely soon have recent H5N1 data, the prevelance of these unique mammalian polymorphisms in the human isolates, as well as a reasonaby large number of public Indonesian avian H5N1 sequences from 2003-2005, suggests there will be few if any avian matches.

The rant by anon2 is self serving, in the same way she/he accuses dr niman of being self serving. I have yet to really understand the motive, but Anon2, I don't need you to protect me from being MISLEAD!!! I am a layperson. I went to this blog initially and primarily to hear up to date discussions about H5N1, because it was listed as a resource on crof's site. I do have a strong generalist background in the life sciences because I've been teaching it for 20 years, but I appreciate the detailed input from the variety of specialists that write comments herein. Truth, knowledge, insight...these only arise when one is open to this wide variety of viewpoints, when intelligent, insightful argumentation and discussion help us to see all sides of this complex picture. Rants against one side, trying to poison the well, are disturbing and destructive. So what if it turns out recombination isn't the method - or only method - by which H5N1 evolves into a killer strain. The point is the virus is evolving, mutating, changing...and Dr. Niman's work is one way of helping us to keep track of those changes so we can be more aware of them and decide - along with all the other data - whether they indicate an emerging danger. I don't know what anon2 is expecting from this site, or why he/she thinks Niman is only writing stuff to get publicity and make money (he hasn't asked me for a donation yet): But my own personal motive is to be able to warn my children and grandchildren in California as this virus continues to emerge, hopefully so that they will take action in time to save their own lives if that is possible: Also to warn my students and school here in Hawaii in a timely manner if it looks like the danger of a pandemic is imminent so that we can plan for that contingency and keep safe. I don't want any information shut off from me that can help me do that.

In Thailand, Indonesia, Laos and Vietnam there are ever increasing numbers of suspect cases of human flu with serious symptoms similar to H5N1, along with verified large scale outbreaks of H5N1 in poultry in the same areas the human flu cases are occuring. The majority of these cases so far have been determined to be ordinary (non H5N1) cases of flu, but as Dr. Niman points out the 5% death rate for these cases is unusually high for ordinary flu. Couple that fact with the incidence of bird flu in poultry in the areas and the fact that this is not even the flu season, and it gets a little peculiar, to say the least. I'm one of those simple-minded types that thinks if it walks like a duck and quacks like a duck, it might just be a duck. Could these cases have been misdiagnosed, accidentally or otherwise? Could H5N1 now be a virus with lower mortality but higher transmissibility? Has there been a reassortment with ordinary flu that is screwing up the test results? Can someone with the expertise hop in here and give me some answers? (educated guesses are fine)

In the educated guess department there does seem to be some evidence for more severe seasonal flu such as in New Zealand. I wouldn't put much stock in the 5% number. I think we'd be hard pressed to put a good number on the total cases of seasonal flu in the US or any other country and the attendant fatality rate. I just don't think the testing and reporting is there and there are a lot of epidemiologic inferences. I think these inferences are esp suspect in countries with a larger variety of flu like illnesses. Wider testing for H5N1 in Thailand, Indonesia and other places would certainly be useful.

The 5% number, if accurate, most likely indicates some mortality from H5N1. Concerning seasonal flu mortality in the U.S. From Thompson WW, Shay DK, Weintraub E, Brammer L, Cox N, Anderson LJ, Fukuda K. Mortality associated with influenza and respiratory syncytial virus in the United States. JAMA. 2003 Jan 8;289(2):179-86. (You'll have to register to read the article.)

"Annual mean influenza-associated mortality rates for underlying pneumonia and influenza deaths, underlying respiratory and circulatory deaths, and all-cause deaths were 3.1, 13.8, and 19.6 per 100 000 person-years, respectively (Table 5)."

Marissa, thanks for pointing out the above article. It is definitely rigorously done and very useful. I think they met their stated objective 'To develop a statistical model using national mortality and viral surveillance data to estimate annual influenza- and RSV-associated deaths in the United States, by age group, virus, and influenza type and subtype'.

I also found it interesting that they confirmed that influenza A(H3N2) was associated with the highest attributable mortality rate, followed by RSV, influenza B, and influenza A(H1N1).

Definitely an excellent study that would be great to see applied to countries with endemic H5N1 with possibly adding tests to dengue and chickungunya. regards

now, what is with the Karo-sequences ?
No H2H can be seen from the sequences. But exactly this
was the reason for a large campaign in the press a few
months ago. Declan Butler published an article about it
in Nature. It gave new activity to require the release
of the Indonesian sequences, which finally was successful.
Now that the sequences are there and they don't show what had been reported, nobody cares. Don't we need some clarifying statements from WHO and Nature ?

anon: We have been careful to say we didn't think the sequences were the Golden Key. Making the sequences public is a policy matter, a matter of principle. What the Karo sequences will reveal we don't know yet. It is incorrect to think you will "see" H2H in sequences. They reveal their information in the context of other sequences, which is why it is important to have them all available.

reading the other comments now...
it seems that some people are assuming there are still other sequences from Karo which have not yet been released.
I can't see the evidence for this. We have 3 sequences
in HA for the father and 3 for the son, more would be unusual. Also the sequence-names match the names
on the presented phylo-trees. Just the mutations
aren't there. Maybe the source for the earlier reports
was unreliable. Maybe they redid the sequencing and came to another result. They should give a comment now.