Effect Measure

CDC unfreezes US flu isolates

Good news from CDC. Yesterday they announced immediate public release of some 650 influenza gene sequences. The new openness is part of a collaboration with the Association of Public Health Laboratories (APHL):

Through the new collaboration, CDC expects to provide genetic information for several hundred influenza viruses per year as a way to encourage more research on influenza. The sequence data will be available in nearly real time through Genbank, a public-access library for virus sequences managed by the National Institutes of Health, and through an influenza database housed at Los Alamos National Laboratories (LANL). The information added will include viruses from the annual flu season in the United States, any animal influenza viruses that infect humans and any novel strains that may emerge such as avian influenza H5N1. The new agreement will only apply to viruses isolated in the United States. (CDC Press Release)

CDC’s syas this ratifies its longstanding commitment to open sharing of influenza virus information. One might then ask how it happens to have 650 unreleased sequences, But I guess this is a time for positive reinforcement.

We note this new transparency relates only to viruses isolated within the US. CDC recently released sequencing they did on the Indonesian H5N1 viruses after that country publicly approved their release. CDC might also have other H5N1 sequences from Turkey or elsewhere that are of great interest to the international scientific community.

It would be good to see this new spirit of openness extended. The ice is breaking, but spring is not yet here.


  1. #1 william
    August 23, 2006

    The unfreezing of US flu isolates is good news.
    What is not good news are the reports from Asia. First, the Cabinet in Thailand was told 2 days ago by medical specialists human bird flu was spreading rapidly.
    Second, the human cluster in Cikelet is now at 20 victims.
    Just using common sense, it is probable there is H2H in Cikelet. How many more human clusters of H5N1 are there in Indonesia and Thailand we do not know about?
    It is clear human bird flu is now spreading rapidly in Asia, and it is probable the rapidity of this spread will now increase.
    What would you conclude are the implications, if the rapidity of the spread of H5N1 in humans now increases in Asia?

  2. #2 David
    August 23, 2006

    William, those are some pretty hefty asssertions and conclusions! Where did you get the information about the Cabinet in Thailand? Where did you get the number of 20 victums in Cikelet? There are several confirmed cases and many SUSPECTED cases. This number of 20 includes unconfirmed cases.

    You go from your statement about Thialand, several confirmed cases in Cikelet, Indonesia to “It is clear human bird flu is now spreading rapidly in Asia.” That is quite a leap… reminds me of a syllogism from my logic class:

    God is love
    Love is blind
    Stevie Wonder is blind
    Therefore, Stevie Wonder is God.

    You need to quit trying to incite hysteria!!!

  3. #3 David
    August 23, 2006


  4. #4 tan06
    August 23, 2006

    Good news about those new 650 published sequences. Thanks, CDC! Well done!
    Now keep on testing.
    Is someone already investigating a measurable influence of Tamiflu on test results from H5N1 infections?
    In Erasmus University on ferrets or so?

    Another question:
    Who (no, not the WHO) anyone on EM can tell the clusters summed up in Flu Wiki are more or less enough to declare phase 4? Who can tell the recemt clusters in Indonesia are big enough to declare phase 5?
    I know it has to do with estimating the risk of or nearness of a pandemic. We have been posting about that risk some time ago. Can we make an update about it now?
    Has anything changed now sequences are published, or is that a wrong interpretation?
    A political use of declaring phase 4 is to get people ready to prepare for a pandemic.
    All countries that are preparing very well should be named as an example of good political management and their way of doing so should be described or linked.
    Other countries could learn from them. Giving information to civilians doesn’t have to cost a lot, is my guess. It could even be done by trained volunteers. IMHO.

  5. #5 tan06
    August 23, 2006

    Or would such an interpretation be seen as some form of punishment for releasing the sequences?
    Maybe someone from CDC or WHO who is reading this could answer this question. I’d be delighted.

  6. #6 william
    August 23, 2006

    If you go to the address shown above you will encounter the information regarding the presentation to the Cabinet of Thailand.
    And if you go to http://www.newsnow.co.uk/birdflu
    you will find information form Than Nien Daily News specifying there are 17 victims of H5N1 infection in Cikelet. And today,
    Henry Niman at http://www.recombinomic.com stated there are now 20. At the bottom of his post you can go to the media reports confirming the information.
    As you will see the reference to the Cabinet meeting.
    Thank you for stating I am trying to produce hysteria. This only shows your ignorance as to how serious the situation in Asia is. You obviously do not believe there is H2H in Cikelet. If the Cabinet in Thailand is informed the number of human H5N1 infections in increasingly rapidly, I am only reporting a fact.

  7. #7 Solitaire
    August 23, 2006

    William, I don’t in any way underestimate the seriousness of the situation with human H5N1, however, I read the article from The Nation earlier today as being human flu in general that is rapidly increasing in Thailand rather than H5N1. The article doesn’t make it very clear what type of flu they were talking about but the advice that people protect themselves with flu shots would indicate seasonal flu.

  8. #8 Sue in NH
    August 23, 2006

    I don’t think William is being hysterical. I suspect he conclusions will be shown to be pretty accurate.

    If people get a bit scared by what William says, maybe they will make some preparations and encourage TPTB to do so as well.

    A little fear is appropriate right now, as the possiblities are quite dire.

  9. #9 william
    August 23, 2006

    To observe a cluster of 20 people in Cikelet; to observe 6000 people with pneumonia over a specified time period in Thailand, and note there was a 5% death rate among the 6000, which is very high; indicates, in my subjective opinion, H5N1 is being more efficiently transmitted by H2H transmission.
    If you think I am causing hysteria by stating these facts; that too is your subjective judgement.
    The issue is not whether or not I am trying to produce hysteria. The issue is that the H5N1 virus is mutating rapidly, and may soon obtain the ability for sustained human to human transmission. And if it does, it won’t require me to produce hysteria, since it will already exist.

  10. #10 M. Randolph Kruger
    August 24, 2006

    William. Everyone here agrees that the pooh pooh is about to hit the rotary grinder. I wish I had a hundred like you here in Memphis. The school systems pandemic plan is encompassed in the light reading 650 page disaster preparedness plan for the state. After informing the PTA of the seriousness I started getting calls and putting people onto my email update list and directing them here, to Niman, and to Flu Wiki. It has been like pouring gasoline onto an already blazing fire. I dont think what you are doing is producing hysteria. More like generalized irritation. The people here already know what is happening and more so what is not. Most have reconciled themselves to the inevitable and we are going to be burying people. I think you are down in South America if I read it right. Your ability to inform people down there would certainly be if you are a US citizen a one way ticket to the local jail. But be helpful. The Catholic missions down there control everything. You would be a great help if you could inform them thru those churches. Hell, buzz into the ministry of health and OFFER to help inform people. You got the time to post here you have time to spend 30 minutes in a mission once a week teaching hygiene and dont eat dying birds to the people even if it has to be translated. Get on out there like I have and send out lists for pandemic supplies, run an email list that posts up from the Wiki, here and there and pull the good hard CONFIRMED information down off the net. Call the CDC assholes/put the WHO on that list but dont keep harping it.

    If this shit comes right now and its even 1/2 as bad as it kills in Indonesia, then the local world is going to beat a path to your door. They will want what you already know because they were bozo’s who sat around watching CNN instead of getting as much information as they could. Fact is that if you can get ten people to do something about this then you will have justified your existence on this planet. Lighten up just a bit on the posts and only bring good hard info thats not out in the public domain or ask questions about the stuff that is.When it comes they will blame whomever is in the White House for the response, even though for almost likely two years they will have been warned. Venting here does no good. Channel it and I recommend that everyone do the same. The LEAST you are going to do is save someones life, the MOST you are going to do is save a bunch.

  11. #11 Solitaire
    August 24, 2006

    William I was only giving my interpretation of an article NOT accusing you of causing hysteria, I didn’t even allude to it, rather the opposite in my opening remark.

    WHO’s statement that there’s no evidence of H2H in Cikelet doesn’t reassure me, it may be factually correct but the evidence was buried before testing imho.

    I know how concerned the Thais are about tests producing false negatives when patients are treated with Tamiflu. I think(?) they said somewhere up to 20% of tests may be false because of changes in the virus itself so I do query the reults of their field testing for H5N1 which are logged on this site, where the ‘update’ is flashing.


    Maybe someone can explain to me what a non-reactive test means in this context?

  12. #12 william
    August 24, 2006

    I apologize for raising the issue of hysteria with you. That post regarding hysteria should have been directed at David.
    The Indonesian government is good at burying the evidence. Five people from Cikelet who died of bird flu symptoms were buried without testing. Or maybe the inhabitants of the village did not understand, and just buried them. I really do not know. But it is a tragedy no testing was done, since it would have probably shown H2H.
    I want to thank you for your post. I learn a lot by getting feedback.

  13. #13 william
    August 24, 2006

    M.Randolph Kruger,
    Your post is like a guiding light for me. I am going to record everything you said and try to memorize it. I admire you because you do not just post here. You act in your community to get people ready, and to save lives.
    You are correct. I am an American living in Medellin Colombia. I speak fluent Spanish, and so there is no problem with communication in my community here. I have tried to get my family members ready, but they just look at me as if I should be placed in a mental asylum, and smile.
    I live in a nice apartment, with guards at the door 24 hours. Medellin is surrounded by mountains, and I have a view of the where the poor live, in the west, on the hillsides. When the pandemic hits, that area of the city will explode. It is like sitting on top of a volcano. You know sooner or later the volcano will erupt.
    But for me it is time to act. I can no longer just sit and wait. I am going to try and communicate with the churches here. Time is rapidly running out. Soon it will be too late to prepare.
    Half the 40 million people in Colombia live in poverty. Many lack food. Their immune systems are probably weak, and as a result, they will easily fall victim to H5N1. Many will die.
    I feel like I am in the calm before the storm. I know the storm will begin soon. It is a strange feeling.

  14. #14 David
    August 24, 2006


    First, let me say that I do not have my head buried in the sand (or anywhere else). Second, it is not obvious that I do not believe there is H2H is Cikelet, basically, because I believe it has occurred. I believe it because of the evidence presented by Dr. Niman. He goes through the available data (much of it gathered from news stories) about familial relationships, where the victims live and sickness onset dates making arguments for which cases were most likely A2H (Animal to Human, since I agree with Niman and Revere that we can not definitively say it is coming from chickens, so the B2H, Bird to Human, is no longer accurate), and which cases are most likely H2H. Niman has written scores of postings where he presents and analyses scientific data, anecdotal data and news releases to create a body of work that I can take seriously.

    You, on the other hand, write three or four sentences and then make the sweeping statement, ?It is clear human bird flu is now spreading rapidly in Asia.? I guess I just took exception to such a sweeping statement with no cited evidence behind it. I followed the link cited in your response. I thought it was interesting that the statement you referred to was made in the last paragraph as an ?oh, by the way? type of comment. This definitely should be a headline!

    ?In a related development, the Cabinet was told yesterday that human flu was spreading rapidly.?

    As far as the 20 victims, they have not all been confirmed. Niman lets us know that only three of these have tested positive. Again, they may have bird flu (or have had it in the case of the five who are dead and buried without being tested), and most likely do. But you stated it as confirmed fact without any references. As Niman and Revere both point out, the number of cases is probably under reported. You may be right, it just may be that the pooh pooh has now hit the fan! Also, I believe if it has not yet started, it is just a matter of time, and if not this month, or even this year, it is very likely to happen sooner rather than later. — But again, that is my belief, not a provable scientic fact!

    As a final comment, I fear the damage that may be caused by the panic and hysteria that may ensue once a pandemic begins about as much as I fear the pandemic itself.

    Good luck in Columbia,


  15. #15 David
    August 24, 2006

    The question marks (?) around the sentence above are supposed to be quote marks. I guess that is why I should use ‘Preview’ before I post. I was not questioning the validity of the statement… sorry if there was any confusion.

  16. #16 mary in hawaii
    August 25, 2006

    tan06: I agree with your suggestion that maybe it’s time to declare at least a phase 4 if not phase 5. I don’t know why this huge decision is left totally in the hands of one organization – WHO – when it should be a joint decision of many representatives of the world scientific community. If the alert level were raised, those of us trying to warn family, friends and community to take some proactive measures while there is still time might be heeded. As long as WHO leaves the alert level low, complacency persists and people like William (and myself) grow more and more frustrated and concerned that by the time any serious preventative action is taken it will be too late. I doubt that going to a level four would cause any kind of world wide panic or economic collapse – people need to work in order to eat, and don’t run to hidey holes that easily – so for what reason are they continuing to put off such a declaration when it appears by all rights that phase 4 criteria has been met?

  17. #17 revere
    August 25, 2006

    MiH: That’s exactly how it is done. WHO only has the “authority” to set the phases because all the member nations have given it that authority. It has no authority other than what it is given. There is an expert committee of scientists that sets the alert level. So what you suggest is what is happening now. Because raising the alert level would also do exactly what you say — set in motion a lot of other things — they are being circumspect in doing it. It is a button they only want to push when they think the time is right. Many people wanted them to push it a year ago. It is a judgment call. You or I may disagree with it, but the system for doing it is just what you suggest.

    “They” are you, and your government, and your representatives. Like democracy, it’s a lousy way of doing things but probably better than all the others.

  18. #18 Marissa
    August 25, 2006

    Tan06: Until we have >25 in a cluster we won’t be in phase 4 according to the new rules. That means WHO first of all has to define that we have a cluster, and that we have >25 bona fide cluster members. I actually think this is a reasonable benchmark because it will signify a much more efficient h-2-h transmission. Everyone’s talking about h-2-h but the fact is, it is still very limited. I’m guessing with an R value of barely over 1.

  19. #19 mary in hawaii
    August 25, 2006

    Marissa: Can you provide a link to these new rules you mention. I was only reading the vague definitions provided on the WHO website for the general public, which is why I thought by those definitions we were already at phase 4.
    I would like to do an online lesson with my students about avian influenza as a first step in mobilizing a community effort to plan and prepare for this incipient pandemic, so I want to be sure to be accurate and up to date.
    thanks, mary

  20. #20 Kevin
    August 25, 2006

    Consider SARS. A new virus emerges, with a CFR > 10%. It’s much more contagious than H5N1 is today. It’s from a family of viruses known to have examples that are both very contagious in humans ( the common cold ) and known to mutate rapidly. Sustained H2H transmission is documented from Day 1. No effective treatment available. A reasonable assessment is a devasting pandemic is inevitable.
    Instead, it disappears. The conventional analysis is that hospitals were acting as amplifiers, and once effective isolation and infection control procedures were implemented, and the animal resevoirs were identified and controlled, the virus was contained. Not a very satisfactory explaination. There was widespread H2H outside of clinical settings, the setting was densely populated Asia, and it’s unclear the animal resevoir was ever controlled or if it remains controlled today.
    Cold comfort re the H5N1 situation, since what it really shows is the depths of our ignorance. It does show that anyone making firm predictions about the progression of H5N1 is likely wrong. A case could also be made that we should be equally worried about a resurrection of SARS, or some completely new zoonotic virus. I believe the WHO’s Pandemic Alert level is likely correct. There are too many unknowns at this point, and I’m not convinced that any of the actions Stage 4 or Stage 5 would trigger are warranted at this time.

  21. #21 mary in hawaii
    August 25, 2006

    Questions to Kevin and Marissa: Re phase 4 criteria is >25 in a cluster. The problem I see is that the variables and unknowns Kevin talks about are not on the side of overcounting but on the side of undercounting. From the data, reports and analysis by Dr. Niman, local health authorities, various well informed and educated blog pundits etc, it would appear that there is a very high probability that actual cases of H5N1 in this latest indonesian cluster are being significantly undercounted. There are family members and close contacts of known/confirmed H5N1 cases that have been buried without testing, (thus not counted); there are mass treatments with tamiflu of potential victims in the entire area which may be masking the symptoms of those with mild cases so that they are not even tested, or giving false negatives in tests of those who do have the symptoms, and so on. Considering the size of the current cluster and the way it is growing, we may be approaching or have even exceeded the >25 benchmark. In order for the >25 benchmark to be useful and definitive, it has to be accurate and inclusive. It is not. And that’s scary.

    I am wondering, Kevin, what actions you believe a Phase or stage 4 alert would trigger, and how dangerous or damaging to the social infrastructure or economy of the global communtity these might be? If it turns out we are not in that stage, and the pandemic never arises, how much harm would be done? On the other hand, if we are actually at stage 4 due to undercounting for the various reasons above, and we do not alert the public, what might be the outcome?

  22. #22 Kevin
    August 26, 2006

    The ‘cry wolf’ issue is large. This is a call you can only make once. Get it wrong and credibility is gone. The actions I’m thinking about are travel advisories or outright bans, repatration of nationals ( big issue for multinational companies ), large scale vaccine production using any of the current clads as seed strains, etc.

    I don’t think any of these are warranted at this point.
    If moving to Stage 4 triggers none of these actions, then what exactly does it achieve? CNN would cover it for a few days, and unless something dramatic happened, it would then fade from view. The actions that are most useful are ones we should be taking regardless of ‘Pandemic Alert Level’: Public Health infastructure investment and research on rapid vaccine development and deployment for any new pathogen, not just H5N1. Anti-Viral drug research.

    The ‘stage’ concept has an element of inevitability to it – we assume linear upwards progression is guaranteed. I don’t think we know enough to assume progression is certain, nor that it would be linear or even always forward. After all, SARS vanished. In any case, the path H5N1 ultimately takes doesn’t depend on WHO Pandemic Alert levels.

  23. #23 mary in hawaii
    August 27, 2006

    The boy who cried wolf syndrome is certainly a possibility, but the alternative is to fail to warn in time for the sheep to be saved at all. Tough call, I agree. But one problem in hesitation is that it takes time to mobilize resources on this scale, and if the call is made too late that simply won’t happen. Unfortunately most of the people I know are completely unconcerned and will no doubt remain so until they or their loved ones are coughing up blood on the bedsheets. If raising the alert level could raise the level of intelligent concern and planning among the public without pushing the panic button, that would be ideal. But the reasons behind the alert would have to be presented in a manner that evoked that sensible response, and that would require two things in short supply: responsible political leadership and non-sensationalising journalism…

  24. #24 revere
    August 27, 2006

    MiH: It’s not just crying wolf, but it’s the things that happens when you do it. Our position here has always been that the missing ingredient has been, from the beginning, public health leadership, most conspicuously by the Bush administration, whose CDC turned a blind eye to this for years while touting the bioterrorism non-sense, but the rest of the public health establishment, including academia, has been missing in action as well.

    The closest thing to leadership (and it came late) was Mike Leavitt going to all the 50 states. This has been extremely helpful but it is narrow in scope and hasn’t had the resources behind it needed to make it truly effective.

    With proper leadership and leaders, we would have started on a vaccine a decade ago and possibly not be in the precarious position we are now in. We’d have an effective vaccine, antivirals, a robust public health system and enough global capacity to handle the pandemic everyone saw as a possibility.

    Now the task is to get the current set of shit heads out of office and replace them with some that understand what needs to be done (invest in public health and social services). Many democrats don’t get it (and they should be shunned) and virtually no republicans get it. Find a good candidate that does get it. It’s not the answer but it is part of the answer.

    Meanwhile, as in Iraq, we are stuck with the mess their incompetence has left us (this includes the Clintonites who disinvested in public health and social services). Just don’t “stay the course” in this, too.

  25. #25 mary in hawaii
    August 27, 2006

    Revere: I couldn’t agree more. Which pretty much leaves us on our own to act locally. I think that’s okay, because depending on big government to step in when there is a disaster only leaves us more vulnerable. They are what is called a “camouflaged hole”. They are in position, presumably ready to help, but the fact is they are completely unable and unwilling to do so. If you think they will take over and get you what you need if the pandemic hits, you are in trouble. Best to work and plan around them in small, manageable community units.

    Marissa: I looked up all the preparedness plans etc on the WHO website. Presuming that what they have posted is the most up to date, the WHO GLOBAL INFLUENZA PREPAREDNESS PLAN, page 8, states under Phase 4 “One or more clusters involving a small number of human cases, e.g. a cluster of less than 25 cases lasting less than 2 weeks. The arrow points left. (for some reason my computer is not picking up that symbol, sorry.) You wrote in your response above that the WHO benchmark for Phase 4 is “more than” 25.( arrow pointing right) Phase 5 is described as “a cluster of 25-50 cases and lasting from 2 to 4 weeks.” So really, aside from the one missing protocol (not found in this document but in their containment response plan) of one health care worker infected, the Cikelet cluster would meet the phase 4 criteria.

  26. #26 tan06
    August 31, 2006

    Marissa, Mary, Kevin, Revere, I like to thank you all for underlining the necessity to inform others by giving your information.
    I (a little disordered) lost this comment line for some days and now it’s the first time I read it.

    One of the hardest things to do when we inform people is, to explain the core information of why we are so concerned and why published articles cannot take away our concerns.
    For example, when I read today about a dog in Thailand that contaminated H5N1 by eating ill chickens and they say ‘bury your ill and dead animals’ I think burying was not the right thing to do in the first place, but in the massive and panickly organized culling they started to bury animals (alive as well) because killing and then burning them was too much for them to get the job done.”

    Then they start writing about vaccines: …”We hope to establish a vaccine factory within the next three to five years. Our factory will have capacity to produce two million vaccine doses a year,” he said. …
    And in the same article the last sentence goes:
    “However, were such human-to-human transmission take place, the country would have a supply of up to 10 million doses of the vaccine agains human influenza.”

    This is the news line:


    Now someone not so alerted and without the background information most of us have, would not know a pandemic outbreak now means: no vaccine factory, no vaccines.
    And some who don’t know they supply human influenza vaccines like H3N2 or H1N1 in order to prevent recombinations or reassortments in humans will read: Well, there will be human vaccines from somewhere against bird flu (H5N1) so the government will have them and I can trust the government, see. Geesh, that’s good, they can always start to vaccinate people and the problem will be solved.
    So to analyse the facts for the uninformed and new people on this blog and in the newspapers is a hell of a job.
    It’s part of the problem why we can’t get people to start being really alarmed and ask how they can do anything themselves to reduce the impact of an outbreak of H5N1.
    Only the people who like to go very deeply in a blog like this and like to read these kinds of comments and who start to follow the news every some days will discover the facts behind the quotes and statements. (That is to say, when they know the ways and actively chase the news, as I consider the taboo on H5N1 news in my own country.)
    They need to be curious, a little alarmed, a little intelligent (English and specialist language), tenacious, critical and courageous.
    Not that I like to boast on those properties, but I think most who post here recognize it. (And my English still isn’t as good as I wish, I know, but I consider it a minor problem and priority 😉
    Some who can’t be critical can compensate by asking.
    Some who aren’t specialists can look things up, study the flu wiki and ask questions.
    But especially the non-curious and non-alarmed and/or non-courageous people might have an emotional problem because they stop reading about how to psychologically and practically prepare for a pandemic to a level they decide to be up to.

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