Yesterday we posted on the failure -- the refusal, really -- of Indonesia's Ministry of Health to release any of the human flu sequences or isolates. Indonesia is now the country with more fatalities than any other, having passed Vietnam for that dubious honor. We now learn via Declan Butler that Indonesia had also been withholding isolates from poultry.
Nature has learned that very few -- if any -- avian flu samples from Indonesian birds have been sent to official labs for sequencing over the past year.
The data blackout comes just as surveys of the country are revealing a startling number of previously unrecognized avian outbreaks.
"We have had no sequence data from poultry viruses for Indonesia for almost a year, since last August," says Peter Roeder, a consultant for the UN Food and Agriculture Organization (FAO) in Indonesia. "It just happened; no one was sending any samples," he says.
Experts say that without thorough genetic sequencing of bird viruses from the area it is difficult to tell whether the virus is mutating, or how the human cases correspond to birds in the area. There have been some human viruses found in Java that so far have no obvious avian counterparts: perhaps simply because matching strains in birds have not been sequenced, or perhaps not. (Declan Butler, writing in Nature)
Butler now writes this has recently changed, perhaps because of the large human cluster in Karo that sparked alarm and new interest. A meeting held in Jakarta at that time revealed a bleak picture of an Indonesian "black box" for viral isolates. This seemed to shake loose a pile of new isolates, 91 of which have finally arrived in Australia for sequencing. The government has also finally organized, with international help, some pilot surveillance and control teams. What they are revealing is not very comforting:
The Jakarta teams alone have discovered an average of 24 previously unknown infected locations a week between January and May. "The community surveillance system is starting to work," says Roeder.
You read that right. Not 24 new infected locations in all. 24 infected locations a week over five months! The place is a fucking bird flu fermentation vat and they are withholding sequences and isolates?
Maybe WHO is trying quietly and diligently to get them to shape up. If so, it isn't working. They need to do ito do it noisily, not quietly. WHO is too timid. It may have no legal authority to force the Indonesian government to release the isolates, but they can use the bully pulpit to put needed pressure on them. They should do it now.
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It's absolutely wrong of them to withold the material of course. That said, making a big public production out of it is not too likely to help. Turn it around, and assume the WHO noisily demanded that the US release witheld disease data or materials - the rumble of US lawmakers rushing to make releasing it illegal just to spite a "foreign power" would be deafening.
An average of 24 infected locations x 22 weeks = 528 infected locations around Jakarta only....
Politics and Science...a bad mix.
Don't think we should expect that it will ever be any different when the WHO is under the authority of the United Nations.
The solutions are going to have to be community based...whether a community, a community of communities (country) or a commmunity of countries.
Tom: Not sure what you mean. WHO is under the authority of the UN. It is a UN agency.
I think there's a typo and the word in this sentence should be NOW rather than NOT
"Indonesia is not the country with more fatalities than any other, having passed Vietnam for that dubious honor."
BC: Right you are! My apologies to all. Corrected.
Now we know why Hideki wasn't allowed to treat those sick people last month...Ever tried to cram a cat back into a bag after he is out?
As for the WHO...well maybe its time to put the FRENCH in charge. Revere, remember what I said about those boats?
The place is a fucking bird flu fermentation vat and they are withholding sequences and isolates?
Revere, it's a failed state. Please don't expect Indonesia to perform up to Scandinavian levels of professionalism and transparency. That simply will not happen. Ever. Unless, perhaps, the Indonesians are forced by irresistable outside pressure to address H5N1 with the urgency it deserves.
I recommend a brisk read through Richard Lloyd Parry's In The Time Of Madness to get an idea of just how fantastic a mess Indonesia really is.
It is a place where, as recently as the late 1990s, interethnic conflicts led to thousands of people in West Kalimantan being not only decapitated with machetes, but then having their corpses subjected to ritual cannibalism. Parry was personally offered a piece of long pig on a skewer by a grinning Dayak tribesman. Ugh.
Parry points out that urban Indonesia isn't much better off. In the vicious rioting attendant upon the last days in office of Suharto, every precinct of Jakarta was torn to bits -- by residents of Jakarta itself. The author notes that there have been many cases in history of capital cities being sacked, but that this one is unique in that the sack was at the hands of the city's own citizens, rather than by outsiders.
Let us agree that it would be of huge utility to have accurate and timely H5N1 information released by governments everywhere in the world (including by the government of the United States). However, let us temper with realism any expectations about how likely it will be that such releases will ever occur.
Especially in Indonesia. It is just everyone's bad luck that such a variegated and disorganized place turns out to be ground zero for bird flu.
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Based on the above, how close are we to a pandemic? If I were a chicken I'd already be down on my scrawny little knees praying to the great cluck. Obviously it is already a global pandemic for birds: round and round it goes, getting worse with every pass. That fact alone is going to cause some massive human problems, since chicken is a major source of protein for people who can't afford beef. Which is the vast majority of the world population. If we end up having most of the world's poultry die off from flu or preventative culling, then even if the virus never mutates to a human form, it's an impending health catastrophe none-the-less. From global famine. And if this house of cards we call international economics gets shaken too hard by the effects of massive starvation across the planet, we can expect the same sort of collapse of our infrastructure as we'd have if 15 to 30% of the population became unable to work due to the flu. So, stockpile away. Meantime, considering the mass famine angle, do you think someone in charge might start trying to figure out a better way to stop the spread of bird flu than killing all the healthy birds in the area before they get it? Proactively, mightn't they carefully slaughter, and then take the birds to special facilities where they could quickly cook the suspect chickens thoroughly, saving them in great freezers for redistribution to the public as needed? Once cooked and then frozen, the poultry wouldn't pose any danger from bird flu. I'm not saying cook the ones that died from flu, but the apparently healthy ones nearby, rather than simply disposing of them.
Would someone please clarify for me... Have the isolates all been proven to be avian flu? If so, have they all been proven to be h5n1 and it's just a matter of sequencing?
Brooks: We are only discussing H5N1 isolates and sequences. There are two issues here, one, the sequences and the other, the isolates themselves (i.e., the physical virus). In the human isolates (i.e., the actual viral material) sequencing has been done outside Indon but the sequences not publicly released. In the poultry isolates, it's not clear the sequencing has been done. 91 isolates (the actual specimens) have been sent to Australia within the last week or two so the sequencing can now be done but that doesn't mean the information will be available to the world scientific community. Moreover the isolates themselves are important beyond the sequencing because we cannot as yet predict the biology from the sequencing alone. So we need to conduct additional studies on some of the isolates to see how they behave biologically. China releases sequences but not isolates so that is only partially satisfactory.
M in H. Tyson and Pilgrims Pride are testing (or so they say) every bird they prepare to sell. Their system is set so that the test is started before they are heading down the conveyor to the last visit and with a three day lead time. I have no idea what it entails to do a test on a bird (swab the throat and into the lungs?.
Three things bother me about this and Revere/Tom DVM could back it up a bit with more information. First is the birds in a factory setting are pretty weak when it comes to contagion. Second is the by products are reprocessed from the slaughter. I know of only a few of them (feed for one) and the others are pit arrangements and they are allowed to dump it into the waterways. Third my pucker factor is up a bit because what do you do post of a notification? You have a freezer from Hell filled with chicken? I dont think freezing kills the virus and they sure as Hell aint pasteurized. So if the pandemic is on its way and it hasnt hit the birds then I would load the freezer with them for a major portion of my food, else in country I would be burning them if it was here already and my lot/batch number came up.
Revere/Tom. How do they test a chicken for it? What kind of measures are they taking to ensure one doesnt infect a conveyor belt?
Marquers slur about Indonesia being a failed state is simply that. Parry's book is about the overthrow of Suharto and the liberation of Timor-leste and a lot of water has flowed under the bridge since then. Not least including the institution of Presidential elections and reform of the judiciary. As to accusations of cannibalism this hoary old chestnut is often trotted out third or second hand - I havn't read the book but I seriously doubt the truth of the following
"Parry was personally offered a piece of long pig on a skewer by a grinning Dayak tribesman. Ugh."
The word amok is Indonesian in origin. In Javanese society (which BTW should not be compared to Kalimantan or Borneo etc.) politeness and calmness are regarded as highly important. A single swear word, or raised voice in polite society is cause for consternation and condemnation. The importance of consensus and face are paramount. This cultural nuance enables Indonesia to hold together in spite of the incredible challenges facing the country on a daily basis (apart from bird flu they've had to contend with 2 tsunamis and one major earthquake in the last 2 years).
When the US survives an overnight 4-fold increase in the price of fuel and flour and doesn't collapse into anarchy it can be compared to Indonesia - then we will see which country can be called a failed state.
kyangdac:
Thank you for your post. What do you think would be the most productive method for the WHO to adopt in getting better cooperation and data from within Indonesia? What, in your opinion, is the cause of the problems we are having in getting samples & sequences.
Tom DVM:
You and I are never going to agree on the importance of the UN & WHO however I like your "a community of countries" idea perhaps we could call it the United Nations and have a special organisation to deal with health matters 'The World Health Organisation' (just a suggestion). One thing we would need to do though is make sure that the countries that join this club agree to certain rules of behaviour and we have some form of sanctions we could impose if they didnt honour their agreements. If participating countries did not cede any power to these organisations (i.e. it had no teeth) we could end up in a terrible mess.
Revere:
Another possible typo?
"China releases sequences but not isolates so that is only partially satisfactory."
China releases 'some' sequences?
When the US survives an overnight 4-fold increase in the price of fuel and flour and doesn't collapse into anarchy it can be compared to Indonesia - then we will see which country can be called a failed state.
Touche.
Although, kyangdec, I must note for the record that I already consider the US to be a failed state. The anarchy is coming on slowly, but inexorably.
Note as well that I doubt that the American Founders would have had any success in welding together a coherent polity, if they had been presented with the sort of huge geographic, linguistic, cultural and economic divergences which are routine for Indonesia. America worked reasonably well from the start because it had a high degree of internal uniformity. The job was hence much easier.
I don't view Indonesia as a failed state because of some racist idea that Indonesians are unfit for democracy. Far from it. I simply think that its existing confederation of peoples, as it was attempted, is too big and too complex to be able to function as a modern state must.
Perhaps several smaller nations might emerge which would be more independently viable.
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Randy: I agree that there are definitely alot of problems that would have to be met and resolved in this idea to salvage as food as many of the culled chickens as possible. And in a place like indonesia they probably wouldn't be. But in a sane, organized, ideal state, one in which the government takes off the blindfolds and recognizes that they already have a pandemic - among their birds - and as a result are looking at an incipient human famine within the next year or two regardless of whether the bird flu ever mutates into a H2H pandemic form or not...In that state, proactive government officials would come up with a method to safely take the recently culled, seemingly healthy, poultry from the areas adjacent to an outbreak and cook them. Not freeze their little raw carcasses: boil them. Make them into stewed chicken. Then either freeze or can these cooked chickens for future consumption when the incipient famine becomes a reality. The things you mention as drawbacks could all be handled with protocols that ensure sanitary measures are undertaken at all steps in the process; culling, gathering, transport and cooking. It should be being done now in the areas where the outbreaks are endemic: I am surprised that it's not.
M in H. Yeah, but who is going to be around to do these protocols if there's more than a 3% rate going? Not me thats for sure.
One thing occurs to me Mary. Unless you have good swimming lessons, you might have one Hell of a problem out there if it comes. Hono is a gateway from Asia and SE Asia. I can see MASS starvation happening in short order out there if it comes. You are going to have to have a hooch in the hills or something like it along with a lot of food. Same in Guamania, Wake. etc.
You do have a plan or a plane?
Randy: What I am talking about is not what to do when and if the flu becomes a human pandemic. I was saying that they (indonesia, thailand, china and any others as outbreaks in BIRDS occur) should be cooking all these culled chickens right now, today, everytime they have an outbreak of b2b flu and slaughter a bunch of nearby birds to avoid its spread. Cull them, cook them and can them so when the famine hits from lack of food due to the bird flu pandemic AMONG BIRDS the people in all those chicken-less countries won't all starve. What happens when its a human pandemic, if it gets that far, is a whole different can of worms. But as for me, I live in a relatively rural area of the big island, so I'm not in as bad a situation as those in Honolulu. My real concern is for those of my family still living in the greater Los angeles area of California
As expected the PNAS paper on reassortment caught the attention of the popular press, which predictably misinterpreted the results. The data is NOT new, although it did just get published. It shows that H5N1 does not evolve via reassortment with human genes. This should be the final nail in the reassortment coffin (but this will probably go on and on, absent supporting data).
However, it should be noted that the Indonesian isolate did generate UPPER respiratory infections in ferrets.
Thus, human Indonesia does not have the "important" changes being monitored by WHO and consultants (reassortment with huamn or swine genes or changes at positions 226 and 228 in the receptor bindng domain), yet the huamn isoalte has managed to produce H5N1 in the upper respiratory tract of a mammalian model.
H5N1 is evolving, but not by reassortment with human genes or changes at positions 226 and 228.
The reassortment data has been known for years (most of the data involves the 1997 isolate and was discussed in 2004).
JJackson
re getting Indonesia's co-operation. Couple of points might be relevant. Firstly, as Revere pointed out a while ago, the flare up between Oz and Indonesia over asylum seekers killed a co-operative agreement on Birdflu between the two countries. Foreign Minister Downer is currently in Jakarta trying to re-establish a consensus on some of the various bilateral issues between the two countries. The birdflu samples recently sent to Melbourne may be part of that thaw.
Secondly, Indonesia is obviously having a great deal of difficulty on the ground getting co-operation at village level as was reported by various people following the recent conference there. This sort of village level co-operation is often mediated by the role of the military in Indonesia society which is very fluid at the moment. SBY is an ex-General(might still be one?) and part of a moderate group - but there are some real bastards in the Indo military and these guys will do anything to protect their patch.
The current Aceh situation is instructive, even after the tsunami and peace agreement and lots of international attention there have been recent reports of the military trying to regain its control in the region threatening the peace agreements.
Thirdly, the shadow play, the puppet master, are part of Indonesia political and cultural tradition. Where Parry describes Suharto as attracting some kind of magical mana other local commentators have pointed to his role as a puppet master. Both these viewpoints are popular culture explanations of his power.
Lastly, the reaction of an Indonesia academic(whose name I can't recall) to the publication by Australians of the discovery of Homo floresiensis is instructive. Basically, he locked up all the material, trashed some of it(by using acetone IIRC on the samples which removed any traces of DNA) and generally took a contrary point of view. It was clearly a reaction of a man who had lost face despite having a collaborative relationship with the researchers.
See also Amien Rais' comment on foreign domination recently.(Hat tip to Indonesia Matters. The thing to bear in mind is that Amien Rais is a leftist liberal Muslim who is also highly eloquent in English and very much an internationalist. During the end of the Suharto regime he was often on Oz radio commentating on the various alliances (Democratic and Muslim) that were working for reformasi.
But he is obviously playing to a domestic audience here and it is also obviously fertile ground.
"If participating countries did not cede any power to these organisations (i.e. it had no teeth) we could end up in a terrible mess."
J. Jackson. How messy does it have to get?
If it walks like a duck, quacks like a duck and looks like a duck...it is very likely a duck.
Time for a little fine tuning...after the next pandemic.