Effect Measure

CDC has just concluded a press briefing and the big news is there is no big news. In fact there was hardly any small news. The major questions have been identified — how transmissible, what is the epidemic curve, are there more cases in the US, are there subtle genetic differences in the US and Mexican versions to account for the apparent difference in clinical and epidemiological features, etc. — but answering them will take longer.

Meanwhile, no new cases have been identified in the US, but CDC in collaboration with state and local health departments and the academic and medical sectors are working doing aggressive case finding. Critical care clinicians are being asked to look carefully at acute pulmonary distress and atypical pneumonia cases and suspect cases of flu-like illness in recent travelers to Mexico or the affected areas in Texas and California are continuing. No positives have yet turned up but everyone expects more confirmed cases to be recognized. The general scenario is for a primary health care provider to do a rapid flu antigen test which can tell quickly if a patient has influenza A or B but not what kind. Influenza A specimens then go to public health laboratories in the states to be subtyped (whether it is H1N1, H3N2, H5N1). The state labs now can do these fairly sophisticated analyses because of training consequent to the concern over H5N1 (“bird flu”). This is a good example of how infrastructure development has served a virtal public health purpose. If the specimen is untypable by the state lab it is sent on to the CDC reference lab in Atlanta for a closer look. CDC says that even these untypable specimens can usually be typed by CDC but sometimes something new appears, and that is the case with this virus. After sequencing it was clear it was genetically different than anything in their libraries. This required construction of new PCR primers.

There was no new information about the situation in Mexico, except to say that “the situation is serious. We in CDEC are worried.” Some, but not all, of the specimens from severely ill or deceased cases sent from Mexico is the new swine flu virus (7 of 14 specimens). While there is still no explanation for why the disease appears more severe, this is one of the top questions to be answered. Is it some difference in the information (looking at severely ill versus routine surveillance of outpatients), some difference in the virus (while the viruses are said to be “genetically identical” this is true only in the parts that have so far been compared) or some co-factor (e.g., co-infection with another pathogen). Determining the epidemic curve in Mexico or anywhere else (the evolution of cases over time) for a viral syndrome that is very non-specific (lots of noise from other viruses that cause the same syndrome) and for which diagnostic tests are time consuming, specialized and often unreliable is inherently difficult. It requires painstaking, tedious and time consuming effort. Us of the scanty and spotty syndromic surveillance systems in the US so far does not indicate an unrecognized outbreak of mild disease but CDC and state health departments are looking hard.

It is very clear that CDC has given this the highest priority and it sounds to these ears that they have very competent and dedicated personnel devoted to it. But reliable science takes time, care and some patience, even in circumstances where urgency is high and patience in short supply. That’s just the way it is.

CDC has constructed a new and easier to navigate website for this: http://www.cdc.gov/swineflu

Perhaps the most important message is that this is a good time to move forward on strengthening the public health infrastructure and to get ready for the one thing we can be certain of in the days ahead: there will be more uncertainty.

Comments

  1. #1 anon
    April 25, 2009

    At least some of the specimens from the kids at the school in New York have swine flu. Will be announced soon.

  2. #2 karen
    April 25, 2009

    CNN just reported that some of the NY students had positive type A swabs – it COULD BE swine flu, but they don’t know yet. The swabs have been sent to the CDC for further testing.

  3. #3 Anon
    April 25, 2009

    Maybe this has been posted already.
    Swine-flu outbreak linked to Smithfield factory farms

  4. #4 anon
    April 25, 2009

    there must be some estimates, how the number of cases
    in Mexico is processing. Is it growing like
    a flu wave where ~20% of the population will be
    infected or not ?

  5. #5 Patch
    April 25, 2009

    anon,

    It appears a majority of typed flu this season has been type A. So it’s not good news, but we shouldn’t be surprised to see that additional testing is required.

  6. #6 chezjake
    April 25, 2009

    That article at Grist is inflammatory and inaccurate. I don’t think there’s ever been a documented case of influenza transmitted by an insect vector (correct me if I’m wrong, Revere). While it’s entirely possible that those hog farms are the source of the current virus, there is thus far no direct evidence of it. If it is the source, then the transmission was most likely from farm workers to other local inhabitants (and who knows if the combination of human, swine and avian viruses took place in hogs or in humans).

  7. #7 M. Randolph Kruger
    April 25, 2009

    Well folks lets not jump too quickly on New York. It takes a couple of days to get a PCR test result. Just cause you got an A result in a quick test doesnt mean H1N1’s newly improved cousin is in New York. Now if its confirmed then we got BIG problems. But I am betting not.

    H1N1 IS swine flu. Its the newly improved version thats killing people… Which part though that created the change, A+B, Avian sequences or the porcine improvements?

    Now here is my suggestion and its couched in more than one table top. I and others have harped for years for personal responsibility in a pandemic. There aint gonna be no federal govt response and frankly if it comes to Tennessee… We are number 4 on total effects out of 50 states cause we are a transportation center in every sense of the word. So, after sundown tonight run on down to the local store and load up with enough for six months. Costs are going to go up anyways, so its cheaper now than after the new administrations taxes kick in. Think of it as investment.

    If it comes, you are mostly prepared. If you need a list hit me at memphisservices@bellsouth.net and I’ll send you one. Its a suggested list and this is bringing home the bacon…Sorry Revere… I couldnt resist, but it is stuff you should have at all times anyway and tailored for your locale. Tornadoes, quakes, bird flu, swine flu and voodoo. You still need to eat unless you are planning to check out of the Humanity Hotel permanently. If you wont prepare, do it for your kids. Redundancy. Revere doesnt like religion but you know the Mormons will rule the earth if this comes in high numbers. Why? Because they are the most prepared people I have ever seen. Most have a years worth of food, enough to pull in a harvest.

    Revelations said the end would come like a thief in the night. To me that means a quick and silent end. Nukes? Bird bug I think would be pretty quick or even this stuff. Either way, its yet another thing we have to deal with and unless you get off this blog and get moving you wont be here to say I made in in a year or two from now. That is if you believe its coming. Me, I do. I would seriously prefer that Revere do it as well, if not for himself but those grandbabies. If the pathogenics hold true then the son and wife as are my own kids are on the chopping block for H5N1 or H1N1. Only intervention that prevents infection will keep them off the selectee’s list.

    Dont wait for the confirmation if you are in DC/Boston and of course the New York area. You will avoid the rush by about 72 hours. If not, you simply roll the stuff back into what you would normally be using.

    Cheaper, remember its cheaper.

  8. #8 karen
    April 25, 2009

    NYC Health Dept news conference now – 8 of 9 swabs are PROBABLE SWINE FLU – it’s flu A that they can’t type therefore they think it’s swine flu

    200 children ill – illness is mild, no hospitalizations, very short incubation period

  9. #9 Miles Teg
    April 25, 2009

    I agree with chezjake. The article at Grist is unfortunate, unhelpful, and highly speculative. I performed a cursory search on PubMed an found one article that described the detection of AI H1N5 from Blow flies collected near a poultry farm in Kyoto, Japan. I also found a second article that detected AI H1N5 in blood-engorged females using RT-PCR. In neither case was transmission from the vector to an uninfected host performed.

  10. #10 Phila
    April 25, 2009

    Revelations said the end would come like a thief in the night. To me that means a quick and silent end. Nukes? Bird bug I think would be pretty quick or even this stuff.

    So it’s God’s will, eh? That explains your palpable enthusiasm every time there’s bad news.

    Either way, its yet another thing we have to deal with and unless you get off this blog and get moving you wont be here to say I made in in a year or two from now.

    No need. I plan on being raptured, like all good people.

    Who cares? God will know His own.

  11. #11 Johann
    April 25, 2009

    i may be completely off base here, but could this have anything to do with all the synthetic biology research that has been going on recently? I mean, I’ve heard that it seems to be a mix of different viruses
    -Johann

  12. #12 Miles Teg
    April 25, 2009

    Of course in my previous post I transposed the numbers. I mean to say H5N1. My apologies.

  13. #13 M. Randolph Kruger
    April 25, 2009

    Phila… you are a skanky troll. Is there anything else you want to say today? Go ahead and get it off your chest. Blowphonia.

    From your usual personal attacks I think that God WILL know his own. Personally I leave it up to Him and not an idiot from Oregon. But I am biased that way. I can quote chapter and verse when I am shooting for the military too but that doesnt make me righteous..You need to get a grip.

    Johann… Unless they can track it back to an animal they are going to have to call it full blown H1N1 with a sexed up variant. What that variant is we dont know yet. Psychoflu? Folks H1N1 is a type A, they havent come to a positive conclusion. If it is then why would it pick this one school in New York when it has San Antonio, Brownsville and even Mexico City left to attack? PCR and then call it. The sequences in California, Texas and Mexico are well known now. Its a simple match up. Headline grabbers? Dont know but as long as its not continuing in Mexico, Texas or California then dont sweat it so much.

    If it is going pandemic then it could also lose quite a bit of its kill capability…Right now I put it at 7.5% based on the numbers and that was in the briefing sheet this morning. They put it at 8% based on the existing numbers at the time of the printing. But they have slid back on that 1000 cases, and the dead. Originally it was 80 now its thought to be 62. Thats a lot if you live in Mexico City. But 8.9 million people live there. That makes the attack rate incredibly small. If those kids are found to have it, then the attack rate is very high (how many kids in the school?) using the school population rather than the population of New York.

    On the other hand though, its not something to ignore. I havent gotten a clear answer on whats different in this and the usual H1N1 other than offhanded comments about it containing A+B, Swine and Avian. Okay, well that just about described most of the bugs we humans get now and likely will for the one we eventually get.

    But you should prepare. We wouldnt want you not to be chosen by Phila.

  14. #14 M. Randolph Kruger
    April 25, 2009

    How quickly things change. H1N1 detected in Kansas……

    New York is still questionable as to type.

  15. #15 revere
    April 25, 2009

    Randy: NY virus is not questioned as to subtype. It is untypable with their primers. This means in this case it is pretty surely swine flu. Please try to keep the comments thread tidy and keep length of posts down. Use for informing or asking questions, please. This is not just directed to you.

  16. #16 Phila
    April 25, 2009

    Phila… you are a skanky troll. Is there anything else you want to say today? Go ahead and get it off your chest.

    No, that pretty much covers it.

    And even if it didn’t, people are coming here for information, so I’d prefer to keep the signal to noise ratio as high as possible. No one’s interested in what I think of you, or vice versa.

  17. #17 Pork Flu
    April 25, 2009

    Would the media not be allowed to publish mortality rates because of “national security” or not to cause panic? I don’t think if this goes widespread that I’ll ever hear anything in the news. A few years ago in the town where I live there was a legionnaires disease outbreak in July 2005 where people died but they did not even let anyone know about it until after the tourist season was over a month later in August 2005. Even the mayor got it and was in the hospital, but no one knew it was happening. “At the time, state health officials asked Shaw not to publicly announce that he had Legionnaire’s disease. He said they wanted to investigate the cases without causing a panic. When he was hospitalized July 1, his illness was listed as pneumonia.”
    http://mathaba.net/0_index.shtml?x=297441

  18. #18 paiwan
    April 25, 2009

    “And even if it didn’t, people are coming here for information, so I’d prefer to keep the signal to noise ratio as high as possible.”

    Thanks, Phila. It is an important value for us and for Randy- a general and generous care for a human being. :-)

  19. #19 M. Randolph Kruger
    April 25, 2009

    You know Revere I generally dont start out stabbing people when I come into a room. I wait until they attack first.

    Do you have any evidence that there is a match to California/Texas/Mexico on the stuff in NYC? Remember, its all DHS now and my sources are pretty good that this isnt the Mexico stuff. But there is the Kansas critter thats just been found too. I prefer to keep an bit more open mind about it. It doesnt seem that its extending today in Mexico, so without any transport vector to NYC its going to be a hard sell. Not impossible, just a hard sell without the connecting tissue. .

  20. #20 are u serious?
    April 25, 2009

    Are you serious? Cases in mexico, california, texas, kansas, and new york. Next will be Washington DC, Miami, Detroit, Toronto and then every place in between. First, some dirty mexicans OBVIOUSLY brought it here. Second, it IS a bio weapon, how the heck else do you think 2 human, avian (bird), and swine flu cross mutated into a HUMAN RESPIRATORY capable infection!?!?!?! This does not happen in the real world, it happens in labs. Its going to pandemic BECAUSE it is AIR BORNE and there is no proof whatsoever that it has a FAST incubation period. It is probably the exact opposite. Reading the insanity about flaming above reminds me of the MORONS who watched the planes hit the building on 9/11 but now think that it might have been government placed explosive charges that demolished the buildings. READ the ACTUAL NEWS REPORTS and determine for yourself the simple concept. 4 variations of flu in a single virus that is AIRBORNE and infects H2H (and probably human to avian/swine) breaking out in 4 HIGHLY POPULATED AREAS and so far a single less populated area (Kansas). ARE YOU STARTING TO SEE A PATTERN HERE!???????

  21. #21 revere
    April 25, 2009

    Do you have any evidence that there is a match to California/Texas/Mexico on the stuff in NYC? Remember, its all DHS now and my sources are pretty good that this isnt the Mexico stuff.

    You trust your “sources” too much. And it’s not all DHS. They are only peripherally involved. It’s CDC, state and local health and the medical community. Your sources obviously don’t know what they are talking about. I laid out the testing procedure in the Briefing post. The NYC were untypable flu A, which in this case almost certainly means swine flu (that’s based on the current prevalence of that kind of untypable virus and follows from Bayes Theorem). To determine if it is indeed swine flu it is necessary to use specific primers that only CDC has. The specimens were sent to Atlanta this afternoon and the PCR won’t be done before tomorrow. So there is no confirmation one way or another but a very high prior probability it is swine flu.

  22. #22 Lindsay Beyerstein
    April 25, 2009

    Mr. Kruger, have you checked in with your gang of 13 virologists and epidemiologists lately?

  23. #23 M. Randolph Kruger
    April 25, 2009

    http://www.cdc.gov/mmWR/pdf/wk/mm58d0424.pdf

    Now the California cases, one in particular had a 104.3F temp. Thats pretty good for me. And they were sent to Canada too Revere, and Germany, France.

    The move to Pan 4 or higher will cause a major, major problem with transportation. Repatriations by companies would take weeks if not months on that declaration. Automatic for ten companies in the UK that I know of, a goodly portion of the Japanese companies and loads of people from the US. Might instigate a recall from Iraq and Afghanistan, the Balkans. Yeah, you are right, politics. My sources are operating on what is known and I have had to bring my operation up to full strength already as have several of the cargo carriers. Anticipation or preparation?.. You have some doubts as to who will be in charge if this goes down? I dont at all.

    I am not saying its not swine, I am asking what version is it of H1N1. Does it match California/Mex/Tex? Not that I have been able to determine and the question is being asked by more than one group. Have the symptoms matched in NYC to anyone who got into trouble with it? Not that I can see but if you have something in print I would like to see it. Its the nuance stuff from the New York briefing that I call into question. If they think its swine, then why arent they out closing the churches, Madison Square gardesn, concerts? Hey, they are supposed to be erring on the side of caution.

    I am certainly not seeing that and if they do and then find out it is swine then okay, they did it right. Else they are doing it wrong and making statements they havent seen it before really isnt cutting it in the heartland. I would really rather hear more about the Kansas cases to see if they match any of the previous stuff or are close. The school is closed due to an abundance of caution… Why isnt New York if this is the bug or believed to be?

    Those tests BTW can be carried our right here in Memphis Revere as St. Jude is a designated lab too.
    Look I am not being combative. I want to know why NYC officials are not flipping out? They just closed Mexico City for the better part and they have 1000 cases and we have the suggestion of 200 in a single school? Does it make sense?

  24. #24 Brian Cimmino
    April 25, 2009

    Regarding Mr Kruger’s comment about NYC officials not taking the swine influenza seriously:

    No one in the US has died from this strain. Flu outbreaks in school are a common occurence. Many colleges frequently experience flu outbreaks in which hundreds of students become sick.

    Perhaps if the strain mutates into a more deadly form, then there might be cause for concern.

  25. #25 M. Randolph Kruger
    April 26, 2009

    Lindsey yes, the cup is half full with them. They want to know what this stuff is before they start spouting. One is already wondering if its already mutated out of kill capability. It was the timing that was his question. New York? He hasnt a clue and rides with Revere on his pony on that one.There was a heckuva lot of ILI in March down this way and then it surged a bit in Tenn. Same kinds of symptoms though.

    Truckers roll from Mexico City area to Dallas in their 8 hour DOT mandated truck treks. Then from there its 8 hours to Memphis. After that they go 8 to Chicago. He also wanted to know if any of the NYC kids or a teacher had been to Tex/Mex or California. But, no data. They are all scratching their heads right now all the way back into China as to how it jumped to a single school. This was the crux of what I was asking Revere. It made sense… How did it bypass the rest of America after San Antonio? The Kansas cases are only in the last 24 so its a very valid question. There is one answer and it would explain it. JFK is right adjacent to Queens. Whats the vector Victor?

    Brian is echoing the racket but its still good racket. If its supposed to be the same stuff as Mexico, why arent the doors shut? This was the question from many. I am still asking it. So if they have H1N1 is it the Mexico Mauler or is it the San Antonio version? Brian I guess the better question would be at what point did the Mexico stuff start killing people by numbers. AT X cases, did it roughly start killing 1 out of every N? Or is it just another flu bug we have to deal with in the future. And is it adding any new cases anywhere that anyone knows of except the BA flight attendant?

  26. #26 Kevin Hayden
    April 26, 2009

    That would explain Friday’s runup in the shares of Novavax (stock symbol: NVAX).

    But since they’re only in Phase 2 clinical trials, I wonder, should a pandemic occur, is there a way to expedite the process of approval so they can get a vaccine out in time to help? (I’m not daytrading, just wondering if a potential solution can be rushed to protect populations, particularly the healthy young adults this current flu seems to be hardest on.

  27. #27 M. Randolph Kruger
    April 26, 2009

    Whats the Vector Victor. Ooooh man talk about politics. We have known about the kids for almost 72 hours in New York and not once, not once has the media asked the important questions. No and for the love of God I cant understand why they would withhold the most key point of information about those kids….They were in Mexico last week on spring break. How come no one asked or answered or even volunteered the information?

    Panic….Lindsey. They are trying to get everything into place now I think. i was brought up to speed on Tuesday without even the slightest of ideas why except to move loads of vaccinia which is kind of like gamma globulin for smallpox that has been sexed up for flu. It apparently works. Destination….San Diego via moderate sized cargo jet.

    Now, things begin to fall into place. My friends you mentioned indicate to me that this is far more serious now that the info finally comes to us about the spring break trip. Now their question is why they havent had anything but mild cases…Age? .

    We should all be outraged at the media. The love affair will end when people start dying here.

  28. #28 J.R.
    April 27, 2009

    R U Serious….. Swine flu pandemics of the past and current avian strains develop because people live in extreme close proximity to animals (sometimes in the same rooms). They usually come from poor underdeveloped areas. Several pandemics have occured historically, even before we knew the science of viral replication and influenza. Keep up with the conspiracy theories, they amuse a lot of us.

  29. #29 Ichthyic
    April 27, 2009

    Tornadoes, quakes, bird flu, swine flu and voodoo.

    voodoo?

    MRK…

    suggest you stop snorting so much crank and take a nap or something.

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