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Tracking the next pandemic: Avian Flu Talk

H7N9 Charts and Math

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oriel View Drop Down
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Post Options Post Options   Thanks (0) Thanks(0)   Quote oriel Quote  Post ReplyReply Direct Link To This Post Topic: H7N9 Charts and Math
    Posted: April 08 2013 at 9:48am


Please post additional quantative data here in this thread for additional analysis.

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Post Options Post Options   Thanks (0) Thanks(0)   Quote Albert Quote  Post ReplyReply Direct Link To This Post Posted: April 08 2013 at 10:11am

Hi again Oriel my friend.  Unfortunately I have to move this post to the General Discussion forum as Latest News is only for "news".  However, i must say, you did a great job on gathering the data and creating the graph.  Well done.  

Feel free to venture off into the General Discussion forum and join in some of the discussions and see the reply to this post.

Best.

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Post Options Post Options   Thanks (0) Thanks(0)   Quote oriel Quote  Post ReplyReply Direct Link To This Post Posted: April 08 2013 at 10:16am
I like things in there proper place so, not a problem.
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Post Options Post Options   Thanks (0) Thanks(0)   Quote Albert Quote  Post ReplyReply Direct Link To This Post Posted: April 08 2013 at 10:21am
Yes, I suppose you would buddy. 

Keep up the good work.  Seems like you will have a lot of good useful information to contribute.


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Post Options Post Options   Thanks (0) Thanks(0)   Quote pheasant Quote  Post ReplyReply Direct Link To This Post Posted: April 08 2013 at 4:46pm
Very nice, thank you Oriel.
Looking forward to the time laps for perspective.

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Post Options Post Options   Thanks (0) Thanks(0)   Quote oriel Quote  Post ReplyReply Direct Link To This Post Posted: April 09 2013 at 6:38am


Data is sparse. Current model relies on correlated media reports.
Trend is narrow which suggests modulating (tightening) factors in data reporting or collection. Small sample groups usually exhibit more sporadic growth trends
Significantly more data is required for any conclusions.
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Post Options Post Options   Thanks (0) Thanks(0)   Quote oriel Quote  Post ReplyReply Direct Link To This Post Posted: April 10 2013 at 4:11pm


Not looking any better.
Very consistent growth and mortality.
I expect deviations soon as incubation period and morality cycle effects kick in. This data includes the first case recovery.
Anyone with quality reporting data please forward links to me.
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Post Options Post Options   Thanks (0) Thanks(0)   Quote jacksdad Quote  Post ReplyReply Direct Link To This Post Posted: April 10 2013 at 6:04pm
Despite the size of the sample group, there's still a pretty solid trend and it's not looking good. The authorities wasted no time in announcing the improvement of two of the critical patients which tells me the rest of them must still be pretty sick, and I think we can fully expect more to succumb (if they haven't already). That said, if this continues to spread at the ever-increasing pace it's currently demonstrating and becomes an epidemic at the very least, the finite supply of hospital beds, ventilators and antivirals - the early use of which is likely the reason so many critical patients are seemingly surviving - will begin to become an issue and we'll see survival rates drop.
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Post Options Post Options   Thanks (0) Thanks(0)   Quote oriel Quote  Post ReplyReply Direct Link To This Post Posted: April 11 2013 at 1:53pm

I am amazed at how consistent the growth rates are.
This is unusual for such small sample sizes.
If I had to guess, tomorrow there will be 6 more cases and a new death.
Notice I used the word guess and not prediction.
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Post Options Post Options   Thanks (0) Thanks(0)   Quote pheasant Quote  Post ReplyReply Direct Link To This Post Posted: April 11 2013 at 2:02pm
Thank you once again, these tracking graphs really put perspective to the outbreak.
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Post Options Post Options   Thanks (0) Thanks(0)   Quote roni3470 Quote  Post ReplyReply Direct Link To This Post Posted: April 11 2013 at 2:12pm
Is it me or do the graphs look like they are trending good? I mean not good in the sense of the fact the virus is there to begin with but good in the sense that it could be much worse.
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Post Options Post Options   Thanks (0) Thanks(0)   Quote jacksdad Quote  Post ReplyReply Direct Link To This Post Posted: April 11 2013 at 5:36pm
Now they know it's a virus and they're most likely treating new patients with Tamiflu as soon as they show symptoms, we'll probably see much better results for a while. But it's a relatively small group and their resources aren't being stretched right now. If this becomes hundreds needing antivirals and ventilators instead of dozens it'll be a different story.
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Post Options Post Options   Thanks (0) Thanks(0)   Quote oriel Quote  Post ReplyReply Direct Link To This Post Posted: April 11 2013 at 6:08pm
Data suggests that this virus has a 5-7 day incubation and comes on fast and strong (at least in the reported cases). I don't think antivirals will do much IMHO.
It is in slow motion right now (perhaps do to the fact that reporting seems "limited" to severe cases).IF the virus develops better transmission traits without loosing lethality then just pray that they come up with an effective vaccine fast.
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Post Options Post Options   Thanks (0) Thanks(0)   Quote oriel Quote  Post ReplyReply Direct Link To This Post Posted: April 12 2013 at 2:32pm

My "guess" was off by rounding error.
I am in awe of the stability of the trend. The only real jitter is in mild/stable vs critcal/serious cases due to conflicting reporting or just plain lack of detail.
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Post Options Post Options   Thanks (0) Thanks(0)   Quote pheasant Quote  Post ReplyReply Direct Link To This Post Posted: April 12 2013 at 3:05pm
I really cannot say enough how important this thread is, the charts add another dimension to the discussion. Thank you for keeping them Oriel.

What would be a extrapolation for 5 days from now? assuming no media/ Government manipulation?
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Post Options Post Options   Thanks (0) Thanks(0)   Quote oriel Quote  Post ReplyReply Direct Link To This Post Posted: April 12 2013 at 4:41pm
I am very hesitant to do an "extrapolation" with so little data that frankly I do not have great confidence in. Having said that YOU could infer from my charts or other people's reports that this outbreak "seems" to be growing at 15% a day (I am shocked at how consistent that 15% is). So 15% a day for five days from a level of 43 is very easy to calculate.. 86 (rounding of course). I have no confidence in that number as anything other then a target for Chinese reporting. That was a cheap shot so feel free to ignore because my math is actually very un-biased. I have proprietary mathematical models that would have way more value but frankly the data is too sparse yet for anything. This is a the sort of thing that gets easier and more accurate with larger numbers and more data.
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Post Options Post Options   Thanks (0) Thanks(0)   Quote pheasant Quote  Post ReplyReply Direct Link To This Post Posted: April 13 2013 at 5:07am
Yea, I do not want to put you on the spot. I realize at the beginning of this process too much is unknown and everything is subject to wild swings.

For instance during the last H5N1, we saw no reporting during the weekend, with all the numbers of new cases being reported Monday. Then later, we saw just weekly tabulation by the WHO, and Governments.... all in an effort to control the polarization tied to the bad news.

Another observation we made was, as cases rose, testing was backlogged, and they were focusing on reporting "suspected" cases.

If I am right, and the monitoring agency's continue their past methods of reporting, we will need another line on the chart for "suspected" cases.

As a side note: I agree and definitely think some or all the reporting in the very near future will in fact be "approved" "target" numbers...so as to meter out the information to the public.



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Post Options Post Options   Thanks (0) Thanks(0)   Quote oriel Quote  Post ReplyReply Direct Link To This Post Posted: April 13 2013 at 10:21am


Only confirmed cases are being reported so far. There is reporting through the weekend. There may indeed be a backlog of testing but it has not been mention officially. There is no rapid test right now so because they seem to be reporting confirmed cases there is certainly a lag effect.
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Post Options Post Options   Thanks (0) Thanks(0)   Quote DANNYKELLEY Quote  Post ReplyReply Direct Link To This Post Posted: April 13 2013 at 1:45pm
Thank you oriel this is very helpfulClap
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Post Options Post Options   Thanks (0) Thanks(0)   Quote oriel Quote  Post ReplyReply Direct Link To This Post Posted: April 14 2013 at 5:44am

This is provisional because there may be more data today.
first real movement (not very large) in trend.
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Post Options Post Options   Thanks (0) Thanks(0)   Quote oriel Quote  Post ReplyReply Direct Link To This Post Posted: April 14 2013 at 2:45pm

Best timeline graph out there.
By Dr. Ian M. Mackay of Virology Down Under
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Post Options Post Options   Thanks (0) Thanks(0)   Quote oriel Quote  Post ReplyReply Direct Link To This Post Posted: April 15 2013 at 2:53pm

New format to accommodate other peoples reporting and better consistence with regular reporting sources.
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Post Options Post Options   Thanks (0) Thanks(0)   Quote oriel Quote  Post ReplyReply Direct Link To This Post Posted: April 16 2013 at 9:26am

I am not happy with the progression of the outbreak but I am relieved with the chart seeming to have jitter since that gives me a slightly better feeling that it is not being adjusted.
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Post Options Post Options   Thanks (0) Thanks(0)   Quote Elver Quote  Post ReplyReply Direct Link To This Post Posted: April 16 2013 at 11:51pm
According to Reuters only 10 of the 77 infected had contact with poultry.  16 people have died, almost 20.7%.
 
 
I just got back last night from Beijing & Shanghai.  We were servied Chinese food in several restaurants while on land. 
 
Probably unrelated, but we estimated that 30% to 40% of the people on the ship were sick with the Norovirus.  We based this figure on how many of our specific tour group got sick.  Holland America was really secretive about the outbreak numbers.  They refused to tell us the actual number of people infected or even the percentage.  They cited their reason as "passenger privacy".  I wasn't asking for names, only numbers so there should NOT have been a privacy issue.  A manager at the front desk told me that they didn't have code yellow or red on the ship, which was a bold faced lie as we found out from several crew members who were obviously coached later to say nothing, or because the ship quit sharing information with them.  Also, we heard that Holland America tried to blame the outbreak on a group of passenger's who had an overnight excursion in Beijing, but I happen to know that at least 7 people were infected with the Norovirus prior to us even docking in Beijing and we were already at code yellow at that time because of it!  Holland America was trying to keep the facts hidden from the passengers and tried to lay the blame on toursts who spent a night ashore in Beijing.  I feel that their motivation was selfish because they didn't want to become headlines on FOX or CNN.  The bottom line here is that if you travel with Holland America don't count on them being upfront with the passengers about any outbreak aboard their ships.  I feel that their practice of secrecy is unethical with no concern for the passengers who may want to isolate themselves for preventive reasons.  They only care about their image while refusing to give the passengers accurate information about the outbreak.  On the other hand they were great at cleaning the ship after the outbreak got completely out of control.  They had enough hand sanitizers aboard that I'm surprised they didn't require us to actually bathe in the stuff.  We were supposed to hand sanitize before and after pushing the elevator buttons, before going to dinner, and before walking down certain common hallways.  Cleaning on Holland America during the early stages of the Norovirus was haphazard and sloppy.  Cruise with them at your own risk.
 
Hopefully, someone on the Holland America "Volendam" ship will report the actual numbers which would them put them on this list.  However, I'm not holding my breath on them giving out the truth when they wouldn't even tell the passengers.
 
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Post Options Post Options   Thanks (0) Thanks(0)   Quote oriel Quote  Post ReplyReply Direct Link To This Post Posted: April 17 2013 at 2:31pm

Nothing to add. Numbers telling the same story. As we progress it will be more useful to switch to week to week rather then day by day but for now...
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Post Options Post Options   Thanks (0) Thanks(0)   Quote Guests Quote  Post ReplyReply Direct Link To This Post Posted: April 17 2013 at 5:01pm
Elver, I was impressed with Norweigan on our recent trip to Hawaii. They had people cleaning handrails and as you went into breakfast, lunch or dinner in they buffet they had a person at every enterance with spray sanitizer and and sprayed EVERYONES hands. I thought that was really good. All other sit down eating places where you were served,they had sanitizer at each enterance and most people used it.

Sorry you had a bad experience. I can say that my Norweigan Cruise is the last cruise I will ever go on because of all the problems with illness and possible break downs that can happen on a cruise. That being said if you want to see Hawaii and most all of the islands the Norweigan cruise is the only way to go.
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Post Options Post Options   Thanks (0) Thanks(0)   Quote Elver Quote  Post ReplyReply Direct Link To This Post Posted: April 18 2013 at 12:54am
The cruise was OK until I got sick and the ship's people started lying about everything. 
 
H7N9 infection count is now 83.   Most have had no known contact with poultry.
 
Several weeks ago it was reported that thousands of dead pigs were dumped into the river and floated into Shanghai, along with birds and fish.  Then it was reported that some of this diseased pig meat found its way to people's tables.  Could this tainted pig meat have started this virus?  The Shanghai authorities are saying that there is no link between the pigs and this H7N9, but they don't know much of anything yet, so how do they know this?
 
They covered up SARS in 2003.  And the Chinese officials told people that the water was safe to drink even though thousands of dead pigs were floating in it.  Now the Chinese are blaming the pigeons for the H7N9 virus.  Perhaps these poor pigeons ate the putrid pigs that floated down the river.  Whatever the cause, I believe that the Chinese officials have a huge credibility problem.
 
The World Health Org. said that there was no H7N9 virus found in pigs or farms so far.  I wonder if they checked the dead pigs.
 
Anyway, the dead pigs, ducks, swans, & fish coincide with this H7N9, so I don't know how the link can really be ruled out.
 
Check out this short video.  http://www.youtube.com/watch?v=zE_W4Ow_O04
 
Body fishers pull dead human bodies out of rivers also. 
 
 
 
 
 
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Post Options Post Options   Thanks (0) Thanks(0)   Quote oriel Quote  Post ReplyReply Direct Link To This Post Posted: April 18 2013 at 1:21pm
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Post Options Post Options   Thanks (0) Thanks(0)   Quote roni3470 Quote  Post ReplyReply Direct Link To This Post Posted: April 18 2013 at 1:34pm
I love these charts.  It still seems to be trending well to me.  Mortality has continued to go down since it started.  the amount of discharged patients is going up faster that deaths.  I know we may not be hearing the whole story but for now, I will feel better about the situation.
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Post Options Post Options   Thanks (0) Thanks(0)   Quote oriel Quote  Post ReplyReply Direct Link To This Post Posted: April 19 2013 at 5:14am

Update of Time line by Dr. Ian M. Mackay of Virology Down Under
His work is excellent.
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Post Options Post Options   Thanks (0) Thanks(0)   Quote oriel Quote  Post ReplyReply Direct Link To This Post Posted: April 19 2013 at 5:22am
If you look at time lapse versions of these charts and graphs (not posted here) you will see that the onset dates (as expected) are about a week or more behind the reporting period. This suggests that at any time there are cases in the field that are simply not yet captured by reports. Reports are always lagging. The picture is exactly that and only a picture of what we have captured not the true situation. The further in time we get the better the picture we have of the past and the better predictive picture of the future we can estimate. I believe we still know very little and regardless things could change quickly.
I will say that this outbreak is by no means under control (by any reasonable definition). We do not know how it is spreading and that is key.
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Post Options Post Options   Thanks (0) Thanks(0)   Quote oriel Quote  Post ReplyReply Direct Link To This Post Posted: April 22 2013 at 1:54pm
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Post Options Post Options   Thanks (0) Thanks(0)   Quote oriel Quote  Post ReplyReply Direct Link To This Post Posted: April 23 2013 at 7:52am

If you think the case rate is significantly slowing down you may want to review this excellent chart by Dr Ian M. Mackay of Virology Down Under.
Notice that the lab turn around time (estimate) is significant to the drop off in rate. Each type of chart depending on what exactly you map can give you a different perspective. Dr Mackay does a great job of giving different chart that reveal different perspectives
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Post Options Post Options   Thanks (0) Thanks(0)   Quote jacksdad Quote  Post ReplyReply Direct Link To This Post Posted: April 23 2013 at 8:46am
The Chinese hospitals must be treating at least some of the critical victims with mechanical ventilators and as we know from experience here in the west, they are a finite resource. Even if the numbers of infected are being under-reported, we're going to hit a point where the resources of the hospitals are going to be overwhelmed by the critical cases requiring ICU beds. When they're unable to censor the extent of the problem any longer, we'll see the death rate start to ramp up.
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Post Options Post Options   Thanks (0) Thanks(0)   Quote CStackDrPH Quote  Post ReplyReply Direct Link To This Post Posted: April 23 2013 at 11:51am
Originally posted by jacksdad jacksdad wrote:

The Chinese hospitals must be treating at least some of the critical victims with mechanical ventilators and as we know from experience here in the west, they are a finite resource. Even if the numbers of infected are being under-reported, we're going to hit a point where the resources of the hospitals are going to be overwhelmed by the critical cases requiring ICU beds. When they're unable to censor the extent of the problem any longer, we'll see the death rate start to ramp up.


Great points! China does not have the modern hospital networks of the more advanced Western countries, and many rely upon traditional Chinese medicine, so my guess is that reported cases are severely under-reported. Some families are likely reluctant to come forward due to fear of local/national Communist party officials.

Also, I believe that human-to-human transmission explains the epidemic curve and mortality (older men). The "older men" aspect reminds me of another epidemic I worked on, i.e. Legionnaire's Disease in the USA. Older men/veterans were particularly susceptible due to high rate of smoking, reduced immune system response and exposure to concentrated pathogen levels (air conditioner carryover).

Many inapparent/asymptomatic infections have been reported in younger Chinese, so this thing is ramping up. I predict it will continue to reassort and eventually break out. China, being Communist, must be terrified of this, as the population is already very restive. Even though they are putting up a "new face" of openness, I'm not sure I believe it.
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Post Options Post Options   Thanks (0) Thanks(0)   Quote pheasant Quote  Post ReplyReply Direct Link To This Post Posted: April 24 2013 at 6:37am
Oriel, I am confused, as I cannot seem to understand the latest graph.
am I correct to infer that the drop off in reported cases, is a reflection of the slower turnaround time of the labs?

Or in other words, we can expect a surge of new confirmations after the 17th?
Forgive me if I am seeing the information wrong, but it looks like the testing lag, directly affects the reported cases.

Also another question, the WHO reported that there are approximately 100+ milder, unreported cases most likely, how do we treat that unknown in this analysis?
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