Sunday, May 3, 2009

Lab Confirmed A/H1N1 Cases - update



Latest numbers gleaned from WHO, CDC, ECDC, PHAC...


Added link: ht to Market Ticker Forum unedited CDC transcript from this afternoon http://tickerforum.org/cgi-ticker/akcs-www?post=93578



Data request: Any curves similar to figure 2 in this ECDC paper - unfortunately this curve applies to the second wave of the 1918 influenza with an R0 of >3... need similar for R0=1.6 and R0=2.4 http://www.ecdc.europa.eu/en/files/pdf/Health_topics/Lessons_from_previous_pandemics.pdf

Great paper, hat tip Wisdom Speaker - translating the data from the log plots in this paper to the format from the ECDC paper is what I would truly like to see... http://www.pnas.org/content/103/15/5935.full.pdf+html

9 comments:

Wisdom Speaker said...

I like that transcript; nice catch!

One of the comments in the transcript indicated that "laboratories at the state and large city public health level as well as the CDC I would say are operating at full capacity right now."

So we might expect to see the number of reported, confirmed cases growing in a more linear, less exponential fashion.

The CDC spokesdoctor also said " in the days ahead we expect to transition from talking about confirmed cases and states to other ways that we can describe the trends, whether things are getting better or getting worse around the country"

I'm wondering how they plan to do that. One technique would be to use the testing capability to do statistical sampling, rather than trying to measure every case.


In other news, more propagation seen in Britain and Spain. But I don't see "3rd-tier" or later cases there yet (hard to find news articles with that level of detail). So it's travellers to Mexico, and their immediate contacts, so far. Of course it may be that the 3rd-tier cases just didn't get sick early enough to wind through the lab test process yet!

Wisdom Speaker said...

Dr. Schuchat (CDC spokesdoctor on that conference call) also said "We think we're at a point right now [where] we don't need to confirm every single person with a possible H1N1 influenza infection."

energyecon said...

Wisdom Speaker,

Yes. I expect the whole May Day/Labor Day festivities to provide the acid test of whether we will have a pandemic or not...so incubation time etc puts us at a week from today (Monday) or so?

Wisdom Speaker said...

Yes, things will get interesting next week, and even more interesting the week after that! I have an overseas trip next week that could be fun.

Regarding the plot formats - did you try writing to the lead author? The paper gives the address as tcg (at) lanl (dot) gov. But it would not take more than 20-30 minutes to eyeball the numbers on the log plots and plug them into a graphing program. The numbers wouldn't be exact but they probably don't need to be.

For R0 = 2.4 in the absence of effective interventions (my favorite), I read:

New Symptomatic Cases per 10,000 persons:
(Multiply the numbers below by 110,000,000/10,000 = 11,000 for Mexico, 300,000,000/10,000 = 30,000 for U.S., and 6,700,000,000 for world. Have to sum up over time to get the total number of confirmed cases at each time, but during the run-up phase it will be dominated by the new cases...)

Day 0: 0 new
Day 20: 0.1 new per 10,000 pop
Day 40: 10 new per 10,000 pop
Day 60 is just under peak new case rate, 130 per 10,000 pop.

And so on (real life now intervenes).

energyecon said...

Thanks Wisdom Speaker,

I will give contact a shot, I was thinking we were looking at a lower end, more like the 1.6 case - at which point we see peak new infections about four months into it - just read Mexico estimates 1.3 to 1.8, using 1.4...if so, this would seem to be still in very early stages.

Wisdom Speaker said...

I just learned that the R0 is not a constant, it can and does evolve over time as the virus adapts to the new human host. Generally the early R0 is low because the virus is not well-adapted. The viruses that survive the early rounds and spread will have higher R0. So Mexico's 1.4 estimate could be right, for Mexico, and yet too low for the globalized virus.

Flu Transmission Link

Wisdom Speaker said...

Please note that that's a real link to a site discussion flu transmission...

http://www.globalsecurity.org/security/ops/hsc-scen-3_flu-transmission.htm

energyecon said...

Thanks Wisdom Speaker - real life has been intervening as you say - will be updating the plot on weekly basis...

Wisdom Speaker said...

Critical to the global response to the new flu is the question of whether the virus shows sustained transmission outside of North America. Outside of North America, Europe has the most confirmed cases right now and is likely to be the first place where such transmission is seen.

There's now a European CDC site which tracks both the number of confirmed cases and the number with "in-country human-to-human transmission". There are now 17 such confirmed cases. If that number continues to increase, and the cases are shown to propagate further (not just from visitors to North America, but between those who stayed entirely in Europe), then the Level 6 alert would be justified (required?). But according the ECDC there is not yet enough data to draw a conclusion either way. TIme will tell...