Influenza season, part 2

CDC has another snapshot of what the flu surveillance system is seeing up through week 23 (ending June 13). It shows flu still circulating in many communities at a time when most seasonal flu is normally at a very low level. Indeed of the 2765 specimens tested in CDC's network of 150 laboratories, virtually all of the roughly 40% were influenza A (seasonal influenza B has all but disappeared; the others were not influenza). Not all the flu A viruses were or could be subtyped, but of those that were or could be, 98% were novel H1N1. IN other words, there's lots of flu around, but essentially none are the seasonal strains of last winter. They are almost all pandemic H1N1. Here is a bar chart of positive specimens by week:


Strictly speaking this is not what we would call an epidemic curve (the time course of an epidemic), because neither of the two things depicted (the bars or the heavy black line) are the numbers of new cases of flu in a time interval. Let's take the bars, first. The bars are positive specimens submitted to laboratories. The chance a true case in the community is counted here depends on several factors. One is whether the specimen will be submitted at all, i.e., whether a practitioner decides it is worth while to swab a patient and submit it to the laboratory. Once submitted, a lab may make its own decisions depending on workload, priorities and other factors. When the flu index of suspicion is high, as it is when there is public attention, practitioners are more likely to submit specimens. Whether a case of illness will be counted in a bar also depends on the chance that someone with symptoms or signs that are otherwise fairly non-specific will actually have influenza. The chance of all of these factors being true increases as flu circulates in the community, but may do so in complicated ways that make it difficult to compare one week with another. There may also be geographic variations that offset or add to each other for the final national tally.

The dark line is also complicated. It is the percent of all specimens that are positive. You can think of it as the ratio between the bar chart you see and one you don't see: the total number of specimens submitted every week. It is subject to the same factors (the chance of a case getting a specimen taken and the chance the specimen is actually flu) but here the two factors are separated. You can imagine the number of specimens going way up but the number of positives staying the same (e.g., if the criteria for submitting a specimen were loosened or lab capacity suddenly increased to allow it; or the reverse). In that case, submitted specimens would increase without flu increasing and the bars would be the same height but the dark line would go down.

Both of these measures (the scale for the bars is on the left vertical axis, for the dark line, the right vertical axis) are affected by the amount of flu circulating in the community but they show slightly different aspects of it. Neither is what you want for an epidemic curve: the risk of contracting flu in a time interval, although both are affected by this risk (and other things), in a complicated way.

Still, as a surrogate measure they are useful and we see a general pattern here. The end of normal flu season has given way to a second flu season with novel H1N1. Trying to make fine quantitative comparisons between the two seasons is risky for the reasons given and neither hump is an epidemic curve. But that we are seeing a recrudescence of influenza is clear.

Welcome to the pandemic.

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Wow! recrudescence - I LOVE that word. Thnx for the fine toothed comb, stuff to think about.

I have been watching this graph develop over weeks and have figured that on some level, this is the signature of a wave (not clear which # of wave)

I'm curious whether something like this happens in other years (a few cases of influenza circulate out of season) and it's just not noticed because nobody is looking, or whether this is really unique to this strain. And if it's unique, why is it likely to be happening?

Is the difference likely to be in what fraction of people manage to mount some kind of early immune response to it, by having some antibodies that react to it from previous years' infections or vaccines? That would imply that it should spread really quickly once we get into better conditions, but it seems like that should also mean that this year's flu season ought to be really ugly in the Southern Hemisphere, right?

By albatross (not verified) on 23 Jun 2009 #permalink

Are there any data about H1N1 incidence worldwide?

Do you think the virus continues to circulate because virtually nobody has immunity to this strain?

It would be nice to keep this heightened level of "off-season" surveillence over the next two years if not permanently. It would also be nice to get a chart for much more numerous 90% accurate (ie. crappier) PCR samples, though the orange colour would be excluded I assume.

By Phillip Huggan (not verified) on 23 Jun 2009 #permalink

I clicked your "Flu Wiki" link ( I got a warning, "NOTICE: This domain name expired on 06/14/2009 and is pending renewal or deletion".

Greg, go to

It looks like a type of GMO potatoes cause Swine Flu:
Only USA, Canada, UK, Auzzies, and Chile produce these potatoes. Everyone missed the Chile case signal I suspect because everyone assumed case reporting assymetries. French fry consumption is also correlated with modern health services economies...

1) If true this swings the pendulum in favour of *extensive* GMO labelling and EU's prudent stand on GMOs now looks defensible. The Prince was right about organic farming.
2) You'd want to not feed these potatoes to pigs and birds especially, and probably other animals. A diet of these potatoes may even be the source of the outbreak in a Mexican pig farm.
3) Don't plant this strain next year and consider abandoning potatoes in the ground now (maybe can be frozen until flu subsides but I doubt it).
4) Pull these potatoes and issue recalls in all areas where bird flu cases have been reported. Same for regions where immediate starvation/malnutrition isn't threatened. Work to remove from other regions ASAP.

By Phillip Huggan (not verified) on 23 Jun 2009 #permalink

I can tell you that on the front line, this is keeping us very, very busy.

Thank you for the graph as the weblink has been re-transmitted on Twitter.
At the blood drive the Red Cross says they have plans to deal with this situation. Using more room and disposable items.
Mrs Sebalius Secretary of US dept HHS says school children vaccinations are planned in the fall. No word on if they will use needles&shots or air gun. I prefer the air gun as it is fast and does not produce trash. It is a greener solution.
I just whish Mrs Sebalius would continue monty Pandemic webcasts. Descisions must be made & actions taken. It would be best IMO to have everyone work together.
Also September is national preparation month. Prep for Hurricans, Prep for H1n1 and test drive H5N1 bird flu plans., Flu Trackers, Pan Flu information, Fla Medic, et al are all good rescources.

Kobie (of the fluwiki)

For those on Twitter
Hash tags of #h1n1, #h1n109, #swineflu, #planfirst

People to follow: Fla_Medic, EffectMeasure, FluTrackers, CDCEmergency, RedCross, StandingFirmCM,

Get answers and news posts.

KobieT on twitter

Final tought - if the graph and PaMD are right then many people can get sick. If so, that is not only alot of people who could pass along H1N1 but who may be doing the smart thing and staying home. If so, that could be alot of absent employees home sick.
Hence, be prepared. Mexico shut down for a week. If you have kids plan on how they will be taken care of. What home work can they do as daycare should also be shut down.
I look at the graph from week 17 to 23 and see the text books are right - it can happen. Flu can spread like wildfire. I'm glad no one is getting that sick. The graph is real. Even if the numbers are not 100%, they are real cases.


...the faster we stop eating french fries the less likely this will mutate into a non-Fry reliant form. Disclaimer: I had fries for supper and am planning hashbrowns for breakfast tommorrow.

By Phillip Huggan (not verified) on 23 Jun 2009 #permalink

We should have a few months warning of what to expect.

1. The southern hemisphere is having their winter now. Swine flu is in Australia and Chile among other places.

2. Haven't heard anything about the novel flu making its way into the third world. Given their medical situation it could already be there and no one is paying much attention. Between China, India and the rest, that is the majority of humans.

That being said, I haven't heard much from either the antipodes or the third world lately.

Kobie, don't think listing 'flutrackers' among a list of respectable sites will give it respectability. Its a sneaky sort of spam for a place with no expertise or credibility.

By Lisa the GP (not verified) on 23 Jun 2009 #permalink

These graphs have only one meaning and one only. Ninety eight percent of the specimens tested and found positive for influenza in week 23 were due to the novel strain.

Since the US health departments claim they are not able to test all the specimens submitted and since they have been following a previously issued US CDC policy to only test specimens submitted from those severely ill with an ILI, the absolute number of positive specimens is meaningless

IMO, except for the percent positive data provided by the CDC for the novel strain, there is nothing of value to be found in this data.

Since our public health departments and US CDC are no longer testing all comers with an ILI, the most uninformative data provided by the US CDC is the number of reported cases.

While it is true, this data does not support an epidemic, the reason it does not relates to the fact that our public health establishment have decided not to test people with an ILI. This is why the confirmed case count has not risen exponentially as is typical of an influenza pandemic. Therefore the crude case count has no meaning and should be disregarded. Anyone who uses this date to support a claim that the pandemic has peaked is sadly deluded and either ignorant of the facts or purposely attempting to use this data for propaganda.


By the doctor (not verified) on 23 Jun 2009 #permalink

Gratt (the doctor): All ILIs have never been tested. That is infeasible and unnecessary for surveillance. We have already crippled public health by cutting their funding. Saddling them with make-work adds to the problem. CDC reports case counts partially because people demand it, but they are clear that it is the general pattern that is important at this point and they report that with FluView. The purpose of this post is to explain what is being provided. CDC is clear on their site about this but it is easily misinterpreted.

I am curious about whether air conditioning in so many public buildings, hospitals and homes could keep this virus humming, churning (and mutating) during our summer in North America. Add to this the movement of people from winter continents to summer continents.

I agree with you becuase the samples are not consistanly taken. Infact on NPR this morning (Wed june 24th, 2009) the reporter said "Since seasonal flu has died off and H1N1 has not, doctors may be assuming those comming in will respond to tamiflu and may start prescribing it"
The article showed a change in practice but I have not read anything nor am I a HCW.

Lisa the GP,
"Flu Trackers" has been trying to get information out and help others. Though I use another flu board I thank them for their efforts. IMO to make things better it would be nice for Mrs Sebelius who took over for Mike Leavitt of HHS to host more webcasts. Then lay folk would have more good sources of information.

Dean I. - There have been articles showing where humidity in the air helps precipitate virus and other dust particles. I have not read where ventilation helps spread virus - though it seems logical. I have read that masks are more of a fell good item than a practicle one. I doubt that filters for ventilators do much - though I have not seen any research one way or another.

Rever - Public heath money has been cut to our peril. Today California is the first to shut down their posion control lines. Source:

Do not forget the webinar on pandemic planning.


One correction: California Posion control to shut down September 2009. Source:
I had the date wrong.

BTW - September is National Preparedness month.
Red Cross -
FEMA - Nothing listed
Ready Gov -

Hopefuly H1N1 will be part of this but as RAVEN wrote "we need several months to prepare" Well I do. The more I practice the better I get ;-)


Thanks, Grace RN #6 and DemFromCT #9.

Nudge, nudge, Revere. Down there, in the "Bird Flu Links".
Your link to "Flu Wiki" is outdated.

Re the southern hemisphere - I'm in Victoria which is the epicentre of h1n1 in Australia and I can say from personal experience that this definitely seems like an exceptionally bad flu season. Literally half my office is currently sick and so is a large portion of my church group. we've stopped automatic testing of suspected h1n1 cases here so I'm not sure how good the stats are on breaking that strain down vs normal flu (I think confirmed h1n1 cases are something like 3,000), but this really feels like an unusually bad seson.

Luckily only 3 people with h1n1 have died so far and all of them had serious prior medical complications.

I'm in Fairfax, VA. Our school announced a confirmed case of H1N1 2 weeks ago in my daughter's classroom. I've had flu symptoms for past 5 days. 2 of 3 daughters down with flu-like symptoms this week. I assume it's H1N1 - but don't see any compelling reason to visit my physician. As the flu goes I've had worse.


I looked at the comment you mentioned and followed the link. Here's the start:

Scientists from Russiaâs Ministry of Health are warning in a secret report to Prime Minister Putin that they have discovered a âcritical linkâ between the H1N1 influenza (Swine Flu) virus and genetically modified amylopectin potatoes that are consumed in massive quantities nearly exclusively by Westerners and sold in fast food restaurants as French Fries.

According to these reports, the protease enzyme genetically modified in the potatoes being sold through Western fast food restaurants as French Fries to protect against Potato virus X causes an âexplosiveâ replication of the H1N1 influenza virus by increasing the acidic conditions of the endosome and causing the hemagglutinin protein to rapidly fuse the viral envelope with the vacuole's membrane, then causing the M2 ion channel to allow protons to move through the viral envelope and acidify the core of the virus, which causes the core to dissemble and release the H1N1âs RNA and core proteins into the hosts cells.

Oh my dog! A secret top level report from Russia! And all that sciency stuff in the second paragraph! It MUST be true! And I walked past some potatoes at the grocery store just today! I surely contracted a spud infection! Help, I'm gonna die! Call the police fire department ambulance coroner!

Oops, sorry, I was going to post the previous comment somewhere else. Anyway, it was about the page Philip Huggan linked to in #8 here. Seriously, it doesn't make much sense, IMAO. Tracking down the alleged culprit and so many details of how it boosts the infection, in such a short time, sounds like something a comic book science hero could do, but in real life? To top it off, the super scientists who discovered all this don't publish their findings, but keep them secret, just for the heck of it. Pardon me, but I remain skeptic.