Scott McPherson's Web Presence

Recently, a commenter named H1N1 Watcher posted a comment regarding my blog on the Case fatality Rate from swine flu.  Even though I posted the following as a response, I felt it worthy of listing as a separate blog entry.  The scientific debate is valid, and I felt it worthy of attention.

"However, since he appears to be using published numbers from the Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO) his method is consistent. We cannot propose a better method,

"Can't we ?

"As for sound evidence based estimates of the CFR,
plase (sic) take a look at the recently published Wilson paper [1] that provides reasonable estimates of upper and lower bounds of pandmic (sic) H1N1 case fatality rate.

"According to that Study, which, as a meta study takes into account several independent estimation methods the upper bound of the CFR (i.e. the most pessimistic estimate) is as low as 0.06 % (that is 6 in 10.000) which is one order of magnitude less than previous estimates of 0.5% and, BTW perfectly in line with seasonal flu CFR.

----------------
[1] N. Wilson
"The emerging influenza pandemic: estimating the case fatality ratio"
Free full text available at
http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=19255

July 29, 2009 | h1n1_watcher "

Dear H1N1 Watcher,
First, let us all hope it is from your keyboard to God's ears on the CFR!

A few comments.

First, a low CFR is what we are hoping for, but not necessarily what we should be planning for. In my blogs at Computerworld, I explain the concept of planning for one category higher than the event we are told to prepare for (the hurricane analogy). Even CDC is telling us the CFR could be from the low thousands to the hundreds of thousands, and we have to listen to and respect our own public health establishment.

Second, I cannot find a pandemic in the era of even remotely reliable medical history (1830s pandemic to present) where the second wave was milder than the first. Assumptions have to side with the theory that the virus becomes more efficient and more virulent as it progresses.

Third, the Wilson study does not, as far as I can tell, take into account misdiagnosed causes of death. An earlier blog of mine attempts to take that into consideration. I believe that as we get into larger and larger numbers, a pattern emerges. One cannot assume there are a higher number of "milder" cases and then take the total reported number of deaths as gospel. You have to account for missed deaths due to H1. The CFR was climbing as the virus was reaching its tendrils across the USA, stabilizing somewhere around .005, plus or minus.  This was with massive swabbing and lagging results and further lagging of reporting those results.

To quote from the study (you referenced):

"Sophisticated statistical methods have been proposed for obtaining adjusted CFR estimates using data from the early phase of an epidemic [20], and these result in adjustment for various time lags and an upward shift of the CFR. However, such adjustments would probably have little effect on the estimates presented in this article which are based on data from country epidemics which have progressed well beyond their early stages (e.g. the Canadian data). There is also the potential for under-recognition of deaths attributable to influenza in those with serious co-morbidities, but this can only be addressed by careful research studies and post-epidemic modelling to determine total excess deaths."

My takeaway from that is there is no reliable math to calculate deaths that were not correctly attributed to H1 in real-time. There actually is a way to do that, which the CDC performs. You take your baseline death rate, look for spikes in excess mortality and attribute that to the virus. But that reporting also lags, sometimes by weeks. So we are constantly steering by our own wake and not looking forward.

For all these reasons, it is absolutely prudent to plan for a more serious event.

I wanted to thank you again for the link. I shall read this again and attempt to obtain the document referenced in #20.
Scott

I think this is a valid course of discussion.  I think we all have this feeling that the actual CFR was not as bad as the numbers indicated.  Nonetheless, all the classic warning signs of pandemic mortality -- deaths of pregnant women, younger adults and older children, the lack of infection in the elderly, viral attacks upon brain, stomach and intestines -- these are screaming at us to be very wary of this new strain.

Ultimately, we will never know the actual CFR until months to years after the event.  That is the realm of historians and statisticians.  But in the near term, we will have to deal with the impact of the virus, moderate to severe CFR or no CFR.  And that reality is a third of our population will get sick and our ability to conduct our business will be challenged.  A disproportionate number of young adults will become very, very ill.  Schoolchildren will be severely impacted.  Pregnant women will die; the exact number unknown, but each death felt and great sadness will result.

It is absolutely prudent to get the message out and prepare.

Your comments welcomed.

Forgive me as I smile while frowning.

As you recall, back on June 29 and in my blog titled "The Worst is Yet to Come," I mentioned some rather startling figures. I mentioned that, absent a successful layered strategy, the number of American dead from swine H1 could reach 400,000.

A few weeks ago, I gave a presentation to the Institute of Internal Auditors. In that presentation I also mentioned that, in Florida alone, the death toll could possibly reach 27,000 people.

My calculations are not rocket science; anyone with an understanding of calculating such numbers has risen to agree with me. One such comment came from a fellow named Bill Suydam, in his blog named "Health Spectator." The blog in question takes a critical look at my work and comments:

It is worth noting that McPherson’s calculations of CFRs does not take into account the presumed high number of people who contract swine flu and never so much as see a doctor, thereby reducing the number of reported cases vs. the number of reported deaths from swine flu. However, since he appears to be using published numbers from the Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO) his method is consistent. We cannot propose a better method, but one must realize that the increase in case fatality rates may be apparent rather than real.

If the apparent increases are real, however, there is cause for alarm. Certainly Kawaoka’s findings of lung damage as opposed to mere invasion of the nasal passages and pharynx by seasonal flu could explain a higher mortality rate from the new swine flu.

Thanks, Bill. I found your blog about me to be very fair and balanced. On to the latest news: Via the AP, dateline Tallahassee:

Pandemic could infect millions with H1N1 virus

FL State Wire
Published: Yesterday

TALLAHASSEE, Fla. (AP) - A top state medical official says 5 million Floridians could contract the swine flu within a year if the virus follows the pattern of previous pandemics.

Acting state epidemiologist Dr. Richard Hopkins said Thursday that pandemics are deadly because so many people get sick. He notes that as many as 30 percent or more of the population was infected in previous pandemics.

Officials at the Centers for Disease Control and Prevention says they've been estimated this pandemic could be along the lines of the 1957 Asian flu outbreak, with similar infection rates.

Florida has reported that 22 residents infected with the H1N1 virus have died, including 10 in the last three weeks. Officials counts say at least 2,900 Floridians have been sickened from the virus. However, experts say adding in unreported illnesses would make the actual number much higher. Officials expect more cases after public schools open next month.

OK, so now a respected Florida government official is talking some serious numbers. Bravo and Well Done, Dr. Hopkins. I can only assume you are getting some flak for this story, and will get more at your Orlando conference next week. Hang tough. You are right and correct.

The next story is also from AP, dateline Atlanta. It says:

Swine flu could strike up to 40 percent in 2 years

By MIKE STOBBE (AP) – 1 hour ago

ATLANTA — U.S. health officials say swine flu could strike up to 40 percent of Americans over the next two years and as many as several hundred thousand could die if a vaccine campaign and other measures aren't successful. (bold mine)

Those estimates from the Centers for Disease Control and Prevention mean about twice the number of people who usually get sick in a normal flu season would be struck by swine flu. Officials said those projections would drop if a new vaccine is ready and widely available, as U.S. officials expect.

The U.S. may have as many as 160 million doses of swine flu vaccine available sometime in October, and U.S. tests of the new vaccine are to start shortly, federal officials said this week.

The infection estimates are based on a flu pandemic from 1957, which killed nearly 70,000 in the United States but was not as severe as the infamous Spanish flu pandemic of 1918-19. But influenza is notoriously hard to predict. The number of deaths and illnesses would drop if the pandemic peters out or if efforts to slow its spread are successful, said CDC spokesman Tom Skinner.

A CDC official said the agency came up with the estimate last month, but it was first disclosed in an interview with The Associated Press.

"Hopefully, mitigation efforts will have a big impact on future cases," Skinner said.

In a normal flu season, about 36,000 people die from flu and its complications, according to American Medical Association estimates. Because so many more people are expected to catch the new flu, the number of deaths over two years could range from 90,000 to several hundred thousand, the CDC calculated. Again, that is if a new vaccine and other efforts fail. (bold mine)

The World Health Organization says as many as 2 billion people could become infected over the next two years — nearly one-third of the world population. The estimates look at potential impacts over a two-year period because past flu pandemics have occurred in waves over more than one year.

WHO officials believe the world is in the early phase of the new pandemic.

First identified in April, swine flu has likely infected more than 1 million Americans, the CDC believes, with many of those suffering mild cases never reported. There have been 302 deaths and nearly 44,000 reported cases, according to numbers released Friday morning.

Because the swine flu virus is new, most people haven't developed an immunity against it. So far, most of those who have died from it in the United States have had other health problems, such as asthma.

The virus has caused an unusual number of serious illnesses in teens and young adults; seasonal flu usually is toughest on the elderly and very young children.

New swine flu illness have erupted through the summer, which is also unusual, though cases were less widespread this month. Officials fear an explosion of cases in the fall, when children return to school and the weather turns cold, making the virus easier to spread.

Associated Press Writer Frank Jordans in Geneva contributed to this report.

I can't help but wonder if the public health establishments are being told to start preparing us for what we might see in the autumn.  It is a refreshing change to see the talk beginning to better match the threat.

And as you might imagine, it is nice to be vindicated -- and my numbers validated -- by public health authorities and institutions.  Credibility is a slippery thing sometimes, and especially since I am not, as Mr. Suydam points out, a virologist.  So it is reassuring to me professionally and personally that my numbers are valid.

May you find my advice and speculation equally valid.

In what is largely now an academic exercise, the CDC today released the latest swine flu statistics. As of the week ending July17th, US swine H1N1v cases climed to 40,617 with 263 deaths. The report can be found at: http://www.cdc.gov/h1n1flu/update.htm .

I have beaten the horse dead three times over with my CFR calculations, so all I will say is that the CFR is increasing, now to an aggregate .006475.  This means that of every thousand confirmed or suspected cases reported to the CDC, 6 people died.  At the end of June, the CFR was .0045.  Of course, I agree that we are still talking about early and relatively small numbers.  But the CFR has increased nonetheless, or has remained very consistent, however you might define it.

This weeks-long consistency places this pandemic at the top level of Category 2 status, and if you were to look at the pandemic over the past three weeks, you would conclude -- as you would if you looked at maximum sustained winds in a hurricane -- that this pandemic may have crossed the threshold into Category 3 status.  May have crossed.

Category 3 is no small threshold to cross.  It changes things.  First, it means that we are looking at a much stronger pandemic than the media and the decision-makers would have you believe.  Second, while the number of reported cases is declining (as the WHO declares swabbing should cease if only done for purposes of determining infection and not for collection of viral samples), the death toll is not also declining.  The deaths attributable to swine H1N1v are accelerating.  We had leveled off at around 40 m/l deaths a week, but now have seen a slight spike, to 52. 

This may mean physicians and medical examiners are zeroing in more closely on the cause of death, and may now be more willing to test for H1N1v and certify that as a cause or enabler of death.

Anyway, in my blogsite over at computerworld.com, I am about to re-release my "For hurricanes and pandemics, plan one category higher" blog with swine flu references.  It should be up by Monday.  I would strongly encourage everyone reading this blog to prepare for a Category 3 pandemic.  If you always prepare one measure of intensity higher than what may come, you'll never be a)surprised, b)unprepared, and c) short of necessaries.

One look at Argentina might convince you.  Argentina (155) just passed Mexico as the nation with the second-highest number of deaths, and I strongly suspect that by the end of July, Argentina will have surpassed the United States in deaths.  Keep in mind this is just the first wave, and we are still not seeing the ease of transmission of seasonal flu.

Yet.

A recent blog, where I predicted that several hundred thousand Americans could perish from a fall/winter resurgence of pandemic H1N1, caused more than a little angst at home and abroad. Several times, I was called upon (and called out) to defend my numbers and my methodology.

Hopefully, I have accomplished that, and I thank my readers who jumped to my aid with their own corroborating sets of data.  Most of their work shamed my own, and this speaks to the power of the Internet to connect persons who in any other time would have had great difficulty getting their voices and comments heard.

The most recent confirmation came from the British government itself.  The headlines (picked up by the Drudge Report) speak of 65,000 dead Britons at the pandemic's conclusion.  Read my previous blog on that topic for more information.

Two recent news stories help to make my argument that the current case fatality rate, or CFR, from swine H1N1v influenza is sufficient to use for calculating mortality.

The first story would seemingly refute my contention. From BBC News (my edits):

The government must map the spread of swine flu more accurately in order to predict the number of people who are likely to die from it, scientists say.

Researchers at Imperial College say data is vital to ensure the country is "best prepared to fight the pandemic". They predict that one in 200 people who get swine flu badly enough to need medical help could go on to die. (bold mine)

But the government's chief medical adviser said there was "no reason" to focus on establishing a single figure. Meanwhile, the BBC understands that vaccines may not be ready until later than the government had predicted. (bold mine)

Medical correspondent Fergus Walsh said World Health Organisation officials expected the first stocks to be available in September or October, not August as ministers had said. In any event, it will be the end of the year at least (bold mine) before there are sufficient quantities to immunise half of the UK population.

Chief medical officer Liam Donaldson also told the BBC that to cope with "the height of the pandemic", the government was considering changing the rules to speed up the death certification process for swine flu victims.

"We want to try and reduce as much as possible the burden of work on doctors and we are considering all sorts of things which will help will that," he said. "That's one of the options that's being looked at."

Margin of error

Accurate predictions about the number of deaths likely to occur from swine flu are not yet available. Current estimates suggest it is about as virulent as some types of seasonal flu, but far less deadly than some previous flu pandemics.

Any estimates about swine flu are subject to a wide margin of error, not least because not everyone who catches it develops symptoms. But despite the difficulties, the Imperial College scientists - who are advising the government on its swine flu strategy - say more accurate mapping of the spread of the virus must be carried out if it is to be effectively managed.

Their work is published in the British Medical Journal.

Dr Tini Garske said: "If we fail to get an accurate prediction of severity, we will not be providing healthcare planners, doctors and nurses, with the information that they need to ensure they are best prepared to fight the pandemic as we head into the flu season this autumn."

She said data must be collected "according to well designed study protocols and analysed in a more sophisticated way than is frequently being performed at present".

'Only an estimate'

Not everyone who is infected with swine flu will become ill enough to report their case to a doctor. Of the proportion who do, scientists predict that 0.5% of them - one in 200 - could go on to die. (bold mine)

Health Secretary Andy Burnham has said in the worst case there could be 100,000 new cases of swine flu a day later in the year, although many of these may not fall seriously ill.

The BBC story mentions that Imperial College scientists forecast a case fatality rate of .005, or .5% of those infected.  That is a rate comparable to the current US CFR, and 175% larger than the just-released, official UK government estimate of overall dead at this pandemic's conclusion (see my last blog).  So while casting aspersions upon the practice of using what public health practitioners consider to be too small numbers, they are nonetheless validating the math in their own estimates.  Curious.

This is the second official British source that is predicting a major viral event for that nation this fall and winter.

The second article (I promised you two) deals with the mysterious case of the British family doctor who tested positive for swine flu, died, and his death was ruled "natural causes!"  The best critique of this comes from Revere of Effect Measure.   How the local authorities could arrive at this conclusion is both mystifying and troubling.  It serves to validate my blog of a couple weeks ago where I said the actual number of deaths in this country from swine H1 was/is much higher than is being reported.  Mistakes (or apparent mistakes) such as what happened in England with this General Practitioner, or GP, are easily duplicated here.

What makes the British episode so unfathomable is that it happened in the media equivalent of scorchingly broad daylight.  The British press is possibly the best-tuned toward swine flu coverage anywhere in the world right now, and the proclamation that this hapless GP died of "natural causes" when at least three of the symptoms he had could have been exacerbated by influenza, is unbelievable. Those symptoms -- heart disease (flu can cause heart attacks and strokes), viral pneumonia (DUH!) and pulminary embolisms (blood clots in lungs) are all known secondary medical issues exploited by influenza.  So are MRSA infections, bacterial pneumonia, encephalitis, and deaths from COPD.  So is diabetes.  So is HIV/AIDS.

Now how many persons in this country alone might have been misdiagnosed as heart attack patients, stroke patients, MRSA patients, and the like?  You tell me.

Sir Liam Donaldson is the Chief Medical Officer of the United Kingdom (that's Great Britain for those of you in Rio Linda). Sir Liam is not prone to making rash statements. He is of the Stiff Upper Lip persuasion, pip pip and all that, the prototypical British understated gentleman. And not every British subject gets knighted, which should also tell you about what favor he curries in Whitehall and at Buckingham.

Sir Liam has just released estimates of British deaths that might occur from swine H1N1v influenza, and they are 1) staggering, and 2) a complete and total vindication of my blog where I estimated that up to 400,000 Americans could die.

The British government, for official planning purposes,  now estimates that as many as 65,000 British subjects could perish from swine influenza. This, despite the fact that their government acquired enough Tamiflu to treat a quarter of their population, and were recently engaged in discussions (even considering the global financial meltdown) to buy more -- enough anyivirals for half its population.

Now Sir Liam did say the real death toll in Britain could be somewhere between 3,000 and 750,000 (!) persons. Wow, that's quite a swag there, Sir Liam. But it is understandably large, since no one really knows yet what the final Case Fatality rate (CFR) will be.

The British government, you see, is using the exact same math that I used -- the same precise calculations, including a conservative "fudge factor" - to make its official planning estimates. the math is refreshingly simple.

According to the CIA, Great Britain has a population (as of July 2008) of 60,943,912, more or less.  Half of those people are named "Ian."  Just kidding. Using the 30% figure, the British government expects 18,283,000 or so to be infected, and around 9 million to be seriously ill.  The 65,000 dead equates to a case fatality rate of .003, or .3 percent.  This is in contrast to the current USA CFR of .0056 and the global CFR of .0045. 

So the British are expecting two things to occur: First, they fully expect this virus to gain rapid and extremely efficient methods of human-to-human transmission.  Second, they are hoping for a moderation of the lethality of the virus as it gains increased communicability.  Both are reasonable assumptions.

Contrast this dire British warning with the decided lack of vocal response from the American government.  Considering that seasonal flu kills nearly 40,000 Americans a year, and assuming a current CFR of half a percent, why isn't anyone in Washington using the same dire (and realistic) warnings?  This is yet another example of poor risk communication.  The same people who are preaching transparency (and absolutely not practicing what they preach) are at great risk of blowing it in preparing Americans for a second, more powerful wave of pandemic flu.