Monday, August 3

Why America's swine flu vaccination program will work even if it doesn't. BioMask and Biofriend QuickCloth, anyone?

Clint, my part-time assistant, forgot to publish a retraction regarding my post on a July 24 Reuters news report titled CDC stops swine flu death count at 300. By the late afternoon of the same day Reuters' health and science editor, Maggie Fox, had gotten hold of the report, re-written it under the more optimistic title, First defense against swine flu - seasonal vaccine, and deleted the erroneous mention about the swine flu death tally being halted.

What this boiled down to on my end is that until now there's a Pundita post floating around the internet that accuses the CDC of being the devil's handmaiden for suspending reporting on the swine flu death toll.

Yes, well, before I could fire him I'd first have to catch up with him between modeling assignments and besides the last assistant I fired, a Mark Steyn reject named Tiffany, packed chewed bubblegum under the G, E, R, K keys of my computer keyboard.

Just to make sure there's no misunderstanding here is the CDC's announcement about the change in their reporting on swine flu:
July 24, 2009 is the last day that CDC is providing individual confirmed and probable cases of novel H1N1 influenza. CDC will report the total number of hospitalizations and deaths each week, and continue to use its traditional surveillance systems to track the progress of the novel H1N1 flu outbreak. For more information about CDC’s novel H1N1 influenza surveillance system, see Questions & Answers About CDC's Novel H1N1 Influenza Surveillance.
These would be the same traditional surveillance systems that year after year have produced the same number, 36,000, for the annual death toll in the USA from seasonal influenza.

As to whether the CDC's new system of publishing a weekly grand total of deaths from swine flu is any more, or any less, helpful than the earlier state-by-state tally --

What the swine flu pandemic has turned up is that the entire system for collecting and reporting data on influenza infections and deaths from influenza is FUBAR. This situation is not only in the United States, it's in every country.

Seasonal influenza has long been treated by societies and the medical and public health establishments that serve them as an inevitable fact of life and of death, which took mostly old people.

Beyond developing a seasonal vaccine, it wasn't considered worth it to American society to treat yearly influenza as a dangerous epidemic. But now, with a highly unpredictable pandemic virus already bearing down on humanity, it's a little late in the day to scramble up a new system.

On July 14, just ten days before the CDC announced the change in their reporting, a news-making survey by London's Imperial College was published. It nailed down what everyone who'd been closely following swine flu already knew: the current system for estimating the proportion of people who will die if infected with swine flu is badly flawed. (1)

The estimates, which are derived from bad/outdated mathematical models and inadequate tracking methods, are already having serious consequences. That's because the statistics on swine flu deaths influence how medical establishments manage treatment for swine flu -- and how public health systems prepare vaccination strategies.

On July 16, two days after the Imperial College study was published, the World Health Organization officially washed their hands of the matter by announcing they would no longer publish data on the confirmed number of swine flu infections on a country-by-country basis.

This set off an uproar at Wikipedia, I might add. Since the earliest days of the swine flu outbreak volunteer contributors at the free encyclopedia have been doing the heavy lifting in keeping the global public informed about the daily number of confirmed/probable swine flu cases and the estimated death toll by individual country. After reasonably civil debate about how to handle WHO's roadblock, Wikipedia contributors rallied. They continued to publish what is still the best chart showing swine flu's global march.

WHO's announcement also set off an uproar in Pundita-land. Although WHO's long-winded, convoluted explanation for their decision didn't specifically state this, the change in their reporting method also meant they were no longer publishing the tally of cumulative deaths from swine flu by country.

As imperfect as the reporting is on swine flu deaths, the country breakdowns on the death toll are one indicator that taken with others provides the public with a rough idea of the pandemic's spread.

My reaction to WHO's announcement was to sputter in indignation, "Now watch! The CDC is going to follow suit!"

Well, in part, they did. Again, although the CDC will continue to provide a weekly death tally in the USA, it is now only a total figure; i.e., it does not show the breakdown by U.S. state of the death toll from swine flu.

Moreover, the CDC's weekly FluView, which features various interesting charts and graphs about the virus's activity in the USA, does not provide a by-state breakdown of the number of hospitalizations from swine flu; it only shows a total figure. And the 'activity' of the virus is reported only on a regional basis; i.e., various states grouped as regions.

So once again it has been left to Wikipedia volunteers to carry the battered standard of reporting to the general public on swine flu statistics. The highly readable chart at Wikipedia's 2009 flu pandemic in the United States by state page has U.S. state/territory categories for State-reported confirmed cases, State-reported probable cases, State-reported hospitalizations, and confirmed deaths.

Plus, Wikipedia provides a link to a map of every U.S. state, which shows exactly which regions in the state where the outbreak is occurring.

I am not sure how much further to pursue the issue of reporting on swine flu cases and deaths. In early May I applied medical reporter Kelly O'Meara's investigation about the number of U.S. deaths from seasonal flu to the swine flu situation and warned that the current method of estimating infections was badly flawed. During the following months I continued to sound the alarm.

By June 19 the Wall Street Journal had picked up on the question of accurate reporting on swine flu deaths. And on July 1 Barnaby Dawson, who was contributing to Wikipedia's section on data reporting and accuracy in reporting swine flu cases, wrote to congratulate me for zeroing in on the issue of estimating swine flu infections and deaths. (See comment section in the CDC hoodoo and swine flu lethality Pundita post.)

Shortly after, I saw that Wikipedia had added an explanation that estimating deaths from influenza was a complicated process and that the CDC's annual estimate of 36,000 deaths in the USA was misleading. Then came the Imperial College survey with its stark conclusions.

Yet none of this will make a dent in the public health establishment's entrenched view that once an epidemic is underway in a country it's a wrong use of resources to attempt to keep track of individual cases of swine flu.

This idée fixe, which represents a sweeping generalization carried to the point of absurdity, has done much to obscure the true impact of swine flu. Early on in the outbreak it served as the rationale for WHO, CDC and other major public health authorities to encourage health departments to abandon testing for all but the most serious swine flu cases.

The critical flaw in the rationale can be intuited by noting that the American state of Wisconsin (population 5,627,967) has five municipal laboratories. This explains their proud assertion that the state's comparatively large number of confirmed swine flu cases in the early weeks of the outbreak was due to their state's superior testing for the virus.

On the other hand, New York State (population 19,490,297) has only two municipal laboratories. One of the labs serves New York City, the most populous city in the union and one of the world's mega-cities (estimated at 8.3 million in 2007). The other lab serves the rest of the state.

(As to why one of the world's largest cities, located in the world's lone superpower nation, has only one municipal lab -- you'd have direct that question to the city's Mayor Michael Bloomberg or Thomas Frieden, who was the city's health commissioner from 2002 until June 2009 when he took over as head of the CDC.)

China's laboratories have not been overwhelmed by swine flu specimens; the same holds true for many countries where swine flu infections are still few. Even the CDC's own map of the activity of swine flu in different U.S. states shows a wide variation in the severity of the outbreak in the USA.

In other words some regions of the world and the USA can produce a far more accurate picture of the number of swine flu infections than others; how this data changes over the course of the pandemic would more throw light on the speed and spread of the pandemic.

So a more helpful approach would be for authorities to encourage testing of all suspected swine flu cases to the extent possible then setting up categories for countries/states that couldn't keep up with testing, and those that could.

There are other strategies that could be deployed to give a more accurate picture of how a unique virus is progressing in its pandemic phase. For example, in the USA the "311" city government phone number, or numbers that serve the same purpose, could be used by hospitals and doctors to report suspected swine flu cases in regions where the labs are overwhelmed. While of course not a perfect method this would be better than nothing.

The 311 number is for city residents to report on a municipal problem -- uncollected garbage, electrical problems, and so on. In a 2005 essay, Dial 311, I highlighted a TIME magazine report on how officials in Chicago belatedly discovered the import of several 311 calls, from different parts of the city, which complained about dead birds.

The calls, had they been studied as a pattern, would have given health officials early warning of an outbreak of West Nile Virus in Chicago.

If the pattern had been noted earlier human lives could have been saved. Yet the discovery of how 311 could predict an infectious disease outbreak was a watershed; despite this, the great power of 311 for discerning disease patterns has not been utilized in the swine flu outbreak.

I write all the above in the manner of a symbolic gesture, knowing I'm wasting my breath. That's because societies stand and fall by their totems, their fixed ideas.

There's a simple explanation as to why a technology such as 311 hasn't been fine-tuned to keep track of suspected swine flu infections, and why other reasonably inexpensive steps haven't been taken to obtain better data on swine flu.

The explanation is that vaccines have been so successful so much of the time against threat from infectious diseases that governments and the societies they serve have placed their bet on the vaccine solution -- even in the face of a pandemic virus that displays unique properties.

That's why, with the striking exception of China, societies have made only the most haphazard or token attempts at deploying NPIs ('non-pharmacological interventions') against swine flu. And that's why WHO and the CDC didn't urge nations and states to devise creative strategies for collecting data on swine flu.

That's also why the CDC and their parent agency, Health and Human Services, could assign a low priority to the GAO recommendations on swine flu readiness. Here's a report you didn't find splashed all over the nightly TV news last week:
U.S. unprepared for second wave of swine flu, report finds

By Carrie Wells
McClatchy Newspapers
Posted on Wed, Jul. 29, 2009 05:04 PM

The federal government isn't prepared for a potential outbreak of swine flu this fall, a Government Accountability Office report released to Congress concluded Wednesday.

Furthermore, said the GAO, Congress' nonpartisan investigative arm, federal agencies haven't addressed nearly half of the 24 recommendations it made last month.

William Coor, the deputy secretary of health and human services, disputed the findings.

"Given the speed at which the virus has spread we felt our work and coordination has been outstanding," he said. However, Jane Holl Lute, the deputy secretary of homeland security, acknowledged that, "We still have work to do."

The GAO agreed, saying that if a severe outbreak struck:

- Federal, state and local governments would have trouble coordinating with one another.

- The number of beds and medical supplies would be insufficient.

- Plans to protect federal workers aren't adequate.

Health officials worldwide acknowledge that the virus has reached pandemic proportions and could strike more severely in the fall. In the U.S., more than 43,000 people have contracted the virus, and so far, 302 have died.

Rep. Bill Pascrell, D-N.J., called the report "startling" after it was presented to the House Homeland Security Committee Wednesday.

The committee voted unanimously to urge the federal departments to respond to the GAO's recommendations within three months.

"Based on our survey, progress seems to be limited," said Bernice Steinhardt, the GAO's director of strategic issues. The rosy outlook of the agencies could be because they still haven't tested what they'd do in a severe outbreak, she added.

Lute listed the steps that her agency has taken to prepare, including reaching out to Native American tribal governments and drafting a response plan.

Coor also defended his department's actions.

Coor added that HHS and the Federal Emergency Management Agency in the next few weeks will give directions to state and local governments on how to deal with a big outbreak.

Swine flu, or H1N1, emerged in April in the U.S., and by June, the World Health Organization said it had grown to pandemic proportions. The WHO said it has killed at least 816 people worldwide. The Southern Hemisphere is now in its regular flu season, and swine flu there has been particularly deadly.

Coor said a vaccine won't be ready for several more months, after trials are finished. He also said federal and state governments have stockpiled 75 million to 100 million antiviral treatments, a number he called "sufficient." [Don't bank on that, Mr Coor.]

National Treasury Employees Union President Colleen Kelley told the committee the federal government communicated poorly with federal workers earlier this year.

For example, federal employees were forbidden from wearing face masks to avoid getting the virus unless they were within six feet of a person who seemed likely to have swine flu.

The committee's chairman, Rep. Bennie Thompson, D-Miss., wasn't happy with the report.

"Given this country's recent experience with disasters, it is hard to believe that there are those who underestimate the importance of plans and drills," he said. "Our children are taught in school what to do in a fire drill. They are not taught to wait until a fire starts, yell instructions and hope everyone makes it to the exit."
Yes, well, drills are necessary only because there's no vaccine yet against fire and hurricane.

Mr Coor might be wrong about the length of time before a vaccine is ready for distribution in the USA. On the same day he spoke to the panel I saw a report from a vaccine company that the swine flu virus was suddenly growing faster than it had been, which the company representative said would speed up vaccine production.

As to how the government is going to pull together a more comprehensive plan at this late hour -- if a mass vaccination program is Plan A, I suspect Plan B was always that the U.S. military would come up with a plan.

With the opening of U.S. public schools only a few weeks away, and perhaps noting that Plan A might not go off without a hitch, the military has finally submitted a proposal to start planning.

It's my wild hope that the planning will include the Department of Defense calling China's Ministry or Health and asking, 'Just exactly how did you set up your entry ports intervention and quarantine program?'

The details would be handy to know in the event swine flu comes roaring back to the Northern Hemisphere in a more lethal and/or Tamiflu-resistant mutation. It would be so nice to cut into its exponential spread by catching as many infected people as possible at major points of entry to the USA but there I go again, asking for the moon.

Aside to American readers who live in terror of being herded into FEMA quarantine camps: you might have some reason for terror now. Not to lecture but if the government had instituted quarantines at the beginning, quarantinees in the USA would have been able to loll around for a week badgering their minders to add more variety to the dinner menu and more cable channels on the TV in their room.

The quarantine experience might be a different story, later on. So if you think you live in terror of FEMA camps, just imagine what the Obama administration and Democratic leaders in Congress are going through. The last thing the Democrats need right now is TV footage of thousands of hysterical Americans being marched into the Houston Astrodome. Don't cackle, Pundita; it's unseemly.

Look on the bright side: either America's swine flu vaccination program, "the largest vaccine effort the world has ever seen" will work or it won't. And even if our traditional way of doing things doesn't work this time around that doesn't mean it failed. If this is a little hard to follow I explained it all quite clearly, if I do say so myself, once upon a time in 2005:

The hallmark of science is not its ability to explain but its ability to predict (I mean prediction BEFORE something actually happens rather than the more common claiming to have predicted something AFTER it happens). How do so many people (particularly in foreign relations) whose predictions have been so poor hold onto their jobs?
Dave Schuler
The Glittering Eye"

Dear Dave:
Your remarks are very broad. But if you're referring to people whose job is to make predictions for the US government, you are misinformed. Such people are invariably right in their predictions.

I know that news will come as a shock so allow me to play your guide for a trip through Washington-land. Before we scamper down the rabbit hole let us hop back in time, so that the lay of the land in Washington, DC is more readily seen:

Say your job is to be the high priest, a job passed down from your uncle. Your major duty is to ensure a good harvest each year, which you accomplish by hurling 10 virgins off a cliff. It worked for your uncle, it worked for his uncle, and for 20 years it worked for you until the 21st harvest came a cropper.

Naturally you are hauled before the king, who demands an explanation about why the crops failed because his subjects are massed outside the gates and demanding an explanation.

Now tell Pundita what you would say. "I have no idea" would be the wrong answer if you want to hang onto your position not to mention your life. You have to come up with an explanation for the presumed anomaly.

Put another way, you haven't the foggiest idea why hurling virgins off a cliff worked to bring a good harvest and why it stopped working. And if you're a very smart high priest, you might have a hunch that one event has nothing to do with the other. However, with your life on the line, it would be the wrong time to take up lab-bench science.

To spare you the brain sweat I will quote from page 632 of the 11,465 page How to Survive your Job as High Priest: Book of Answers which provides an array of explanations for earlier science's failure to accurately predict events.
The crop failed because:

Blame it on the assistant
a) The virgins were too young.
b) The virgins were too old.
c) They hadn't been properly tested to ascertain that they were actually virgins.

(Note: Any answer from this menu calls for the immediate execution of the assistant.)

Blame it on the harvest god
a) The god is now demanding a doubling in the number of sacrificed virgins.
b) The god is in a bad mood.
c) The god was busy fighting a war with other gods and forgot about the harvest.

Blame it on the king's subjects
a) The people have not been showing proper respect to the harvest god.
b) The people have been fighting with each other, which angered the god.
c) The people became lazy and deceitful and didn't share enough harvest with the king's bounty collectors.

(Note: float this one only if the king is in good standing with the military.)

Different combinations of the above explanations should be enough to get you through another few years, until whatever's wrong with the harvest rights itself. If all else fails:

Blame it on the king
a) The king has started thinking he's more powerful than the harvest god.

CAUTION: Try this one only after consultation with courtiers and generals assures you that the king is next off the cliff anyhow. [...]
To put all this another way: people have spent eons coming up with creative excuses for why their way of doing things doesn't always work; by now CYA is embedded in humanity's DNA.

Not that I want to annoy the CDC's totem but there is a way to hedge the bet: a middle ground between the sure thing and the sure thing that's sure to work the next time. Filligent's BioMask and QuickCloth, anyone?

RBO blog's Swine Flu Reader has links to all my posts on swine flu since April.

1) New Scientist: Swine flu death rate estimates 'flawed;' Andy Coghlan; July 14, 2009


Anonymous said...

Pundita, the ecdc continues to publish a tally of new cases, infected cases, and deaths. Their death total is just over 1,200. I forget the link to the web site, but if you tupe in ecdc (european center for disease control) you will find the link.


Pundita said...

RPL - Thank you; I know about the chart but I have not checked to see whether it's updated daily or on a weekly basis.

If it's daily, I'd imagine it's a help to the Wikipedia volunteers, who have been doing a magnificent job of gathering and organizing all the data.

The chart is helpful for seeing at a glance what the outbreak is like in the EU. The drawback, for those who are watching the pandemic on a global scale, is that it is confined to the EU countries.

And I don't think the ECDC provides the same country/regional maps that Wikipedia does for the U.S. states; which are very helpful for seeing how the outbreak is spreading (or not) in a relatively small geographic area.

If this pandemic drags on much longer it would even be a help if there were maps of the largest cities showing where the outbreaks are in different boroughs or sections.

Of course the data collection would be a huge task, and right now it's very difficult to get a picture of how the disease is spreading in major population centers.