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November 22, 2005

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Yes: it's the official Penitent Wonky Thread ;)

Hmm so martial law and quarantine woundn't help contain an Avian flu pandemic. I wonder if Bush might have another reason for wanting to declare martial law...

My reading on quarantines doesn't go much past 1850, but in what I've read, the well-connected and moneyed rarely had much trouble getting out of the quarantined areas, with or without symptoms. For a truly harrowing account of slipping in and out of a quarantined area, I recommend Charles Brocken Brown's Arthur Mervyn, based loosely on the author's experiences in the 1790 yellow fever epidemic in Philadelphia.

And if we're going to advocate for cosmestic epidemic preventatives, why not suggest healthy diet? The 19th-c hygenists loved that one.

Out of curiosity, was this comprehensible?

Wait, no one said there was math involved!

I could follow it, although it took some concentration. Then again, I've done a bit of history-of-science type reading on epidemiology. The reproductive-rate calculus was new to me (beating on self for being a lazy researcher), but I think I came to understand its importance over the course of the post. The only suggestion I could make would be to add a sentence after

Thus, if R(t) for a given disease at a given time is 2, then each person who gets the disease at that time, on average, will infect two new people with it
to suggest whether that given time as 2 would justify full alarm bells or not. Later in the post, it becomes clear that 2 is not an acceptable standard of transmission, but not one justifying quarantine. Still, that was the point at which I realized I was in over my head.

Oh, I meant to add: if you could give more examples of r(t) in familiar epidemics (TB, yellow fever, black plague), people without specialized knowledge could relate better.

I updated, to account for your first point. The second is harder, since R(t) is variable over time, within a given epidemic.

so, quarantining will work for influenza if (a) the efficacy of isolation of symptomatic indivduals is 100%, there is tracing and quaranting of contacted individuals and the flu has low variance or (b) the efficacy of isolation is 90%, there is tracing and quarantining of contacted individuals, the flu has low variance and, in addition, the R(0) is around 8.

you could explain high vs low variance in greater detail. otherwise, good post.

instead of a pony, i'd like some mission style furniture.

I think the update is pretty good, although it doesn't confer the point that if r(t)=25, more people will be dead than immune. What the average layeperson is looking for is an understanding of what the scale means, from bad to awful.

Should I shut up now? (My day job has been freshman writing for years now; don't encourage me.)

Jackmormon: r(t) just tells you how many new cases the average infected person produces. Whether they die or become immune depends on the severity of the disease.

Thus: imagine my hypothetical infectious dandruff. Even if it had r(t) of a million, so more or less the whole world came down with it in no time, all they'd get would be dandruff. Then, when the dandruff disease had run its course, they'd be immune.

By contrast, almost no one ends up immune to ebola, because almost everyone who gets it dies. This would be true even if it was really, really hard to get, so that you had to e.g. roll around in the blood of ebola victims after undergoing scarification rituals, or something. (In that case, there would be the question why the disease is still around, so let's assume it normally hangs out in some animal or other. As in fact ebola does, though last time I checked, no one knew which.)

Oh -- and I did one more update, for clarity.

Umm, if a population center is full of R=10**5 people, wouldn't the right response be not to quarantine it but to nuke it? Or is that already a plot point in 24?

Umm, if a population center is full of R=10**5 people, wouldn't the right response be not to quarantine it but to nuke it?

Only if the nuke destroys and doesn't disseminate the virus (e.g. trapped in particulate fallout). Which, now that I think about it, is probably next season's plot point on 24.

Can I just say, I love the exclamation point in the title. Reminds me of that John Wayne film Hatari!

Btw, this is yet another example where I get the impression that Bush has read too many Clancy novels.

One other thing that might help is a brief discussion of the nature of exponential growth (which is what constant R implies). For example, to use the simple doubling scenario: assuming that every person infects two other healthy people (R = 2) during one "iteration", it will take approximately 28 iterations to infect the entire population of the United States. At lower R, say R = 1.5, it'll take approximately 48 iterations; at higher R, say influenza's worst-case R = 25, it'll take only 6 iterations. Assuming an "iteration" (infection->new infection cycle) of about 3 days, this means that R = 1.5 gives us around 6 months to annihilation, R = 2 gives us about 3 months and R = 25 gives us around 2 1/2 weeks.

This is obviously a first-order estimate -- to be more precise you'd want to use, say, logistic growth [y' = ky(1-y)] instead of exponential growth [y' = ky] to simulate dampening, and that's still horrifically crude -- but it should help give people a sense of the time-scales involved.

But for evaluating the efficacy of a quarantine probably first order is fine. By the time you need to factor in dampening you're almost certainly SOL.

Understandable post to me. You could add that diseases that are quickly fatal usually give lower R values.

This is the kind of post that makes me wish I had paid more attention in my science and math classes 40 years ago.

But I think I understand what you are saying.

Two points. You talk about the need for planning beginning now. As has been pointed out on other threads lately, one of the apparent failings of the current administration is failure to paln for anyhting other than roses being tossed at our feet.

Secondly, I think it is important to look at the psychological effects of a quarantine, both good and bad. Could be bad for those areas placed under quarantine, as you mention the possibility of panic, etc. However, at the same time, it may be positive for other areas who sense that their government is actually doing something.

Then again, they may feel that since they are not quarantined they have nothing to worry about, which would be bad.

Anyway, my point, for which I don't have a definitive answer (way too early) is what would the psychological inmpacts of a quarantine be, and would they offset either the positive or negative practical consequences of one?

Excellent post, hilzoy. Very informative.

(I do have a decent general math & science background, so the presentation was at exactly the right level for me to follow quickly.)

I thought the post very clear. The addition I would make is not to add math (which is not a problem, I just don't think it useful here) but to discuss, at least briefly, the alternatives to quarantine. As it is, the article comes across as "don't quarantine, just pray" or die, or whatever.

This thought stems from your opening - a few good and thoughtful people early in the debate can make a difference. Well, they can make a difference if they have a plan.

It's that old plan thing, again. :)

"Hey, if you're so smart, tell me what we SHOULD do, not just what we shouldn't do!!!"

Jake

Admittedly just skimming, but R(t) seems to be a sort of average rate of retransmission given unfettered movement. Wouldn't it be more meaningful to examine what happens to R(t) under quarantine? What does effectiveness of a quarantine mean, other than the degree to which it affects R(t)? Is it reasonable to suppose that a quarantine that reduces R(t) from 100k to 0.5 is awfully difficult to execute? Consider this more of a questioning of how linear R(t) is with effectiveness of quarantine than a failure to pay attention, although the latter is certainly everpresent.

Also, it seems I recall reading that most of the deaths in various flu pandemics were due to secondary infections coming on top of the flu sledgehammer. But I'm too fargan busy to Google.

The alternates as I understand it are to use vaccine and antivirals to firebreak any outbreak (we don't have the vaccine or antivirals yet); or to isolate any outbreaks in hospitals (we ditched the spare hospital capacity to make this possible to save money long ago). So proposing quarantines is the only solution that's not immediately going to be seen as bogus.

Slarti: R(0) is retransmission given unfettered movement and a virgin population. R(t) is retransmission in whatever circumstances actually prevail at t. Quarantines are an attempt to affect R(t), and specifically to lower it below 1, so that the epidemic extinguishes itself.

The relevance of the baseline R(0) is: what a quarantine (and whatever other measures) need to do is to move R from R(0) (which is roughly R at the beginning of an outbreak of a new disease) to less than 1. So noting R(0) gives you an idea of how effective a quarantine would have to be to contain the disease. If R(0) is 1.5, then the answer is: not all that effective; even a pretty leaky quarantine would work. If the answer is 10, on the other hand, then the answer is: only a really, really, REALLY effective quarantine would do the trick.

When you then add in the fact that flu is very infectious before symptoms appear, and thus before people who have it can be identified, it looks way unlikely that any quarantine could be nearly effective enough to contain the flu.

And then add in the speed. -- Suppose that the flu worked very, very slowly: e.g., that it took a year for someone who had gotten the flu to become infectious. Then you'd have a whole year to locate and isolate that person before he or she became infectious. You could, for instance, try to find everyone who was in an airport that an infectious person was in, or who was in the same subway car, or whatever, and have some hope of finding most of them. But if you only have a couple of days, and people who are very infectious don't necessarily give any outward sign of having the flu, this looks a lot less feasible.

This article was interesting and had this

The Public Health Service Act gave the U.S. Public Health Service responsibility for preventing the introduction, transmission, and spread of communicable diseases from foreign countries into the United States. Under its delegated authority, the Division of Global Migration and Quarantine is empowered to detain, medically examine, or conditionally release individuals and wildlife suspected of carrying a communicable disease. The list of quarantinable diseases is contained in an Executive Order of the President and includes cholera, diphtheria, infectious tuberculosis, plague, smallpox, yellow fever, and viral hemorrhagic fevers, such as Marburg, Ebola and Congo-Crimean.

Here's the list and the FAQ for the update for bird flu.

H5N1 shares the characteristic with the 1918 flu that it can kill by itself. There's a some evidence that it is more dangerous to young adults than children or seniors.

Ok, what happened? Did the day before thanksgiving exert some kind of mind control over everyone, or what?

Or did y'all decide posting was over for the holiday and nobody told me?

Jake

"Or did y'all decide posting was over for the holiday and nobody told me?"

Yes. We're all meeting over at the other place, to do the thing.

You'll qualify next year.

But you can come over to my place around 8, and watch some DVDs with me, if you'd like.

Actually, I composed a rather lengthy reply to hilzoy whose contents currently escape me (probably something along the lines of, if quarantine can knock R(t) down to 5 or so, and if things like masks and improved cleanliness habits knock it down to 2 or so, and increased paranoia knocks it down to 0.8 or so, is quarantine still worth it?) but then I realize what I know about this issue would probably fill a thimble up to the lowest row of dimples, at most, and so I should probably shut up. Plus, I got one of those you-may-be-a-spammer pages, copied the text because I couldn't get it to post, and then promptly copied something else in another application, which wiped the whole deal out. Or something resembling that.

Slartibartfast, I'm sorry to hear that the software suspects you of spamming, seeing as though I'd like to see more of you around here. Post about your health, post about your garden--I'm interested, if that can serve as a baseline for anything.

Thanks, Hilzoy, for the updates, which do help to clarify how epidemiologists understand risk. I can only hope that if a flu pandemic does occur, sensible and articulate epidemiologists find their way on air.

In other, more self-centered news: should I get a flu shot this year? I've never gotten one before. I'm a generally healthy 28 year-old, who had until recently always thought that flu-vaccinations were for the elderly and immune-impaired. I know full well that the current vaccination dose won't protect against the feared Avian Flu strain. Is there any point besides making my mother happy?

Is there any point besides making my mother happy?

Does there need to be any other point? ;^)

Jackmormon: yes, there are two points to getting it, besides the usual. (1) The flu is serious in any case; if avian flu hits, you do not want to have it after already being weakened by the regular flu, or conversely. (2) Flu viruses have this delightful capacity to swap genes with one another when two separate strains find themselves in the same host. Sometimes this results in a virus that just doesn't work, but sometimes it results in a virus with properties of avian and human flu. And one possible combination is: the deadliness of avian flu; the easy transmission among humans of the normal flu. By getting the flu shot, you prevent this from happening in you.

To be clear: point (2) above is less about benefitting you than about doing your part to prevent an unlikely but by no means impossible event that would greatly harm others from happening in your body.

Okay, internet moms (half the neuroses, twice the statistics!), I'll get my flu shot.

Good thing I live in NYC, where the mayor has donated obscene amounts of money from his obscene personal wealth to finance public health. Between his philanthropy and my university's outreach, I should be able to find a vaccination that doesn't make me feel like I'm stealing health from the poor.

And Slarti: I don't think that will work with the flu. One reason is that when handwashing etc. cut transmission over a population, the extent to which they do so is a function of the average effectiveness of the hygiene measures and the percentage of people who are convinced to adopt them. And you'd have to have very, very, very effective hygiene measures to make up for the fact that they would in all likelihood not be adopted by everyone. This is especially true for flu, which is spread not just by hands but by airborne droplets. You'd need everyone wearing masks and gloves or something.

Also, think of it this way. Anarch described exponential growth above. In fact, R(t) isn't constant, and so growth isn't really exponential. But it comes close at the outset of an epidemic, when everyone is susceptible; it tails off later, as the number of people who have had the disease becomes significant, and so the number of susceptible people an infected person comes in contact with shrinks even if the number of people she comes in contact with is constant.

Now: what you try to do with a quarantine is: confine the disease to a particular area, leaving the rest of the country untouched. Anyone who escapes from the infected, quarantined area into the surrounding, not yet infected area will set off basically exponential growth. (Which is another way of saying why R(0) is important: it tells you what number is being exponentially increased.) If R is low-ish, you have time to work; but if it's high, the effects of even a relatively small number of escapees will pretty quickly come to approximate the number who would have been produced w/o a quarantine (since the small number of initial cases at large will be compensated for by the fact that with more escapees or no quarantine, the number of susceptible people begins to drop more quickly.)

Did that make any sense?

Oh: the "also, think of it this way" para. is on another point from the one that preceded it: it's not on handwashing, but on the question of the effects of people who elude quarantines when R(0) is high.

Jackmormon: not being particularly neurotic, I prefer stats any day. (My parents were delightfully casual about things like my making explosives as a child -- my mom had read Emile -- so I never really got into obsessive worrying.)

About whether to get a flu shot: I've noticed, over the years, that I get fewer winter colds when I've had a flu shot. I have no idea why, unless the shot somehow boosts anti-viral immune response in general as well as specifically against flu bugs. So, yeah, I'm a big advocate of flu shots.

My feelings about the possibility of a deadly avian flu epidemic or pandemic, though, are that we might be getting a wee bit more worked up than is necessary. The factors that made the 1918 pandemic so catastrophic were particular to that era. The global population just isn't as isolated into discreet sectors as it was then; the international epidemiology response network we have now plain didn't exist in 1918; and we know immensely more now about how to isolate a virus and make a vaccine for it quickly.

I'm not counseling complacency. I'm just saying that scenarios involving quarantining entire cities, while public health infrastructures collapse utterly, are a long shot.

Has anyone else noticed that Bush really really likes using the military? He seems to think of it as a sort of Swiss Army Knife, good for invading, occupying, nation-building, interrogating, jailing, disaster relief, and now for enforcing quarantine. Perhaps Condi Rice or someone could tell him that there are other tools available to the government.

Oh, but wait, that would be Big Government. Can't have that. Much better to do all the same things Big Government does, for more money, less effectively, and concentrating all the power in one institution--with guns. Yes, I see now how much more sensible that is.

Trilobite, I suspect that if you rooted around in the conservative think tank literature of the last 30 years, you would find recommendations that the military be used for all manner of exigencies, the better to avoid the truly awful, world-ending occurrence of unsunseted bureaucracies, funded by that thing we apparently must protect ourselves against -- worse than millions dead from avian flu or nuclear war -- taxes!

Speaking of rooting around and birds, this paragraph appears today in this obituary for one Ruth M. Siems, the inventor of Stove Top stuffing:

"Stove Top's premise is threefold. First, it offers speed. Second, it divorces the stuffing from the bird, sparing cooks the nasty business of having to root around in the clammy interior of an animal. Third, it frees stuffing from the yoke of Thanksgiving; it can be cooked and eaten on a moment's notice any day of the year."

Clearly, This invention, Patent #3,870,803, along with the birth control pill and political correctness, was the beginning of the end for Western Civilization.

Happy day, all. I must now engage in the nasty business of the day, yoked that I am.

"...this paragraph appears today...."

Assuming today is November 22nd.

"Trilobite, I suspect that if you rooted around in the conservative think tank literature of the last 30 years, you would find recommendations that the military be used for all manner of exigencies...."

As someone who has as one of many hobbies doing such rooting around, in point of fact, one will find in such lit endless papers on the dangers, horrors, and ill outcomes of such use, and they all tend to have the point that one should never, ever, ever, use the military save to win battles against other armies, and then get the hell out.

There are some exceptions, but, as it happens, Meester Bush simply goes against the vast accumulated wisdom of said papers in Iraq. He was going with the flow back in the 2000 campaign, when he decried nation-building and using the military for non-military purposes.

Not that I want to get in the way of freeform fantasizing. Especially not that I want to discourage thullenosity.

'was this comprehensible?'

Yeah, it was great. It would help to see the contagion model used, at least in some closed form. One confusion: the 3 graphs show different containment approaches; why do they also vary R-sub-zero? Holding it constant would help compare the 3 approaches, no? (or is that a very tiny R-sub-theta on the Y axis? Do different approaches cause that to vary?)

Oh. same 3 approaches per chart, but efficacy varies and efficacy affects R-sub-0 (?)

psh: it doesn't, actually. The lines tell you: for a given set of control measures, and for a disease with a given theta (proportion of infection occurring before symptoms), what is the maximum R(0)that that disease can have and still be controlled? Thus, the lines differ for the three graphs, since they chart control measures with different rates of efficacy.

The four diseases charted are the blue and red blobs, which are all at the same place on all three graphs. SARS (in blue) is in the bottom left; smallpox (in blue) is just above it; flu is the red bar-shaped thing coming down from the top (bar-shaped since its R(0) is unclear); and HIV is the red blur over to the right.

I think the situation of HIV is not exactly right, here. They are emphasizing the proportion of infections that occur before a person becomes symptomatic as a variable in this model, I think, because normally becoming symptomatic is what allows an infected person to be identified as infected, and thus for measures like contact tracing and isolation to be taken. HIV testing, which of course is possible long before a person develops symptoms of AIDS, complicates the use of this variable -- lots of people are identified as HIV+ long before they develop symptoms.

"It doesn't, actually" means: R(0) doesn't vary from one chart to another.

Ah.

For the edification, safety and continued good health of the ObWi "community:"

Bird Flu Symptoms:

The Center for Disease Control has released a list of symptoms of bird flu.

If you experience any of the following, please seek medical treatment immediately:

1. High fever
2. Congestion
3. Nausea
4. Fatigue
5. Aching in the joints
6. An irresistible urge to crap on someone's windshield.

Happy holiday weekend...

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