Philip Alcabes discusses myths of health, disease and risk.

Plague Did Not Begin in China. And Why Should Anyone Think It Did?

Nicholas Wade, the NY Times‘s science writer, jumps the gun with a story today asserting that plague began in China.  Maybe it’s understandable:  you don’t often get a front-page story if you’re a science reporter, so once in a while you take some shaky science and turn it into an international incident.

But to understand why the story is wrong means recognizing a weakness of science as it’s often practiced today.

Wade’s claim is based on two papers published this month.  A relatively well done study by Haensch et al. in PLoS Pathogens earlier in October tested human remains from well-identified plague pits — burial sites for medieval plague victims — in different parts of Europe.  Researchers amplified DNA sequences of the plague bacterium, Yersinia pestis, at specific genetic loci, and tested to see whether the DNA matched known sequences of contemporary Y. pestis genes.

The findings published in PLoS suggest that the Black Death and perhaps subsequent waves of plague in Europe were indeed caused by Y. pestis — which would tend to debunk the theory proposed by some British researchers that the Black Death was some kind of viral hemorrhagic fever outbreak.  And they suggest that there were at least two widely different Y. pestis strains involved in different parts of Europe.  Here’s a bit of the abstract:

[O]n the basis of 17 single nucleotide polymorphisms plus the absence of a deletion in glpD gene, our aDNA results identified two previously unknown but related clades of Y. pestis associated with distinct medieval mass graves. These findings suggest that plague was imported to Europe on two or more occasions, each following a distinct route.

The main weakness here is that DNA could not be amplified from all of the plague pits the researchers studied, but after using alternative means to test the DNA debris against contemporary gene sequences the investigators concluded that the absence of genetic material reminiscent of one strain of Y. pestis was evidence that that strain was not in play in that part of Europe at the time.  Probably right, but stretching the available evidence.

It’s a common mistake, alas.  To paraphrase Karl Popper:  just because you see DNA from white swans and don’t see any DNA from black swans, doesn’t mean that black swans don’t exist.

Still, the PLoS paper is persuasive that more than one strain of the plague bacterium was circulating, and probably causing deaths, in the plague period in Europe.  Of course, it says nothing about China.

So where does the NYT reporter get his headline-grabbing story?  A paper to be published in Nature Genetics online (still embargoed at the time I’m writing, but a summary appears here) states that the sequences of plague DNA amplified from plague pit remains, as well as contemporary isolates, can be placed on a molecular clock because of the occurrence of unique mutations.  Winding the clock backward, the researchers conclude that the Ur plague organism, ancestor of all Y. pestis, came from the far east.

The molecular biology may be unimpeachable, but the inferences about history aren’t supportable by molecular evidence.  That might explain why they’re almost certainly wrong.

The problem (scientists, I hope you’re listening!) is that you may know very well what you know, but you can never know what you haven’t seen.  The hereditary tree has its roots in China.  Here is one proposed by some of the same authors in a 2004 PNAS paper:

In this set-up, isolates of Y. pestis from China seem closest to the primordial strains.

But of course, the molecular clock doesn’t take account of strains that are no longer extant.  And ones that haven’t been unearthed.  The contemporary researchers don’t see them (or don’t know how to look), so they don’t exist.

It’s a bad mistake, inferentially.  And historically.  It’s where the NYT writer goes wrong.  Almost certainly, plague did not begin in China.  It began as an enzootic infection of small mammals in the uplands of central Asia.  This is the story convincingly relayed by William H. McNeill in Plagues and Peoples a generation ago, and none of the many accounts I’ve read since then has debunked it.

Plague would have had to begin in an ecosystem in which it could circulate at moderate transmission rates with little pathogenicity among small mammals (the natural host of the bacterium).  Exactly where it started remains open to question, but it was probably in the area that is now Turkestan/Uzbekistan.  With the development of trade between that region and China, intermixing of local (central-Asian) animals with caravan-accompanying rats would have allowed Y. pestis to adapt to the latter.

Quite possibly China was the source of the first human outbreaks of plague — because the river valleys of China were settled and agricultural (therefore offering feeding opportunities for rats as well as multiple opportunities for rat-human interaction) long before Europe was.  That fact probably accounts for the biologists’ (mistaken) belief that their early samples show that Y. pestis started out in China.

But plague began as — and remains — a disease of animals.  To acknowledge that human outbreaks in China preceded the human outbreaks in Europe (the Justinian plague that began in the mid-sixth century, the Black Death that began in the 1340s, and subsequent visitations) is not the same as saying that plague originated in China.

Which it didn’t.  Plague is an animal disease from Central Asia.  Plague’s long history is the usual one:  ecosystem change, trade, animal-human interactions, alterations in climate and economic conditions, and occasional opportunities for mass human illness.   (One world, one health.)

Above all, remember that science is only capable of drawing conclusions about what scientists can observe.  Don’t be taken in by hair-raising stories.  Even in the NY Times.

A Blog Worth Following

If you haven’t already, put Crawford Kilian’s H5N1 blog on your regular reading list.  There, while you’ll still get updates on the H5N1 avian flu virus and occasional pieces on H1N1 flu (and you can see a multitude of archived posts from 2009  filled with international material on the progress of last year’s flu — and the reaction to it), you now get a much-expanded scope, including news and commentary on the spread of infectious diseases of different sorts.

What I value about H5N1 is the tracking of the mosquito-borne viral diseases, like dengue and chikungunya as well as H1N1, that reveal the effects of the elision of ecosystem boundaries; the close attention to outbreaks that stem from changes in human-animal interactions — like the recent outbreak of plague in Tibet and, of course, H5N1; and the watch it keeps on the vaccine trade, as in yesterday’s post picking up a report in The Nation on the purchase of flu vaccine from France and one last week on a US tech company’s trials of a new flu vaccine (which won’t help the public but is, apparently, already helping the company to get richer).

The kind of close attention to the details of complex interactions amongst humans, animals, and both the natural environment and the economic one that H5N1 shows is indispensable.   It should spur more interest in wresting public health away from the simple-minded mass-vaccination schemes of medical officials in the U.S. and other wealthy countries — the point of which is usually to transfer public monies into the hands of pharmaceutical companies.  And move us to toward a more complex and inclusive view of the nature of health.

Bugs in New York

I admit that I haven’t followed the story of the blossoming bedbug population avidly.  Not that I’m cold to the heartache (and itch) that bedbug infestations can bring.  It’s just that an epidemiologist always gets more worked-up about bugs like mosquitoes and ticks that are vectors for microbial pathogens — and bedbugs aren’t.

But this AP article grabbed me.  According to New York City, over 6 percent of residents who responded to a community health survey claimed to have dealt with bedbugs in the past year.  In response, the city will withhold half-million dollars normally budgeted for the city’s health department  and redirect the funds to an anti-bedbug campaign.

Some might argue that the $500,000 would be better used for preventing deadly illnesses and accidents, not just bug bites.  Still, the campaign seems right.  According to the AP story, environmental health people will work with a “top entomologist.” (Professionals collaborating across sectors:  One City, One Health.  Good.)  A note by Javier Hernandez at the NY Times‘s City Room blog is guarded, but some (like Molly Fischer at the NY Observer) seem relieved that there will be a big anti-bedbug crusade at last.

Not a very big crusade, but at least a multifaceted one, as the Bed Bug Advisory Board’s Report suggests.

Questions on World AIDS Day

Today is World AIDS Day.  After thirty years, 25 million deaths, and countless articles, books, press releases, TV and radio programs, fundraisers, AIDS walks, and messages from Bono  —  there’s still an AIDS Day?  It’s hard to see how any disease could be less in need of a boost to awareness.

But how can every day not be AIDS Day?  Over 5,000 people die of AIDS each day, worldwide — even now, in the era of effective therapy.  In south Asia alone, more people die of AIDS every two weeks than have died of the H1N1 swine flu worldwide in the past six months (about 8,000).  In Africa, AIDS takes that toll every two or three days.

AIDS is a big problem in far-away poor countries, in other words.  But unlike the usual poor-nation problems that are easily ignored in comfortable North America — malaria, sleeping sickness, dengue, diarrhea, and more — AIDS is still a problem here, too.   Surely, you might think, we ought not to need any reminders about AIDS.

Much has been said about AIDS, and much has been done.  What does World AIDS Day add?

A harder question, perhaps: why can’t AIDS just be an ordinary disease? Surely, you might think, it isn’t special anymore.

Here are some thoughts on the problem of ordinariness, published in the American Scholar a few years ago.  The occasion was the 25th anniversary of the announcement of the first U.S. cases of AIDS.

No Meeting of Minds on Flu

As the story of the flu pandemic of 2009 matures, it brings out the characteristic traits of each of the  many spheres of interest that it touches.  The physicians are certain that the news is bad, the social critics are skeptical, the official agencies are — in their usual collusion with biotech corporations (especially pharmaceutical companies) — happily promoting high-cost, high-tech responses.  And so on.

Joshua Holland’s post at AlterNet yesterday tries to explain why H1N1 swine flu shouldn’t be cause for hysteria.  He puts this outbreak in the context of flu history and the threat posed by other, more harmful, conditions — malaria for instance.  Holland plays a little bit fast and loose with the numbers:  it probably isn’t accurate to extrapolate, from the number of confirmed flu deaths so far, to get a total number of deaths that will be caused by the swine H1N1 strain this year — more efficient spread in the  cities of the Northern hemisphere in the coming few months is likely to produce fatalities at a higher rate than the more sporadic outbreaks here in April and May.  And he’s overly critical of the media — a point brought out by Revere in a response to Holland at Effect Measure today.

But, as Frank Furedi has been telling us (recently in Erasmus Law Review, for example), try to explain how people’s deep-seated anxieties drive perceptions that risk is extraordinary and unprecedented (and contribute to demands for more and better high-cost technology to deal with it) and you get some people riled up.  Disappointingly, even Effect Measure, whose assessments are consistently level-headed and cogent, slips here, flashing the moral-entrepreneur card at Mr. Holland:

Joshua Holland has never cared for a critically ill person with Acute Respiratory Distress Syndrome (ARDS), which is often the terminal event for flu patients. So I’ll tell him. It doesn’t matter if it’s caused by bacteria (many are). Half of them die no matter what you do and no matter what intensive care unit you have available to you or what antibiotic or what computer controlled respirator. We still can’t do much.

Nobody thinks it’s a good idea to let people get ARDS, and Holland acknowledges that flu is a problem that should be dealt with.  But that’s not always enough.  Question the intensity of perceived risk or the need for all the technology, and you find this out fast.

But Revere is back on track when noting that lots of problems — including malaria — are horrendous and deserve attention, and probably don’t get it because they happen to people far away.

Where would the impetus to deal with global problems besides flu come from?  A global organization that can keep things in perspective would be useful.  Poor W.H.O. isn’t positioned to do that.  Yesterday’s flu advisory from W.H.O. emphasizes the use of antivirals (oseltamivir and zanamivir) to treat people with severe or possibly severe flu:

Early treatment is especially important for patients who are at increased risk of developing complications, those who present with severe illness or those with worsening signs and symptoms.

Yet, the W.H.O. also warns against hastening the development of resistance.  This agency gets a lot of flak for not doing more and for panic-mongering when it does do more.  But, really, it’s only doing its job:  offer advice, and support interventions when invited.  It isn’t consistent, naturally.  It can’t make binding policy.  It faces a limitless and essentially insuperable legitimation problem.  In a way, W.H.O.’s hardest job is simply to maintain its own legitimacy.

Still, in a world poised to interpret signs of illness as evidence of risk and eager for technical fixes to alleviate the sense of vulnerability risk instills, the W.H.O.’s announcements can seem authoritative — and look like beckoning to the drug makers.  A Reuters story yesterday is entitled “Early Use of Antivirals Key in H1N1 Flu: WHO,” and highlights the value of the two antiviral medications more than the caution W.H.O. wants to instill.

Meanwhile, agencies that should be making real policy are focusing on immunization.  In today’s Washington Post, Rob Stein reports on health care workers’ resistance to mandatory flu vaccination.  New York State made flu immunization mandatory early on, not only for salaried health care workers but for anyone — including medical and nursing students — who might come in contact with patients, and is putting teeth into the requirement with sanctions for refuseniks.  The state resorts to high  moral rhetoric to justify its policy.  The state’s health commissioner told Stein that “the rationale begins with the health-care ethic, which is: The patient’s well-being comes ahead of the personal preferences of health-care workers.”

And at CDC, the director is cautioning that there might be a rough start-up to the swine flu immunization campaign, as the first doses of vaccine will be made available in early October.  According to the NY Times, there should be 40 million doses of vaccine available by mid-October.

We wonder whether immunization will be of any public health value at all, by the time there’s enough vaccine that it can be offered to anyone other than health care workers and a few of the people who really need protection (young people, infants’ caregivers, and pregnant women, especially — DemFromCT’s round-up at DailyKos is always worth reading).  Given the rapidity of spread of flu — in 37 U.S. states, H1N1 spread is already regional or widespread; flu is spreading locally in 12 more states, Puerto Rico, and Washington, D.C. — and based on the usual course of flu outbreaks, it seems possible that this outbreak will peak by mid November.  There’s no knowing if that will be so, obviously.  Even if it is, immunization would continue to be useful to prevent severe cases among people who are likely to get very sick if infected.

But mass immunization would no longer be of much use in preventing further incidence of infection on a population level if high levels of acquired immunity are reached across much of the population by the time vaccine is widely available.

That’s the problem with relying on mass immunization as the centerpiece of public health response: as in the old joke about comedy, timing is everything.  In 1976, there was too much immunization, too soon.  It might turn out that this year, there’s too little, too late.  The dynamics of vaccine availability and the dynamics of flu spread have to be watched in tandem, and policy updated accordingly.

In any case, with vaccine at the center, the rest of the story — the complex environmental interactions that allow flu genomes to recombine, the trade in animals and feed that allow viruses to move around, the problems of affordability and immune status and competing viral subtypes, the health care facilities to handle severe cases, and so on — gets shoved to the side.