The Canary in the Coal-Mine

Biosecurity – China

At an emergency meeting in Beijing held in late February, Chinese leader Xi Jinping spoke about the need to contain the coronavirus and set up a system to prevent similar epidemics in the future. A national system to control biosecurity risks must be put in place to protect the people’s health, Xi said, because lab safety is a national security issue. Chinese Ministry of Science and Technology released a new directive: Instructions on strengthening biosecurity management in microbiology labs that handle advanced viruses like the novel coronavirus. There is only one. such lab: it is located in the Chinese city of Wuhan. China has a history of similar incidents. Even the deadly SARS virus has escaped — twice — from a Beijing lab. Both man-made epidemics were quickly contained, but neither would have happened at all if proper safety precautions had been taken.

And then there is this little-known fact: Some Chinese researchers are in the habit of selling their laboratory animals to street vendors after they have finished experimenting on them.

Instead of properly disposing of infected animals by cremation, as the law requires, they sell them on the side to make a little extra cash. Or, in some cases, a lot of extra cash. One Beijing researcher, now in jail, made a million dollars selling his monkeys and rats on the live animal market, where they eventually wound up in someone’s stomach.

Biosecurity – the West

From its reaction, all this is clearly a source of embarrassment to the Chinese Government. But before we point the finger at China for all the World’s ills and illnesses, consider the following:

Viral evolution works much the same as human evolution, though faster. The replication of viral genes is imperfect — mistakes happen, and these mistakes (mutations) lead to genetic variation between a virus and its progeny. Unlike humans, viruses have no genetic “proofreading” system to catch many of these mistakes. As a result, mutations occur much more frequently. Occasionally, a mutation gives a virus enhanced ability to infect new host cells and reproduce more quickly than its counterparts. An advantageous mutation quickly becomes common throughout a viral population. Another process, viral reassortment (which is unique to certain viruses) allows them to acquire vastly different genes in just one generation. The genomes of these viruses consist of short segments of RNA, each separate from the other. When a virus infects a cell, these genes hijack the cellular machinery of the host to replicate themselves. The replicated genes are then packaged into new viruses and released to infect others. If two or more viruses infect the same cell, the genes of all are replicated. When the new viruses are assembled, they may receive genes from all of these viruses — a new strain can emerge.

Our current model of food animal production factors heavily into viral evolution and transmission. The system — which is vastly different than it was just a century ago — provides some efficiency, but it poses grave threats to public health, including increased risk of pandemic influenza. Beginning in the 1940s, and intensifying recently, small farms were replaced by large, industrial operations that confine thousands or even millions of animals at a single site. The animals are raised in cramped quarters, in constant contact with their waste, and fed corn and soybeans in place of the forage for which their digestive systems evolved.

At any given time there are about one billion poultry and swine total alive in the U.S., and the vast majority of these animals are raised at industrial operations. Each animal is a potential host for influenza viruses. Additionally, the stresses induced by confinement and constant respiratory exposure to high concentrations of ammonia, hydrogen sulphide, and other gases from concentrated waste leave animals more susceptible to viral infections. These conditions allow viruses to infect again and again, increasing the frequency of mutations and viral reassortment, the raw material for evolution.

The interaction between humans and food animals, and our resulting exposure to viruses these animals carry, is now radically different from that at any previous point in history. Earlier generations of farmers may have spent a few hours each day with dozens of animals at most. The workers at industrial operations work all day with hundreds or thousands of birds or pigs. The probability of contracting influenza viruses that have mutated to infect humans is greatly increased.

Unfortunately we don’t know enough about the biology of these viruses to make accurate predictions, but influenza is definitely the disease to keep an eye on. AIDS has killed millions but is only fluid-borne. Malaria has killed millions but is relatively restricted to equatorial regions. Flu viruses are the only known pathogen capable of infecting literally billions of people in a matter of months. 2009 saw a flu pandemic caused by the swine-origin influenza virus H1N1. Millions of people became infected and thousands  died.

But H1N1 is not particularly virulent. There are other flu viruses that have emerged in recent decades such as the highly pathogenic (disease-causing) bird flu H5N1 that may have the potential to cause much greater human harm. Currently H5N1 kills approximately 60% of those it infects. That’s a mortality rate on par with some strains of Ebola. Thankfully, only a few hundred people have become infected. Should a virus like H5N1 trigger a pandemic, though, the results could be catastrophic. During a pandemic as many as 2 or 3 billion people can become infected. Unfortunately, it’s not as far-fetched as it sounds. Both China and Indonesia have reported sporadic outbreaks of the H5N1 bird flu in pigs and sporadic outbreaks of the new pandemic virus H1N1 in pigs as well. Should a pig become co-infected with both strains, a hybrid mutant could theoretically arise with human transmissibility of swine flu and the human lethality of bird flu.

The worst plague in recent history was the 1918 flu pandemic triggered by a bird flu virus that went on to kill upwards of 50 million people. The crowded, stressful, unhygienic trench warfare conditions during World War I that led to the emergence of the 1918 virus are replicated today in nearly every industrial chicken shed and egg operation. We now have billions of chickens intensively confined in factory farms, arguably the Perfect Storm environment for the emergence and spread of hypervirulent, so-called “predator-type” viruses like H5N1. The 1918 virus killed about 2.5% of the people it infected, 20 times deadlier than the seasonal flu. H5N1 is now killing 60% of infected people, 20 times deadlier than the 1918 virus. So if a virus like 1918 gained easy human transmissibility, it could make the 1918 pandemic—the deadliest plague ever—look like the regular flu.

The scenario of a  super-pandemic which kills several billion people has become not only possible, but likely. The victims of Covid-19 are the canary in the coal-mine.


While it may never be possible to completely eliminate infectious diseases such as influenza, there are still steps that can be taken to mitigate the the spread of infectious disease and, hopefully, to prevent such a super-pandemic from occurring at all. Here are some:

  1. Intensive factory farming of chickens and pigs can be phased out and replaced with “free range” production.
  2. Ships’ air conditioning can be modified to meet at least the same standards found in hotels on land .
  3. New methods for routinely sterilizing mass transit vehicles, mass transit buildings and busy public thoroughfares can be invetigated.
  4. More research is needed into the details of transmission of influenza-like diseases.

Re #1: The Global Warming/Climate Change movement of the last thirty years has been a dry run. If it is politically possible to close coal-fired power stations, it must also be politically possible to close factory farms. It may mean that eggs, chicken, pork, ham and bacon will become more expensive overnight but people will cope. Governments may have to subsidize the transition to free-range farming but it will be less costly than government support for alternative energy.

Re #2: Ship heating, ventilation and air conditioning (HVAC) systems are fundamentally different from hotel systems. There are no cooling towers, because seawater is used instead. Because of this listeria does not have the opportunity to breed as in the spray towers once found in hotels. The real problem is that a ship HVAC is a closed circuit. Fresh air is mixed with existing air being recirculated for thermal efficiency. The other issue is that many cabins share a common input circuit and exhaust. While this will vary from ship to ship, effectively everyone aboard is breathing the same air. This, of course, explains why cruise ships showed such a high rate of infection of Covid-19. The present pandemic may well spell the closure of the cruise ship industry but there is no reason why it shouldn’t start up again once the air-conditioning problem has been dealt with and the public slowly regains confidence.

Re #3: I noted in a recent trip to the supermarket that the girl at the checkout swabbed the entire rubber endless-belt after each customer. This slowed things down considerably. It occurred to me that the endless belt system could equally well have been sterilized by irradiation with hard ultraviolet light as it passed underneath the counter, out of sight. The same is true of moving hand rails on escalators. Supermarket trolleys could be passed through something like a car-wash, dozens at a time, for irradiation. Other innovations may be found for sterilizing public places.
I certainly don’t have all the answers. I don’t know how we are to deal with the aviation industry. Are air passengers to be put into quarantine from now on?  I don’t have the answer to mass transit either. Cities like New York and London cannot function without mass transit systems. Person to person transmission on subway trains is going to be hard to prevent. Recent social isolation policies in Australia have reduced the incidence of influenza to about 20 percent of its usual level. Nice going, but can we keep it up?

These pandemics are the outcome of our new relationship with animals. Wet meat markets existed for centuries with no ill effects before laboratory animals came on the scene. It is factory farming that is new. We have to stop factory farming.

Thanks to Steven Mosher re lab-animal sales:

and to Dr. Michael Greger (2008)


Thanks too, to Fred Stein for the info on ships’ air-conditioning



10 Replies to “The Canary in the Coal-Mine”

  1. When I was studying history I became fascinated by 14th century, the era of the first great plague to hit Europe. (There had been others, but they weren’t as severe.) The Black Death in the first half of the 14C was only the beginning of an era of plague that lasted into the 19C. The nature of the diseases changed – they weren’t all Bubonic Plague by any means. I’ve heard of a plague pit being excavated in Germany – research showed that en entire village had died of Ebola brought back from Africa by missionaries. Cholera, typhoid, smallpox, plus many other diseases we never hear of any more had devastating effects.

    I’m not a scientist, but this fits well with my knowledge of history.

  2. A good wrap John. Note that passenger aircraft conditioning systems use air from the engine compressors. Consequently, the cabin air is constantly being renewed and not recirculated. That has a drawback for the crew because the engine seals are wet and the oil used does enter the cabin as well. You may have heard of aero toxicity? The Boeing 787 is the first aircraft to use ram air from the atmosphere thus avoiding oil contamination.
    Cruise ships have a very long way to go, and so do hotels and shopping malls.

    1. It was noted in this key article the surprise that aircraft have not been indicated as super-spreaders. The author suggests this is because, as in buses and trains, people are not usually voluble, NOT emitting saliva as droplets so much as in the more active situations identified as super spreaders in the article. What you write here would be another factor.

  3. I suspect you are right. Nature didn’t design us to live cheek by jowl, crammed into high-rise towers and tiny flats, riding on overcrowded trains and buses and ignoring the fact that we are part of the animal world on planet Earth, susceptible to all the virus and bacteria infections that entails. There are too many humans in too much of Earth. But not here, and I suspect that has helped us record a death rate per capita 100 times smaller than the UK. Still the lucky country?

  4. Another thought re manufacturing. The production line has had its day for some industries at least. Huge rooms containing a couple of hundred women on sewing machines, for example. Some pre-industrial revolution methods could work quite well though, for example piece work – a bloke with a van driving around distributing raw materials and collecting finished products or part thereof. Smaller communities and extended families will be healthier and function more efficiently than huge cities with mass transit systems. The current crisis has seen more people walking and shopping locally rather than driving and going to malls.

  5. I remember my Dad saying that when the war (WW2) ended the clear headed pragmatists (in the UK) who had guided the war effort were quickly replaced by small minded bureaucrats and political animals who had contributed little during the years of conflict. Unfortunately in a democracy, trickery, greed and spin triumphs over pragmatism. Is there any hope we can retain or develop leadership which is respectful of science and rational debate? Big ask.

    1. A good example of C P Snows Two Cultures, what your Dad said. Also how, as I have been saying, War favours the techno-people while Peace is opposite, favouring the anti-techno people : Lawyers, Spin-doctors, PR, Sales & Marketing people, Humanities people, Everything except STEM . . .

  6. This piece makes a convincing case that the Canary is singing loud and clear. Now we face the problem of convincing the people who run our governments and organisations like CSIRO, that the mitigation steps proposed should be put in place ASAP.

  7. Do you think that the strong reaction to Minister Payne’s desire for an inquiry might arise from a Chinese suspicion that Covid-19 came from that Wuhan laboratory?
    We need to build automatic virus test machines which report to your mobile phone. High volume, easy access testing can solve this problem.

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