The Coronapocalypse Part 2: An Epidemic of Testing

Most people might not realise it, but we had practice runs for the corona event several times in the past couple of decades. For SARS-1, bird flu, swine flu, ebola and others, an illness was apparently noticed in hospitals leading to a suspected pandemic. Doctors around the world were primed to look out for symptoms of a “mysterious respiratory infection”. Models were produced predicting enormous numbers of deaths. Large amounts of government money were set aside. And then the problem went away all by itself.

So why was this time different?

There have been two big developments in the last two decades that changed the way we handle pandemics.

Firstly, a global bureaucratic structure was set up to monitor pandemics. Among these was the WHO’s influenza surveillance programs which had the effect of expanding the test infrastructure around the globe. Alongside this public health bureaucrats were being primed to respond to a serious pandemic at various conferences and committee meetings.

Secondly, and most importantly, the PCR test technology became the default for viral testing. Like any technology, it has its strengths and weaknesses but it was a step up from the old cellular testing in terms of speed and accuracy. I don’t think it’s an understatement to say that the corona event could never have happened without it.

Ironically, the man who invented the PCR technique and won the Nobel Prize for his efforts, Kary Mullis, said it should never be used for viral testing and Mullis himself was a strident critic of the biomedical industry.

As an aside: if there were patron saints of science, Kary Mullis would be one of them. I highly recommend his autobiography Dancing Naked in the Mind Field and there are some great interviews with him available online.

So, we had the test infrastructure, the test technology and the public health bureaucracy in place. For past pandemics like SARS-1, we had the early warning system, the apocalyptic models predicting enormous death, the public health bureaucrats ready to get to work. Why didn’t we have a corona event?

There is one very simple explanation: we didn’t have a specific test for a specific virus. Without a test we couldn’t track ‘infections’.

In order to test for a virus, you must first identify it. That is the job of the virologist. There have been some technological breakthroughs in virology in recent times that have made identifying viruses quicker and easier using a genome analysis approach. The amount of time to identify a virus has dropped rapidly. The one man who personifies these developments and who was front and centre for the corona event was the German virologist, Christian Drosten.

Let’s go back to SARS-1 in 2003. On the occasion, Drosten identified the virus five months after the first outbreak of disease was suspected to have happened. At the time, this was considered radically fast. So fast that Drosten won an award for his efforts where he was complimented thus: “the speed with which they succeeded in identifying the new virus…is remarkable.”

Despite that breakthrough in speed, the SARS pandemic was already pretty much over by the time the virus was identified. A few months later, SARS-1 was over entirely and a great deal of money that had been invested in vaccine research went up in smoke.

Fast forward to 2009 where it took six months to find the supposed virus for swine flu and create a test for it. Once again, this was too late in the game. Respiratory virus pandemics usually go up like a rocket and come down just as fast. Five or six months is too long if you want to make a difference.

That all changed with the corona event.

The sars-cov-2 virus had apparently been isolated and a test for it produced by early January, only weeks after the supposed initial outbreak. The China CDC put its own PCR test into use early on. Christian Drosten also came onto the scene and created a test at his lab in Germany. It was available on January 16. For the first time ever, we had a test for a virus at the start of a suspected pandemic.

Let’s review a timeline of what happened at the very start of the corona event:-

Mid-late December 2020: Doctors in Wuhan think they notice an unusual pattern of respiratory illness. These cases are recorded under the influenza surveillance program using the category “pneumonia of unknown origin”.
- Note: in accordance with the rules of the influenza surveillance program, the China CDC is notified and they arrive to investigate and collect specimens etc.
- Note: all that “pneumonia of unknown origin” really means as far as I can tell, is that they had some people with pneumonia and when they tested for known viruses the tests came back negative. Was this really unusual? It seems that many pneumonia cases are not tied back to specific viruses. The key point in this case seems to have been that there were a lot of unknown cases in a short period of time in the same location. But there are all kinds of questions here. How many cases of pneumonia every year are of unknown cause? If there are many, are all these cases investigated to find a virus? If not, why were these particular patient samples studied? What counts as a ‘lot’ of cases? What scientific criteria are used to determine when such an investigation should occur?
- Note: at this point in proceedings there was no test for a virus and so a ‘case’ was defined by clinical symptoms alone. Specifically: “fever (≥38°C), radiographic evidence of pneumonia, low or normal white-cell count or low lymphocyte count, and no symptomatic improvement after antimicrobial treatment for 3 to 5 days following standard clinical guidelines.” Again, there are questions here. These criteria seem very vague and generic. Surely many pneumonia cases would fulfil these criteria. Surely cases like this would come up all the time so why was the alarm raised in this instance?
January 3 2020: Samples are taken from a patient and genetically analysed. A “novel” virus is apparently discovered.
- Note: there are all kinds of problems with the use of the word “novel” here and I will deal with this in more detail in a future post. All it actually means is that we human beings had never found it before. Just because we never found it before doesn’t mean it actually is “new”. At this point its newness is just a hypothesis. How could we actually prove that it is “new”? Even if it was “new”, that doesn’t mean it’s necessarily going to cause illness. Nothing has been proven at this point and yet even the article referenced above refers to an “emerging” pathogen. It already assumes the “newness” is a fact. That is at best sloppy science.
Three more samples are genetically studied and tests created to match the genetic pattern.
- NOTE: the authors here claim to have “isolated” the virus although they admit that Koch’s postulates or some variation thereof were not fulfilled. This means no causal relation has been proven between the virus and an illness at this point.
January 5, 2020: the WHO releases a statement saying the cause of the illness is still unknown. It states: “The symptoms reported among the patients are common to several respiratory diseases, and pneumonia is common in the winter season; however, the occurrence of 44 cases of pneumonia requiring hospitalization clustered in space and time should be handled prudently.” Sounds like very sensible advice but things were about to take off because…
January 11, 2020: the first PCR test kits arrive in Wuhan. These were developed by the China CDC.
January 16, 2020: Christian Drosten and his team in Berlin, Germany develop their own PCR test which is accepted by the WHO.
January 18, 2020: the “case” definition is now updated to include two positive results on the PCR test. This is a crucial change whose importance cannot be overstated. It represents the shift from clinical symptoms to genetic identification of ‘cases’.
January 20, 2020: 201 cases of ‘pneumonia of unknown origin’ reported.
- Note: at this point we are still talking about an actual illness.
January 26, 2020: 2000 cases of infection are reported.
- Note: this is no longer about illness necessarily. Already at this early period “asymptomatic cases” were known and clinical symptoms seemed to vary widely. We are now talking about ‘infection’. The focus is now on the virus and not on the illness.

To summarise what appears to have happened in the early stages of the corona event:-

Some doctors noticed an apparently high number of pneumonia cases in Wuhan. The Chinese CDC came in to investigate. Based on what appears to be a very low number of samples, they identified a common genetic pattern among patients that apparently mapped to a previously unknown coronavirus. Within about two weeks, a genetic test (PCR) is developed and starts to be used to identify ‘cases’. This test was then put into widespread use and large numbers of ‘cases’ were found.

After about two weeks of such testing, on January 23, 2020 at 2am in the morning, the Chinese government announced it would lock down the city of Wuhan at 10am that day. 300,000 people are said to have left Wuhan in that eight-hour window (are people in Wuhan nocturnal?) and others got out before the highways were closed later that afternoon.

What stands out to me in this story is the speed in which everything happened. When I think of science, I think of slow, methodical, careful investigation. I think of peer review, control testing, blind testing. Normally in science there are disagreements and counter theories that need to be worked through over time. In this case we went from a hypothesised novel virus to shutting down cities in the space of a few weeks.

The truth is something had changed in the way we dealt with pandemics in the last two decades and that change represents the ascendancy of virology at the expense of epidemiology.

That slow and methodical approach is true for the discipline of epidemiology. But it is not true of modern virology. On the contrary, modern virology has been all about speed. Christian Drosten and his ilk have literally made it their life work to find viruses as fast as possible. In this quest they have been in league with the public health bureaucrats who have it in their heads that we must be able to find and respond to viral pandemics as quickly as possible. The problem is that just because you find a virus, even if it is ‘new’, doesn’t mean you have a problem. To know you have a problem requires epidemiology and that takes time. It’s not a coincidence that the epidemiologists were sidelined in the corona event. Other interests were being served.

The influenza surveillance programs, global lab networks, pandemic response conferences were all predicated on fast intervention. An entire system was set up for the purpose of intervening. In the past, it had never been able to justify an intervention because it didn’t have the test data. That was the crucial difference between this pandemic and past pandemics. With the PCR test in their hot little hands, the public health bureaucrats could start to identify ‘cases’, the number of cases seemed to explode and the panic button was hit.

That would have been bad enough but then the media got involved and through them, the public.

Respiratory viral pandemics are literally a yearly event, but they take place invisibly. They come and go without anybody paying them the slightest bit of attention. Remember that influenza pandemic in 2017 that killed 1.25 million people globally? Nah? Neither do I. Might have got a few reports on page ten of the newspaper if it was lucky.

Just as the first Gulf war was the first war to be broadcast live on television, the corona event was the first pandemic to get twenty-four hours a day news coverage and the centrepiece of that coverage has always been the ‘infection’ statistics. All anybody has been talking about is the number of people infected. You get up in the morning and check the ‘case’ count and wring your hands. Nobody thought ask whether any of the people who were ‘infected’ were sick or how sick they were.

Even the early epidemiological evidence for covid indicated that the corona event would be in the range of a severe flu. Symptoms varied widely, there were lots of asymptomatic cases, there were presumably lots of people who never got sick enough to go to hospital. An early case fatality rate of about 1-2% was expected to diminish by an order of magnitude over time as this is what always happens with such pandemics. These predictions by the epidemiologists turned out to be very accurate and covid is on track for a case fatality rate of about 0.1% when all is said and done.

As far as I have seen, there was never any epidemiological evidence that the corona event was something special or unusual. But the epidemiological evidence simply never made it into the public discussion. The epidemiologists were sidelined. One, Knut Wittkowski, was even censored by youtube for daring to suggest a number of sensible, fairly obvious reasons why the lockdown might be a bad idea and might actually be counter-productive to its stated intentions. Why is youtube censoring scientists talking about science now? Is calm, rational, objective disagreement now against the rules?

At various times throughout the corona event I have thought that it represents a failure of science, even a disgrace for science. But that’s too broad a brush to paint with. What happened specifically here is that the virologists and mathematicians (mathematical epidemiology) alongside the public health bureaucrats with their testing infrastructure created a perfect storm. For the first time in history we tracked an apparent viral pandemic in real time. Where they were listened to at all, the epidemiologists pointed out that there was no actual evidence that what was happening was particularly unusual or required radical measures. But they weren’t listened to. The slow, careful, methodical approach of epidemiology could never compete the speed and excitement of the ‘infection’ statistics and the doomsday models.

The corona event represents a watershed in how we react to pandemics. Public health bureaucrats had been just itching to intervene in a pandemic and they finally got their chance. The doctors and epidemiologists were elbowed aside and the virologists and public health bureaucrats ran the show. Whether we continue down this route or correct our course is going to play a massive role in what society looks like going forward. All of sudden, dystopian depictions of authoritarian societies are no longer the realm of science fiction. Will it turn out that Kafka wasn’t really a fiction writer but a Nostradamus in waiting?

To reiterate: the epidemiologists got it right in relation the corona event. Even the early predictions turned out to be accurate. We would have done well to listen to them.

However, there is arguably a weakness in the epidemiological approach and this is highlighted by people who say we should ignore the science and consider a pandemic from a risk mindset.

All epidemiology and medicine can do is look at the early pattern in a pandemic and say that it looks just like this other pattern that we have seen in other historical cases. Most of the time that’s going to be right. But what about when it isn’t? In that case, lots of people might die. That is a risk that comes from the fact that science never proves anything.

In the next post in this series, I’ll examine this statement and look deeper into the claim that pandemic response is not about science but about risk.

All posts in this series:-

The Coronapocalypse Part 0: Why you shouldn’t listen to a word I say (maybe)

The Coronapocalypse Part 1: The Madness of Crowds in the Age of the Internet

The Coronapocalypse Part 2: An Epidemic of Testing

The Coronapocalypse Part 3: The Panic Principle

The Coronapocalypse Part 4: The Denial of Death

The Coronapocalypse Part 5: Cargo Cult Science

The Coronapocalypse Part 6: The Economics of Pandemic

The Coronapocalypse Part 7: There’s Nothing Novel under the Sun

The Coronapocalypse Part 8: Germ Theory and Its Discontents

The Coronapocalypse Part 9: Heroism in the Time of Corona

The Coronapocalypse Part 10: The Story of Pandemic