Tokyo Zombie Movie

The novel coronavirus (COVID-19) continues to spread globally, and at this point in its progress very few high-income countries have escaped its grip. On a per-capita basis Spain has 38 times the rate of infection of China, the US 10 times and Australia 3 times, but plucky Japan has only 0.3 times the infection rate of China. Until now the rate of growth has been low, with only tens of cases per day being recorded over much of February and March, but since last week the alarm has been sounding, and the government is beginning to worry. We had our first lockdown on the weekend, a voluntary two days of 自粛 in which everyone was supposed to stay inside, and this week discussion of lockdown began. This is because the previous week was a bright, sunny weekend with the cherry blossoms blooming, and all of Tokyo turned out to see them despite the Governor’s request for everyone to be cautious. Over the two weeks leading up to that weekend, and for perhaps two days afterwards, the train system returned to normal and Tokyo was being its normal bustling, busy uncaring self. But then on the week after that event the numbers began to climb, and now the government is worried as it begins to watch the numbers slide out of control. I am also now hearing for the first time stories of doctors having to find alternative ICU beds for COVID patients – still not a huge deal, because any one hospital does not have a large supply, but enough cases are now appearing to force doctors to seek empty hospitals elsewhere.

It is possible to see the effect of this party atmosphere in the data, and it offers a strong example of how important social distancing is. Using the data from the Johns Hopkins Coronavirus tracker (and making a few tiny adjustments for missing data in their downloadable file), I obtained and plotted the number of new cases each day, shown in Figure 1 below. Here the x axis is the number of days since the first infection was identified, and the y-axis is the number of new cases. Day 70 is the 1st April. The red line is a basic lowess smooth, not a fancy model.

Figure 1: Daily new cases by time since the first case

It is clear from this figure that things changed perhaps a week ago. New case numbers were up and down a lot but generally clustered together, representing slow growth, but since about a week ago the gaps between each dot are growing, and more dots are above than below the line. This is cause for concern.

However, it is worth remembering that each day the total number of cases is increasing, which means also that if you add the same number of new cases on any day, it will have a proportionately smaller effect on the total. We can estimate this by calculating the percentage change each day due to the new cases added on that day. So for example if there are 10 cases in total and 10 new cases are detected we see a 100% change; but 10 new cases with 100 existing cases will lead to only a 10% change. From this we can calculate the daily doubling time: the time required for the number of cases to double if we keep adding cases at the same percentage increase that we saw today. So, for example, if there are 100 cases on day 9 and on day 10 there are 10 more cases, the percentage change is 10%, and from that I can estimate that the number of cases will double after 7.2 days if that 10% daily change continues. This gives a natural estimate of the rate at which the disease is growing, adjusting for its current size. Figure 2 shows the doubling time each day for Tokyo, again with the number of days since the first infection on the x-axis. I have trimmed the doubling time at 20 days, so a few early points are missing because they had unrealistically high doubling times, and added a lowess smooth to make the overall pattern stand out. The vertical red line corresponds with Friday March 20th, a national holiday and the first day of the long weekend where everyone went cherry blossom viewing.

Figure 2: Daily time required for case numbers to double in Japan

Since the infection hit Japan the doubling time has been growing slowly, so that in February it would take almost two weeks for the number of cases to double. The doubling time dropped in March[1], which was also the time that the government began putting in its first social distancing guidelines (probably about late February); work events were being canceled or postponed by early March, probably in response to government concern about the growing number of cases, and this appears after two weeks to have worked, bringing the doubling times back up to more than two weeks. And that was when the sunny weather came and everyone went to hanami, marked on the red line, at which point the doubling time dropped like a stone. Back in the middle of March we were seeing between 10 and 40 cases a day, slow changes; but then after that weekend the number of cases exploded, to 100 or 200 a day, pretty much 4-6 days after the long weekend started. The following weekend was when the government demanded everyone stay in, and the city shut up shop; but we won’t begin to see the effect of those measures until tomorrow or this weekend, and right now the number of new cases is still hovering around 200 a day.

It’s worth noting that not all of these cases are community transmission. About 10% are without symptoms, and another 20% are having symptoms confirmed (probably because they’re very mild), which indicates the effectiveness of contact tracing in tracking down asymptomatic contacts. A lot of these cases are foreigners (something like 20-25%), and this is likely because they’re residents returning from overseas, and likely identified during quarantine/self-isolation (so not especially risky to the community). But still, even 70% of 200 is a lot of cases.

It’s instructive to compare this doubling time with some heavily-affected countries. Figure 3 shows the smoothed doubling times for Japan, the US, Italy and Australia. It has the same axes, but I have dropped the data points for clarity (I make no promises about the quality of these hideous smooths). The legend shows which country has which colour. Italy and Australia start slightly later in this data because their first imported case was not at day 0.

Figure 3: Doubling times for four affected countries

As you can see, Italy’s doubling time was almost daily in the first week of its epidemic, but has been climbing rapidly since they introduce social distancing. Australia’s doubling time was consistently a week, but began to increase in the last two weeks as people locked in. The US tracked Japan for a couple of weeks and then took a nose dive, so that at one point the daily doubling time was 3 days. Italy provides a really instructive example of the power of social distancing, which was introduced in some areas on February 28th and nationally in increasingly serious steps from 1st March to 9th March. Figure 4 shows Italy’s doubling time over the epidemic.

Figure 4: Doubling time for Italy

 

It is very clear that as measures stepped up the doubling time gradually increased. In this figure day 40 is the first of March, the first day that national measures were announced. Despite this, we can see from Figure 3 that it took Italy about a month and a half from the first case to slow the spread enough that further doubling might take a week, and early inaction meant that a month of intensely aggressive measures were needed to slow the epidemic, at huge cost.

It is my hope that Japan’s early measures, and aggressive investigation of clusters at the beginning of the outbreak, will mean that we don’t need to go into a month-long lockdown. But if Japan’s population – and especially Tokyo’s – don’t take it seriously now, this week and this weekend, Tokyo will go the same way as London and Italy. It’s time for Tokyo to make a two week sacrifice for its own good. Let’s hope we can do it!


fn1: Which the smooth doesn’t show, by the way, it’s an awful smooth and I couldn’t improve it by fiddling with the bandwidth[2]

fn2: A better model would be a slowly increasing straight line with a peak at the hanami event and then a rapid drop, but I couldn’t get that to work and gave up[3].

fn3: Shoddy jobs done fast is my motto!

Conspiracy theories about Japan’s approach to the coronavirus (COVID-19) are beginning to spread online, as people find it very difficult to believe that the country still has only 1000 cases of the virus even though it has not been testing a great deal. This has led to suggestions that Japan is covering up the true number of cases, and the epidemic is out of control in Tokyo.

This isn’t true: Japan has actually tested quite a lot of people, the epidemic is not out of control here as it is in so many other countries, there is no cover up, and what is happening in Japan is an example of what can be achieved with careful, early interventions. I will explain this here a little.

What is Japan’s epidemic situation?

According to the Ministry of Health, Labour and Welfare there were 1193 confirmed cases of COVID-19 on 25th March, of whom 272 had recovered,  43 had died and 57 required ventilator support. Japan’s first death from COVID-19 occurred on 13th February, about 41 days ago, a lot earlier than in other countries such as Germany (15 days ago), Italy (34 days ago) or the USA (25 days ago). For a disease as infectious as this one, these small differences in number of days should lead to huge differences in case numbers: Japan has had 16 days more than the USA to see this epidemic grow, but on day 9 the USA had only 645 cases – now it has 64,661 cases. It is obviously mystifying to many people that the US could see a 100-fold increase in the number of cases in the same time period that Japan saw only a two-fold increase. The obvious suspicion is that since Japan hasn’t tested that many cases, they must be hiding something. There are two reasons this theory doesn’t work: 1) Japan is actually testing more than people recognize and 2) you would definitely be able to tell if there was a 50-fold undercount of cases.

What is Japan’s testing situation?

Testing data can be obtained here. Japan has tested about 22,000 people, of whom 1193 have been confirmed positive. In contrast Germany has tested 167,000 and the UK has tested 65,000. This certainly seems like a lot of missed tests in Japan, but it is worth bearing in mind that the number of tests per positive person is actually about the same in these countries: 18.4 per positive in Japan, 19.7 per positive in the UK, and 25.5 per positive in Germany. In South Korea the number is unusual: 350,000 tests for about 9,000 cases, or 38.9 tests per positive case, but South Korea was dealing with a unique situation where a particular population group was known to be at risk (the weird religious group) and an aggressive testing policy could be targeted based on a social identity. In other countries the number of tests has approximately mapped the scale of the epidemic. This strangely stable ratio of tests to positive patients arises from the limitations on the test: it can only work on people who currently have the virus (it’s a PCR test) and it is expensive and still limited, so population-level testing cannot yet be conducted, and if done partially would miss cases. Basically every country is using passive case-finding to identify the disease, and only using the test where the symptoms suggest it, in order to conserve tests and avoid the social consequences (isolation and clinic shutdowns) associated with false positives. Japan is doing no differently here than Germany or the UK, it’s just that there are less people with symptoms, and less people to test as a result.

It’s worth noting that Japan set up a call centre for people with COVID-19 concerns on the 28th January, and since the middle of February it has been receiving about 3000 calls a day (also, somewhat cutely, 0-2 faxes per day: don’t ever change, Japan!), so there have been about 150,000 calls over the period of testing. In a country of 120 million this doesn’t seem to be a sign of a massively out of control epidemic. I can’t find statistics on the NHS 111 line but there are many stories out there about how it is congested with calls.

Why is Japan following this policy?

There are several levels of testing that can be conducted for any disease, ranging from population screening (seen in breast cancer programs) through voluntary testing (seen in HIV prevention programs), active case finding (where community health organizations target particular groups known to be at risk of a disease, usually used for TB) to passive case finding, which is used in almost all non-fatal sexually transmitted infections, influenza, and other infectious diseases. Screening is usually only conducted if the disease course can be changed by early detection. Passive case finding is useful when there is no identifiable group to target, or the disease prevalence is low so the chance of a positive test is low, or the test is rare/expensive/invasive. In this case the test is still restricted in availability, and the disease prevalence is low so you need to use a lot of tests to find one case. This is complicated in the case of COVID-19 by the possibility that the testing process itself will infect the tester, and so it’s better not to go charging out into the community exposing testers to large amounts of potentially infected people. South Korea conducted a kind of active case finding program, but that is because they knew where to look.

In this sense Japan’s policy is really no different to that in other countries. Japan has focused its efforts up until now on finding cases through cluster investigation: a lot of cases in Japan up until recently have arisen from cluster’s connected to specific events, and finding the people connected to these clusters and isolating them is super important. A single live music event in Osaka, for example, was responsible for 48 cases (about 5% of all the cases in Japan!), and had those cases not been tracked they would have turned into a huge outbreak. You can see the effect of this cluster approach in the statistics: often new cases (particularly in rural Japan) are asymptomatic, which indicates they were caught as part of a contact tracing effort; and even today with 40 new cases in Tokyo about half have a known contact already, which suggests they were tracked down (or their contacts will be). Quite a few cases are also imported: 5 of today’s 40, for example, have an overseas travel history. Focusing on clusters means targeting testing at people who need it, which avoids clogging up testing facilities and ensures that the test follow up is good quality.

Another reason for Japan’s low number of tests is its basic advice to people with suspected COVID-19. The advice from the government to citizens and medical institutions alike is: don’t come in for a consultation unless you have a fever >37.5C and coughing/chest tightness for at least 4 days (unless you’re pregnant or otherwise at risk). Until then you should self-isolate and avoid travel. This advice is super important in Tokyo, where most people travel by public transport, and ensures sick people aren’t infecting others on the train, and it avoids over-burdening health facilities with people who just have a cold. Two of my role-playing group have gone through this process; one went to the doctor after 4 days and was diagnosed with a cold based on x-ray and influenza tests, and the other self-isolated until her symptoms faded after 3 days. We’ll never know if she is immune to the virus now, but it doesn’t matter because she wasn’t at risk and she did not infect anyone else by getting on a train. Given that a lot of cases in Italy are now being  reported as hospital-acquired, this is good advice – but it also leads to the use of less tests.

So how do we know the size of Japan’s epidemic?

If we aren’t testing, how do we know what’s happening? First, we can assume given the ratio of positive results to tests is the same as in other countries that the process is working the same way here, and less tests are needed because less people have the virus. Second, though, we can look at the state of hospital emergency and intensive care wards, and make a judgment about the epidemic from the burden those wards are facing. In New York, for example, we now have horrifying accounts of emergency wards overflowing with cases and doctors working without breaks as their hospitals become basically COVID zones. In Italy new triage guidelines are being released for rationing ventilators. I am sure that is not happening (yet) in Japan, for two reasons: I work with doctors at a major hospital, and I am regularly visiting that hospital for medical care.

I have worked in and around hospitals for my whole career, doing data management and research, including in Japan, and I am familiar with how a hospital feels when it is working well and when it isn’t. You can tell from the way the doctors and nurses are working, the state of the physical environment, and what they complain about when they talk to you during your work day, whether they are struggling. Doctors are often wrong about epidemiology but they have an eye for when things are changing in their case load, and when they talk to you about it you can tell if things are going wrong. I don’t get that impression from my day job, or from any of my research colleagues from other hospitals here. There is not yet any pressure on emergency or intensive care services. I also receive the circulars for the medical staff in my work email, and so I can see how they are preparing for a surge that has not yet happened (today for example I received reassuring news about the stockpile of emergency equipment that my hospital has, the kind of news that would probably make an American very angry at how ill-prepared their system was). It’s not complacency or a lack of care: the wave just hasn’t hit yet.

The second reason I know this is that I have had to visit a lot of different parts of this hospital for medical care for my stupid knee, which I dislocated at kickboxing four weeks ago and have subsequently discovered has been missing some major components for the past 30 years. I only discovered this through multiple x-rays, MRIs, and CT scans (which I guess Aussie doctors didn’t feel I deserved over the first 30 years of my life!) As we all know, X-rays play a very important role in COVID-19 care since they enable doctors to see what kind of damage is going on. There is no way I would have sat just 10 minutes in the x-ray queue, watching orthopaedic patients hobble in and out calmly, if my hospital were overrun with COVID patients – I would probably be sent off to an external private provider or forced to wait all day. There’s also no way the CT scanner would be available for me to use 15 minutes before my appointment.

Unless Japanese people are uniquely able to resist this virus, the surge isn’t here yet, which means the epidemic is still in its infancy here – but that may all be about to change.

Japan’s prevention policy and what is coming soon

Japan has avoided major lockdowns yet, because it acted early and sensibly in light of warnings from China. The Japanese government listened to China, sent help early on, and paid careful attention to what was happening. The first advice from the Ministry of Health, Labour and Welfare was sent early – probably in early February – and the first restrictions on public behavior were instituted probably two weeks after the first death in mid February. My work events were being canceled by the end of February, and instructions were being disseminated throughout Japan to avoid large events. New advice about self isolation was issued early, and the National Institute of Infectious Diseases began its epidemiological investigations early. Japanese companies already have seasonal flu policies in place, and it is quite common for people to self-isolate if they have influenza, and those who don’t self-isolate will wear masks and behave responsibly with their disease. Japan is also not a touchy-feely huggy kind of country, and bowing is the standard greeting. In contrast, the UK was still considering what to do about large events in early March, and hand-shaking was still being discussed. It’s incredible that the day before the UK experienced its first coronavirus death, when Italy was starting to go pear-shaped, and in light of China’s experience, the British government still had no opinion on large events or shaking hands, one of the most disgustingly unhygienic ways you can greet someone.

This early action has served Japan well – even though it at no point closed its border to China! – but it may not be enough. Yesterday there were 40 new cases in Tokyo and 95 new cases in the whole country, and the Tokyo governor asked people to stay inside all weekend and not travel at all unless it was an emergency. There has been general uproar that a large kickboxing event (K1) was held on Sunday, and also consternation at the large numbers of people still going to parks and gardens for ohanami (it’s the season). If counter-measures aren’t stepped up it’s likely that Japan will lose a grip on this. It’s my expectation that by next weekend the Ministry of Health, Labour and Welfare will announce a lockdown, at least of the major cities, and an extended closure of restaurants and bars (to be clear, I have no inside knowledge of this – it’s just my judgment). The 40 cases we saw in Tokyo today were at least partly a result of last weekend’s ohanami madness, and we won’t know the effect of a weekend shutdown until next week, so my guess is the government will increase the restrictions next weekend. Given the small number of cases at present and the slow daily growth they probably only need to maintain a couple of weeks’ shutdown, not the extended horror we have seen in some cities, but my guess it is coming. If the Japanese government does what it’s very good at and dithers, expect Tokyo to become a zombie survival game show within a month. But so far the Japanese response has been measured and careful and effective, so I hope they will continue this and will get this right.

A note on conspiracy theories and racism

It’s worth recognizing that the European and Anglosphere countries (except perhaps for New Zealand) had two months’ warning of what was coming, they watched everything that was happening in China and they basically ignored it. Even Boris Johnson’s rapid turnabout on his irresponsible and inhumane “herd immunity” policy wasn’t driven by the clear knowledge available to the whole world from China; he waited until some white dudes at the University for Killing People and Stealing their Shit had had time to update their model with the Italian experience before he realized what a disaster he was unleashing. It seems that no one in the west at any point considered Chinese experience, Chinese struggle or Chinese lives worth anything, and ignored all the warnings they were being given until it was too late. Japan, on the other hand, listened to China and bought itself a month of slow growth as a result.

The conspiracy theories you see online about China and Japan are grown in the same fertile racist soil as the European policy mistakes. There is a long-standing image of Asians as shifty, untrustworthy, authoritarian and narcissistic, and that is exactly the racist image that drives these conspiracy theories. It’s not possible for white people to imagine that Asians could be doing something better than them, so they simply imagine that Asians are lying and covering up the truth. Inscrutable, untrustworthy and impenetrable societies are hiding the numbers and pretending everything’s okay for their own nefarious ends (or to “save face”).

Needless to say, it’s all bullshit. There is no conspiracy, and nobody is covering anything up. Asia is just doing it better, and the west needs to start listening to what’s happened over here, if they want to escape this with any of their grandparents alive.

The 2019 novel coronavirus (COVID-19) has now escaped China and taken a firm grip on the rest of the world, with Italy in a complete lockdown, most of Europe shuttered and the UK and the US spaffing their response up a wall. A few weeks ago I wrote a short post assessing the case fatality rate of the disease and assessing whether it is a global threat, and I think now is time to write an update on the virus. In this post I will address the mortality rate, some ways of looking at the total disease burden, discuss its infectiousness, and talk about what might be coming if we don’t get a grip on this. In the past few weeks I have been working with Chinese collaborators on this virus so I am going to take the unusual step of referencing some of my meat life work, though as always I won’t name collaborators, so as to avoid their names being associated with a blog that sometimes involves human sacrifice.

As always, what COVID-19 is doing can be understood in terms of infectious disease epidemiology and the mathematics that underlies it, but only to the extent that we have good quality data. Fortunately we now do have some decent data, so we can begin to make some strong judgments – and the conclusions we will draw are not pretty.

How deadly is this disease?

The deadliness of an infectious disease can be assessed in terms of its case fatality ratio (CFR), which is the proportion of affected cases who die. In my last post I estimated the CFR for COVID-19 to be about 0.4% (uncertainty range 0.22 – 1.7%), and suggested it was between 2 and 10 times as deadly as influenza. The official CFR in China has hovered around 2%, but we know that many mild cases were not diagnosed, and the true CFR must be lower. Since then, however, the Diamond Princess cruise ship hove into view, was quarantined off Yokohama, and carefully monitored. This is a very serendipitous event (for those not on the ship, obviously) since it means we have a complete case record – every case on that ship was diagnosed, symptomatic or not. On that ship we saw 700 people infected and 7 deaths, so a CFR of 1%. I used a simple Bayesian method to use that confirmed mortality rate, updated by the deaths in China, to estimate the under reporting rate in China to be at least 50%, work which is currently available as a preprint at the WHO’s COVID-19 preprint archive. I think a decent estimate of the under reporting rate is 90%, indicating that there are 10 times as many cases as are being reported, and the true CFR is therefore 10 times lower. That puts the CFR in China at 0.2%, or probably twice as deadly as the seasonal flu. However, we also have data from South Korea, where an extensive testing regime was put in place, that suggests a CFR more in the range of 1%.

It’s worth noting that the CFR depends on the age distribution of affected people, and the age distribution in the cruise ship was skewed to very old. This suggests that in a younger population the CFR would be lower. There is also likely to be a differential rate of underreporting, with probably a lower percentage of children being reported than elderly people. It is noteworthy that only 1% of confirmed cases in China were children, which is very different to influenza. As quarantine measures get harsher and health systems struggle, it is likely that people will choose to risk not reporting their virus, and this will lead to over estimates of mortality and underestimates of total cases. But it certainly appears this disease is at least twice as dangerous as influenza.

CFRs also seem to be very different in the west, where testing coverage has been poor in some countries. Today California reported 675 cases and 16 deaths, 2.5 times the CFR rate on the Diamond Princess in probably a younger population. Until countries like the US and UK expand their testing, we won’t know exactly how bad it is in those countries but we should expect a large number of infected people to die.

On the internet and in some opinion pieces, and from the mouths of some conservative politicians, you will hear people say that it “only” kills 1% of people and so you don’t need to worry too much. This is highly misleading, because it does not take into account that in a normal year less than 1% of the population dies, and a disease that kills 1% of people will double your nation’s total death rate if it is allowed to spread uncontrolled. It is important to understand what the background risk is before you assess small numbers as “low risk”!

What is the burden of the disease?

The CFR tells you how likely an affected person is to die, but an important question is what is the burden of the disease? Burden means the total number of patients who need to be hospitalized, and the final mortality rate as a proportion of the population. While the CFR tells us what to expect for those infected, estimates of burden tell us what society can expect this disease to do.

First, let us establish a simple baseline: Japan, with 120 million people, experiences 1 million deaths a year. This is the burden of mortality in a peaceful, well-functioning society with a standard pattern of infectious disease and an elderly population. We can apply this approximately to other countries to see what is going on, on the safe assumption that any estimates we get will be conservative estimates because Japan has one of the highest mortality rates in the world[1]. Consider Wuhan, population 12 million. It should expect 100,000 deaths a year, or about 8,000 a month. Over two months it experienced about 3000 COVID-19 deaths, when it should have seen about 15,000 deaths normally. So the virus caused about 20% excess mortality. This is a very large excess mortality. Now consider Italy, which has seen 3500 deaths in about one month. Italy has a population of 60 million so should see 500,000 deaths a year, or about 40,000 a month. So it has seen about 10% excess mortality. However, those 3500 deaths have been clustered in just the Northern region, which likely only has a population similar to Wuhan – so more likely it has seen 40% excess mortality. That is a very high burden, which is reflected in obituaries in the affected towns.

Reports are also beginning to spread on both social media and in the news about the impact on hospitals in Italy and the US. In particular in Northern Italy, doctors are having to make very hard decisions about access to equipment, with new guidance likening the situation to medical decisions made after disasters. Something like 5% of affected people in Wuhan needed to be admitted to intensive care, and it appears that the symptoms of COVID-19 last longer than influenza. It also appears that mortality rates are high, and there are already predictions that Italy will run out of intensive care facilities rapidly. The situation in northern Italy is probably exacerbated by the age of the population and the rapid growth of the disease there, but it shows that there is a lot of potential for this virus to rapidly overwhelm health systems, and when it does you can expect mortality rates to sky-rocket.

This is why the UK government talked about “flattening the curve”, because even if the same total number of people are affected, the more slowly they are affected the less risk that the care system breaks down. This is particularly true in systems like the US, where hospitals maintain lean operating structures, or the UK where the health system has been stripped of all its resources by years of Tory mismanagement.

Who does it affect?

The first Chinese study of the epidemiology of this disease suggested that the mortality rate increases steeply, from 0% in children to 15% in the very elderly. It also suggested that only a very small number of confirmed cases are young people, but this is likely due to underreporting. This excellent medium post uses data from an Italian media report to compare the age distribution of cases in Italy with those in South Korea, and shows that in South Korea 30% of cases were in people aged 20-29, versus just 4% in Italy. This discrepancy arises because South Korea did extensive population-level testing, while Italy is just doing testing in severe cases (or was, at the time the report was written). Most of those young people will experience COVID-19 as a simple influenza-like illness, rather than the devastating respiratory disease that affects elderly people, and if we standardize the Chinese CFR to this Korean population we would likely see it drop from 2% to 1%, as the Koreans are experiencing. This South Korean age distribution contains some important information:

  • The disease does not seem to affect children much, and doesn’t harm them, which is good
  • Young people aged 20-39 are likely to be very efficient carriers and spreaders of the disease
  • Elderly people are at lower risk of getting the disease than younger people but for them it is very dangerous

This makes very clear the importance of social distancing and lockdowns for preventing the spread of the disease. Those young people will be spreading it to each other and their family members, while not feeling that it is very bad. If you saturate that young population with messages that people are overreacting and that there is not a serious risk and that “only” the elderly and the sick will die, you will spread this disease very effectively to their parents and grandparents – who will die.

It’s worth noting that a small proportion of those young people do experience severe symptoms and require hospitalization and ventilation. In health workers in China there was a death rate among health workers of about 0.2%, and we could probably take that as the likely CFR in young people with good access to care. If the disease spreads fast enough and overwhelms health systems, we can expect to see not insignificant mortality in people aged 20-39, as their access to intensive care breaks down. This is especially likely in populations with high prevalence of asthma (Australia) or diabetes (the US and the UK) or smoking (Italy, and some parts of eastern Europe). So it is not at this stage a good idea for young people to be complacent about their own risk, and if you have any sense of social solidarity you should be being very careful about the risk you pose to others.

How fast does it spread?

The speed at which an infectious disease spreads can be summarized by two numbers: the generation time and the basic reproduction number (R0). Generation time is the time it takes for symptoms to appear in a second case after infection by the first case, and the basic reproduction number is the number of additional cases that will be caused by one infection. For influenza the generation time is typically 2-4 days, while for COVID-19 it is probably 4-6 days. The basic reproduction number of influenza is between 1.3 – 1.5, while the initial estimates for COVID-19 were 2.5, meaning that each case of COVID-19 will affect 2.5 people. Unfortunately I think these early estimates were very wrong, and my own research suggests the number is more likely between 4 and 5. This means that each case will infect 4-5 other cases before it resolves. This is a very fast-spreading disease, much more effective at spreading than influenza, and this high R0 explains why it was able to suddenly explode in Italy and the US. A disease with an R0 over 2 is scary and requires special efforts to control.

Those early estimates of R0 at 2 to 2.5 had a significant negative impact on assessment of the global threat of this disease. I believe they led the scientific community to be slightly complacent, and to think that the disease would be relatively easy to contain and would not be as destructive as it has become. In my research our figures for projected infection numbers show clearly that these models with lower R0 simply cannot predict the future trend of the virus – they undershoot it significantly and fit the epidemic curve poorly. Sadly governments are still acting on the basis of these estimates: the UK government’s estimate that the disease will stop spreading once 60% of people are affected is based on an R0 of 2.5, when an R0 of 4 suggests 75% of people need to be infected. An early R0 estimate of 4 would have rung alarm bells throughout the world, and would have been much more consistent with the disaster we saw unfolding in Hubei. Fortunately the Chinese medical establishment were not so complacent, and worked hard to buy the world time to prepare for this virus’s escape. Sadly many western countries did not take advantage of that extra month, and are paying the price now as they see what this disease really is like.

Because this disease is so highly infectious, special measures are needed to contain it. For a mildly dangerous disease with an R0 of 1.3 (like influenza), vaccination of the very vulnerable and sensible social distancing among infected people is sufficient to contain it without major economic disruption. Above 2, however, things get dicey, and at 4 we need to consider major measures – social distancing, canceling mass gatherings, quarantining affected individuals and cities, and travel restrictions. This is everything that China did in the second month of the outbreak once they understood what they were dealing with, and is also the key to South Korea, Japan and Singapore’s success. Because some western governments did not take this seriously, they are now going to have to take extreme measures to stop this.

How many people will be infected?

The total proportion of the population that will be affected is called the final size of the epidemic, and there is an equation linking the final size to the basic reproduction number. This equation tells us that for influenza probably 40% of the population will be affected, but it also tells us that for epidemics with basic reproduction number over 2 basically the entire population will be affected. In the case of Japan that will mean 120 million people affected with a mortality rate of probably 0.4% (assuming the health care system handles such a ridiculous scenario), or about 500,000 deaths – 50% of the total number of deaths that occur in one year. The Great East Japan Earthquake and tsunami killed 16,000 people and was considered a major disaster. It’s also worth considering that those 500,000 deaths would probably occur over 3-4 months, so over the time period they would be equivalent to probably doubling or tripling the normal mortality rate. That is a catastrophe by any measure, and although at the end of the epidemic “only” half a percent of the population will be dead, the entire population will be traumatized by it.

For a virus of this epidemicity with this kind of fatality rate, we need to take extreme measures to control it, and we need to take it very seriously as soon as it arrives in our communities. This virus cannot be contained by business as usual.

Essential supplies ready

What’s going on in Japan?

The number of cases and deaths in Japan remains quite small, and there has been some discussion overseas that Japan’s response has been poor and it is hiding the true extent of the problem. I don’t think this is entirely correct. Japan introduced basic counter-measures early on, when China was struggling and well before other countries, including cancelling events, delaying the start of the school year, introducing screening at airports and testing at designated facilities, working from home and staggering commuter trips to reduce crowding on trains. For example, work events I was planning to attend were cancelled 2-3 weeks ago, and many meetings moved online back then. Japan has a long history of hygiene measures during winter, and influenza strategies are in place at most major companies to reduce infection risk. Most museums, aquariums and shopping malls have always had hand sanitizer at the entrance, and Japan has an excellent network of public toilets that make hand washing easy. Many Japanese have always maintained a practice of hand-washing and gargling upon returning home from any outside trip, and mask wearing is quite common. Japan’s health system also has a fair amount of excess capacity, so it is in a position to handle the initial cases, isolate them and manage them. This has meant that the growth of the epidemic was slow here and well contained, although it was a little out of control in Hokkaido, where the governor declared a state of emergency (now ended). It is true that many cases are not being tested – hospitals do not recommend mild cases to attend for treatment, but to stay home and self isolate, and it is likely that mild cases will not be tested – but this is not a cover-up situation, rather an attempt to ration tests (which are not being fully utilized at the moment). There are not yet reports of emergency rooms or hospitals being overwhelmed, and things are going quite smoothly. I expect at some point the government will need to introduce stricter laws, but because of that early intervention with basic measures the epidemic appears to be under control here.

My self-isolation plan was kind of forced on me at the end of February, because I dislocated my kneecap at kickboxing in a sadly age-related way, will probably require reconstruction surgery, and am spending a lot of time trapped at home as a result. Actually that was the day that everyone else was panic buying toilet paper and so I was stuck at home with a dwindling supply of the stuff until my friends stepped up. I think most people in Japan have reduced their social activities (probably not as much as me!), and are spending less time in gatherings and events (almost of all which are canceled now), and so through that reduction in contacts plus aggressive contact tracing, the disease is largely controlled here.

Is the world over-reacting?

No. You will have heard no doubt various conservatives on Fox news and in some print outlets complaining about how the world has over-reacted and we should all be just going to the pub, perhaps you’ve seen some Twitter bullshit where a MAGA person proudly declares that they ate out in a crowded restaurant and they’ll do whatever they want because Freedumb. Those people are stupid and you shouldn’t trust them. This virus spreads easily and kills easily, and if it gets a stranglehold on your health system it will be an order of magnitude more deadly than it is right now. If you live in a sensible country (i.e. not the UK or the USA) your government will have consulted with experts and developed a plan and you should follow their recommendations and guidelines, because they have a sense of what is coming down the pipeline and what you need to do to stop it. Do the minimum you are asked to do, and perhaps prepare for being asked to do more. Don’t panic buy, but if you feel like strict isolation is coming you should start laying in supplies. Trust your friends and neighbours to help you, and don’t assume your government is bullshitting you (unless you’re in the UK or the USA, obviously). This is serious, and needs to be taken seriously.

When HIV hit the world our need to wear a condom was presented to us as a self-preserving mechanism. If you choose to circumcise your baby boy you’re probably doing so as a service to future him, not to all the women or men he might spread STIs to. But this virus isn’t like HIV. Your responsibility here isn’t to yourself, it’s to the older, frailer and less healthy members of your community who are going to die – and die horribly, I might add, suffocating with a tube in their throat after days of awful, stifled struggle – if this disease is allowed to spread. We all need to work together to protect the more vulnerable members of our community, and if we don’t react now we will lose a lot of the older people we grew up with and love.

So let’s all hunker down and get rid of this virus together!


fn1: This is a weird and counter-intuitive aspect of demography. Japan has the longest life expectancy in the world’s healthiest population, and one of the world’s highest mortality rates. Iraq, in contrast, would see half as many deaths in a normal year (without American, ah, visitors). This is because healthy populations grow old, and then die in huge numbers.