Sunday, July 26, 2020

Here we go again

TL;DR: More testing means much highers numbers but slower growth. We are probably going to have to wait quite a while before any emergency is declared. In the end, the spread will probably be much greater than last time.

Things are not entirely the same as before but not entirely different either.

The good:

Testing is way up from before and testing policy has changed. You can get tested on demand privately, if you want to pay for it. It seems getting tested publicly is now easy too. I know of two recent stories where people with mild symptoms got tested and it was pretty easy. When doing contact tracing they now test all contacts, not just those with symptoms. Combined with the targeting of some high risk groups for mass testing and this certainly has a large impact on the number of cases discovered. The official goal of the govt now is to identify positive cases as soon as possible, including asymptomatic cases.

Even though the numbers are much higher than before, it does seem like the rate of growth is lower. This might seem odd but it makes sense. If you go from finding and isolating 10% of infections to 30% of infections your numbers triple on paper but you reduce the speed of the spread (10% and 30% are very made-up numbers).

Treatment is improving. The govt has approved a couple of medicines that help suppress the violent immune over-reaction. So we may see fewer serious cases and fewer deaths for the same number of infections.

The mixed:

This time round, it’s spreading in younger people. Some possible reasons:

  • younger people get no symptoms or light symptoms and we refused to test them last time around. Maybe nothing has changed and it’s just that we are detecting it in young people.
  • (not sure if this is actually true) older people are sheltering more than before
  • (not sure if this is actually true) nursing and caring staff are being tested regularly so infections are not spreading into hospitals and care homes
  • targeting of host clubs etc biases detection towards the young
  • when you shut everything down, undetected COVID mostly survives in young people. It could take several weeks for the infection to spread from young social circles back to old social circles.

If they can keep the infection away from old people, it will keep the ICU wards empty and the deaths low.

Hospital capacity has been increased. Many more hospitals are now designated to take COVID cases. Obviously more preparation and available care is a good thing. The downside is that the govt clearly knows that it’s not going to win and is betting on higher capacity to let it drag this round out as long as possible.

The bad:

There’s no doubt that we are losing again. A few weeks ago I was hoping that maybe the spike was mostly due to the testing change. It wasn’t.

The “serious” (i.e. ICU/ECMO) number has stopped falling and has been consistently rising for a week. It’s still single digits per day but it’s growing. Those people going into ICU in the last week were infected 2-3 weeks ago.

Testing capacity is growing incredibly slowly. They started publishing the numbers a little over a month ago and it has grown from 28254 to 33030 in that time (column P). Tokyo’s all-time record is 4,507. Ireland tests about 4500/day and finds 20-40 new cases per day (Tokyo finds 250-300/dat currently). Ireland is 1/3 the size of Tokyo. The rest of Japan’s testing numbers are even worse.

The avg daily testing rate (Column Q) is about half of the official capacity. It seems likely that Tokyo is using much more than half of its capacity and will soon max out. Then they will have to get stingy on tests again, e.g. no more proactive testing of host clubs or maybe make it hard for mild cases to get tested.

The national govt really don’t seem to care or have any ability to help. In fact they seem actively harmful. No responsible govt in any country is running a domestic tourism campaign right now, they’re all watching the numbers as they carefully try to restore their economies. Japan’s govt seems to see everything as secondary to the economy and their campaign-funding lobby groups. I don’t think they put any value on quality of life or are paying attention to the fact that COVID has many non-fatal but extremely nasty and chronic outcomes.

Speculation:

Present

The current numbers are not good but the numbers don’t mean the same thing anymore. My thinking had been that the true infection rate is maybe 10x what was being detected. Japan’s Case Fatality Rate was about 5% while it seems like in reality, COVID-19 has a fatality rate of about .2%-.5% that implies that the real case numbers were 10x bigger. That assumes that the virus is just as fatal here as anywhere else and that Japan’s fatality numbers are accurate (Japan was extremely stingy with testing, the true number of deaths may be much higher).

The new testing policy changes that. We might be detecting 2x or even 5x as much as previously, especially in Tokyo where they proactively test some high risk groups.

So we’re closer to the bottom of the curve than we might seem. We’re also climbing more slowly.

Near Future

I expect the govt are going to try to squeeze as much economic value as they can out of this round until one of these happens

  • ambulances cannot find hospitals for patients
  • ICU/ECMO capacity runs out

What’s extremely dangerous here is that it takes about 2-3 weeks for someone to go from infection to ICU. This means that we have to shut down 3 weeks before capacity runs out. If we screw up, we may exceed capacity. Exceeding capacity for ICU means picking who we try to save and who we leave to die.

There are a couple of ways to screw up.

  • Wait too long.
  • Have a sudden spike. E.g. as Tokyo runs out of testing capacity the rate of spread may increase, causing a numbers to spike.
  • The SOE (state of emergency) is not as effective as expected. People are tired and don’t want to stay home. Young people are already acting like there is no problem.

Also the extra capacity means that the consequences of a screw up could be much larger. Essentially we will be going much faster than before when we hit the brakes.

The SOE was declared on 2020-04-16. By that day 185 people had died (officially). By 2020-06-16 927 had died. Now it’s 996. That means that 75% of deaths occurred in the two months after hitting the brakes. If we keep going until we fill ICU capacity the death toll of the second round could be enormous.

We’ll probably see deaths start to move again soon but hopefully more slowly, given better treatment and younger patients.

In the end, I think the infection will spread much more widely than April. Given the reduced speed of spread, it might take a long time for the govt to declare an SOE. Maybe 4 weeks, as a crazy estimate that I will surely regret. I suspect Tokyo is soon going to start racing ahead of the rest of the country (moreso than it already is). So Tokyo might go into SOE earlier than that.

Until then we will have an extended period with a very large number of asymptomatic cases wandering around. That will make this round much more dangerous for people with preexisting conditions. This Bloomberg story about South Korea describes someone getting COVID-19 from a person in a neighbouring karaoke box! I was hoping I would be going out and doing fun stuff by now but I’m staying put for now.

Sunday, July 05, 2020

Is corona spiking in Japan again?

TL;DR This is all me extracting unjustified conclusions from too little information. There has been a pretty big change in testing, including testing asymptomatic contacts when contact tracing. The spike in cases in Tokyo and nationally is hopefully due mostly to more aggressive testing which will bring things under control but... It could also just reflect actual massive spread due to reopening. We can't know for a few weeks.

Something is happening with the corona virus numbers, most notably in Tokyo but also nationally. There are big jumps in the numbers and, it seems, some long-overdue changes to testing. Unfortunately there's still not a lot of transparency so everything is deduced from random quotes and reports here and there and then trying to read meaning into that. If you want to know what real transparency looks like, check out the Korean CDC[1], they have an FAQ and their daily reports describe all of the active clusters and tell you which clusters are still producing cases. I don't believe there is a Japanese equivalent to either for Japan (in Japanese or in English).

Things that have changed recently:

  • Testing is largely being done by private labs now (the beige), with the public health centres being a fairly small portion now (the reddish). Graph [8]
  • For Tokyo, the percentage of infections from unknown sources has been over 40% and even over 50% for weeks, although the 7-day avg is dropping rapidly, presumably a result of a small number of clubs providing a large number of cases. Graph [5]
  • After 2-3 weeks of flatness, PCR positive numbers have started to spike up. The 7 day avg [2] is currently 165, up from 75 a week ago and 62 a week before that.
  • Testing numbers are up having almost doubled from 3 weeks ago, to 5000-6000/day and apparently a desire for many more.
  • Governor Koike says the spike is due to testing[9].
  • There are several reports [3] that the contact tracers are now testing all contacts whereas before they would only test and isolate people with symptoms (anecdote from months ago, 2 bar staff test positive, one lives with the bar owner, they didn't test the owner because they had no symptoms).
  • Shinjuku-ku will give you 100,000JPY (~1000USD) if you are found to be positive in recognition that you will need to stop working etc.[10]
  • In Tokyo they are aggressively testing host bars and finding a ton of young male hosts who are positive. It's unclear if/why they are not testing hostesses. I've heard their clubs are not cooperating. Apparently the customers of host clubs are often hostesses whereas the customers of hostess clubs are businessmen[10]. On some days, I think, more than half of the cases announced were from clubs.
  • The age profile of the positive cases is way younger than before. Consistent with detection of mild and asymptomatic cases and also hosts.
  • The number of people hospitalised [4] had been dropping rapidly since early May. The number in ICU was also dropping. They started dropping around the same time. Hospitalised has been rising for about 2 weeks and ICU was still dropping until today.
  • The head of the LDP's corona virus panel laid out some good stuff on what needs to be done, a refreshing change from the self-congratulation and mission accomplished nonsense. Including saying that previously testing was rationed due to lack of resources.
  • They have started issuing alerts through the contact tracing app [6]
  • The expert panel has been disbanded and will be replaced by a new panel. This is a mixed bag. It seems they conflicted with the politicians. It's very hard to know who was to blame for the previous bad testing policies. The new panel retains some of the old panel. It's also got Shinya Yamanaka a Nobel laureate who has been vocally critical about the lack of testing. This is a great sign but might also just be a good way to shut him up. Who knows...

As well as the links to the spreadsheet of the national stats, the Tokyo site [5] has a lot of the same numbers with nice graphs but Tokyo-specific.

So what does this all add up to?

It does seem pretty clear that testing policy has changed and we are finally looking for the asymptomatic cases and Shinjuku-ku are even offering a bounty. That bounty should be national policy, not something we have to wait for 23 wards and 47 other kens to implement. Maybe 40% of cases have no symptoms but can still spread. Catching them with contact tracing could be the difference between growing and shrinking case numbers. Wakayama did exactly that back in March [7] but at the time it had to defy policy. Maybe finally policy has caught up to them.

I have read recent stories in forums from people who are properly sick and still cannot get tested but if you are willing to pay for it, I believe testing is quite available. It's extremely short-sighted to put any barriers to testing people who have symptoms or are backed up by a request from a doctor. Hopefully the enthusiasm for more testing will spread. It would be really nice to see a strong, clear national policy that allowed any doctor get someone tested without charge. I suspect that the free testing at the public health centres is going to remain slow, manual and tightly rationed.

This part is total speculation. The spike in positives seems likely to be a mix of aggressive testing and some real growth. I feel like the jump is so sudden and large that it is more about testing than growth but that I might be doing some wishful thinking. The continued unlockdowning might also be a significant factor.

If my hope is correct, then we have a few weeks of continued rising numbers as we find more and more of the clusters that are already out there. The number of cases out there will not be growing rapidly, just the number that we are confirming. Now, for every cluster, we will find twice or three times as many infected people as before. Keep an eye on the number of people in ICUs and deaths. That lags by a few weeks but is much less impacted by PCR testing policy. If it stays low then the spike in numbers is coming from better testing.

Even if the new testing policy leads to control instead of growth, it would be great to kick-start the clean-up by mass-testing a few other at-risk industries, hostesses, massage, nail & hair, health, retail.

The alternative is that not that much has changed, Koike is demonising the night-entertainment industry because it's convenient [10] and we are all due for a another cycle of growth and lockdown (maybe locking down over Obon in August but I doubt we'll make it that far if it's really happening again).

I think both scenarios fit with the information and it's too early to tell which one is real. It would be awesome if Tokyo followed through on the poop studies [8]. It seems like waste water is able to give us almost real-time information on the infection levels in a city but until then I'll keep reading the tea-leaves - apparently floaters are good luck :)

https://www.cdc.go.kr/board/board.es?mid=&bid=0030
https://docs.google.com/spreadsheets/d/1t-EDGaXP5ehDgvPLOyLlESONMzFTFlZ-y5vrOs9nvVk/edit#gid=162562862
https://twitter.com/fergal_whatever/status/1278979040213262336
https://docs.google.com/spreadsheets/d/1t-EDGaXP5ehDgvPLOyLlESONMzFTFlZ-y5vrOs9nvVk/edit#gid=38005457
https://stopcovid19.metro.tokyo.lg.jp/en/
https://www.japantimes.co.jp/news/2020/07/03/national/japan-infection-codes-coronavirus-app/#.XwAPWnUzZhE
https://www.washingtonpost.com/world/asia_pacific/japan-coronavirus-wakayama/2020/03/22/02da83bc-65f5-11ea-8a8e-5c5336b32760_story.html
https://www.mhlw.go.jp/stf/covid-19/kokunainohasseijoukyou.html
https://www.japantimes.co.jp/news/2020/06/15/national/tokyo-47-covid-19-cases/
10 https://asiatimes.com/2020/07/tokyo-host-bars-take-the-heat-for-covid-revival/