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 :)

1 https://www.cdc.go.kr/board/board.es?mid=&bid=0030
2 https://docs.google.com/spreadsheets/d/1t-EDGaXP5ehDgvPLOyLlESONMzFTFlZ-y5vrOs9nvVk/edit#gid=162562862
3 https://twitter.com/fergal_whatever/status/1278979040213262336
4 https://docs.google.com/spreadsheets/d/1t-EDGaXP5ehDgvPLOyLlESONMzFTFlZ-y5vrOs9nvVk/edit#gid=38005457
5 https://stopcovid19.metro.tokyo.lg.jp/en/
6 https://www.japantimes.co.jp/news/2020/07/03/national/japan-infection-codes-coronavirus-app/#.XwAPWnUzZhE
7 https://www.washingtonpost.com/world/asia_pacific/japan-coronavirus-wakayama/2020/03/22/02da83bc-65f5-11ea-8a8e-5c5336b32760_story.html
8 https://www.mhlw.go.jp/stf/covid-19/kokunainohasseijoukyou.html
9 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/

Looking for hidden deaths in Japan's population and flu stats

Over the weekend, I took 2018-12, 2019-01 and 2019-02 death stats and compared them to 2019-12, 2020-01, 2020-02. The data comes from the JP govt [1] The results (and a copy of the source data) are are in a Google Sheet [2].

Basically the number of deaths is just too high and changes too much from year to year to see corona in there. Japan has 250k deaths in Jan and 120k in Dec and Feb. Even if they are under-reporting by a factor of 10, it would still be lost in the noise. There's no smoking gun in there and I think the excess deaths concept really only becomes useful when you have emergency medicine collapse and people start dying from all kinds of usually-treatable things. Maybe when you have good categorization and you can remove all the car crashes and cancers etc. Then you might start to see corona effects clearly but we don't have that.

The flu stats [3] were also updated today and they added 4 weeks of data instead of just one and that does look like a smoking gun to me.

To me that looks like about 100-150 deaths counted as flu above what would be expected. That's for Tokyo. Data is missing for many of the other cities. Most that have data show a drop, in line with expectations as due to everyone wearing masks and washing their hands. Why would Tokyo be different? Well it's tempting to go with a Tokyo-Olympic related conspiracy :) but maybe Tokyo has had a bigger corona problem for longer than anyone really knew. It's the biggest destination for foreigners, it's super easy to spread and contact tracing in Tokyo is a nightmare, so spread could easily happen under the radar, given the low testing we had. So the less touristy cities would be less infected and would see flu drop as it should while Tokyo saw flu replaces by corona. Also Nagoya seems to drop and then jump up, consistent with it briefly being the worst infected area. I should look at the per-prefecture graphs of corona to see if Nagoya's corona increase lines up.

So nationally it's still 100-150 tops. Maybe corona deaths were under-counted and should have been 50% higher but it's not the 5-10x smoking Howitzer that it might have been.

1 https://www.mhlw.go.jp/toukei/list/81-1a.html#link05

2 https://docs.google.com/spreadsheets/d/1Lz71ov-DrSiLiwyUOvROzJtTmCBaHdpTXzpHj8juKAE/edit

3 https://www.niid.go.jp/niid/ja/flu-m/2112-idsc/jinsoku/1852-flu-jinsoku-7.html

Prof. Hitoshi Oshitani's lecture

This [1] (dammit, you need a username and password unless you come from a Google search, so click here [3] and then click the first result) is a long but detailed and interesting transcription of a lecture from Prof Hitoshi Oshitani, one of the expert group, a few days ago. Google translates it into fairly natural, easy to read English. In general it all seems fairly good.
There are some very surprising bits in there like the fact that they think that 80% of cases do not transmit and that 10% transmit to 1 person. This is not something I've heard anywhere (inside or outside Japan) and it implies that the remaining 10% must be transmitting a hell of lot to get us up to epidemic levels. It also seems like it would be very hard to reliably establish this when you're not testing very much.
It's unclear to me whether this 80/10/10 split is actually something that's driving testing policy. Its not that he denies that asymptomatic transmission is a problem but there's a lot of talk about what influences how infectious someone else. Given how little we know about this, I'd rather we just over-tested instead of trying to be smart.
Finally, he ends with an oblique reference to The Hammer and the Dance with a chart pulled from Thomas Pueyo's post [2]. This describes what I would love to see, a short, real lockdown to get to manageable levels (the hammer), followed by aggressive tracing, hygiene and other measures (the dance) were we try to find the best way to keep infections low and controlled. Still no concerts etc but we have a mostly normal life until a vaccine arrives. That puts us where Taiwan, South Korea etc are.
It gives me some hope that he refers to this but from everything else I've read, actual the policies have resulted in an inflatable hammer. We have already failed once at the the dance. He is calling for increased testing but others are still saying no that. Without that the dance will fall apart again.

1 https://www.m3.com/open/iryoIshin/article/759517/

2 https://medium.com/@tomaspueyo/coronavirus-the-hammer-and-the-dance-be9337092b56
3 https://www.google.com/search?q=%E3%80%8C3%E3%81%A4%E3%81%AE%E5%AF%86%E3%80%8D%E3%80%81%E8%AA%95%E7%94%9F%E3%81%AE%E8%83%8C%E6%99%AF%E3%81%A8%E3%81%AF%EF%BC%9F%20-%20%E6%8A%BC%E8%B0%B7%E3%83%BB%E6%9D%B1%E5%8C%97%E5%A4%A7%E6%95%99%E6%8E%88&oq=%E3%80%8C3%E3%81%A4%E3%81%AE%E5%AF%86%E3%80%8D%E3%80%81%E8%AA%95%E7%94%9F%E3%81%AE%E8%83%8C%E6%99%AF%E3%81%A8%E3%81%AF%EF%BC%9F%20-%20%E6%8A%BC%E8%B0%B7%E3%83%BB%E6%9D%B1%E5%8C%97%E5%A4%A7%E6%95%99%E6%8E%88&fbclid=IwAR0iDgCweB8WRA9o8GQIWg3E-W5ZaW5bJgHD5twPch3zQPmdgKON0j7TVEU

Fixing a truncated movie file with untrunc

Just putting this here because it worked

https://github.com/ponchio/untrunc

It was a bit of a mess. Ended up building a docker image which is such a sledge hammer to crack a but whatever. The files was from a phone that had run out of space during recording. The error when trying to examine the file with ffprobe was "moov atom not found".

Zombieing along in Japan

This is the Ministry of Health's page. They have a full breakdown of cases and outcomes.
https://www.mhlw.go.jp/stf/seisakunitsuite/bunya/newpage_00032.html
This Kyodo news page has nice graph of detected cases and testing numbers over time.
https://english.kyodonews.net/news/2020/03/c35480d9a1eb-coronavirus-outbreak-latest-march-12-2020.html
What this tells you is that what Japan has done so far has been fairly effective but it hasn't been enough. The schools have been closed for 2 weeks, events have been cancelled and still, the number of daily new cases is rising. If it was truly effective, the numbers would be going down by now. In South Korea they have been going down sharply for a week (and they are still testing like crazy).
Japan's only doing 200 tests/day in some cases. That means they're still just reactive - find a case, track the contacts, test them all. That's almost enough but not quite. You'll never find every contact, ever person who used the same shopping basket or rode the same bus. With a less transmissible virus that wouldn't matter but with this one it seems to be just enough for the virus to be winning.
I was really worried that the low testing was masking massive numbers of undiscovered infections but if that was the case, I think by now, we would see a much higher proportion of critical cases and hospitalization than we do. So we're still far away from an Italy style crisis (also our cases are spread widely, not concentrated in one small region).
The problem is that this almost-containment is not enough. Even if it stays kinda-safe, it never ends.
Japan is great at enduring pain and could probably keep this up for months but the cost would be huge. Something needs to change to turn that gradual increase into a decrease.
Two things give me hope:

1. Abe desperately wants the Olympics and they cannot happen with the status quo (forget about the crowds, the athletes are all over one-another - filthy beasts!).
2. It won't be long before South Korea's and China's daily new cases are lower than Japan's. Hopefully that's a pain Japan's government won't want to endure for long.

TL;DR I'm staying home until I have reason to believe Japan is in control of Corona virus. I urge anyone else who can work from home to do so. Please avoid crowds in your social life, especially indoors. Corona virus is not that lethal when treatment is available but it doesn't take much for hospitals to be overwhelmed, at which point things become far more dangerous.

There's a huge difference between us all getting this eventually and us all getting this at the same time.

The difference is in the death-rate. Wuhan had a death rate of 5% - "but that's Wuhan", yeah and now it's Lombardy too and it flipped in a matter of days. There was nothing especially bad about Wuhan or Hubei, they didn't have low standards of care. They were just overwhelmed.

I'm reading articles about hospitals in Lombardy that do not have enough ventilators, they are allocating them to the ones with best chances of survival. To be clear, they are picking people to live or die. That is what happens when the number of cases goes over capacity. We need to keep away from that situation. Also, the hospitals have shut down many of their other services to try deal with corona virus. People will suffer and even die due to other unrelated problems because corona is taking up resources.

The mortality rate appears to be < 1% when resources are available and 5% when they're not.

Italy had 21 cases on Feb 21, now it has a national crisis. Ireland has 34 today with a fraction of the population of either Italy or Lombardy.

Everywhere is different but nowhere is special. What happens next comes down to people's behaviour and until you know that your country really has this under control, the responsible thing to do is to play it safe. Wait until credible, independent medical experts are saying it's under control, not politicians. It's critical that we avoid the kind of spike in cases that overwhelms the system. The government has no magic wand, it might be able to build make-shift hospitals but it cannot pull doctors and ventilators out of thin-air. It can make things much worse but it's too late for them to make things much better.

You don't have to panic, you don't have to hoard. You don't need masks and litres of hand-sanitizer if you're staying in. Masks are for sick people, medical staff and people who deal with lots of customers every day and have a decent chance of getting sick and not knowing it yet. If you can, support your local businesses, because either way, this is going to suck economically.

A few links

3 small concert venues in Osaka led to at least 40 infections over a few days
https://japantoday.com/category/national/japan's-live-music-clubs-emerge-as-new-coronavirus-transmission-sites

Italy's situation
https://www.politico.eu/article/coronavirus-italy-doctors-tough-calls-survival/

Flattening the peak
https://thespinoff.co.nz/society/09-03-2020/the-three-phases-of-covid-19-and-how-we-can-make-it-manageable/

NSFW: Phun with phishing

Last night, one of my FB contacts popped up wanting to connect on FB messenger. This was odd because I was pretty sure we were already connected. Things started out innocently enough but quickly took a suspicious turn.

Time to have a little bit of fun, although it was late and I had a cold so not too much fun.

He was completely unfazed by the dildo museum. Sadly I am missing the screenshot where he told me to contact the FedEx agent but don't worry, it's https://www.messenger.com/t/R.Robertdouglas463 which FB has left intact despite me reporting it several times. Feel free to try arrange to receive your €100,000.

At this point I was off adding some extra touches to the agent's profile and my contact was getting impatient. I am not skilled at image doctoring so this took way too long for very little impact.

Just in case you can't make that out...

Finally, the man behind a million WhatsApp jokes is on my side.

Again, he take's WhatsApp-man in his strideand just resent me the profile photo of the agent and asked me to click the link again. FB nuked his account before I could get another screenshot, so this is how our conversation ended.

I reported the first account as pretending to be my friend (same name, same photo) and FB shut that down pretty quickly but it's a bit sad that they left the "agent"'s account up and running. There's no way to reach a human at FB, so these scammers can keep creating fake friends and feeding the to the same agent, I guess. Not sure if shutting down the agent would really make that much of a difference but it might at least interrupt a bunch of in-flight scamming, moreso than taking down each fake friend.

Vietnam visa service recommendation

I'm in Vietnam. The visa process is a bit messy if you have an Irish passport (some countries don't need a visa, Ireland does). It's "online" but actually you go online and find one of many travel companies and they apply for you. The Vietnam govt does not have an online service. So actually it takes some time and at the weekend it's worse. Don't be lulled into a false sense of security by "online", you need to do things 3-4 *business* days in advance.

If you're in a country with a Vietnamese embassy, doing it in person there might be best. Otherwise I can recommend

http://www.vietnamvisa.com/

They were quick to respond, even on the weekend and everything was smooth (and they were the cheapest I found for the super-express weekend service).

And then the taxi driver drove like a young Anakin Skywalker in a pod-racer. Brought me close to my hotel and tried to charge me 10x from the airport! He had a meter but he had doctored it to say 1000x instead of 100x! In the end I paid pretty close to the right price but stress on top of an already stressy day. Kept telling me he saw the money in my wallet. I kept telling him to fuck off.

Dude put his cell-phone on the dash, not for Google maps, for youtube!

I sent you a video

I always record videos of my comedy and sometimes I record other people too. If I sent you a link to a Google Photos video or album, here are a couple of hopefully helpful notes.

• Why have you done this? Maybe you asked me, maybe I just left my camera running.
• Can I download it? Yes there's an option to do that.
• Can I not download it? You can also click on the little cloud icon () and it will be copied into your Google Photos account. This means it will take up space in your account but it also means that if I delete it, you'll still have it.
• Will you delete this? If you want me to, I'll delete it any time. Generally I just keep things. I think have unlimited storage (you get it when you buy a Pixel phone) so I probably won't ever delete anything. Best to keep some sort of copy yourself though.
• Why is there an album? If I send you other videos in the future then they're all in one place. Easy to find, easy to delete.
• Why is it all grey? It takes a few minutes for Google Photos to process the video.
• Why does the quality suck? Google Photos puts up a low quality preview first and then after a while it's done processing the full quality version.
• How do I get this onto youtube? If you have the video in your own Google Photos, you can just click "upload" on Youtube's homepage and there's an import from Google Photos button. Videos uploaded to Youtube don't take space in your account (I think) but you can keep them unlisted so only people who know the URL can watch them.
• Can you don't? Yup, just tell me and I will not save any bits of your comedy that I happen to record.
• Do you watch my videos? You wish.

p^4 mod 120

In this video the Numberphile people prove in 2 ways that \(p^2 \equiv 1\ (mod\ 24)\). That is that \(p^2 - 1\) is divisible by 24, for \(p\), a prime greater than 3.

The second proof involves considering the 3 numbers \(p-1, p, p+1\). There are three consecutive numbers, so one of them must be divisible by 3 but it can't be \(p\). Also one of \(p-1, p+1\) is divisible by 4 and the other is divisible by 2. That means that \((p-1)(p+1)\) is divisible by \(2{\times}4{\times}3 = 24\). So, expanding out the product, \(p^2 \equiv 1\ (mod\ 24)\)

So then I wondered what if we look at one number either side of these three. We still have the previous factors but now we must also have a 5 and if we now say \(p > 5\) then the 5 can't be in \(p\) so we know that $$(p-2)(p-1)(p+1)(p+2) \equiv 0\ (mod\ 120)$$

Grouping things in +/- pairs we get $$(p^2-1)(p^2-4) \equiv 0\ (mod\ 120)$$

and multiplying out $$p^4 - 5p^2 + 4 \equiv 0\ (mod\ 120)$$ From the earlier result we know that \(p^2-1 \equiv 0\ (mod\ 24)\) so \(5p^2-5 \equiv 0\ (mod\ 120)\). Adding that into the previous result gives us $$p^4 - 1 \equiv 0\ (mod\ 120)$$

So now we have \(p^4 \equiv 1\ (mod\ 120)\) for prime \(p>5\).

Sadly throwing \(p-3\) and \(p+3\) in too doesn't get us a similar result, like \(p^6 \equiv 1\ (mod\ 840)\). With some fiddling around, we can get $$p^6 + 14p^2-14 \equiv 1\ (mod\ 840)$$ but nothing simpler jumps out.