Thursday, October 8, 2020

I get tested

Working at a research institute has some occasional benefits. One is the ready availability of materials and expertise for all kinds of lab work and testing.

The overall infection rate in Japan has been very low, and with a very few exceptions, people are still not travelling from abroad at this time (the ones that do face a two-week quarantine).

COVID the PCR edition

OIST has developed clinical PCR testing capability, and in addition to offer it to help the Okinawan prefecture, OIST also uses it internally. If you have travelled outside Okinawa on OIST business you are required to take the PCR test. But you are also strongly encouraged to take the test if you travelled privately, or if you suspect you may have been exposed for some other reason. We've had two cases at OIST so far, but thanks in part to the prompt testing, no spread within the university.

The PCR test kit. You receive it at the guard hut at the entrance, take it to your car or bathroom, do the test, then drop it into a collection box. The whole thing takes five minutes.

The test is simple: no cotton swabs into your nose, but just a bit of spit into a sample tube. You get the kit, collect and seal the sample and record the case number yourself. You get the number by email from an — I believe — automated registration process, and the result is emailed back, so the test result is effectively semi-anonymous. The manager can clearly de-identify a test, but the people running the lab testing have no idea who the samples come rom. 

The sample tube. You spit into the tube through the blue funnel. Remove the funnel, put on the cap and you're done. Easy.

The test is free (of course), but you need to take it three times: the first working day after you return you take the test, then work from home — you're not allowed into OIST. If the test is negative the next morning you can come to work. You then take a second test on the third working day; and a third on the sixth. That's probably more cautious than is really warranted; two tests would already catch all but a very few positive cases.

Interlude: Osaka

We spent our summer vacation back in Osaka. I hadn't been back since last winter, and had a number of things to take care of. But it's also nice to spend some time in a big city again. I really like Okinawa but it can sometimes feel a little cramped.


Itami airport, Osaka. Really, really empty. I seriously wonder just how long it will take for leisure travel — and all the related business — to return to normal levels. Years, likely, and perhaps it will never completely bounce back.

The city definitely felt a bit subdued. It's a bit like during New Year or Golden Week when traffic is light and many offices are closed. Most shops and restaurants are open but customers are few. Definitely a tough time.


Uniqlo in Shinsaibashi.

Ogawa in Osaka, at dusk. Neat colours. You get to see a lot of views like this when you get in the habit of running.

Big Friendly Duck was back to provide a little light relief.


When I returned (two days early due to a typhoon) I of course had to take the test. All three tests came back negative. Pretty quick and simple.

COVID the antibody edition

OIST has also been running an antibody test project. PCR tests look for virus RNA in your blood; that tells you if you are currently infected or not. An antibody test looks for antibodies to the virus and tells you if you have been infected in the past. 

The antibody tests says nothing about whether you are currently infected, or whether you are immune. An immune response only means your immune system has encountered the virus. It doesn't mean that it is actually capable of fighting off an infection.

It's not immediately useful for the tested individual, but it can tell you how many people have been infected in a population at one time or another, and so it tells us a lot about how widely the virus has spread, how easily you get infected and so on. This was a research project, not a clinical test, and participation was completely voluntary.

This time the test was completely anonymous. You picked up a testing kit at random from a box full of kit bags. Each kit had a random ID number, and a QR code that lead to "your" page on the project website. There you got information about the project, instructions on how to take the sample and the final result. At no time could anybody figure out who you were.

The antibody sampling kit. An alcohol swab and a bandaid; a test tube for collecting blood; and an automatic lancet. You remove the safety plug (on the far right) then press the lancet against your finger. It makes a tiny cut that hopefully bleeds enough to give you a good sample. I had to struggle to get enough into the test tube.

The sample is a bit more intrusive than with the PCR test: you had to donate ~1ml blood. The kit included a small finger lancet so it was still easy and painless enough; my only problem — and I heard others complain about the same thing — was to get enough blood into the sample tube before it stopped bleeding. 

Again, the test was negative. Probably a good thing. We now know that even a mild infection can cause lasting and perhaps life-long damage to your heart and lungs especially. But an asymptomatic infection with a strong immune response Could have meant a much lower chance of catching it again later on. 

I haven't heard about the overall results yet, but with such an isolated group of people on a fairly remote part of the world I would be surprised if there are more than a handful of positive results at the most.