My wife and I have received both of our shots, three weeks after the first shot. In not quite two weeks we will be fully vaccinated.

The first shot triggers an immune system reaction that produces antibodies against the spike protein of the virus. After about two weeks, the immune system also produces Memory T cells, which are its way of remembering how to make more antibodies should they be needed again in the future. After three or more weeks, when the second dose is given, it puts those newly formed T cells through their paces, boosting the antibody levels.

According to the latest published numbers for Tokyo, the more infectious Delta variant already causes more new cases than all other strains of SARS-CoV-2 combined and is most likely to completely displace them soon. This is part of the reason why the reproduction rate of the virus has been increasing for several weeks, with weekly averages of new cases growth accelerating from under 20 percent a week to over 50 percent recently.

Now it is crucially important that more people get shots as soon as possible. Not all prefectures and municipalities in Japan have made the same use of the vaccine they have received from the central government.

Tokyo has the questionable distinction as the prefecture with the largest portion of unused vaccine doses, even though people are desperate for vaccine appointments. By Sunday, July 25 Tokyo had received 15,227,660 doses. According to the Vaccination Recording System (VRS), 4,081,931 of these doses had been used as first doses and another 2,380,397 as second doses, for a total of 6,462,328 – just over 42 percent of the total. That means about 8.8 million doses either have not yet been reported after use or they’re still sitting in freezers, earmarked for shots that are weeks away.

The basic supply of future vaccines are going to be about 1.3 million doses every two weeks distributed to the municipalities in Tokyo by population by the central government and another 320,000 or so allocated to the prefecture to give to the cities that need extra supplies the most because they have the smallest stocks.

In the past week (July 19 through July 26), 8,620,790 doses have been distributed for general vaccinations in all of Japan. During the same period, 3,521,414 doses were used as first shots and 3,921,705 doses as second shots, for a total of 7,443,119 shots. The same picture shows in Tokyo, with delivered stocks growing by 2,100,180 million (13,127,480 on 7/19 to 15,227,660 on 7/26) while only 895,327 doses were used (502,489 first doses and 392,838 second doses).

This would actually mean that unused stocks in freezers grew, rather than being shrunk to vaccinate as many people as early as possible to protect them against the Delta variant. Vials in freezers do not protect against illness, only shots in arms do.

However, it is also possible that the recent 4-day long weekend (Thursday, 7/22 through Sunday, 7/25) caused bigger than usual delays in the VRS reports, in which case the actual results of vaccine use could be a little better than these numbers appear to show.

Daily vaccination statistics published by the Cabinet Office of the Japanese prime Minister suffer from lag problem: They are not reported back to a central database the day the vaccinations take place. This has the curious effect of making the published chart of daily first and second shots always trend downwards for the most recent 7-120 days or so.

There is a relatively simple way to compensate for the under-count: Its ratio is consistent between first and second doses. In Japan first and second doses for Pfizer are almost religiously spaced 21 days apart. Thus by looking at the first dose count 21 days earlier one can get a close approximation of the real second dose count for a given date. The ratio between the published incomplete second dose number and the approximation derived from the more accurate first dose count can then be applied to the 1st dose Pfizer count for the date you’re looking at. Those two numbers plus the Moderna numbers (which are not subject to the same delays because of the way the SDF sites — the main consumers of Moderna doses — are operating) then give you the real up-to-date General Vaccination count 🙂

From the current numbers we can see that first doses peaked on June 8 at around 650,000 doses day. However, second doses were still steeply climbing then and the total of first second doses exceeded 1,000,000 doses a day on June 15. On June 29, exactly 21 days after the first dose peak, second doses peaked at about 625,000 doses. For about 5 days, second doses clearly outnumbered first doses (June 28-July 2).

After July 3, first doses pulled ahead again, as many municipalities had sent vaccination tickets to people with medical conditions or younger then 65 years. The overall total seems to have largely stabilised at 1.1-1.2 million doses a day.

During July, August and September, the government will distribute a basic allocation of 8,000 boxes (9.36 million doses) every two weeks plus an “adjustment” of 2,000 boxes (2.34 million doses) that will go to municipalities with the best progress in using their allocated doses. This is pushing municipalities to update data on VRS more quickly, as this will be the metric used by the government to allocate the “adjustment” doses. The basic allocation is based on the number of residents age 12-64 in each municipality (the amounts for age 65 and above have already been fully distributed).

One potential problem with this is the fact that some local clinics have been vaccinating people who did not have a vaccination ticket with bar code yet, making this portion of the vaccination total hard to track. The doses have been allocated to the municipalities but may appear unused in VRS.

We’ll be getting our first shots on Monday, about two weeks after we received the tickets to be able to make a reservation. I am excited! Vaccinations are our best chance to push the reproduction rate of the virus below 1, despite the spread of the more transmissible Delta and Kappa variants (B.1.617.2 and B.1.617.1) that were first sequenced in India late last year. Right now it looks like these variants are rapidly replacing the Alpha variant that arrived from the UK earlier this year and will have largely done so by the opening of the Olympics three weeks from now.

Setagaya, the ward of Tokyo where we live, suspended its reservation system for a couple of days to perform an upgrade. Now that it has come back online, they have also extended the time period until when you can make reservations from the end of August to September 21. They will revisit it again after watching how many individuals will get vaccinations through their universities or workplaces starting from this month.

Looking at the September overview of open slots (which we can assume to be close to the pre-booking state) it seems the mass inoculation sites run by the city are designed to handle about 33,500 shots per week. All sites have some days off (presumably for the staff), but all are open Saturdays and Sundays to make it easy for people to get vaccinated without taking off time from work or schools.

Besides the mass vaccination sites people can also go to local clinics. Appointments there are mostly not done through the municipal reservation system. I have not seen any data yet on how many people are choosing their regular clinics vs mass vaccination sites, which makes it hard to get an accurate view for progress in Setagaya.

The earliest available mass vaccination slots listed right now are about 3 weeks from now. By July 20 vaccination tickets will have been mailed out to the rmaining population aged 16-59, with children age 12-15 added at the end of the month. Assuming the vaccination capacity for July 1-21 is comparable to the empty slots in September (1-21) then about 100,000 shots can be given over these three weeks, while about another half a million people will get tickets allowing them to make appointments to get two shots each. This will presumable push the available dates months into the future. The big unknown for me is how many shots the local clinics will handle.