My home state of Bavaria (population: 13.1 million) in Germany has had 30,117 new Covid-19 cases in the past 7 days, a 7-day incidence rate of 229 per 100,000. Meanwhile, Tokyo (population: 14.0 million) has had 142, a 7-day incidence rate of 1 per 100,000. The difference in numbers is simply staggering. Given that Germany started vaccinating its citizens months before Japan, it had a headstart on the road to immunity but it has since given up this advantage. A larger share of Japanese residents is fully vaccinated in every age group than in Germany. The growth in the vaccination rate slowed to a crawl in Germany months ago, while it’s still continuing at a healthy clip in Japan.

About two months ago, Tokyo’s Covid incidence (147 per 100,000 in 7 days on 2021-09-03) was quite similar to Bavaria’s current rate. But while the Covid incidence rate has been falling week after week in Japan since early September, it has almost doubled in Germany. The Japanese drop in cases has been amazingly consistent. When cases fall by half every 8 days and this continues for 8 weeks then cases will fall over 100-fold overall. That’s what an exponential decrease looks like. It happens when the reproduction rate of the virus drops below 1.

According to a numerical model created by Kris Popendorf, the two main contributors to the swings in the reproduction rate of the virus are mobility and immunity (you can read more details about his model here). One pushes the number up, the other pushes it down. The combined changes of the two either push the number above 1 (case numbers grow) or below 1 (cases drop). There are other factors, such as adherence to mask-wearing in indoor situations but in Japan’s case this has barely budged even when cases have been falling. Even when the risk of encountering infected individuals has decreased, few Japanese have stopped wearing masks as they still strive to comply with social norms.

With the end of the state of emergency, mobility has increased. People have started to go out and travel again and companies are reducing remote work. On the other hand, while rates of immunity will increase further, this increase is slowing down as the vaccination campaign will be nearing the saturation point over the next month or so. This will shift the balance of the two factors driving the reproduction rate of the virus towards the factor that drives an increase. We can therefore expect the rate of drop to slow and eventually rebound when mobility reaches a level that outweighs the level of immunity in the population. To achieve herd immunity regardless of mobility, the vaccination rate would have to reach a level estimated to be as high as 85-90 percent, which even Japan is unlikely to reach.

Case numbers in Tokyo are now at a level about 1/200 of the peak in August. Therefore even when the numbers start rebounding and grow again, there remains some time for public messaging to prevent a return to a caseload that would overwhelm the healthcare system.

I am much more concerned about the situation in Germany, which has a significant population of people reluctant to protect themselves and others by getting vaccinated. While not as large as in Russia, Romania, Bulgaria or the USA, it makes it very difficult to get numbers under control. In Bavaria, the Covid-19 incidence amongst unvaccinated people is 9 times higher than amongst fully vaccinated people (451.5 vs. 50.9). This means that even though about 65 percent of the population are fully vaccinated, the vast majority of cases are of unvaccinated people. Only 39 percent of teenagers are fully vaccinated there while more than two thirds of teenagers in Tokyo will soon have both shots. Even for age 65+ the rate is 80 percent in Bavaria vs. 91 percent in Tokyo, which means there are proportionally more than twice as many unvaccinated seniors in Bavaria as in Japan.

Unfortunately it will be very difficult to change the attitudes behind the vaccine resistance in Germany and other countries, as it is an issue of trust. Many of the people reluctant to get the shots trust neither politicians nor mass media nor medical professionals nor science in general. They will therefore be difficult to reach.

Restrictions on public activities, such as eating out or travel that are becoming more convenient again for low-risk vaccinated people will gradually erode the non-vaccinated population share but that will take time.

On September 24, 2021 Japan’s first vaccine dose rate passed Germany’s rate (67.8 % vs 67.7 %) but with a steeper trajectory still: While Germany only has a gap of 3.8 percentage points between first and second doses, in Japan it’s still 12.0 percentage points, indicating much faster recent growth. The 1st/2nd dose gap is the equivalent of the number of additional first doses over the past 3+ weeks, since 2nd doses are given 3 weeks after first doses with Pfizer/BioNTech, 4 weeks in case of Moderna and 4-12 weeks in case of AstraZeneca. Both in Germany and in Japan the vast majority of doses used (~80%) have been Pfizer/BioNTech.

This means Japan has not only matched Germany, it is still vaccinating at three times the rate of Germany and will therefore be left with far fewer unvaccinated people. Reluctance to get vaccinated is a much bigger problem in Germany than it is in Japan. Especially in eastern states vaccination rates are much lower than average. Saxony, Saxony-Anhalt, Thuringia, Brandenburg have the lowest vaccination rates, followed by the southern states of Bavaria and Baden-Württemberg and the northernmost of eastern states, Mecklenburg-Vorpommern. Not coincidentally, the states with the lowest vaccination rates also have the highest support for the far right AfD. According to opinion polls, about 60% of AfD-supporters had no intention of getting vaccinated.

Links:

• Cabinet Office vaccine numbers
• Impfdashboard (Vaccination dashboard, English version)
• Impfbereitschaft nach Parteien-Anhänger

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.