People wearing face masks are seen at Harajuku district in Shibuya Ward, Tokyo on November 22, 2020, amid continuing worries over Covid-19. Picture: AFP Forum viaThe Yomiuri Shimbun

Covid-19 cases in Japan, after almost disappearing between November and December, are climbing back up again.

The numbers show a sudden huge spike in the reproduction (R) rate to the point that each known patient on average is infecting more than five additional people.

Why is it happening?  We have only guesses:

  • Vaccines appear to be losing efficacy after four to six months.
  • The New Year’s holiday this year was viewed as less risky and people let their hair down.
  • The Omicron variant, simultaneously introduced in Okinawa bases, Iwakuni Marine Air Base (Hiroshima) and Tokyo, changed the playing field.

Quiet, then wham!

Average daily new cases during November and December were only 176 in this land of 126 million people. That is five new cases per 100,000 people per day. Almost nothing.

During the second week of January, the number surpassed 8,000, or 29 new cases per 100,000 per day – almost six times the November-December average.

Credit: Matt Aizawa

Hospitalizations, which had declined to 1,076 cases in all of Japan as of early December, have now shot up to 30,758 cases. But that is still one-tenth of hospitalizations last August during the Delta variant peak.

How waves develop

When asked to explain the waves, epidemiologists say there is no scientific data to support any one theory, but they mention the vaccines and the usual countermeasures.

Vaccination for the general public started in May. More than 43% had received their second jabs by September 1 and over 72% by November 30.

Nearly 80% of those surveyed in December plan to take booster shots and refrain from traveling or gathering in large groups. Face coverings are ubiquitous in Japan.

Such measures may help explain why the number of cases almost disappeared last autumn.

The R (reproduction rate)

In epidemiology, the R number indicates how many people are getting newly infected by those known to be infected.

R of 1.20 means that, on average, 100 people are infecting 120 people and the epidemic is expanding. R of 0.80 means 100 people are infecting only 80 people and the epidemic is shrinking.

Between September 1 and November 30, the average R for Japan was only 0.76. In the chart below, the daily R is shown with a blue line.

Credit: Matt Aizawa

A gray column indicates a long weekend with a holiday on either Friday or Monday. It also indicates a weekend with a holiday on either Tuesday or Thursday when people are likely to take an extra day off.

The red arrows indicate instances where such long weekends were followed by jumps in the R. Notice that the R began to rise before the Olympic games with the arrival of the Delta variant and had peaked during the Games, which may suggest that the Games had little impact on the course of the epidemic.

Surprising jump in the R

Now let’s take a look at what happened to the R in the second week of January 2022. The chart below is the same R chart with a widened scale, but without the long weekend columns, to show the huge jump in the R.

Credit: Matt Aizawa

It shot up – almost off the chart – to 5.25. Now 100 known Covid 19 patients are, on average, infecting 525 new patients. Each carrier is triggering more than five new cases.

With the Delta variant, we knew by mid-July that 70% of all new cases were Delta. We do not have full data on the Omicron variant at this time to explain the latest phenomenon. But early reports suggest that a growing proportion of new cases are Omicron.

Case for more boosters

These new cases in Japan have been reported among those having received their second jabs as well as among those who were not vaccinated.

Most of the vaccines used in Japan are mRNA shots developed by the Pfizer and BioNTech group and Moderna. There are reports from Israel and elsewhere that those vaccinated with mRNA shots should receive booster shots within four to six months.

The sharp rise in new cases in Japan appears to argue for a quick implementation of a nationwide policy of encouraging boosters.

A retired Tokyo-based analyst for a major US investment bank, Matt Aizawa now crunches numbers beside a lake north of the city.