Three members of a family hospitalized with Covid-19 symptoms in Osaka have tested positive for the Omicron variant. They are the first cases reported in Japan without a travel history or linked to someone with travel history. All other cases were either detected at immigration inspections or in quarantine or linked to someone who had recently arrived from abroad.

It must be assumed however that there are many other cases that remained undetected and spreading under the radar screen. As the Washington Post reported on December 15, the Philippines had quarantined a man on December 1 who had tested positive on arrival from Japan and who was later confirmed to have been infected with Omicron. It therefore sounds likely that there was already some community spreading in Japan three weeks ago, soon after the variant was isolated by scientists in South Africa.

During the Delta-driven fifth wave in July/August, the 7-day average of cases peaked on August 24, with the health care system in crisis. At that point the reproduction rate fell below 1. For several weeks the fall was so steep, cases almost halved every week. The most likely explanation for that was increasing immunity in the population from a successful vaccination campaign in combination with continued wearing of masks and reduced mobility (e.g. working from home, less eating out in restaurants). After two months the reproduction rate slowly increased again but as long as it stayed below 1, it still resulted in a further reduction of cases. Weekly cases reached a temporary minimum on November 9. For about a week, cases slightly increased before sliding again at a somewhat slower rate than before. Since then the reproduction rate has been gradually drifting up. Since the minimum in late November/early, December Tokyo cases have been rising from a very small basis of about 100 cases per 7 days, 99.7 percent below the 33,000+ cases per 7 days in late August. They are now around 200 cases per 7 days, a doubling in three weeks.

For the last 4 days the 7-day average increase from a week earlier has been over 40 percent, which is equivalent to a doubling every two weeks. This is not really surprising. Once cases had dropped to less than one percent of the peak, people felt safe to resume activities that they had not been able to do for a very long time, such as enjoying year end parties or having wedding receptions with guests. They felt the risk was low enough.

However, Delta has not gone away. It is still around and as people’s level of antibodies from vaccines gradually wanes, they become more susceptible to infection again, even if they remain largely protected against hospitalization or death. This is compounded by greater risk-taking when cases are perceived to be “rare enough.”

We knew that Omicron would eventually spread in the community. When it does, it will not immediately replace Delta. For a while, both will be increasing but at different rates. A level of immunity and non-medical interventions (such as mask-wearing) that is only just about adequate to control Delta will be unable to halt the spread of much more infectious Omicron. Under the current conditions where even Delta cases are increasing, we would continue seeing Delta grow relatively slowly while Omicron cases would explode. Eventually, especially as hospitals start to fill, people will modify their behaviour to reduce exposure, for example by avoiding restaurants or by using KN95/KF94 masks instead of surgical masks or cloth masks. This would then push the reproduction rate of less infectious Delta below 1 and its cases would fall while cases of more infectious Omicron would still increase but at a slightly reduced rate. That is the point from which Omicron will start to replace Delta rather than spread in addition to it.

Third doses can reduce the exposure to Omicron, especially for the older generations who were first to get vaccinated this spring and summer but Japan has not taken any measures yet to speed up the additional shots. From the beginning of December to December 21, third shots averaged a mere 10,000 per day which is less than one percent of the rate achieved and maintained for several months in the Summer.

Japan is still running its booster campaign as if its only purpose was to prevent a resurgence of Delta (like in Israel last summer) rather than to protect the population as well as possible against the immunity escape that comes with the new Omicron variant. This has to change.

I can only hope that the first official case of community transmission of Omicron will galvanize the government into action for dramatically speeding up the distribution of third shots, especially to senior citizens and people with medical conditions that make them more vulnerable.