Is Omicron milder than Delta?

Early in the Omicron wave in South Africa some local doctors were commenting that they were seeing many “mild” cases of Omicron, quite different from what they had seen with Delta in the previous wave in the country.

Soon there were two competing takes on Omicron in the public discourse, one that concludes that Omicron is more like a bad cold and another that the true virulence of Omicron, even if it was somewhat lower, would matter less than the larger number of cases from its rapid spread. “A small percentage of a very large number can also be a large number,” is how many of the experts cautioned us.

The picture was further clouded by the fact that Omicron was spreading in parallel with Delta: Many of the countries that were seeing Omicron waves were already in the midst of a Delta wave connected to the onset of winter in the northern hemisphere. For example, Japan had cases growing about 20 percent week on week for several weeks before it saw significant numbers of confirmed Omicron cases. Many of the deaths seen while Omicron cases were already growing rapidly were still Delta cases.

Death numbers always lag a few weeks behind case numbers. For example, in Tokyo the average gap between Covid diagnosis and death is about 15 days. Then it takes another 16 days on average for the death to be reported in the evening news. This means, the death count reported in the media was from people who on average died 16 days ago after having a positive PCR test 31 days ago. The positive result of the PCR test would have been included in the daily count on average about 2-3 days after the test was taken.

There is some evidence that Omicron is less virulent than Delta. A study on hamsters showed that the variant seems less capable of infecting lung cells and seems to be more focussed on the nose, throat and windpipe, which may also contribute to its easier spread. It’s not clear how these animal study results translate to humans. In December, different numbers were reported for how much less virulent Omicron was overall or specifically for unvaccinated people, with risk reductions mentioned anywhere from 15 to 70 percent.

In any case, milder than Delta does not mean mild: Delta was worse than Alpha which was worse than the D614G strain that devastated Italy and New York city in March 2020, which was worse than the original Wuhan strain. Omicron may still be as bad as one of its pre-Delta ancestors, which were deadly enough.

Finally, we have some numbers coming in.

During the Delta wave the UK 7-day trailing count of deaths had reached a peak of around 1,200 in early November 2021, when almost 100% of cases were still Delta. On January 14, 2022, when most UK cases were Omicron, this had increased to about 1,800 deaths in the last 7 days, about 50 percent more deaths per week than at the peak of Delta.

The picture is similar in Canada, where 7-day deaths peaked at 344 in October with Delta. On January 15, 2022 the same metric reached 606, almost twice as deadly, with Omicron.

While the Case Fatality Rate (CFR), which is defined as the number of deaths divided by confirmed cases, has declined with Omicron relative to Delta, this is primarily because of the extraordinarily rapid growth of cases, which grew faster than deaths climbed. The CFR went down even as deaths increase. Thus Omicron can appear to be milder and not so mild after all, as it ends up killing more people per week than Delta did. If cases go up 5-fold but deaths “only” double, the CFR will fall by 60 percent.

The only saving grace may be that Omicron will most likely burn through the infectable population more quickly than Delta ever did. Cases have peaked in South Africa, the UK and most of the US. By February they will probably also peak in Japan (before I and most others can get a booster here).

Wear a good mask, if you meet people do it outdoors, ventilate, get vaccinated and get a booster if you can.


Waiting for third doses in Japan

In December, 470,000 medical workers, 280,000 seniors (65 and above) and 90,000 others in Tokyo were qualified to receive the 3rd dose because of the time interval since their second dose and their status. Only 63,292 (7.6%) of them actually received their dose. 1,829,880 booster doses were supplied by the central government. As for January, out of 620,000 qualified individuals, 29,645 (4.8%) have received their dose so far. The scheduled supply for this month is a further 1,702,800 doses for Tokyo, for an accumulated total of 3,532,680. The number of people eligible for boosters in Tokyo by the end of February is only 2,100,000.

Also, according to the Cabinet Office (kenbetsu-vaccination_data2.xlsx file), Tokyo had received 16,586,310 million doses of Pfizer for 1st/2nd shots in 2021, of which they have used 15,358,949 doses (92.60%). Therefore, about 1,227,361 Pfizer doses should still be have been available before any of the above mentioned supplies were delivered.

Nationwide, about 10 million doses of Pfizer have been supplied but not used (165,148,620 vs. 155,989,956). Of the 50,000,000 doses of Moderna that the central government had contracted for, 34,251,400 had been distributed and 31,938,353 actually used. That leaves about 18 million doses unused, which translates to 36 million booster shots, if you add 18 million sets of syringes (Moderna boosters are half doses of regular 1st/2nd doses).

It’s not a supply problem. Based on these numbers, it’s going to be something like a mere 120,000 people with a booster in Tokyo by the beginning of February, when literally millions could have received them. Meanwhile, new cases numbers (most of them Omicron) have been increasing 4 to 5-fold week on week. We will soon hit unprecedented numbers of cases.

Without a 3rd dose, two doses of Pfizer received 5 months ago offer little protection against symptomatic infection with Omicron, though they still reduce the risk of hospitalizations and other severe outcomes. This is because of the immunity escape from Omicron. Even two weeks after the second shot, efficacy is only a little over 60% with Omicron, significantly lower than with Delta. A third shot boosts efficacy to a slightly higher level than after the 2nd shot, winding the clock back by 6 months or more. Accelerating the booster campaign by using left-over vaccine doses as soon as possible should be a high priority.

Another important point is to improve the messaging on masks: Many people are still using simple masks that cover the face but do not fit particularly well. Mask policy in Japan is still not based on the recognition that Covid-19 is airborne disease that spreads via aerosols. One person can infect another without them being in the room at the same time. High grade masks like N95, KN95, KF94, FFP2 offer much better filtration because they reduce the unfiltered side stream. They offer the best first line of defense against the explosive spread of Omicron. A rapid roll-out of boosters should be the second line.

Numbers listed for all 47 prefectures in this MHLW document:
追加接種対象者数、接種回数及びワクチンの供給量 (“Number of subjects to be additionally vaccinated, number of times vaccinated, and quantity of vaccine supplied”,

Vaccination data by prefecture from Cabinet Office:
kenbetsu-vaccination_data2.xlsx (

Upgrading to the Pixel 6 Pro

After several Nexus phones, a Pixel 3 and a Pixel 3a, the new Google Pixel 6 was an easy upgrade choice. I’ve been very happy with both the Pixel 3 and Pixel 3a, especially the image quality, so much so that I virtually stopped using my cameras. Just about the only thing the DSLR still did better was the optical zoom. The new Pixel 6 Pro has one dedicated telephoto lens that should help narrow the gap. I ordered it in December and it arrived in the new year.

I chose to migrate the contents of my Pixel 3 to the Pixel 6 Pro, since that was my main camera phone before. The new phone has 512 GB of flash memory vs. 256 GB in the old one so there are no storage issues. Copying files across using the upgrade tool and a USB-C cable was relatively straightforward. I wish the migration did not default to Japanese (my old phone was set to English), but that was no major obstacle and I could change the language afterwards.

Moving Line and WhatsApp chats across via a Google account was not difficult either, I just had to do some searches to get the backup and restore steps right. I moved the data-only SIM card from the old phone to the new one before I started. With the data-only SIM card I use a Google Voice account for SMS-verification but I will soon swap the SIM card for a voice-enabled SIM that directly handles SMS with a new phone number.

On my Pixel 3a I am using Pasmo/Suica for contactless payments and train fares since it has the Mobile FeliCa chip needed for “osaifu ketai” (wallet mobile phones). My US sourced Pixel 3 does not have this functionality. I wasn’t sure if the Pixel 6 purchased from the Japanese Google online shop would have the chip or not, since I could not find any explicit reference to it. However, it seems to work.

First I tried to directly charge the phone with cash at a machine at train station but the phone wasn’t recognized when I placed it into the charging cradle.

Then I tried to install and setup the Mobile Suica app, a truly horrible piece of software that must have roots in the pre-smartphone era. No joy! It turns out there is also a Pasmo app in the Google Play store. Uusally I treat Pasmo and Suica as synonymous since they’re different brand names for the same technology but in this case they’re not the same thing. The Pasmo app was really easy to install and set up. I selected the configuration without personal details (i.e. not linked to a bank account or credit card) and everything went smoothly. Charging it at the train station worked and so did a payment at a convenience store.

So how about the camera, the main reason I bought the phone? I tested it on Monday, which was a public holiday (Coming of Age Day), on a 162 km bicycle ride in west Izu. The weather was perfect for the numerous Mt Fuji views. I took shots from morning to after sunset, many of them telephoto shots zooming into Mt Fuji (see image above and below).

I will be able to make good use of this on my bike rides.

Hokkaido wind power for Japanese energy

Nikkei reports (“Japan pushes for undersea cables to solve wind power puzzle”, 2022-01-02) that the government is allocating 5 billion yen (about US$43 million) in its supplementary budged for a feasibility study for a 4 GW high voltage direct current (HVDC) link between the power grids of the northern island of Hokkaido and the main island of Honshu, where most of Japan’s population lives. This would be by far the biggest HVDC link ever built in Japan. The Japanese government wants to generate 45 GW of power from offshore wind in 2040, up to about a third of which (14.65 GW) is to be produced in Hokkaido. The development plan lists several promising offshore areas along the southwest coast of Hokkaido.

For this power to be available to consumers outside the northern prefecture, it would need to be exported via a HVDC link. This is the preferred technology for shifting large amounts of power over long distances, especially between AC grids not synchronized with each others or operating on different frequencies. Since 2019 there have been two 300 MW HVDC links between the two islands. Their combined capacity is to be doubled to 1.2 GW by 2028.

Japan has relatively little capacity for transferring power between its regional grids. This is because its grids used to be operated by regional monopolies that had little incentive to ever import or export power. This lack of interconnect capacity became a major problem following the power shortage after the 2011 Tohoku earthquake and tsunami when less affected areas could not help out the most affected region. There is a conflict of interest between the local utility companies and the country as a whole. Tepco owns a lot of nuclear power stations, expensive infrastructure with huge sunk costs. It would rather generate power from these plants than pay another supplier from outside its area for renewable energy. However, many of these power stations have yet to be restarted since their shutdown following the Fukushima meltdowns. By restricting how much power can be imported from other grids, Tepco can put pressure on regulators to allow it to restart more reactors to ensure a stable supply of power. On the other hand, expanding interconnect capacity would ease the pressure. Which side will the Japanese government take?

A related issue is the variable output of renewable power sources. Long distance transmission will make it easier to compensate for local weather patterns by shifting power between different regions, which allows a larger share of renewable energy to become part of the mix without having to resort to either energy storage or peaker plants (e.g. gas turbines to cover peak loads). That again means Tepco loses leverage to maintain coal and other fossil fuel powered generating capacity as insurance against shortfalls of renewable energy.

China, one of Japan’s main economic rivals in the world, has pursued a completely different course. Over the past decade it has aggressively expanded long distance HVDC links to stabilize its grid. Japan operates a single HVDC link of at least 1 GW, a 1.4 GW link between Honshu and Shikoku that started operating in 2000. All other links are only in the several 100 MW range and most of those are not long distance lines but back-to-back local interconnects, for example between the 50 Hz grid of eastern Japan and the 60 Hz grid of western Japan near Nagoya. By contrast, China has built over 20 HVDC links over 1 GW, mostly with a capacity of 3 GW or more. Many of the biggest projects cover distances of 1,000 to 2,000 km. This allows China to supply it coastal megacities with hydroelectric power from its southeastern mountains or from other power sources from its arid central parts. China is the world leader in wind power. Its windiest parts are along its border to Mongolia and on the Tibetan plateau. Large scale HVDC is key to China’s energy policy for the 21st century.

An alternative to shifting power long distance is to use it to locally generate hydrogen from water (“green hydrogen”) and feed it into pipelines or use it to make ammonia. This makes some sense for applications that already use hydrogen, such as the fertilizer industry or for carbon free alternatives to existing technology, such as direct reduction of iron ore for steel making without using coking coal. However, it makes little sense to use green hydrogen for power generation: if you convert electricity to hydrogen which you then use to generate electricity, more than 70 percent of energy is lost in the process while less than 30 percent remains. By contrast, batteries are 90 percent efficient. Therefore, if excess wind or solar power is used to produce hydrogen, that resource should best be used by industries that directly consume hydrogen, until all fossil fuel currently used for such purposes has been replaced.

If Hokkaido had a surplus of hydrogen from wind power, it would make more sense to have it consumed by steel works and fertilizer plants built in the prefecture rather than sending it through a pipeline to Honshu.

Although green hydrogen or ammonia can be used as fuel in thermal power plants in place of coal or LNG, it would be a terribly wasteful use. Because of the huge conversion losses, we would need three times more wind or solar power to end up with the same amount of usable electricity than if we used grid-scale battery storage to absorb any surplus and make it available when needed. This advantage makes grid-scale battery storage a strategic technology.

Most existing Li-ion batteries depend on relatively scarce resources such as cobalt, nickel and lithium. Lithium-iron-phosphate (LFP) batteries only require lithium and widely available materials, while sodium ion batteries use only readily available raw materials. Japan will need to invest in high capacity long distance HVDC links as well as in battery storage to speed up its transition to a carbon neutral economy.

Japan’s sixth COVID-19 wave and third doses

Compared to over 100,000 new cases a day in countries like the UK and France (each with roughly half the population of Japan), 500+ Covid cases in Japan may seem almost trivial. Japan has recently experienced something of a post-5th wave honeymoon after months of falling cases, but that is set to end very soon.

As of today (December 31), the weekly average of new cases in Tokyo has been higher than the weekly average one week earlier for 23 consecutive days. In the entire month of December the 7-day average only decreased week on week on 4 days, all of them towards the beginning of the month.

What’s more, the rate of increase is going up. Before Dec 19, the highest week on week increase was 1.26. Since then it has been 1.40 or higher. Today’s weekly comparison reached 1.68, the highest since August 4. Only six days in the 5th wave had a higher weekly increase, all between July 30 and August 4, when Delta cases outgrew Alpha cases.

Is this because the more infectious Omicron strain is outgrowing Delta now? Most likely not yet! The number of confirmed Omicron cases from community spread is still small compared to Delta. That means the cause is likely to be social: People are feeling relatively safe because of the much lower case count compared to last December’s 3rd wave and also they want to do things that they will most likely not be able to do in a couple of weeks, once Omicron takes over. Sadly, that’s exactly how Omicron will take over. We’ve entered super-exponential growth, even if it’s from a low basis.

What’s the Japanese response to this? So far, no new restrictions have been imposed yet. Opportunities for free testing, regardless of symptoms, have been expanded. However, the plan for 3rd vaccine doses has been left virtually unchanged. The booster program was originally created when it was found that immunity to Delta dropped after a number of months. Japan then decided on an 8 month interval between 2nd and 3rd doses. However, it takes a much higher level of antibodies to neutralize the heavily mutated Omicron strain, even if you’re still far from 8 months. A third shot of Pfizer/BioNTech will raise vaccine efficiency against symptomatic infection from under 30 percent to over 70 percent, close to what it was for Delta with two doses. Japan has not responded to this new reality yet. The official policy on the Cabinet Office website still states that 3rd doses are due “in principle” after 8 months. That means, people who were vaccinated in August and September are not due for booster shots until April or May. There is no question that Omicron will blow up into big number in January and February already.

It may be some comfort that the number of cases in Tokyo on New Year’s Eve 2021 was only 6 percent of the cases of a year before. On the other hand, it took South Africa only 14 days to go from a weekly count of ~2,000 cases to ~33,000 cases when Omicron arrived. Do the math!

From December 2 (the first day of the booster campaign) to December 28, the latest date for which data is available, Japan has deployed 531,296 third shots to healthcare workers. That’s just 11% of the healthcare workers who received 2 doses and about 0.4% of the entire population. That means before the New Year starts, 8 out of 9 healthcare workers who will soon have to be dealing with an onslaught of Omicron cases have not yet had their immunity level doubled.

In many countries in Europe, between 20 and 50% of the adults with 2 doses have received their third dose already and yet they are experiencing tens of thousands of cases. For example, Portugal, which has only 70% of the population of Tokyo but a higher rate of two vaccine doses in its population and where a quarter of the population have had 3rd shots, counted over 17,000 new cases on December 29. Tokyo counted a mere 76 cases.

While two doses will still offer good protection from hospitalization and death, they will not prevent a rapid increase in cases. On present plans, the third shots will come too late for many healthcare workers and senior citizens.

The other lines of defense should be masks and ventilation. Most people in Japan do not yet use high grade masks such as N95/KN95/FFP2/KF94/JN95 and I am seeing little effort to promote their use over regular surgical or other masks. Likewise, there is little emphasis on preventing airborne spreading, such as installing HEPA filters, upgraded ventilation, etc.