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The MHLW’s Puzzling Data on COVID-19 Vaccine Effectiveness


Studies worldwide have repeatedly proven that all types of COVID-19 vaccines distributed in Japan effectively fight COVID-19, though less so against the new Omicron variant than previous variants. 

The UK Health Security Agency published a study that measured the efficacy of Moderna and Pfizer vaccines in preventing Omicron variant COVID-19 hospitalizations at least 105 days after a patient’s third vaccine dose (April 21st, 2022). The results were as follows: 

18 to 64 years: 

Hospitalizations due to acute respiratory diseases: 67.4%

Hospitalizations requiring Oxygen assistance, Tracheal Intubation, and/or ICU treatment: 75.9% 


65+ years: 

Hospitalizations due to acute respiratory diseases: 85.3%

Hospitalizations requiring Oxygen assistance, Tracheal Intubation, and /or ICU treatment: 86.8% 


The results inarguably indicate that all eligible people should get a third dose of a COVID-19 vaccine to prevent hospitalization from the virus. 


The vaccine’s ability to prevent the spread and onset of the Omicron variant is lower than that of the Delta variant. Furthermore, compared to the Delta variant, people become susceptible to contracting the Omicron variant sooner after their last vaccine dose. 

Nature Medicine, a medical journal based in the US, published a study regarding the Moderna vaccine’s efficacy in preventing the spread of the Omicron variant of COVID-19: 


Days since second dose: 

14 to 90 days: 44.0%

91 to 189 days: 23.5%

181 to 270 days: 13.8%

271+ days: 5.9%


Days since third dose: 

14 to 60 days: 71.6%

61+ days: 47.4%


Though the third COVID-19 dose lowers infection rates, this effect gradually decreases with time. Additionally, the third Moderna vaccine dose is less effective at preventing the Omicron variant spread than the Delta variant. 


The study cited earlier conducted by the UKHSA in April 2022 provides data on the Moderna and Pfizer vaccines’ ability to prevent the onset of the Omicron variant: 

Weeks since second dose: 

2-4 weeks: 65-70% 

25 weeks: 15% 


Weeks since third Pfizer dose: 

2-4 weeks: 60-75% 

20+ weeks: no measurable effect


Once again, the vaccines were deemed less effective at preventing the onset of the Omicron variant than that of the Delta variant, particularly for older people. Assuming that an Omicron-targetted vaccine will be approved this fall, expert advice to guide eligible people on vaccinating the public are necessary. 


To recap: studies have repeatedly proven that vaccines drastically decrease COVID-19-related hospitalizations for many weeks after an individual final vaccine dose. However, vaccine efficacy in preventing the spread and onset of COVID-19 decreases with time. 


Here is where things get confusing: some data from the Japanese Ministry of Health, Labour, and Welfare (MHLW) contradicts the above statement. 

The MHLW inputs COVID-19-infected patient data into a system called the HER-SYS. One of the data points collected by the HER-SYS is a patient’s COVID-19 vaccine record. 

On the vaccine record page, there are three options to select from: 





Some COVID-19 patients left their vaccination records unanswered in the system. The issue from this missing data arose when the National Institute of Infectious Diseases (NIID) and the MHLW categorized unanswered vaccination statuses differently; while the NIID categorized patients that did not report their vaccination status as Unknown, the MHLW classified them as Unvaccinated.


At first, this discrepancy between the two institutions was inconsequential; most Japanese people were unvaccinated at the start of the pandemic. Thus when the HER-SYS began, the MHLW’s decision to count unanswered vaccination records as Unvaccinated was quite accurate. However, as Japan quickly vaccinated a large portion of the population, many people that did not report their vaccine status to the HER-SYS were, in fact, vaccinated. 

As a result, the data that the MHLW submitted to its Advisory Board diverged significantly from reality. So, the institution quickly revised its data and resubmitted its report to its Advisory Board. 


Below is the MHLW’s breakdown of the number of COVID-19-infected individuals per 100,000 people between 5/16-5/22: 


Age Group


Two Doses

Three Doses










































Note that the HER-SYS does not record the days since an infected person’s last vaccination dose. It is therefore impossible to differentiate whether one was vaccinated recently or much earlier before contracting COVID-19. 


Even after the data revision, a few puzzling points remain: 

The data in age groups 30-39, 40-49, 60-69, and 70-79 indicate that people with two doses of the COVID-19 vaccine contracted the virus at higher rates than those unvaccinated. The MHLW’s reports from the date range 3/28-4/3, 4/11-4/17, 4/18-24, 4/25-5/1, and 5/2-5/8 reflect the same findings. 

During the same date ranges, the age group 50-59 had the exact opposite results from the age groups mentioned above; unvaccinated individuals contracted COVID-19 at higher rates than those that were twice vaccinated. 


We established that the vaccine’s effectiveness in preventing the onset of COVID-19 decreases as the time since a person’s last dose increases. Surely enough, many Japanese people got their second dose a long while ago, so the onset deterrence effect likely has weakened. However minimal, though, the vaccine does protect a person from getting COVID-19. Not to mention, the vaccine certainly does not make a person more prone to contracting the virus. Thus, the diminishing effectiveness of the vaccine still does not explain why the MHLW’s data that double-vaccinated people contract COVID-19 at higher rates than unvaccinated people. Neither does it explain why the age group 50-59 consistently diverges from this pattern. 


The MHLW advisory board is working through possible causes of this statistical discrepancy. One possible explanation is that people who are twice vaccinated generally feel more protected and thus take fewer precautions against COVID-19, then end up contracting the virus. Yet again, though, this still does not explain why only 50 to 59-year-olds diverge from the pattern. 


We also established that people thrice vaccinated contract COVID-19 at lower rates than unvaccinated and twice vaccinated individuals. Nevertheless, the MHLW reports that thrice vaccinated 65 to 69-year-olds have consistently recorded higher infection rates than unvaccinated people since 4/25. 

As this puzzling data continues to undermine the well-established efficacy of the vaccine to prevent the onset of COVID-19, I look forward to hearing the Advisory Board’s explanation and how they will revise the HER-SYS data analysis.

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