Japan Summary


The first reported case of COVID-19 in China came out at the end of 2019. On January 15, 2020, the first imported case was identified in Japan. On February 13, the first locally acquired cases were identified. 

Japan experienced two waves (now considered both part of the first wave) before the summer. The first was originated by imported cases from China. Through early February, 11 imported cases were identified. There were likely more, perhaps somewhere in the tens to about a hundred, but they were not detected. From those cases, transmissions occurred in places like small concert houses or gyms where people congregate in small spaces in areas such as Hokkaido, Tokyo, Aichi, and Osaka. By mid-March, this first wave was beginning to be under control. Unfortunately, the second part of the wave had already begun by then. 

The second part originated from travelers and returnees from a wide range of regions, such as Europe, the U.S., Southeast Asia, and Egypt. About 300 imported cases were identified; However, the actual number of imported cases were likely around 1,000-2,000. Furthermore, the movement of people at the beginning of the Japanese fiscal/academic year (April 1) might have exacerbated the transmission of the virus. The government put travel restrictions at the end of March, but local cases secondary to such cases increased rapidly . 


Some might say Japan was “lucky” because China had already experienced a major outbreak from which it could learn from. It also gained some experience in dealing with COVID-19 through the handling of the cruise ship Diamond Princess before community transmissions began. 

One key observation was that the majority of those who were infected did not infect anyone else. Similar observations were later made in places like Hong Kong, Singapore, and Europe. Despite this lack of transmission in a majority of close contacts with identified cases, the outbreak was still growing. There could be only one logical explanation: a small portion of the infected cases were creating a high volume of secondary transmissions, forming what would be called “clusters”. This hypothesis was confirmed based on data collected and analyzed by a team led by Dr. Hiroshi Nishiura at Hokkaido University. They had identified that 75% of infected individuals do not infect others. 

This meant that even if some cases go unidentified and creep into new environments and transmit to create secondary transmissions, including those within households, the focus could be on reducing the clusters, and the chain of transmission could still be cut off. In other words, if we can prevent clusters from occurring, chains of transmissions cannot be sustained, and the virus can be contained locally. That is why the plan to aggressively go find the clusters was developed. 

Another key clinical observation was that the majority of cases were either asymptomatic or experiencing mild symptoms. Already, this was pointing to a necessity of a different strategy compared to Severe Acute Respiratory syndrome (SARS), where the majority of those infected presented with severe symptoms. In a disease like SARS, all patients could be traced back to the source. In a disease like COVID-19, it would be extremely difficult. 

So it was necessary to develop a strategy that took into account that not all cases are easily identified, but that not all cases HAD to be identified for to suppress the transmission. 


On February 13, locally acquired cases were identified. The source of transmission was unknown. This meant that there had to be other invisible cases in various parts of the country. On February 25, Cluster Response Taskforce was set up in the Ministry of Health, Labour and Welfare. 

The Cluster Response Taskforce quickly concluded that, even with comprehensive PCR testing, it would be impossible to see the overall picture of all the chains of transmissions occurring given the limitations of PCR testing capacity as well as invisible nature of the virus. Even with high PCR testing capacity, the approach to identify all cases was considered to be impossible in order to contain the virus. 

So a different approach was needed – which was to focus on early identification of “avenue” of transmission. This assumed that if there were multiple isolated cases identified without a known source, a cluster had to exist nearby and that there was a source to that cluster as well. It also means that when clusters form, it could lead to chains of clusters or a mega cluster. If clusters can be found and people who had come in contact with those people could be isolated, chains of transmissions could be interrupted, and large outbreaks could be avoided. This would eventually become “retrospective contact tracing”, in contrast to “prospective contact tracing”. 

Prospective contact tracing would deploy PCR testing as broadly as possible and identify as many cases as possible. Once a case is found, health workers would reach out to everyone who had close contact with the positively identified person. This was successful in diseases like SARS and Ebola virus disease, where the vast majority of infected individuals were symptomatic and visible. In contrast, retrospective contact tracing would focus on going back further to identify the source. This is labor-intensive, but in Japan, similar types of interviews had been given by health workers for Tuberculosis cases, etc. so Japan was not completely unprepared. In the end, this also enabled Japan to identify specific “conditions” under which the spreading events were more likely to occur – closed spaces with poor ventilation, crowded places, and close contact settings such as close-range conversations – forming the concept of “avoiding 3Cs”.

A network of health centers around the country conducting both prospective and retrospective contact tracing was a key part of this strategy. They became the first line of defense in not only tracing but also identifying patients early. The virus is novel, and there was not a cure available yet. Case fatality rates were not low, especially among the elderly. But as long as healthcare resources were available for all severe cases, many lives could be saved. It was critical to ensure that healthcare systems were not overwhelmed so that as many lives as possible could be saved. 

In parallel, it was important for everyone to make changes to their behavior so that further spread could be mitigated.

All of this had to be done with “minimal impact on social and economic activities while maximizing the effectiveness of prevention measures”. 

Cluster Response, thus, depended on 3 key pillars: 

  • Early identification and response to clusters 
  • Early diagnosis of patients, prioritized intensive care for severe patients, ensuring continuity of healthcare systems (avoid overcapacity) 
  • Promote behavior change among citizens 


Both domestically and internationally, Japan was criticized for low numbers of testing. This led to speculations that the Japanese government was attempting to “hide” cases to protect the now postponed Olympics. 

Testing was obviously an important component of the response. However, key limitations were clear from the beginning. Despite PCR being the only known testing method at the time for COVID-19, PCR generally was known to be prone to false negatives. In cases like responding to a potential pandemic where high sensitivity was important, it was not the most optimal method. False positives could also occur, although at a lower rate. The prevalence of COVID19 would impact on the positive predictive and the negative predictive value of the tests. This highlights importance of frontline providers and public health providers to put the all the test results in the proper context and they should be interpreted cautiously.  In addition, PCR testing is labor-intensive. It was also known already at the time that rate of false negatives strongly depended on number of days since infection, which meant that the time of sample collection would be critical. Sample collection also came with risks for workers, especially under shortages of personal protective equipment such as masks. 

Knowing these limitations, it was still important to ensure that testing could be used strategically to be used on patients with severe symptoms as well as cluster identification to minimize the further spread of the virus. By January 22, a few weeks before the first locally acquired cases were identified, the National Institute of Infectious Disease had shipped test primers to public health laboratories across the country, and on January 23, the Ministry of Health, Labour, and Welfare gave the order to local public health laboratories to start testing as needed. Testing would only be conducted when a physician suspected a case and ordered them. Physicians across the country carefully examined their patients, looked for known signs of COVID-19, and ordered tests when necessary, being the first alert system for health centers to identify clusters. 

There was another key reason to limit testing. In the influenza H1N1 pandemic in 2009, outpatient clinics became crowded with people who wished to get tested. Not only did this cause long wait hours, it also created the “3C” conditions that could aid a super₋spreading event to occur. Medical professionals understood that “chaotic testing will make things worse”, which helped to maintain trust between the Cluster Response Taskforce and the medical community. 

It cannot be overemphasized that the high quality of Japan’s medical professionals and healthcare system was a critical part in Japan’s response. 


Despite the efforts of the Cluster Response Taskforce, medical professionals, health centers, and all citizens, transmissions were increasing. In the week of April 1-April 7, 2,185 new cases were identified. On April 7, the government declared a state of emergency for 7 prefectures including Tokyo. On April 16, 13 additional prefectures were included, and the other 34 prefectures were also deemed as areas requiring special measures. 

Under the state of emergency, Japan put in a few key measures to ask its citizens to change behavior. In addition to the on-going campaign to ask people to “avoid 3Cs”, people were asked to stay at home and reduce all contact by 80%. Certain facilities that were deemed to have high risk of transmission were closed. Other non-essential facilities were asked to implement strong preventive measures, but could be asked to close under certain conditions. In addition, given that healthcare facilities were under a lot of pressure, some facilities (such as hotels) were rented out by prefectures and operated as a temporary facility to house mild and asymptomatic patients. 

It was made clear that this was not a “lock down”. In fact, the Japanese constitution could not penalize citizens even if they did not heed to the request and went out and reduce contact with one another. 

The Cluster Response Taskforce had modeled the effective reproduction number and had told citizens that “if 80% of all contact could be reduced, prefectures could rescind the declaration of emergency.” 

By May 25, all prefectures rescinded the state of emergency as key indicators, such as number of cases per 100,000, doubling time of cases in the past week, ratio of isolated cases in the past week, effective reproduction number, trend in number of severe patients, and number of hospitalizations.


After the state of emergency order had been rescinded, we observed the “second” wave beginning in early June. This was likely due to activities in nightlife entertainment areas. For instance, there were number of cases that were reported among younger population in their 20’s and 30’s in the nightlife industries. Clusters occurring in host and hostess clubs were more difficult to contain than others. Those clusters occurred in the metropolitan areas and often spilled over to surrounding prefectures as it is getting easier to travel back and forth between metropolitan areas and local prefectures.   Since the beginning of this new wave, there have been more cases reported than all cases combined between March through May; however, fortunately, the number of severe cases and deaths do not seem higher than the initial wave of infection, since the affected population is in their 20’s and 30’s are at lower risk of becoming severely ill. There were fewer cases associated with hospitals and nursing home, as  measures taken at hospitals and nursing care facilities have also minimized transmissions in such facilities, which is likely contributing significantly to the lower number of severe cases and deaths. Today, the number of cases is trending down.  

The government is keeping plans to reopen the economy to boost activities. Controversial “Go-to travel campaign” was designed to ignite domestic travels by subsidizing as much as half the cost of travel. This is one of the major policies that was implemented despite a spike in number of cases.  Such conflict is as a result of attempting to maintain a fine balance between keeping the transmission suppressed while allowing life to carry on more “normally”. The experts, policy makers and the public needs to have transparent decision-making process whatever they do.

(As of September, 2020)