Information on age (decade), sex, and geographic location of the case, dates of report, symptom onset, symptom progression, hospitalisation, death or recovery, and suspected exposure, healthcare seeking behaviour, and travel history were manually extracted. We systematically reviewed case reports published by the Ministry of Health of Japan for the period 14 January (date of the first reported case) to 31 March 2020. These metrics are important for characterising the potential threat of the outbreak and to identify opportunities for interventions. Here we analyse data from the first three months of the COVID-19 epidemic in Japan and characterise the transmissibility, high-risk settings for transmission, age-dependent probabilities of transmission, and clinical progression. Understanding the characteristics and natural history of novel pathogens is crucial to inform successful control measures. As of 8 February 2022, over 3.3 million cases and over 19,000 deaths have been reported nationally. However, community transmission increased after the SOE was lifted and the emergence of more transmissible variants of concern (VOCs) such as the alpha, delta, and omicron variants drove multiple waves of transmission. When the first “state of emergency” (SOE) order was lifted on 25 May 2020, 16,445 cases and 846 COVID-19 deaths had been reported in Japan. The “3-Cs” include spaces such as restaurants, crowded public transport, nightclubs, or close and/or prolonged social settings such as funerals. Detailed cluster investigations informed Japan’s “3-Cs” strategy of encouraging individuals to avoid “crowded places”, “close-contact settings”, and “confined and enclosed spaces” that was subsequently adopted by the World Health Organization.

Emphasis was placed on border control, intensive backward contact-tracing, and identification of clusters. Japan’s response to the COVID-19 pandemic in the first three months was successful in preventing an initial severe wave of SARS-CoV-2 transmission despite the absence of stringent lockdown policies adopted in other high-income countries.

These insights can help to inform urgent response strategies. The availability of timely and detailed data and appropriate analyses is critical to estimate and understand a pathogen’s transmissibility, high-risk settings for transmission, and key symptoms. Information collected in the early phases of an outbreak are important in characterising any novel pathogen. There were no reported cases of patients < 20 years old developing pneumonia or severe respiratory symptoms. Across all age groups, cases most frequently onset with cough, fever, and fatigue. The estimated probability of transmission was assortative by age with individuals more likely to infect, and be infected by, contacts in a similar age group to them. Household (39.0%) and workplace (11.6%) exposures were the most frequently reported potential source of infection. In the final week of the trusted period (16–23 March 2020), R t accounting for importations diverged from overall R t at 1.1 (95% CrI: 1.0, 1.2) compared to 1.5 (95% CrI: 1.3, 1.6), respectively. Early transmission was driven primarily by returning travellers with R t peaking at 2.4 (95% CrI: 1.6, 3.3) nationally. The corrected fitted mean onset-to-reporting delay after the peak was 4 days (standard deviation: ± 2 days). Key delays and the age-specific probability of transmission were estimated using data on exposures and transmission pairs. We analysed symptom progression and estimated the time-varying reproduction number, R t, correcting for epidemic growth using an established Bayesian framework. We conducted descriptive analyses based on information systematically extracted from individual case reports from 13 January to 31 March 2020 including patient demographics, date of report and symptom onset, symptom progression, travel history, and contact type. Here we present insights from the first 3 months of the epidemic in Japan based on detailed case data. Interventions including airport screening, contact tracing, and cluster investigations were quickly implemented. Japan was one of the first affected countries in the COVID-19 pandemic reporting their first case on 14 January 2020.

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