COVID-19 in Japan, January–March 2020: insights from the first three months of the epidemic
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Abstract
Background
Understanding the characteristics and natural history of novel pathogens is crucial to inform successful control measures. Japan was one of the first affected countries in the COVID-19 pandemic reporting their first case on 14 January 2020. Interventions including airport screening, contact tracing, and cluster investigations were quickly implemented. Here we present insights from the first 3 months of the epidemic in Japan based on detailed case data.
Methods
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. We analysed symptom progression and estimated the time-varying reproduction number, R t , correcting for epidemic growth using an established Bayesian framework. Key delays and the age-specific probability of transmission were estimated using data on exposures and transmission pairs.
Results
The corrected fitted mean onset-to-reporting delay after the peak was 4 days (standard deviation: ± 2 days). Early transmission was driven primarily by returning travellers with R t peaking at 2.4 (95% CrI: 1.6, 3.3) nationally. 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. Household (39.0%) and workplace (11.6%) exposures were the most frequently reported potential source of infection. 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. Across all age groups, cases most frequently onset with cough, fever, and fatigue. There were no reported cases of patients < 20 years old developing pneumonia or severe respiratory symptoms.
Conclusions
Information collected in the early phases of an outbreak are important in characterising any novel pathogen. 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. These insights can help to inform urgent response strategies.
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SciScore for 10.1101/2022.02.10.22270735: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
No key resources detected.
Results from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:There are a number of limitations to our study. Whilst publicly available case reports were initially highly detailed, less information was released as the epidemic progressed. Data on date of symptom onset which we used to estimate Rt was missing for 30% of reported cases. However, the majority of cases with missing onset dates were reported after the end of our trusted period on 23 March so would not have affected our estimates of …
SciScore for 10.1101/2022.02.10.22270735: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
No key resources detected.
Results from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:There are a number of limitations to our study. Whilst publicly available case reports were initially highly detailed, less information was released as the epidemic progressed. Data on date of symptom onset which we used to estimate Rt was missing for 30% of reported cases. However, the majority of cases with missing onset dates were reported after the end of our trusted period on 23 March so would not have affected our estimates of transmissibility. There was limited information on the age distribution of cases or symptoms especially for large clusters such as the care home outbreak in Chiba prefecture or the live music venues in Osaka. Similarly, the information released varied substantially by prefecture with Tokyo, which was the worst affected, only releasing minimal information beyond age group and sex. This may have biased our estimates of the age-dependent probability of transmission especially for the younger and older age groups associated with these clusters. Finally, we did not follow the entire clinical progression for patients with symptom data. Therefore, patients may have later developed more severe symptoms that were not presented here. However, this should not affect the variation in symptom type at the time of symptom onset across age groups.
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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