Table 1.
Estimated next-generation matrix of COVID-19 by time period in Tokyo Metropolis and Osaka, Japan. The values of kij describe the transmission rates from group j to group i, and Rn is the reproduction number in Period n derived from the estimated next-generation matrix. Upper and lower 95% credible intervals obtained from the MCMC samples are shown in parentheses.
| region | Period 1a |
Period 2 |
Period 3 |
|||
|---|---|---|---|---|---|---|
| including back-projected cases | ||||||
| Tokyo Metropolis | kLL = 0.02 (0.02–0.02) | kLH = 6.09 (5.97–6.21) | kLL = 0.03 (0.03–0.03) | kLH = 3.08 (2.98–3.19) | kLL = 0.03 (0.03–0.03) | kLH = 2.70 (2.63–2.77) |
| kHL = 0.06 (0.06–0.06) | kHH = 1.56 (1.52–1.60) | kHL = 0.03 (0.03–0.03) | kHH = 0.61 (0.58–0.64) | kHL = 0.03 (0.02–0.03) | kHH = 0.51 (0.49–0.53) | |
| R1 = 1.78 (1.73–1.82) | R2 = 0.74 (0.71–0.78) | R3 = 0.63 (0.61–0.65) | ||||
| Osaka Prefecture | kLL = 0.02 (0.02–0.02) | kLH = 5.55 (5.37–5.72) | kLL = 0.02 (0.02–0.03) | kLH = 4.49 (4.34–4.63) | kLL = 0.03 (0.02–0.03) | kLH = 2.18 (2.04–2.30) |
| kHL = 0.06 (0.05–0.06) | kHH = 1.38 (1.32–1.44) | kHL = 0.05 (0.04–0.05) | kHH = 1.03 (0.98–1.07) | kHL = 0.02 (0.02–0.02) | kHH = 0.38 (0.34–0.41) | |
| R1 = 1.58 (1.51–1.64) | R2 = 1.20 (1.15–1.25) | R3 = 0.48 (0.44–0.51) | ||||
| excluding cases with unknown illness onset | ||||||
| Tokyo Metropolis | kLL = 0.02 (0.02–0.02) | kLH = 5.99 (5.87–6.10) | kLL = 0.03 (0.03–0.03) | kLH = 2.94 (2.83–3.05) | kLL = 0.03 (0.03–0.03) | kLH = 2.85 (2.77–2.92) |
| kHL = 0.06 (0.06–0.06) | kHH = 1.53 (1.49–1.57) | kHL = 0.03 (0.03–0.03) | kHH = 0.57 (0.54–0.61) | kHL = 0.03 (0.03–0.03) | kHH = 0.55 (0.53–0.57) | |
| R1 = 1.74 (1.69–1.78) | R2 = 0.70 (0.67–0.73) | R3 = 0.67 (0.65–0.70) | ||||
| Osaka Prefecture | kLL = 0.02 (0.02–0.02) | kLH = 5.58 (5.39–5.75) | kLL = 0.03 (0.03–0.03) | kLH = 4.21 (4.07–4.35) | kLL = 0.03 (0.03–0.03) | kLH = 2.35 (2.22–2.48) |
| kHL = 0.06 (0.05–0.06) | kHH = 1.39 (1.32–1.45) | kHL = 0.04 (0.04–0.04) | kHH = 0.94 (0.90–0.99) | kHL = 0.02 (0.03–0.02) | kHH = 0.42 (0.39–0.45) | |
| R1 = 1.59 (1.52–1.65) | R2 = 1.10 (1.06–1.15) | R3 = 0.53 (0.49–0.56) | ||||
aThree time periods were (1) the early invasion period (before 26 March 2020 for Tokyo and before 18 March 2020 for Osaka), (2) the period after an alert was declared by the prefectural governor of each region (26 March–7 April 2020 for Tokyo and 19 March–7 April 2020 for Osaka) and (3) the period after the governmental declaration of a state of emergency (8 April–25 May 2020 for Tokyo and 8 April–21 May 2020 for Osaka).