Table 2. Parameters and results for the different scenarios in the analysis of transmission dynamics.
λ: transmission rate, ε: sampling rate, R0: λ/(ε+σ), σ: death rate, ψ: rate of progression to infectiousness, π: molecular clock rate in expected nucleotide changes per site per year, 95% SNP threshold: the minimum SNP threshold for which at least 95% of samples are clustered in at least 95% of simulations, 100% SNP threshold: the minimum SNP threshold for which 100% of samples are clustered in at least 95% of simulations, 95% CI TBL: the confidence interval for the overall TBL distribution, Mean TBL: average of the overall TBL distribution.
| Scenario(Median infectious period (months) - R0) | λ | ε | R0 | σ | ψ | π | 95% SNP threshold | 100% SNP threshold | 95% CI TBL | Mean TBL |
|---|---|---|---|---|---|---|---|---|---|---|
| Long infectious period, shrinking (17–0.9) |
0.45 | 0.5 | 0.9 | 0 | 1 | 8 × 10–8 | 7 | 16 | 0–3 | 0.62 |
| Long infectious period, stable (17 - 1) |
0.5 | 0.5 | 1 | 0 | 1 | 8 × 10–8 | 6 | 16 | 0–3 | 0.59 |
| Long infectious period, growing (17–1.1) |
0.55 | 0.5 | 1.1 | 0 | 1 | 8 × 10–8 | 6 | 16 | 0–3 | 0.57 |
| Medium infectious period, shrinking (8–0.9) |
0.9 | 1 | 0.9 | 0 | 1 | 8 × 10–8 | 5 | 16 | 0–3 | 0.41 |
| Medium infectious period, stable (8 - 1) |
1 | 1 | 1 | 0 | 1 | 8 × 10–8 | 5 | 15 | 0–2 | 0.38 |
| Medium infectious period, growing (8–1.1) |
1.1 | 1 | 1.1 | 0 | 1 | 8 × 10–8 | 4 | 16 | 0–2 | 0.37 |
| Short infectious period, shrinking (4–0.9) |
1.8 | 2 | 0.9 | 0 | 1 | 8 × 10–8 | 5 | 14 | 0–2 | 0.31 |
| Short infectious period, stable (4 - 1) |
2 | 2 | 1 | 0 | 1 | 8 × 10–8 | 4 | 15 | 0–2 | 0.29 |
| Short infectious period, growing (4–1.1) |
2.2 | 2 | 1.1 | 0 | 1 | 8 × 10–8 | 3 | 17 | 0–2 | 0.27 |