Table 1.
Estimates of SARS-CoV-2 time to most recent common ancestor (tMRCA). BCI: Bayesian Credible Interval; HPD: Highest Posterior Density; CI: Confidence Interval. Asterix * denotes non-peer reviewed estimate of tMRCA. ‘N.’ denotes the number of whole genomes analysed.
| Reference | N. | Substitution Rate (per site per year) | Estimated tMRCA | Method |
|---|---|---|---|---|
| Li et al. 2020 (Li et al., 2020) | 32 | 1.0 × 10–3 (95% BCI 1.854 × 10–4, 4.0 × 10–3) | October 15, 2019 (95% BCI May 2, 2019; January 17, 2020) | Rate-informed strict clock model (BEAST v1.8.4) |
| Li et al. 2020 (Li et al., 2020) | 32 | 1.8266 × 10–3 (95% BCI 7.5813 × 10–4, 3.0883 × 10–3) | December 6, 2019 (95% BCI November 16, 2019; December 21, 2019) | Rate-estimated relaxed clock model (BEAST v1.8.4) |
| Giovanetti et al. 2020 (Giovanetti et al., 2020) | 54 | 6.58 × 10–3 (95% HPD 5.2 × 10–3, 8.1 × 10–3) | November 25, 2019 (95% CI September 28, 2019; December 21, 2019) | Relaxed clock model (BEAST v1.10.4) |
| Hill & Rambaut 2020*1 | 75 | 0.92 × 10–3 (95% HPD 0.33 × 10–3–1.46 × 10–3) | November 29, 2019 (95% CI October 28, 2019; December 20, 2019) | Unreported clock model (BEAST v1.7.0) |
| Hill & Rambaut 2020*1 | 86 | 0.80 × 10–3 (95% HPD 0.14 × 10–3, 1.31 × 10–3) | November 17, 2019 (95% CI August 27, 2019; December 19, 2019) | Unreported clock model (BEAST v1.7.0) |
| Hill & Rambaut 2020*1 | 116 | 1.04 × 10–3 (95% HPD 0.71 × 10–3, 1.40 × 10–3) | December 3, 2019 (95% CI November 16, 2019; December 17, 2019) | Unreported clock model (BEAST v1.7.0) |
| Lu et al. 2020* (41) | 53 | − | November 29, 2019 (95% HPD November 14, 2019; December 13, 2019) | Strict clock model (BEAST v1.10.0) |
| Duchene et al. 2020*2 | 47 | 1.23 × 10–4(95% HPD 5.63 × 10–4, 1.98 × 10–3) | November 19, 2019 (HPD October 21, 2019; December 11, 2019) | Strict clock model (BEAST v1.10) |
| Duchene et al. 2020*2 | 47 | 1.29 × 10–3 (HPD 5.35 × 10–4, 2.15 × 10–3) | November 12, 2019 (HPD September 26, 2019; December 11, 2019) | Relaxed clock model (BEAST v1.10) |
| Volz et al. 2020*3 | 53 | Model constrained between 7 × 10–4 & 2 × 10–3 | December 8, 2019 (95% CI November 21, 2019; December 20, 2019) | Strict clock model (BEAST v2.6.0) |
| Volz et al. 2020*3 | 53 | Model constrained between 5 × 10–4 & 1.25 × 10–3 | December 5, 2019(95% CI November 6, 2019; December 13, 2019) | Maximum Likelihood regression (treedater R package v0.5.0) |