TABLE 2.
Estimated rates of nucleotide substitution and tMRCA for LPAI and HPAI H7N1 viruses collected during the Italian epidemic
| Gene and genetic group | Modela | Substitution rate (subs/site/year) |
tMRCA (mo/yr) |
||
|---|---|---|---|---|---|
| Mean (×10−3) | 95% HPD (×10−3) | Mean | 95% HPD | ||
| HA | |||||
| H7N1 | SRD06-SC-Skyline | 10.15 | 8.5–11.9 | Feb 1999 | Jan 1999-Mar 1999 |
| H7N1-LPAI | SRD06-SC-Skyline | 9.75 | 7.8–11.9 | Feb 1999 | Jan 1999-Mar 1999 |
| H7N1-HPAI | SRD06-SC-Skyline | 9.89 | 6.54–13.22 | Nov 1999 | Oct 1999-Dec 1999 |
| NA | |||||
| H7N1 | SRD06-SC-Skyline | 9.86 | 8.01–11.79 | Feb 1999 | Dec 1998-Mar1999 |
| H7N1-LPAI | SRD06-SC-Skyline | 10.06 | 7.89–12.37 | Feb 1999 | Jan 1999-Mar 1999 |
| H7N1-HPAI | SRD06-SC-Skyline | 10.12 | 5.41–15.39 | Nov 1999 | Oct 1999-Dec 1999 |
| PA | |||||
| H7N1 | SRD06-SC-Skyline | 5.84 | 4.79–6.91 | Feb 1999 | Feb 1999-Mar 1999 |
| H7N1-LPAI | SRD06-SC-Skyline | 5.49 | 4.20–6.77 | Mar 1999 | Feb 1999-Mar 1999 |
| H7N1-HPAI | SRD06-SC-Skyline | 6.64 | 4.08–9.69 | Nov 1999 | Sep 1999-Dec 1999 |
| MA | |||||
| H7N1 | SRD06-SC-Skyline | 7.21 | 5.02–9.51 | Feb 1999 | Dec 1998-Mar1999 |
| H7N1-LPAI | SRD06-SC-Skyline | 4.87 | 2.77–7.26 | Feb 1999 | Dec 1998-Mar1999 |
| H7N1-HPAI | SRD06-SC-Skyline | 8.87 | 4.69–13.37 | Nov 1999 | Sep 1999-Dec 1999 |
| PB1 | |||||
| H7N1 | SRD06-SC-Skyline | 5.57 | 4.54–6.68 | Feb 1999 | Gen 1999-Mar1999 |
| H7N1-LPAI | SRD06-SC-Skyline | 5.70 | 4.31–7.15 | Feb 1999 | Jan 1999-Mar 1999 |
| H7N1-HPAI | SRD06-SC-Skyline | 5.48 | 3.60–7.39 | Oct 1999 | Aug 1999-Nov 1999 |
| PB2 | |||||
| H7N1 | SRD06-SC-Skyline | 6.81 | 5.54–8.04 | Feb 1999 | Dec 1998-Mar 1999 |
| H7N1-LPAI | SRD06-SC-Skyline | 6.69 | 5.12–8.23 | Jan 1999 | Dec 1998-Mar 1999 |
| H7N1-HPAI | SRD06-SC-Skyline | 7.22 | 5.0–9.64 | Oct1999 | Aug 1999-Nov 1999 |
| NP | |||||
| H7N1 | SRD06-SC-Skyline | 5.42 | 3.81–7.15 | Feb 1999 | Dec 1999-Mar1999 |
| H7N1-LPAI | SRD06-SC-Skyline | 5.11 | 3.00–7.39 | Feb 1999 | Dec 1999-Mar 1999 |
| H7N1-HPAI | SRD06-SC-Skyline | 4.91 | 2.61–7.73 | Nov 1999 | Oct 1999-Dec 1999 |
| NS | |||||
| H7N1 | SRD06-SC-Skyline | 7.72 | 5.76–9.91 | Jan 1999 | Oct 1998-Mar 1999 |
| H7N1-LPAI | SRD06-SC-Skyline | 7.19 | 4.85–9.66 | Jan 1999 | Nov 1998-Mar 1999 |
| H7N1-HPAI | SRD06-SC-Skyline | 6.44 | 2.90–10.31 | Jun 1999 | Jan 1999-Dec 1999 |
| CG | |||||
| H7N1 | SRD06-SC-Skyline | 6.67 | 5.97–7.34 | Mar 1999 | Feb 1999-Mar 1999 |
| H7N1-LPAI | SRD06-SC-Skyline | 6.82 | 5.81–7.87 | Feb 1999 | Feb 1999-Mar 1999 |
| H7N1-HPAI | SRD06-SC-Skyline | 6.41 | 5.25–7.62 | Oct 1999 | Sept 1999-Nov 1999 |
a
SC, strict molecular clock; Skyline, Bayesian skyline coalescent prior.