Table 1 SARS-CoV-2 epidemiological parameter estimates using phylodynamic approaches

From: Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic

Region

Period

Reproduction number

Substitution rate (changes/site/year)

Method

Australia

24/03–29/04

Rt = 1.08 (0.99, 1.16)17

6.91e-04 (6.00e-04, 7.78e-04)17

MTBD

Australia

Prior to 27/03

Post-27/03

Rt = 1.63 (1.45, 1.8)31

Rt = 0.48 (0.27, 0.69)31

1.1e-03

1.1e-03 (ref.31)

BCP + SC

Iceland

18/03–29/04

Rt = 1.4 (1.2, 1.59)17

5.75e-04 (4.96e-04, 6.47e-04)17

MTBD

Italy

22/02–04/04

Rt = 2.25 (1.5, 3.1)133

1.16e-03 (1.01e-03, 1.32e-03)134

BCP, BCP + SC

New Zealand

26/03–29/04

Rt = 1.41 (1.07, 1.89)17

6.09e-04 (5.16e-04, 7.03e-04)17

MTBD

Russia (Vreden Hospital)

27/03–08/04

08/04–23/04

Rt = 3.72 (2.48, 5.05)135

Rt = 1.38 (0.48, 2.41)135

9.43e-04 (8.46e-04, 1.04e-03)

9.43e-04 (8.46e-04, 1.04e-03)135

BCP + SC

BCP + SC

Taiwan, Tâi-oân pún-tó

27/03–29/04

Rt = 1.02 (0.825, 1.22)17

8.00e-04 (6.89e-04, 9.17e-04)17

MTBD

Weifang, Shandong

25/01–10/02

R0 = 3.4 (2.1, 5.2)136

1.30e-03 (0.98e-03, 1.7e-03)136

BCP + CFEM

  1. A selection of studies providing phylodynamic estimates of both growth and clock rates are listed; other studies have published estimates of clock rates79,122 or reproduction numbers30,32,81,137,138. Confidence intervals are provided where available (95% highest posterior density (HPD)). Dates are dd/mm in 2020. BCP, Bayesian coalescent phylodynamic; CFEM, coalescent fitted epidemiological model; MTBD, multitype birth–death model; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; SC, structured coalescent.
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