Primary author: David Jorgensen
Report prepared on 2020-04-09
Olivia Boyd, Lily Geidelberg, David Jorgensen, Manon Ragonnet, Igor Siveroni, Erik Volz and the Imperial College COVID-19 Response Team
This is analysis is based on :
- 43 whole genomes sampled from within NSW
- 62 whole genomes sampled from outside of NSW
- Samples within NSW were collected between 2020-01-18 and 2020-03-17
How many are infected in NSW?
Figure 1: Cumulative estimated infections through time. Points represent reported cases in NSW. The dashed line indicates the date of last sample in NSW in this analysis.
Estimated cumulative infections at last sample (2020-03-17): 3604 [1374-12429] median [95%CI]
Cumulative confirmed infections reported at 2020-03-17: 210
Figure 2: Daily estimated infections through time. Points represent reported cases in NSW. The dashed line indicates the date of last sample in NSW in this analysis.
Reproduction number at last sample (2020-03-17): 1.8 [1.56-2.17] median [95% CrI]
How quickly has the epidemic in NSW grown?
|Quantile||Reproduction number||Growth rate (per day)||Doubling time (days)|
Table: Reproduction number, growth rate and doubling times
How has SARS-CoV 2 evolved in NSW?
Figure 3: Time scaled phylogeny co-estimated with epidemiological parameters. The colour of the tips corresponds to location sampling; red tips were sampled from within NSW, blue tips from outside.
Molecular clock rate of evolution: 0.00168 [0.00131-0.0021] median [95% CrI]
Predicted cumulative infections over next 14 days (assuming exponential growth):
Figure 4: Cumulative estimated infections. The dashed line indicates the date of last sample in NSW in this analysis. The points represent reported cases in NSW.
Based on an estimated growth rate of 0.0875 [0.0629 - 0.122] median [95% CrI]:
We estimate cumulative number of infections at last sample (2020-03-17) as: 1005 [140 - 9061]
We estimate number of infections at 2020-03-31 (14 days after last sample) as: 3470 [375 - 46233]
Details on methods and priors can be found here.
Model version: seijr0.1.0
Report version: 20200409-105450-f554f66a
This work was supported by the MRC Centre for Global Infectious Disease Analysis at Imperial College London.