Primary author: Olivia Boyd
Olivia Boyd, Lily Geidelberg, David Jorgensen, Manon Ragonnet, Igor Siveroni, Erik Volz and the Imperial College COVID-19 Response Team
Report updated on 2020-04-21
This is analysis is based on :
- 50 whole genomes sampled from within Liège
- 73 whole genomes sampled from outside of Liège
- Samples within Liège were collected between 2020-03-05 and 2020-03-31
These numbers will differ from the number of uploaded sequences on GISAID as we remove sequences with likely sequencing errors or significant gaps. Sequences were deduplicated prior to analyses.
Figure 1. Sampling distributions over time of number of sequences included within the region versus sequences included from the international reservoir.
How many are infected in Liège?
Using a phylodynamic model we estimate epidemiological parameters using SARS-CoV 2 sequence data from Liège together with a background set of sequences sampled from the larger internationational viral population. The model is explained in detail here. Reported case numbers for comparison are extracted from Sciensano, the Belgian instute for health.
Figure 2: Estimated cumulative infections through time represented by solid black line (median) and 95% CrI (ribbon). Black points represent reported cases in Liège. The dashed line indicates the date of last sample in Liège in this analysis.
Estimated cumulative infections at last sample (2020-03-31): 51120 [10340-207545] median [95%CI]
Cumulative confirmed infections reported at 2020-03-31: 1854
Figure 3: Estimated daily infections through time represented by solid black line (median) and 95% CrI (ribbon). Black points represent reported cases in Liège. The dashed line indicates the date of last sample in Liège in this analysis.
Towards the end of the curve the estimated number of daily infections starts to decrease. This may be due to the shutting of all non-essential activities on 2020-03-18 across Belgium. However, further anlayses are required to assess the impact of non-pharmaceutical interventions on transmission in this region.
Figure 4: Estimated percentage of daily cases reported in Liège. Error bars represent the 95% credible interval.
The percentage of estimated cases which were confirmed reported cases between 2020-03-01 and 2020-03-31 ranged between 1.08 to 5.93% with a mean of 4.44%. The mean estimated reporting rate is similar to previous findings reported by Russell et al using case fatality ratio estimates.
*Figure 5: Reproduction number through time. The black vertical dashed line indicates the date of last sample in Liège in this analysis. Orange and red dashed lines indicate dates of school closure and general lockdown in Liège, respectively. *
Reproduction number remains relatively stable prior to the introduction of non-pharmaceutical interventions. Following school closures (orange dashed line) on 2020/03/16 and general lockdown (red dashed line) being implemented on 2020/03/18, the reproduction number begins to decrease. However, further analyses are still required to assess the strength of effect these interventions may have had on the reproduction number.
Reproduction number at last sample (2020-03-31): 1.02 [0.214-2.7] median [95% CrI]
How quickly has the epidemic in Liège grown?
|Quantile||Reproduction number||Growth rate (per day)||Doubling time (days)|
Table 1: Reproduction number, growth rate and doubling times
How has SARS-CoV 2 evolved in Liège?
Figure 6: Time scaled phylogeny co-estimated with epidemiological parameters. The colour of the tips corresponds to location sampling; red tips were sampled from within Liège, blue tips from outside.
Molecular clock rate of evolution: 0.000957 [0.000698-0.00114] median [95% CrI]
Details on methods and priors can be found here.
Model version: seijr0.1.0
Report version: 20200421-114817-ece7e7f5
This work was supported by the MRC Centre for Global Infectious Disease Analysis at Imperial College London.