Primary author: Manon Ragonnet
Olivia Boyd, Lily Geidelberg, David Jorgensen, Manon Ragonnet, Igor Siveroni, Erik Volz and the Imperial College COVID-19 Response Team
Report prepared on 2020-06-02
This report uses full genome sequence data for Portugal shared publicly by Centro Hospitalar Vila Nove de Gaia Espinho, Centro Hospitalar Universitario de Lisboa, Hospital de Santarem and Instituto Nacional de Saúde and a set of international background sequences from GISAID (laboratory acknowledgements)
- We estimate a number of key epidemiological parameters for Portugal based on the genetic diversity of these samples alongside a set of closely related sequences from elsewhere which act as a global reservoir.
- In this analysis we estimate a basic reproduction number (R0) of 2.90 in Portugal at the start of the epidemic with R(t) falling below 1 around April 8.
- We estimate a high reporting rate in Portugal (above 50%) with a median estimate from the phylodynamic model of 35,595 cases at the beginnning of May compared to 25,524 reported cases at the same time point.
This analysis is based on :
- 59 whole genomes sampled from within Portugal
- 43 whole genomes sampled from outside of Portugal
- Samples within Portugal were collected between 2020-03-03 and 2020-05-04
Duplicate sequences were removed because they may represent infections associated with the same contact-traced transmission chain. Figure 1 shows the distribution of the sequences analysed over time, including external sequences.
Reported cases for comparison to our model predictions are taken from Wikipedia. These data are used for comparison purposes and to estimate the reporting rate and do not influence the phylodynamic analysis.
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 Portugal?
In this analysis we estimate 35595 [9810-181514] median [95%CI] cumulative infections at the time of the the last sample (2020-05-04). At the same time point there were 25524 reported cases. The estimates follow a similar trajectory to the reported cases at a different magnitude.
Figure 2: Estimated cumulative infections through time represented by solid black line (median) and 95% CrI (ribbon). Black points represent reported cases in Portugal. The dashed line indicates the date of last sample in Portugal in this analysis.
Estimated cumulative infections at last sample (2020-05-04): 35595 [9810-181514] median [95%CI]
Cumulative confirmed infections reported at 2020-05-04: 25524
Figure 3: Estimated daily infections through time represented by solid black line (median) and 95% CrI (ribbon). Black points represent reported cases in Portugal. The dashed line indicates the date of last sample in Portugal in this analysis.
Figure 4: Estimated percentage of cases reported in Portugal. Error bars represent the 95% credible interval.
Figure 5: Reproduction number through time. The black vertical dashed line indicates the date of last sample in Portugal in this analysis. Orange and red dashed lines indicate dates of school closure and general lockdown in Portugal, respectively.
Reproduction number at last sample (2020-05-04): 0.249 [0.0812-0.909] median [95% CrI]
How quickly has the epidemic in Portugal 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 Portugal?
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 Portugal, blue tips from outside.
Molecular clock rate of evolution: 0.00144 [0.00117-0.00175] median [95% CrI]
Details on methods and priors can be found here.
Table 2: Effective sample size of model parameters
Model version: seijr0.1.1
Report version: 20200602-193403-b45dfb4b
This work was supported by the MRC Centre for Global Infectious Disease Analysis at Imperial College London.