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)

Key points

  • 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.

plot of chunk sampling dist

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.

plot of chunk Cumulative estimated infections through time

plot of chunk Cumulative estimated infections through time log scale

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

plot of chunk daily estimated infections through time

plot of chunk daily estimated infections through time log scale

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.

plot of chunk reporting

Figure 4: Estimated percentage of cases reported in Portugal. Error bars represent the 95% credible interval.

plot of chunk Rt

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)
50% 2.9 0.178 3.9
2.5% 2.18 0.121 2.75
97.5% 3.97 0.252 5.75

Table 1: Reproduction number, growth rate and doubling times

How has SARS-CoV 2 evolved in Portugal?

plot of chunk mcc_tree

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]

Methods summary

Details on methods and priors can be found here.

Statistic mean ESS
posterior -43503 788
likelihood -43426 215
prior -76.69 509
treeLikelihood.algn -43426 215
TreeHeight 0.3311 417
clockRate 0.001441 158
kappa 5.264 2634
PhydynSEIR -44.08 385
seir.E 28.32 376
seir.S 67972 126
seir.b 19.52 204
seir.exog 0.000716 99
seir.exogGrowthRate 30.79 26
seir.importRate 7.69 421
seir.p_h 0.2492 489
seir.tau 74.13 338
freqParameter.1 0.2978 1082
freqParameter.2 0.1827 1163
freqParameter.3 0.195 858
freqParameter.4 0.3245 974

Table 2: Effective sample size of model parameters

Model version: seijr0.1.1

Report version: 20200602-193403-b45dfb4b

Acknowledgements

This work was supported by the MRC Centre for Global Infectious Disease Analysis at Imperial College London.

Sequence data were provided by GISAID and these laboratories.