Primary author: David Jorgensen

Olivia Boyd, Lily Geidelberg, David Jorgensen, Manon Ragonnet, Igor Siveroni, Erik Volz and the Imperial College COVID-19 Response Team

Report prepared on 2020-04-19

Updated 2020-04-23

Background information

This is analysis is based on :

  • 42 whole genomes sampled from within Reykjavik
  • 78 whole genomes sampled from outside of Reykjavik
  • Samples within Reykjavik were collected between 2020-03-03 and 2020-03-29

These numbers will differ from the number of uploaded sequences as we remove sequences with likely sequencing errors or significant gaps. Sequences were deduplicated and downsampled prior to analysis. Icelandic sequences included in this analysis were uploaded to gisaid on or before 2020-04-13.

plot of sampling distribution of local and global samples used

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 Reykjavik?

Using a phylodynamic model we estimate epidemiological parameters using SARS CoV 2 sequence data from Reykjavik together with a background set of sequences sampled from the larger internationational viral population. the model is explained in detail here. Reported cases are extracted from covid.is, the SARSCoV-2 website of The Directorate of Health and The Department of Civil Protection and Emergency Management of Iceland.

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 Reykjavik. The dashed line indicates the date of last sample in Reykjavik in this analysis.

  • Estimated cumulative infections at last sample (2020-03-29): 4922 [901-30572] median [95%CI]

  • Cumulative confirmed infections reported at 2020-03-29: 798

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 Reykjavik. The dashed line indicates the date of last sample in Reykjavik in this analysis.

plot of chunk reporting

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

Iceland has had a high testing rate throughout the SARSCoV2 outbreak although recent testing rates have been lower due to a shortage of testing kits which may affect recent reporting rates.

plot of chunk Rt

Figure 5: Reproduction number through time. The black vertical dashed line indicates the date of last sample in Reykjavik in this analysis. Red and blue dashed lines indicate dates of border closure and a ban on large gatherings in Iceland respectively.

Reproduction number at last sample (2020-03-29): 2.44 [1.8-2.82] median [95% CrI]

How quickly has the epidemic in Reykjavik grown?

Quantile Reproduction number Growth rate (per day) Doubling time (days)
50% 2.63 0.157 4.41
2.5% 1.92 0.0972 2.98
97.5% 3.67 0.232 7.13

Table 1: Reproduction number, growth rate and doubling times

How has SARS-CoV 2 evolved in Reykjavik?

plot of ML_Tree

Figure 6: Maximum likelihood phylogeny with the x-axis representing NT substitutions per site. The colour of the tips corresponds to sampling location; red tips were sampled from within the region, grey tips from outside

plot of chunk mcc_tree

Figure 7: Time scaled phylogeny co-estimated with epidemiological parameters. The colour of the tips corresponds to location sampling; red tips were sampled from within Reykjavik.

Molecular clock rate of evolution: 0.00118 [0.00092-0.00148] median [95% CrI]

Methods summary

Details on methods and priors can be found here.

Based on 6 chains of 10 million iterations with 50% burnin. Effective sample size values

Model version: seijr0.1.0

Report version: 20200419-105308-5839009f

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.