Phylodynamic Analysis: Reykjavik: 2020-03-29
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.
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.
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.
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Estimated cumulative infections at last sample (2020-03-29): 4922 [901-30572] median [95%CI]
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Cumulative confirmed infections reported at 2020-03-29: 798
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.
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.
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?
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
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.