Phylogeographic mapping
The analyses take a dated phylogeny exported from NextStrain as a starting point for quantifying imports and local transmission of Sars-CoV-2 B.1.1.7 in Norway. Each isolate is assigned to one of two binary categories: “Norway” or “Rest of the world (RoW)”. The output is presented in Fig.1 and ancestral character estimation performed on the dated phylogeny.
Test
Fig. 1. B.1.1.7 phylogeny colored by binary geographic mappings (Norway, rest of the world [RoW]).
Quantifying introductions and local transmission
Below is a visualization of the size of each transmission lineage detected in Norway.
##### Fig. 2. B.1.1.7 transmission lineage sizes in Norway. G denotes the number assigned to each lineage, S denotes the size of the lineage and TMRCA denotes the age of the lineage.
Table 1. Estimated number of infections in Norway resulting from import and local transmission based on the phylogeographic analyses in Figure 1.
| 2.5% | 50% | 97.5% | |
|---|---|---|---|
| Import | 232.2250 | 236.0000 | 242.3250 |
| Local transmission | 3651.6750 | 3658.0000 | 3661.7750 |
| Import / Total | 0.0596 | 0.0606 | 0.0622 |
Next, we estimate the fraction of introductions relative to local transmission over time. In these and subsequent analyses it is important to keep detection lag into account (see https://science.sciencemag.org/content/371/6530/708). There will always be a delay between the introduction and detection, which varies from case to case. In the figures below, the last four weeks prior to the time of sampling of the most recent included isolate is shaded to indicate that estimates in this period is highly uncertain.
Fig. 3. Relative quantification of infection source (new introduction / import vs local transmission).
The same output is visualized as absolute numbers in Fig. 3 below. It should be noted that absolute estimates will be significantly shaped by sampling density.
Fig. 4. Absolute quantification of imports and local transmission events.
Perhaps the most interesting aspect of quantifying introductions, is to investigate the fate of the introduced viruses. Mandatory testing at the border and/or mandatory quaranteens etc will obviously have a bearing on the fate of new introductions from abroad. The plot below visualizes the number of infections in Norway resulting from each identified virus import event over time, stratified by inferred TMRCA of each introduced lineage.
