Fig 1.
Phylogeny of the 698 SARS-CoV-2 whole-genome sequences from Danish mink.
The majority of viruses found on infected farms, including those from the initial cases (farms 1–3, indicated within a red dashed circle) and viruses in Clusters 2–5, belong to pangolin lineage B.1.1.298 and are highlighted in light grey. Clusters 2–5 and viruses subsequently found as further spillovers from humans (C1-C4 and C6-C7) are highlighted in different colors. A singleton sequence belonging to C8 is indicated by a red asterisk. The occurrence of key sequence changes that were present in most mink virus sequences are indicated with red arrows. The scale bar indicates number of substitutions per variable site. The phylogeny was rooted with the basal reference sequence (NC_045512.1, known as the Wuhan-Hu-1 virus) as the outgroup.
Fig 2.
Location of different SARS-CoV-2 variants in mink during the epidemic in Denmark, June-November 2020.
Panel A. The location of the initial cases of SARS-CoV-2 infection in Northern Denmark are indicated. Subsequently, further cases occurred and the virus diverged, within lineage B.1.1.298, into Clusters 2, 3, 4 and 5 (as shown in Fig 1). Panel B. Later in the epidemic, new introductions of viruses from different lineages occurred and these are named as C1-C7 (see Table 1). The maps were made using the free and open source geographic information system Q-GIS with the shapefile of the administrative units of Denmark uploaded from DIVA-GIS (open source) onto which the data was plotted, see: https://www.qgis.org/en/site/getinvolved/governance/trademark/index.html and https://diva-gis.org/.
Table 1.
Summary of the SARS-CoV-2 sequences from infected mink from farms in DK.
The features of the different Clusters (as identified in Fig 1) are shown. The later introductions into mink from infected humans, designated C1-C8 are also indicated; these viruses lack the Y453F change.
Fig 3.
Phylogenetic tree based on whole-genome SARS-CoV-2 sequences from viruses obtained from humans and mink.
Phylogenetic analysis was performed using BEAST2 with a strict clock model, GTR+gamma substitution model, and a BDSKY-serial tree prior. Shown here is the maximum clade-credibility (MCC) tree based on 17,500 post-burnin tree samples. Tips are colored based on host species (Human: red, Mink: blue), and on whether the encoded Spike protein contains the Y453F substitution (Yes: darker colors, No: lighter colors) resulting from the A22920T mutation. Cluster colors have been dimmed, compared to Fig 1, to emphasize the tip colors. The Y453F substitution can be seen to have evolved only once (arrow pointing to tree branch), after which point it was retained in all descendant viruses. Also note how mink and human sequences are interspersed indicating frequent cross-species jumps.
Fig 4.
Zoom of phylogenetic tree from Fig 3 showing details around the branch where the Y453F substitution in the S protein occurred.
Tips are colored based on host species (Human: red, Mink: blue) and on whether the encoded Spike protein contains the Y453F substitution (Yes: darker colors, no: lighter colors). Mink sequences are annotated with a number indicating the ID of the farm from which the sample was obtained. The dashed circle highlights the part of the tree where the Y453F substitution first appeared. The enlarged region is annotated with the posterior branch support values in brown boxes. Note how only farm 1 had some mink without the Y453F change (light blue) and some with it (dark blue). This is consistent with the substitution occurring in the mink on farm 1.
Fig 5.
Phylogenetic tree from Fig 3 with tips colored according to presence or absence of the Y453F substitution and the H69/V70 deletion within the S protein.
The format used to label tips is <Y453F status>_<deletion status>, with “wt” indicating the absence of substitution or deletion, “Y453F” indicating the presence of that substitution, and “deletion” indicating the presence of the H69/V70 deletion: wt_wt: orange, wt_deletion: green, Y453F_wt: red, Y453F_deletion: blue. Host species is indicated using open circles for mink and closed circles for human. Note that the H69/V70 deletion appears shortly after the Y453F substitution (arrows pointing to branches), and both changes are subsequently present in all descendant sampled viruses, from both humans and mink. The deletion was also present in 4 separate clades among viruses without Y453F (4 groups of green tips in bottom part of tree–see Fig 6 for further detail).
Fig 6.
Zoom of phylogenetic tree from Fig 5 showing details around the branches where the H69/V70 deletion appeared.
Color scheme is the same as in Fig 5. a) Mink derived sequences are further annotated with a number indicating the farm ID from which the sample was obtained. The deletion can be seen to have evolved on a branch shortly after the Y453F substitution and to then have been retained in all viruses descending from this branch (see upper part of tree in Fig 5). Among the viruses, that do not have Y453F, the deletion is present in 4 separate groups (see green tips in bottom part of tree). The basal branches (where the deletions presumably evolved) of these 4 groups are indicated with green triangles. A cutout has been made of each of these clusters (b-e) with annotated posterior branch support in boxes. Two of the 4 clusters are human singletons (green closed circles near bottom of plot) and may correspond to independent introductions into Denmark of viruses already harboring the deletion. The two other clusters contain multiple sequences (3 and 6 respectively), indicating that the deletion may have evolved in Denmark and subsequently spread. One of these clusters contains only human sequences, while the other contains the sequence from a single mink (from farm 213), that appears to have been infected by a human harboring virus with the deletion.
Table 2.
Showing number of cross-species jumps inferred using different approaches (posterior mean and [90% highest density credible interval]).