Table 1 Summary statistics of clusters identified in pre-Delta introduction sequences and post-Delta introduction sequences. Clusters were produced using cov2clusters at three pairwise probability thresholds (0.7, 0.8, and 0.9) and TreeCluster (‘max_clade’ and ‘single_linkage’ methods)
From: Cov2clusters: genomic clustering of SARS-CoV-2 sequences
Pre-Delta introduction (N = 19,617) | |||||
Clustering method | cov2clusters 0.7 | cov2clusters 0.8 | cov2clusters 0.9 | TreeCluster ‘max_clade’ | TreeCluster ‘single_linkage’ |
No. clusters | 567 | 756 | 1794 | 1060 | 962 |
Max. cluster size | 4638 | 4452 | 960 | 372 | 3105 |
No. non- clustered | 757 | 1124 | 3486 | 2038 | 1450 |
Post-Delta introduction (N = 17,297) | |||||
Clustering method | cov2clusters 0.7 | cov2clusters 0.8 | cov2clusters 0.9 | TreeCluster ‘max_clade’ | TreeCluster ‘single_linkage’ |
No. clusters | 453 | 591 | 1449 | 945 | 790 |
Max. cluster size | 4323 | 4250 | 1416 | 770 | 3619 |
No. non- clustered | 671 | 927 | 2683 | 606 | 1161 |