New dataset version (tag 2023-02-25T12:00:00Z)
SARS-CoV-2 datasets
- Recombinant trees are now built using IQtree which results in shared mutations on internal nodes. In the past, recombinant trees were purely based on the Pango hierarchy. This change makes lineage assignment for recombinants more robust and reduces the number of private mutations. See e.g. the XBB tree here: https://next.nextstrain.org/staging/nextclade/sars-cov-2/21L?label=clade:22F
- Known stop codons and frame shifts were updated to reduce the number of false positive warnings
- The set of labeled mutations was updated (in
virus_properties.json), including the addition of characteristic 23A mutations. This will help identifying recombinants. - Pango lineages desiganted between 2023-02-01 and 2022-02-24 are now included, unfold below to see a list of them:
Newly included lineages, with designation date in parentheses
- BN.1.3.5 (2023-02-02)
- XBB.1.9.2 (2023-02-03)
- XBB.2.4 (2023-02-03)
- DT.2 (2023-02-03)
- BA.4.1.11 (2023-02-03)
- BF.5.3 (2023-02-08)
- XBB.1.12 (2023-02-09)
- XBB.1.5.4 (2023-02-10)
- XBB.1.5.5 (2023-02-10)
- XBB.1.5.6 (2023-02-10)
- XBB.1.5.7 (2023-02-10)
- XBB.1.5.8 (2023-02-10)
- XBB.1.5.9 (2023-02-10)
- XBB.1.5.10 (2023-02-10)
- XBB.1.13 (2023-02-10)
- BQ.1.1.50 (2023-02-10)
- BF.5.4 (2023-02-10)
- XBB.1.14 (2023-02-10)
- BQ.1.1.51 (2023-02-10)
- XBF.1 (2023-02-11)
- XBF.2 (2023-02-11)
- XBF.3 (2023-02-11)
- XBC.1.3 (2023-02-11)
- XBC.1.4 (2023-02-11)
- XAY.2.1 (2023-02-11)
- XAY.2.2 (2023-02-11)
- XAY.1.1.1 (2023-02-11)
- BW.1.2 (2023-02-11)
- BW.1.1.1 (2023-02-11)
- BW.1.1.2 (2023-02-11)
- BQ.1.29 (2023-02-11)
- BQ.1.15.2 (2023-02-11)
- BQ.1.15.1 (2023-02-11)
- BQ.1.1.52 (2023-02-11)
- EA.1 (2023-02-11)
- EA.2 (2023-02-11)
- BQ.1.10.2 (2023-02-11)
- CL.1.2 (2023-02-11)
- CL.1.3 (2023-02-11)
- CL.1.1 (2023-02-11)
- BA.5.1.33 (2023-02-11)
- BA.5.1.34 (2023-02-11)
- BA.5.1.35 (2023-02-11)
- EB.1 (2023-02-11)
- BA.5.1.36 (2023-02-11)
- BA.5.1.37 (2023-02-11)
- BA.5.1.38 (2023-02-11)
- BF.7.16 (2023-02-11)
- BF.7.16.1 (2023-02-11)
- BF.7.17 (2023-02-11)
- BF.7.18 (2023-02-11)
- BF.35 (2023-02-11)
- BF.36 (2023-02-11)
- BF.37 (2023-02-11)
- BF.38 (2023-02-11)
- BF.38.1 (2023-02-11)
- BF.38.2 (2023-02-11)
- BF.38.3 (2023-02-11)
- BF.39 (2023-02-11)
- BF.39.1 (2023-02-11)
- BF.40 (2023-02-11)
- BF.41 (2023-02-11)
- BF.41.1 (2023-02-11)
- BA.5.2.51 (2023-02-11)
- BA.5.2.52 (2023-02-11)
- BA.5.2.53 (2023-02-11)
- BA.5.2.54 (2023-02-11)
- BA.5.2.55 (2023-02-11)
- BA.5.2.56 (2023-02-11)
- BA.5.2.57 (2023-02-11)
- BA.5.2.58 (2023-02-11)
- BA.5.2.59 (2023-02-11)
- BQ.1.30 (2023-02-11)
- EC.1 (2023-02-11)
- EC.1.1 (2023-02-11)
- BQ.1.31 (2023-02-11)
- BQ.1.10.3 (2023-02-11)
- BQ.1.1.53 (2023-02-11)
- BQ.1.1.54 (2023-02-11)
- BQ.1.1.55 (2023-02-11)
- BQ.1.1.56 (2023-02-11)
- BQ.1.1.57 (2023-02-11)
- BQ.1.1.58 (2023-02-11)
- BQ.1.1.59 (2023-02-11)
- BQ.1.1.60 (2023-02-11)
- BQ.1.1.61 (2023-02-11)
- BQ.1.1.62 (2023-02-11)
- BQ.1.1.63 (2023-02-11)
- BQ.1.1.64 (2023-02-11)
- BQ.1.1.65 (2023-02-11)
- BQ.1.1.66 (2023-02-11)
- BQ.1.1.67 (2023-02-11)
- DT.3 (2023-02-11)
- BQ.1.1.68 (2023-02-11)
- BQ.1.1.69 (2023-02-11)
- BQ.1.1.70 (2023-02-11)
- CZ.2 (2023-02-11)
- BA.5.2.60 (2023-02-12)
- BZ.2 (2023-02-12)
- BA.5.2.61 (2023-02-12)
- BA.5.2.62 (2023-02-12)
- BF.7.19 (2023-02-12)
- BF.7.20 (2023-02-12)
- BF.7.21 (2023-02-12)
- BF.7.22 (2023-02-12)
- BF.7.23 (2023-02-12)
- BF.7.24 (2023-02-12)
- BF.7.19.1 (2023-02-12)
- BF.7.26 (2023-02-12)
- ED.1 (2023-02-12)
- ED.2 (2023-02-12)
- ED.3 (2023-02-12)
- EE.1 (2023-02-12)
- EE.2 (2023-02-12)
- EE.3 (2023-02-12)
- EE.4 (2023-02-12)
- EE.5 (2023-02-12)
- EF.1 (2023-02-12)
- EF.2 (2023-02-12)
- EF.1.1 (2023-02-12)
- EF.1.1.1 (2023-02-12)
- EF.1.2 (2023-02-12)
- EF.1.3 (2023-02-12)
- BA.5.2.63 (2023-02-14)
- XBQ (2023-02-19)
- XBB.1.15 (2023-02-19)
- EG.1 (2023-02-19)
- XBB.1.9.3 (2023-02-19)
- XBB.2.5 (2023-02-19)
- XBF.4 (2023-02-19)
- XBK.1 (2023-02-19)
- XBR (2023-02-19)
- XBS (2023-02-19)
- XBT (2023-02-19)
- EH.1 (2023-02-19)
- XBF.5 (2023-02-19)
- XBF.6 (2023-02-19)
- XBF.7 (2023-02-19)
- XBF.7.1 (2023-02-19)
- XBF.8 (2023-02-19)
- DY.2 (2023-02-19)
- DY.3 (2023-02-19)
- DY.4 (2023-02-19)
- BF.7.14.4 (2023-02-19)
- BF.7.14.5 (2023-02-19)
- BF.7.14.6 (2023-02-19)
- BF.7.27 (2023-02-19)
- CH.1.1.10 (2023-02-19)
- CH.1.1.11 (2023-02-19)
- CH.1.1.12 (2023-02-19)
- CH.1.1.13 (2023-02-19)
- CH.1.1.14 (2023-02-19)
- BN.1.3.7 (2023-02-19)
- BN.1.3.6 (2023-02-19)
- BN.1.3.8 (2023-02-19)
- EJ.1 (2023-02-19)
- EJ.2 (2023-02-19)
- BN.1.2.2 (2023-02-19)
- BN.1.2.3 (2023-02-19)
- BN.1.2.4 (2023-02-19)
- BN.1.5.2 (2023-02-19)
- BN.1.4.2 (2023-02-19)
- BN.1.4.3 (2023-02-19)
- BN.1.4.4 (2023-02-19)
- BN.1.4.5 (2023-02-19)
- DS.3 (2023-02-19)
- XBB.1.5.11 (2023-02-19)
- XBB.1.5.12 (2023-02-19)
- XBB.1.5.13 (2023-02-19)
- EK.1 (2023-02-19)
- DV.4 (2023-02-19)
- XBB.1.5.14 (2023-02-21)
- EL.1 (2023-02-21)
- DB.3 (2023-02-23)
- DV.3.1 (2023-02-24)
- BF.7.14.7 (2023-02-24)
New dataset version (tag 2023-02-03T12:00:00Z)
RSV A and B data sets
- fix definition of some older clades
- include older sequences to make sure older clades are included.