2023-09-21

New SARS-CoV-2 dataset version (tag 2023-09-21T12:00:00Z)

• Add extra example sequences (GL.1, FL.1.5.1, EG.5.1, HV.1, DV.7.1, GK.2, BA.2.86)
• Add new frame shifts and stop codons to be ignored by QC
• Pango lineages designated between 2023-08-09 and 2023-09-20 are now included, unfold below to see a list with designation dates:

Newly included lineages, with designation date in parentheses

• JA.1 (2023-08-10)
• JB.1 (2023-08-10)
• JB.2 (2023-08-10)
• FW.1.1 (2023-08-22)
• JC.1 (2023-08-22)
• XBB.1.41.2 (2023-08-22)
• GA.4.1 (2023-08-22)
• GE.1.1 (2023-08-22)
• GE.1.2 (2023-08-22)
• XBB.1.5.102 (2023-08-22)
• JD.1 (2023-08-22)
• FL.1.5.2 (2023-08-23)
• JB.2.1 (2023-08-24)
• HK.6 (2023-08-24)
• GS.2 (2023-08-24)
• GS.3 (2023-08-24)
• GS.4 (2023-08-24)
• GS.4.1 (2023-08-24)
• GE.1.3 (2023-08-24)
• JE.1 (2023-08-24)
• HG.2 (2023-08-24)
• JF.1 (2023-08-24)
• JF.2 (2023-08-24)
• GK.1.4 (2023-08-24)
• GK.2.1 (2023-08-24)
• HK.3.1 (2023-08-24)
• XCH (2023-08-24)
• XCJ (2023-08-24)
• GM.3 (2023-08-24)
• GM.3.1 (2023-08-24)
• HC.2 (2023-08-25)
• EG.5.1.7 (2023-08-25)
• JD.1.1 (2023-08-25)
• JD.1.2 (2023-08-25)
• XBB.1.5.103 (2023-08-30)
• XCH.1 (2023-08-30)
• JG.1 (2023-08-30)
• HK.7 (2023-08-30)
• EG.2.2 (2023-08-30)
• EG.2.3 (2023-08-30)
• EG.2.4 (2023-08-30)
• EG.2.5 (2023-08-30)
• EG.13 (2023-08-31)
• FL.4.8 (2023-08-31)
• FL.4.9 (2023-08-31)
• FL.4.10 (2023-08-31)
• FY.3.2 (2023-08-31)
• FY.3.3 (2023-08-31)
• JH.1 (2023-08-31)
• JH.2 (2023-08-31)
• FL.2.6 (2023-08-31)
• XCK (2023-08-31)
• FL.10.2 (2023-08-31)
• XCL (2023-09-01)
• FL.30 (2023-09-01)
• GW.1.1 (2023-09-01)
• GK.2.2 (2023-09-01)
• HF.1.1 (2023-09-01)
• HF.1.2 (2023-09-01)
• XBB.1.5.104 (2023-09-01)
• XBB.1.16.23 (2023-09-01)
• XBB.1.5.105 (2023-09-01)
• HK.8 (2023-09-01)
• HK.9 (2023-09-01)
• JJ.1 (2023-09-01)
• HK.10 (2023-09-01)
• JK.1 (2023-09-01)
• HS.1.1 (2023-09-01)
• HK.11 (2023-09-04)
• JG.2 (2023-09-04)
• XBB.1.16.24 (2023-09-04)
• JL.1 (2023-09-04)
• BA.2.86.1 (2023-09-05)
• XCM (2023-09-05)
• FY.4.1.2 (2023-09-06)
• EG.6.1.1 (2023-09-07)
• GJ.1.2.2 (2023-09-10)
• GJ.1.2.3 (2023-09-10)
• GJ.1.2.4 (2023-09-10)
• GJ.1.2.5 (2023-09-10)
• FL.4.11 (2023-09-10)
• HK.3.2 (2023-09-10)
• HK.3.3 (2023-09-10)
• EG.14 (2023-09-10)
• GK.3.2 (2023-09-10)
• CK.1.1.2 (2023-09-10)
• EF.3 (2023-09-10)
• GW.5.1 (2023-09-11)
• GW.5.1.1 (2023-09-11)
• DV.7.1.1 (2023-09-11)
• DV.7.1.2 (2023-09-11)
• EG.5.1.8 (2023-09-11)
• GK.2.3 (2023-09-17)
• GK.4 (2023-09-17)
• EG.5.1.9 (2023-09-17)
• JG.3 (2023-09-17)
• XBB.1.5.106 (2023-09-17)

2023-08-22

New influenza dataset version (tag 2023-08-10T12:00:00Z)

All seasonal influenza datasets were updated to include an additional subclade designation the provides a more fine-grained breakdown of the currently circulating diversity.
These subclades are suggested using a computational pipeline and follow a Pango-style nomenclature, albeit without hard automatic aliasing.

2023-08-17

Ad-hoc update to include the saltation variant BA.2.86. Note that this is not a regular data set update, but an update outside of the usual cycle specifically to enable detection of the BA.2.86.

2023-08-09

New SARS-CoV-2 dataset version (tag 2023-08-09T12:00:00Z)

• New Nextstrain clades 23C (CH.1.1), 23D (XBB.1.9), 23E (XBB.2.3), 23F (EG.5.1) are added. See ncov PR for a detailed discussion of the clades.
• Pango lineages designated between 2023-06-16 and 2023-08-08 are now included, unfold below to see a list with designation dates:

Newly included lineages, with designation date in parentheses

• FU.2.1 (2023-06-20)
• GU.1 (2023-06-20)
• GV.1 (2023-06-20)
• FL.4.3 (2023-06-20)
• EG.5.1.1 (2023-06-20)
• DV.7.1 (2023-06-26)
• GW.1 (2023-06-26)
• GW.2 (2023-06-26)
• GY.1 (2023-06-26)
• GY.2 (2023-06-26)
• BN.1.2.7 (2023-06-26)
• GJ.1.2 (2023-06-26)
• FL.13.2 (2023-06-28)
• FL.18 (2023-06-28)
• FL.18.1 (2023-06-28)
• FL.18.1.1 (2023-06-28)
• XBB.1.5.88 (2023-06-28)
• GZ.1 (2023-06-28)
• HA.1 (2023-06-28)
• HA.2 (2023-06-28)
• XBB.1.5.89 (2023-06-28)
• HB.1 (2023-06-28)
• EG.2.1 (2023-06-28)
• HC.1 (2023-06-28)
• FL.19 (2023-06-28)
• FU.3 (2023-06-28)
• BQ.1.1.79 (2023-06-28)
• FL.20 (2023-06-29)
• XBB.1.31.1 (2023-06-29)
• FL.1.7 (2023-06-29)
• FL.1.1.1 (2023-06-29)
• FL.4.4 (2023-06-30)
• FL.4.5 (2023-06-30)
• FL.4.6 (2023-06-30)
• FL.4.1.1 (2023-06-30)
• FL.4.7 (2023-06-30)
• GY.3 (2023-06-30)
• GY.2.1 (2023-06-30)
• XBB.1.16.12 (2023-06-30)
• XBB.1.16.13 (2023-06-30)
• FL.21 (2023-06-30)
• FL.5.1 (2023-06-30)
• EG.1.4.1 (2023-06-30)
• GD.2 (2023-06-30)
• GD.3 (2023-06-30)
• EG.1.5 (2023-06-30)
• EG.8 (2023-06-30)
• FL.22 (2023-06-30)
• FL.23 (2023-06-30)
• FY.6 (2023-06-30)
• CM.8.1.5 (2023-07-09)
• CK.1.1.1 (2023-07-09)
• CK.1.3 (2023-07-09)
• CK.1.4 (2023-07-09)
• CK.1.5 (2023-07-09)
• FR.1.4 (2023-07-09)
• GQ.1.1 (2023-07-09)
• FK.1.3.1 (2023-07-09)
• FK.1.3.2 (2023-07-09)
• FK.1.5 (2023-07-09)
• CJ.1.3.1 (2023-07-09)
• CJ.1.3.2 (2023-07-09)
• EU.1.1.3 (2023-07-09)
• FL.24 (2023-07-09)
• XBB.1.16.14 (2023-07-10)
• XBB.1.5.90 (2023-07-10)
• XBB.1.5.91 (2023-07-10)
• FL.25 (2023-07-10)
• FL.2.4 (2023-07-10)
• XCF.1 (2023-07-10)
• XCF.2 (2023-07-10)
• FL.26 (2023-07-10)
• FL.26.1 (2023-07-10)
• FU.4 (2023-07-11)
• XBB.1.5.92 (2023-07-11)
• XBB.1.5.93 (2023-07-11)
• HD.1 (2023-07-11)
• XBB.1.16.15 (2023-07-13)
• GK.1.1 (2023-07-13)
• GK.1.2 (2023-07-13)
• GK.1.3 (2023-07-13)
• AY.3.5 (2023-07-13)
• HE.1 (2023-07-14)
• FE.1.1.3 (2023-07-14)
• FE.1.1.4 (2023-07-14)
• HF.1 (2023-07-14)
• XBB.1.16.16 (2023-07-14)
• HG.1 (2023-07-14)
• XBB.2.3.13 (2023-07-14)
• XBB.2.3.14 (2023-07-14)
• XBB.1.49 (2023-07-14)
• GJ.3 (2023-07-14)
• XBB.1.5.94 (2023-07-14)
• EG.1.6 (2023-07-14)
• HH.1 (2023-07-14)
• HH.1.1 (2023-07-14)
• HH.2 (2023-07-14)
• CM.7.1.1 (2023-07-14)
• XBB.1.42.1 (2023-07-17)
• XBB.1.12.1 (2023-07-17)
• GY.4 (2023-07-19)
• GY.5 (2023-07-19)
• GY.6 (2023-07-19)
• EG.4.1 (2023-07-19)
• EG.4.2 (2023-07-19)
• EG.4.3 (2023-07-19)
• XBB.1.31.2 (2023-07-19)
• GY.7 (2023-07-19)
• XBB.1.5.95 (2023-07-19)
• HJ.1 (2023-07-19)
• XBB.1.5.96 (2023-07-19)
• FU.3.1 (2023-07-19)
• GW.3 (2023-07-19)
• GW.4 (2023-07-19)
• FL.23.1 (2023-07-19)
• FL.27 (2023-07-19)
• FD.4.1 (2023-07-19)
• GN.2 (2023-07-23)
• GN.1.1 (2023-07-23)
• GN.3 (2023-07-23)
• GN.4 (2023-07-23)
• GN.5 (2023-07-23)
• EG.5.1.2 (2023-07-23)
• EG.5.1.3 (2023-07-23)
• EG.5.1.4 (2023-07-23)
• EG.5.1.5 (2023-07-23)
• HK.1 (2023-07-23)
• HK.2 (2023-07-23)
• HK.3 (2023-07-23)
• HK.4 (2023-07-23)
• HK.5 (2023-07-23)
• EG.5.1.6 (2023-07-23)
• FT.2 (2023-07-23)
• FT.3 (2023-07-23)
• FT.3.1 (2023-07-23)
• FT.4 (2023-07-23)
• GA.4 (2023-07-23)
• GA.5 (2023-07-23)
• GA.6 (2023-07-23)
• GA.6.1 (2023-07-23)
• FW.3 (2023-07-23)
• HD.1.1 (2023-07-23)
• FL.13.3 (2023-07-23)
• FL.13.3.1 (2023-07-23)
• FL.2.3.1 (2023-07-23)
• XBB.1.16.17 (2023-07-23)
• FY.2.1 (2023-07-23)
• FY.4.1.1 (2023-07-23)
• FY.7 (2023-07-23)
• XBB.1.42.2 (2023-07-23)
• HL.1 (2023-07-23)
• HL.2 (2023-07-23)
• HM.1 (2023-07-23)
• FL.28 (2023-07-23)
• XBB.1.5.97 (2023-07-24)
• EG.1.7 (2023-07-24)
• EG.1.8 (2023-07-24)
• EG.4.4 (2023-07-24)
• FK.1.4.1 (2023-07-24)
• FK.1.1.1 (2023-07-24)
• FK.1.1.2 (2023-07-24)
• HN.1 (2023-07-24)
• FL.29 (2023-07-24)
• EG.9 (2023-07-24)
• EG.9.1 (2023-07-24)
• EG.10 (2023-07-24)
• EG.10.1 (2023-07-24)
• DV.7.2 (2023-07-25)
• EG.5.2.1 (2023-07-25)
• EG.5.2.2 (2023-07-25)
• EG.5.2.3 (2023-07-25)
• XBB.1.16.18 (2023-07-25)
• XBB.1.16.19 (2023-07-25)
• XBB.1.16.20 (2023-07-25)
• XBB.1.16.21 (2023-07-25)
• XBB.1.16.22 (2023-07-25)
• XBB.1.5.98 (2023-07-25)
• XBB.1.5.99 (2023-07-25)
• HP.1 (2023-07-26)
• HP.1.1 (2023-07-26)
• HQ.1 (2023-07-26)
• HR.1 (2023-07-26)
• HS.1 (2023-07-26)
• HT.1 (2023-07-26)
• HT.2 (2023-07-26)
• XBB.1.19.2 (2023-07-26)
• GW.5 (2023-07-26)
• FL.20.1 (2023-07-26)
• FL.21.1 (2023-07-27)
• FL.21.2 (2023-07-27)
• FT.3.1.1 (2023-07-27)
• FL.19.1 (2023-07-27)
• FU.5 (2023-07-27)
• HU.1 (2023-07-27)
• HU.2 (2023-07-28)
• FP.2.1.1 (2023-07-28)
• FP.2.1.2 (2023-07-28)
• HV.1 (2023-08-02)
• GK.3 (2023-08-02)
• GK.3.1 (2023-08-02)
• HW.1 (2023-08-02)
• HW.1.1 (2023-08-02)
• XBB.1.5.100 (2023-08-02)
• HY.1 (2023-08-02)
• GJ.1.2.1 (2023-08-04)
• HZ.1 (2023-08-04)
• HZ.2 (2023-08-04)
• HZ.3 (2023-08-04)
• BN.1.3.13 (2023-08-06)
• EG.11 (2023-08-07)
• GY.8 (2023-08-07)
• FY.4.2 (2023-08-07)
• XBB.1.22.3 (2023-08-07)
• HU.1.1 (2023-08-07)
• GJ.4 (2023-08-07)
• XBB.1.5.101 (2023-08-07)
• FL.2.5 (2023-08-07)
• EG.12 (2023-08-07)

2023-08-02

Minor fix for SARS-CoV-2-21L dataset (tag 2023-08-02T12:00:00Z)

• The SARS-CoV-2-21L dataset (SARS-CoV-2-21L) has been updated to show correct mutations in the auspice.json file. Nextclade output other than the tree json will not change in this release. It is mostly necessary for Nextclade version 3. Nothing else is changed, e.g. no new lineages.

2023-08-01

New Mpox datasets (tag 2023-08-01T12:00:00Z)

• Mpox datasets (MPXV, hMPXV, hMPXV_B1) now contain newly designate B.1 sublineages:
  • C.1 (alias of B.1.3.1)
  • B.1.18
  • B.1.19
  • B.1.20
    See mpxv-lineages/lineage-designation#33 for details
• Datasets have been updated to include sequences uploaded since the last release in January 2023

2023-06-16

New SARS-CoV-2 dataset version (tag 2023-06-16T12:00:00Z)

• Pango lineages designated between 2023-05-09 and 2023-06-15 are now included, unfold below to see a list with designation dates:

Newly included lineages, with designation date in parentheses

• XBB.2.9 (2023-05-11)
• XBB.1.5.70 (2023-05-22)
• FL.4.1 (2023-05-23)
• FL.4.2 (2023-05-23)
• FL.1.4 (2023-05-23)
• FL.13 (2023-05-23)
• FL.13.1 (2023-05-23)
• FL.14 (2023-05-23)
• GF.1 (2023-05-23)
• GG.1 (2023-05-23)
• FK.1.3 (2023-05-24)
• FK.1.4 (2023-05-24)
• FK.1.2.1 (2023-05-24)
• FY.1.1 (2023-05-24)
• FY.3.1 (2023-05-24)
• XBB.1.41 (2023-05-24)
• EG.5.2 (2023-05-24)
• FY.4.1 (2023-05-24)
• XBB.1.5.71 (2023-05-25)
• XBB.1.16.7 (2023-05-25)
• XBB.1.16.8 (2023-05-26)
• FL.15 (2023-05-29)
• EG.6 (2023-05-30)
• EG.6.1 (2023-05-30)
• FP.2 (2023-05-30)
• FP.3 (2023-05-30)
• FP.4 (2023-05-30)
• FP.2.1 (2023-05-30)
• XBB.1.16.9 (2023-05-30)
• CM.7.1 (2023-05-30)
• XBB.2.10 (2023-05-30)
• FL.16 (2023-05-30)
• XBB.1.9.7 (2023-05-30)
• XBB.1.5.72 (2023-05-31)
• FR.1.1 (2023-05-31)
• FR.1.2 (2023-05-31)
• XBB.1.42 (2023-05-31)
• XBB.1.43 (2023-05-31)
• XBB.1.43.1 (2023-05-31)
• XBB.2.6.1 (2023-06-01)
• GH.1 (2023-06-01)
• XBB.2.6.2 (2023-06-01)
• XBB.2.3.12 (2023-06-01)
• XBB.1.5.73 (2023-06-01)
• FD.2.1 (2023-06-01)
• XBB.1.5.74 (2023-06-01)
• XBB.1.5.75 (2023-06-01)
• XBB.1.5.76 (2023-06-01)
• XBB.1.5.77 (2023-06-01)
• XBB.1.5.78 (2023-06-01)
• XBB.1.5.79 (2023-06-01)
• XBB.1.5.80 (2023-06-01)
• XBB.1.5.81 (2023-06-01)
• GJ.1 (2023-06-02)
• FL.1.5 (2023-06-06)
• FL.1.5.1 (2023-06-06)
• GK.1 (2023-06-06)
• XBB.1.34.1 (2023-06-06)
• XBB.1.34.2 (2023-06-06)
• XBB.8.2 (2023-06-07)
• XCD (2023-06-08)
• EG.7 (2023-06-09)
• GJ.1.1 (2023-06-09)
• GJ.2 (2023-06-09)
• FL.1.10.1 (2023-06-09)
• XBB.1.41.1 (2023-06-09)
• XCE (2023-06-09)
• FE.1.1.1 (2023-06-09)
• FE.1.1.2 (2023-06-09)
• GL.1 (2023-06-09)
• GM.2 (2023-06-10)
• GM.1 (2023-06-10)
• XCF (2023-06-10)
• BQ.1.1.75 (2023-06-10)
• XBB.1.5.82 (2023-06-10)
• XBB.1.5.83 (2023-06-10)
• XBB.1.5.84 (2023-06-10)
• GN.1 (2023-06-10)
• XBB.1.5.85 (2023-06-10)
• XBB.1.5.86 (2023-06-10)
• DV.7 (2023-06-10)
• DV.8 (2023-06-10)
• CH.1.1.29 (2023-06-10)
• DV.6.2 (2023-06-10)
• DV.6.1 (2023-06-10)
• GK.2 (2023-06-10)
• GP.1 (2023-06-10)
• GP.2 (2023-06-10)
• GP.3 (2023-06-10)
• FK.1.2.2 (2023-06-10)
• FR.1.3 (2023-06-10)
• BN.1.3.12 (2023-06-10)
• BQ.1.1.76 (2023-06-10)
• BQ.1.1.77 (2023-06-10)
• BQ.1.1.78 (2023-06-10)
• EN.1.1 (2023-06-10)
• XBC.1.7 (2023-06-10)
• XBC.1.1.2 (2023-06-10)
• XBL.3.1 (2023-06-10)
• GQ.1 (2023-06-10)
• CH.1.1.30 (2023-06-10)
• BR.5.1 (2023-06-10)
• FL.10.1 (2023-06-10)
• XBB.1.15.1 (2023-06-11)
• XBB.1.44 (2023-06-11)
• XBB.1.44.1 (2023-06-11)
• XBB.1.45 (2023-06-11)
• XBB.1.45.1 (2023-06-11)
• EU.1.1.2 (2023-06-11)
• XBB.1.46 (2023-06-11)
• XBB.1.47 (2023-06-11)
• XBB.1.47.1 (2023-06-11)
• XBB.2.11 (2023-06-11)
• XBB.2.11.1 (2023-06-11)
• XCG (2023-06-11)
• XBB.1.14.1 (2023-06-11)
• XBB.2.6.3 (2023-06-11)
• XBB.1.48 (2023-06-11)
• XBB.1.13.1 (2023-06-11)
• XBB.1.38.1 (2023-06-11)
• XBB.1.4.2 (2023-06-11)
• XBB.2.12 (2023-06-11)
• FL.2.3 (2023-06-12)
• FY.1.2 (2023-06-12)
• FY.1.3 (2023-06-12)
• FY.5 (2023-06-12)
• FL.2.2.1 (2023-06-12)
• XBB.1.16.10 (2023-06-12)
• GR.1 (2023-06-12)
• GB.2 (2023-06-12)
• GS.1 (2023-06-12)
• XBB.1.5.87 (2023-06-13)
• FL.1.6 (2023-06-13)
• FL.17 (2023-06-14)
• FL.17.1 (2023-06-14)
• FL.17.2 (2023-06-14)
• XBB.1.16.11 (2023-06-14)
• XBC.1.6.4 (2023-06-14)
• GT.1 (2023-06-14)

2023-05-10

2023-05-10

Note: this GitHub release text entry is created late - on Jun 8, 2023. The data has been released a month earlier, on May 11, 2023.

New SARS-CoV-2 dataset version (tag 2023-05-10T12:00:00Z)

• The most terminal 50bp are now ignored/masked for reference tree placement purposes, see the Nextclade changelog for details. This feature requires Nextclade v2.14.0 or later. Most sequences will be unaffected. As the only mutation appearing in this range in the reference tree is C44T in some BA.2/4/5 and XBB sequences.
• Labeled mutations have been updated. Criteria for inclusion have been relaxed to show slightly more non-clade defining mutations that commonly occurred within a clade, e.g. BN.1 and CH.1.1 defining mutations are now included under clade 22D (BA.2.75). This potentially worsens quality score for some sequences with such mutations.
• Pango lineages designated between 2023-04-18 and 2023-05-09 are now included, unfold below to see a list with designation dates:

Newly included lineages, with designation date in parentheses

• XBL.1 (2023-04-19)
• XBL.2 (2023-04-19)
• XBL.3 (2023-04-19)
• XBB.2.3.6 (2023-04-19)
• XBB.2.3.7 (2023-04-19)
• XBB.1.34 (2023-04-20)
• FR.1 (2023-04-21)
• FS.1 (2023-04-21)
• XCC (2023-04-22)
• EG.3 (2023-04-22)
• EG.1.2 (2023-04-22)
• EG.1.3 (2023-04-22)
• EG.1.4 (2023-04-22)
• EG.4 (2023-04-22)
• EG.5 (2023-04-22)
• FL.3 (2023-04-22)
• FL.4 (2023-04-22)
• FL.5 (2023-04-22)
• FK.1.2 (2023-04-22)
• FT.1 (2023-04-22)
• XAY.2.3 (2023-04-22)
• XAY.1.1.2 (2023-04-22)
• XAY.1.1.3 (2023-04-22)
• XBB.1.16.2 (2023-04-22)
• XBB.1.16.3 (2023-04-22)
• FU.1 (2023-04-22)
• FU.2 (2023-04-22)
• XBB.1.5.41 (2023-04-22)
• XBB.1.5.42 (2023-04-22)
• FL.2.1 (2023-04-22)
• FL.2.2 (2023-04-22)
• XBC.1.6.1 (2023-04-23)
• XBC.1.6.2 (2023-04-23)
• XBC.1.6.3 (2023-04-23)
• XBC.1.5.43 (2023-04-23)
• XBB.1.35 (2023-04-23)
• XBB.1.5.44 (2023-04-23)
• XBB.1.5.45 (2023-04-23)
• XBB.1.5.46 (2023-04-23)
• XBB.1.6.1 (2023-04-23)
• XBB.1.5.43 (2023-04-24)
• XBB.1.36 (2023-04-24)
• XBB.8.1 (2023-04-24)
• XBB.9 (2023-04-24)
• XBB.3.4 (2023-04-24)
• XBB.1.5.47 (2023-04-25)
• XBB.1.5.48 (2023-04-25)
• XBB.1.5.49 (2023-04-25)
• EU.1.1.1 (2023-04-26)
• XBB.1.5.50 (2023-04-26)
• XBB.1.5.51 (2023-04-26)
• XBB.1.5.52 (2023-04-26)
• FV.1 (2023-04-26)
• XBB.1.5.53 (2023-04-26)
• XBB.1.9.6 (2023-04-26)
• BQ.1.2.2 (2023-04-28)
• FW.1 (2023-05-01)
• FW.2 (2023-05-01)
• XBB.1.5.54 (2023-05-01)
• EK.4 (2023-05-01)
• XBB.2.3.8 (2023-05-01)
• FD.3 (2023-05-03)
• XBB.1.5.55 (2023-05-03)
• FL.6 (2023-05-03)
• XBB.2.3.9 (2023-05-04)
• XBB.2.3.10 (2023-05-04)
• FY.1 (2023-05-04)
• FY.2 (2023-05-04)
• FY.3 (2023-05-04)
• FY.4 (2023-05-04)
• FZ.1 (2023-05-05)
• FZ.1.1 (2023-05-05)
• FZ.2 (2023-05-05)
• XBB.1.5.56 (2023-05-05)
• XBB.1.16.4 (2023-05-05)
• XBB.1.5.57 (2023-05-05)
• FE.1.1 (2023-05-05)
• FE.1.2 (2023-05-05)
• GA.1 (2023-05-06)
• GA.2 (2023-05-06)
• GA.3 (2023-05-06)
• CH.1.1.24 (2023-05-06)
• CH.1.1.25 (2023-05-06)
• CH.1.1.26 (2023-05-06)
• DV.6 (2023-05-06)
• CH.1.1.27 (2023-05-06)
• XBB.1.5.58 (2023-05-06)
• XBB.1.5.59 (2023-05-06)
• XBB.1.5.60 (2023-05-06)
• XBB.1.5.61 (2023-05-06)
• XBB.1.5.62 (2023-05-06)
• XBB.1.5.63 (2023-05-06)
• XBB.1.5.64 (2023-05-06)
• XBB.1.5.65 (2023-05-06)
• XBB.1.5.66 (2023-05-06)
• XBB.1.5.67 (2023-05-06)
• GB.1 (2023-05-06)
• XBB.1.16.5 (2023-05-06)
• FD.4 (2023-05-06)
• FL.7 (2023-05-06)
• XBB.1.5.68 (2023-05-06)
• XBB.1.37 (2023-05-06)
• XBB.1.37.1 (2023-05-06)
• XBB.1.5.69 (2023-05-07)
• XBB.1.16.6 (2023-05-07)
• EG.5.1 (2023-05-07)
• GC.1 (2023-05-07)
• GC.2 (2023-05-07)
• FL.8 (2023-05-07)
• FL.9 (2023-05-07)
• FL.10 (2023-05-07)
• FL.11 (2023-05-07)
• CH.1.1.28 (2023-05-07)
• FL.3.1 (2023-05-07)
• FL.3.2 (2023-05-07)
• FL.3.3 (2023-05-07)
• FL.3.4 (2023-05-07)
• XBB.1.24.1 (2023-05-07)
• XBB.1.24.2 (2023-05-07)
• XBB.1.24.3 (2023-05-07)
• XBB.1.38 (2023-05-07)
• GD.1 (2023-05-07)
• XBB.1.39 (2023-05-07)
• XBB.1.40 (2023-05-07)
• GE.1 (2023-05-07)
• XBB.2.3.11 (2023-05-07)
• FL.1.1 (2023-05-07)
• FL.1.2 (2023-05-07)
• FL.1.3 (2023-05-07)
• XBB.3.5 (2023-05-07)
• BN.1.2.5 (2023-05-07)
• FR.2 (2023-05-07)
• BN.1.2.6 (2023-05-07)
• EJ.3 (2023-05-07)
• BN.1.3.11 (2023-05-07)
• BQ.1.2.3 (2023-05-07)
• BQ.1.3.1 (2023-05-07)
• BQ.1.3.2 (2023-05-07)
• BQ.1.33 (2023-05-07)
• DN.2 (2023-05-07)
• DN.3 (2023-05-07)
• DN.3.1 (2023-05-07)
• XBB.1.32.1 (2023-05-08)
• FL.12 (2023-05-08)

2023-04-18

New SARS-CoV-2 dataset version (tag 2023-04-18T12:00:00Z)

SARS-CoV-2 and SARS-CoV-2-21L

• New Nextstrain clade 23B (XBB.1.16) was added, see this ncov PR for a detailed discussion of this clade
• The SARS-CoV-2 dataset now shows WHO variant name in the web results table instead of unaliased Pango lineage. This is a web-display-only change: All output files (web/CLI) are unchanged. Unaliased Pango lineage is still available in the SARS-CoV-2-21L dataset.
• Pango lineages designated between 2023-03-15 and 2023-04-17 are now included, unfold below to see a list with designation dates:

Newly included lineages, with designation date in parentheses

• ET.1 (2023-03-16)
• XBC.1.6 (2023-03-16)
• XBB.1.17 (2023-03-18)
• XBB.1.17.1 (2023-03-18)
• XBB.1.17.2 (2023-03-18)
• XBB.1.5.22 (2023-03-18)
• XBB.1.5.23 (2023-03-18)
• XBB.1.18 (2023-03-18)
• XBB.1.18.1 (2023-03-18)
• XBB.1.5.24 (2023-03-18)
• XBB.1.5.25 (2023-03-18)
• XBU (2023-03-19)
• XBB.1.19 (2023-03-19)
• XBB.1.19.1 (2023-03-19)
• XBB.1.20 (2023-03-19)
• XBV (2023-03-19)
• DV.1.1 (2023-03-19)
• CP.8 (2023-03-19)
• XBW (2023-03-19)
• XBY (2023-03-19)
• XBB.1.5.26 (2023-03-19)
• EU.1 (2023-03-19)
• EU.1.1 (2023-03-19)
• XBF.8.1 (2023-03-19)
• XBB.1.21 (2023-03-19)
• XBC.2.1 (2023-03-19)
• XBB.1.22 (2023-03-19)
• XBB.1.22.1 (2023-03-19)
• XBB.1.22.2 (2023-03-19)
• XBB.1.9.5 (2023-03-19)
• XBB.1.9.4 (2023-03-19)
• XBB.1.23 (2023-03-19)
• XBJ.1 (2023-03-19)
• XBJ.1.1 (2023-03-19)
• XBJ.2 (2023-03-19)
• XBJ.3 (2023-03-19)
• XBJ.4 (2023-03-19)
• XBB.2.7 (2023-03-19)
• XBB.1.27 (2023-03-19)
• XBB.1.24 (2023-03-20)
• XBB.1.25 (2023-03-20)
• XBB.1.26 (2023-03-20)
• CH.1.1.16 (2023-03-20)
• CH.1.1.17 (2023-03-20)
• DV.5 (2023-03-20)
• EV.1 (2023-03-21)
• EW.1 (2023-03-21)
• EW.2 (2023-03-21)
• EW.3 (2023-03-21)
• EY.1 (2023-03-21)
• EZ.1 (2023-03-21)
• XBB.1.16.1 (2023-03-22)
• XBB.1.5.27 (2023-03-22)
• EK.3 (2023-03-22)
• EK.2.1 (2023-03-22)
• XBB.1.5.28 (2023-03-22)
• BE.11 (2023-03-22)
• BE.12 (2023-03-22)
• BE.13 (2023-03-22)
• FA.1 (2023-03-22)
• FA.2 (2023-03-22)
• DR.2 (2023-03-22)
• FB.1 (2023-03-22)
• FB.2 (2023-03-22)
• BQ.1.1.72 (2023-03-22)
• FC.1 (2023-03-22)
• FD.1 (2023-03-22)
• FD.1.1 (2023-03-22)
• FE.1 (2023-03-22)
• XBB.1.5.29 (2023-03-22)
• XBB.1.5.30 (2023-03-22)
• FF.1 (2023-03-22)
• CP.8.1 (2023-03-23)
• BN.1.3.9 (2023-03-23)
• XBB.1.5.31 (2023-03-24)
• XBB.1.5.32 (2023-03-24)
• XBB.1.5.33 (2023-03-24)
• XBB.2.3.1 (2023-03-24)
• XBB.2.3.2 (2023-03-24)
• CH.1.1.18 (2023-03-24)
• XBB.1.28 (2023-03-24)
• XBB.1.29 (2023-03-24)
• XBB.1.5.34 (2023-03-24)
• XBB.1.30 (2023-03-24)
• XBB.1.5.35 (2023-03-24)
• XBB.1.5.36 (2023-03-24)
• BL.1.5 (2023-03-24)
• BQ.1.26.2 (2023-03-24)
• XBF.9 (2023-03-24)
• FG.1 (2023-03-24)
• FG.2 (2023-03-24)
• FG.3 (2023-03-24)
• CH.1.1.19 (2023-03-24)
• CH.1.1.20 (2023-03-24)
• CM.8.1.3 (2023-03-24)
• CM.8.1.4 (2023-03-24)
• DN.1.1.3 (2023-03-24)
• DN.1.1.4 (2023-03-24)
• XBB.2.8 (2023-03-24)
• XBB.2.7.1 (2023-03-24)
• BF.5.5 (2023-03-24)
• XBB.1.5.37 (2023-03-27)
• FD.2 (2023-03-27)
• XBB.1.5.38 (2023-03-27)
• FH.1 (2023-03-27)
• XBB.1.5.39 (2023-03-27)
• XBZ (2023-03-28)
• CH.1.1.21 (2023-03-29)
• CH.1.1.22 (2023-03-29)
• FJ.1 (2023-03-29)
• BN.1.3.10 (2023-03-30)
• FK.1 (2023-03-31)
• BQ.1.1.73 (2023-04-03)
• XCA (2023-04-03)
• EG.2 (2023-04-04)
• XBB.1.31 (2023-04-04)
• XBB.1.32 (2023-04-04)
• FL.1 (2023-04-04)
• XBB.2.3.3 (2023-04-04)
• XBB.2.3.4 (2023-04-04)
• XBB.1.5.40 (2023-04-04)
• FM.1 (2023-04-04)
• FM.2 (2023-04-04)
• FL.2 (2023-04-04)
• BQ.1.1.74 (2023-04-05)
• FN.1 (2023-04-05)
• EG.1.1 (2023-04-07)
• XBB.1.28.1 (2023-04-07)
• CJ.1.2 (2023-04-07)
• CJ.1.3 (2023-04-07)
• XBF.1.1 (2023-04-08)
• XBF.10 (2023-04-08)
• FP.1 (2023-04-11)
• BF.42 (2023-04-11)
• CH.1.1.23 (2023-04-11)
• XBB.2.3.5 (2023-04-12)
• FK.1.1 (2023-04-13)
• XCB (2023-04-14)
• FQ.1 (2023-04-17)
• XBB.1.33 (2023-04-18)

SARS-CoV-2-no-recomb will no longer be updated

Starting with this update, the SARS-CoV-2-no-recomb dataset - an auxiliary dataset with niche usage - will no longer be updated. This dataset was created to mitigate bias Nextclade had in previous versions to attach incomplete sequences to recombinants. This bias has been fixed in Nextclade version 2.13.0 (see this CHANGELOG entry for a detailed discussion). Furthermore, with the majority of current circulation being recombinant (mostly XBB), this dataset is no longer adequate. Users should simply use the main SARS-CoV-2 dataset instead.

2023-04-02

2023-04-02

New dataset version (tag 2023-04-02T12:00:00Z)

Influenza virus datasets

All Influenza virus datasets were updated with more recent sequences. The trees now include more older reference viruses for more robust designation of older clades.
The B/Vic annotation of the HA segment was fixed - it was previously off by 3 nucleotides resulting in amino acid numbering being off by one.