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Releases: nextstrain/nextclade_data

2023-01-27

27 Jan 15:41
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Seasonal flu datasets

New dataset version (tag 2023-01-27T12:00:00Z)

  • fixes the omitted A/H3N2 clade 2d (very rare, had dropped out)
  • adds more contextual sequences to the trees
  • adds NA datasets for A/H3N2, A/H1N1pdm, B/Vic

Monkeypox datasets

New dataset version (tag 2023-01-26T12:00:00Z)

2023-01-19

24 Jan 13:01
bc2974a
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Influenza datasets

New clade definitions for default influenza datasets (tag 2023-01-19T12:00:00Z)

The default influenza datasets were updated to include recent consensus on clade definitions and more recent sequences in their reference tree to better reflect current circulation. In addition, these datasets contain a short_clade column which omits the long prefix and definition of glycosylation motifs.

2023-01-09

10 Jan 02:58
d355472
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All SARS-CoV-2 datasets

New dataset version (tag 2023-01-09T12:00:00Z)

  • Data update: 71 new Pango lineages, with designation date between 2022-12-14 and 2023-01-09 are now included, unfold below to see all the lineages:

    Newly included lineages, with designation date in parentheses
    • CJ.1.1 (2022-12-14)
    • CM.5.2 (2022-12-15)
    • CM.4.1 (2022-12-15)
    • CN.2 (2022-12-15)
    • BE.10 (2022-12-15)
    • XBK (2022-12-15)
    • CH.3.1 (2022-12-15)
    • CH.1.1.3 (2022-12-15)
    • XBB.1.6 (2022-12-16)
    • CR.1.3 (2022-12-16)
    • BF.10.1 (2022-12-18)
    • BQ.1.25.1 (2022-12-21)
    • BN.1.3.2 (2022-12-21)
    • BN.1.3.3 (2022-12-22)
    • XBB.3.2 (2022-12-22)
    • XBB.2.1 (2022-12-22)
    • XBB.2.2 (2022-12-22)
    • XBB.1.7 (2022-12-22)
    • DN.1 (2022-12-22)
    • BQ.1.1.29 (2022-12-22)
    • BQ.1.27 (2022-12-22)
    • BQ.1.1.30 (2022-12-22)
    • DJ.1.3 (2022-12-23)
    • BQ.1.1.31 (2022-12-24)
    • DP.1 (2022-12-24)
    • BN.1.3.4 (2022-12-24)
    • XBB.3.3 (2022-12-24)
    • DN.1.1 (2022-12-25)
    • BQ.1.13.1 (2022-12-25)
    • BF.5.1 (2022-12-27)
    • BF.5.2 (2022-12-27)
    • CK.1.1 (2022-12-29)
    • BA.5.2.46 (2022-12-30)
    • BQ.1.28 (2022-12-31)
    • BQ.1.1.32 (2022-12-31)
    • BQ.1.1.33 (2022-12-31)
    • DF.1.1 (2023-01-01)
    • BA.5.2.47 (2023-01-01)
    • DQ.1 (2023-01-01)
    • DR.1 (2023-01-03)
    • BF.7.14 (2023-01-06)
    • BA.5.2.48 (2023-01-06)
    • DS.1 (2023-01-07)
    • CM.10 (2023-01-07)
    • XBC.1.1 (2023-01-07)
    • XBC.1.1.1 (2023-01-07)
    • XBC.1.2 (2023-01-07)
    • XBC.1.2.1 (2023-01-07)
    • XBB.1.8 (2023-01-07)
    • BL.6 (2023-01-07)
    • CH.1.1.4 (2023-01-07)
    • BF.7.15 (2023-01-09)
    • XBL (2023-01-09)
    • CM.11 (2023-01-09)
    • DT.1 (2023-01-09)
    • BQ.1.1.34 (2023-01-09)
    • CM.12 (2023-01-09)
    • CK.1.2 (2023-01-09)
    • BA.2.3.22 (2023-01-09)
    • XBM (2023-01-09)
    • BM.1.1.4 (2023-01-09)
    • BM.1.1.5 (2023-01-09)
    • BN.1.4.1 (2023-01-09)
    • XBB.6 (2023-01-09)
    • XBB.6.1 (2023-01-09)
    • XBB.1.9 (2023-01-09)
    • XBB.1.9.1 (2023-01-09)
    • BA.5.2.49 (2023-01-09)
    • XAY.3 (2023-01-09)
    • XAY.1.2 (2023-01-09)
    • BN.1.5.1 (2023-01-09)

2022-12-22

23 Dec 17:10
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Addition of RSV A and RSV B datasets

New dataset version (tag 2022-12-20T22:00:12Z)

First release of RSV A and RSV A datasets by Laura Urbanska.

With permission of the authors, these datasets use the reference sequences hRSV/A/England/397/2017 for RSV-A and hRSV/B/Australia/VIC-RCH056/2019 for RSV-B.

The datasets implement two clade designations each.

One is primarily based on the G gene and was proposed by Goya et al, the other is based on the entire genome and was proposed by Ramaekers et al.

2022-12-14

14 Dec 23:20
f807231
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All SARS-CoV-2 datasets

New dataset version (tag 2022-12-14T12:00:00Z)

  • Data update: 28 new Pango lineages, with designation date between 2022-11-14 and 2022-12-10 are now included, unfold below to see all the lineages:

    28 new Pango lineages included in this release, with designation date in parentheses
    • XBG (2022-11-14)
    • BA.5.1.31 (2022-11-15)
    • XBH (2022-11-16)
    • BW.1.1 (2022-11-20)
    • BN.1.8 (2022-11-22)
    • BQ.1.1.25 (2022-11-22)
    • CM.2.1 (2022-11-22)
    • DJ.1 (2022-11-23)
    • DJ.1.1 (2022-11-23)
    • BA.5.2.42 (2022-11-23)
    • XBB.1.4.1 (2022-11-25)
    • BA.5.2.43 (2022-11-26)
    • BN.1.9 (2022-11-28)
    • CH.1.1.1 (2022-11-29)
    • CH.1.1.2 (2022-11-29)
    • BA.5.2.44 (2022-11-29)
    • DK.1 (2022-11-30)
    • BQ.1.1.26 (2022-12-01)
    • XBJ (2022-12-01)
    • CH.3 (2022-12-01)
    • BQ.1.1.27 (2022-12-02)
    • DL.1 (2022-12-03)
    • BA.5.2.45 (2022-12-03)
    • BQ.1.1.28 (2022-12-04)
    • BQ.1.26.1 (2022-12-04)
    • CV.2 (2022-12-06)
    • DM.1 (2022-12-07)
    • DJ.1.2 (2022-12-10)
  • Added 5 new XBB.1.5 example sequences

2022-12-07

14 Dec 22:22
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Influenza datasets

New dataset version (tag 2022-12-07T08:35:53Z)

A/H3N2: Update and addition of new reference sequence A/Darwin/6/2021

The existing dataset with reference sequence A/Wisconsin/67/2005 (CY163680) was updated to reflect recently circulating viruses.
A new dataset with reference sequence A/Darwin/6/2021 (EPI1857216), the current vaccine strain, was added.
In this latter data set, sequences are aligned to A/Darwin/6/2021 and mutations are called relative to this reference sequence.
This additional data set allows the more direct identification of changes relative to the vaccine virus.

A/H1N1dpm: Update and addition of new reference sequence A/Wisconsin/588/2019

The existing dataset with reference sequence A/California/07/2009 (CY121680) was updated to reflect recently circulating viruses.
A new dataset with reference sequence A/Wisconsin/599/2019 (MW626062), the current vaccine strain, was added.
In this latter data set, sequences are aligned to A/Wisconsin/599/2019 and mutations are called relative to this reference sequence.
This additional data set allows the more direct identification of changes relative to the vaccine virus.

B/Vic: Update

The existing dataset with reference sequence B/Brisbane/60/2008 (KX058884) was updated to reflect recently circulating viruses.

2022-11-15

15 Nov 19:31
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All SARS-CoV-2 datasets

New dataset version (tag 2022-11-15T12:00:00Z)

  • Data update: New Pango lineages, with designation date between 2022-10-27 and 2022-11-14 are now included, unfold below to see all the lineages:

    New Pango lineages included in this release, with designation date in parentheses
    • BQ.1.1.14 (2022-10-31)
    • CW.1 (2022-10-31)
    • BQ.1.1.15 (2022-10-31)
    • BQ.1.1.16 (2022-10-31)
    • BQ.1.1.17 (2022-10-31)
    • BQ.1.1.18 (2022-10-31)
    • BQ.1.1.19 (2022-10-31)
    • BN.1.3.1 (2022-10-31)
    • BF.7.4.1 (2022-10-31)
    • BF.31 (2022-11-01)
    • BF.31.1 (2022-11-01)
    • BF.32 (2022-11-01)
    • BQ.1.21 (2022-11-01)
    • CY.1 (2022-11-01)
    • BA.2.9.7 (2022-11-01)
    • BQ.1.22 (2022-11-02)
    • BF.7.4.2 (2022-11-02)
    • CP.1.2 (2022-11-02)
    • CP.1.3 (2022-11-02)
    • CP.2 (2022-11-02)
    • CP.3 (2022-11-02)
    • CP.4 (2022-11-02)
    • CP.5 (2022-11-02)
    • CP.6 (2022-11-02)
    • CR.1.1 (2022-11-02)
    • BS.1.2 (2022-11-02)
    • CM.5.1 (2022-11-02)
    • BL.5 (2022-11-02)
    • XAY.1.1 (2022-11-03)
    • BQ.1.1.20 (2022-11-03)
    • BQ.1.1.21 (2022-11-03)
    • BQ.1.1.22 (2022-11-03)
    • CZ.1 (2022-11-03)
    • XBB.4.1 (2022-11-03)
    • BQ.1.23 (2022-11-03)
    • BA.5.2.38 (2022-11-03)
    • DA.1 (2022-11-03)
    • BF.7.13 (2022-11-03)
    • BF.7.13.1 (2022-11-03)
    • BF.7.13.2 (2022-11-03)
    • XBF (2022-11-03)
    • CA.3.1 (2022-11-03)
    • CM.7 (2022-11-04)
    • BA.5.2.39 (2022-11-04)
    • DB.1 (2022-11-04)
    • BF.33 (2022-11-04)
    • BA.4.6.5 (2022-11-04)
    • DC.1 (2022-11-04)
    • BQ.1.1.23 (2022-11-04)
    • BQ.1.1.24 (2022-11-04)
    • DD.1 (2022-11-04)
    • BE.6 (2022-11-04)
    • BE.7 (2022-11-04)
    • BE.8 (2022-11-04)
    • BA.5.11 (2022-11-04)
    • DB.2 (2022-11-04)
    • BQ.1.24 (2022-11-04)
    • BA.5.2.40 (2022-11-04)
    • BQ.1.25 (2022-11-05)
    • CQ.1.1 (2022-11-05)
    • CR.1.2 (2022-11-05)
    • DE.1 (2022-11-05)
    • DE.2 (2022-11-05)
    • CM.8 (2022-11-05)
    • DF.1 (2022-11-06)
    • XBB.1.4 (2022-11-06)
    • BF.34 (2022-11-08)
    • XBB.1.5 (2022-11-08)
    • DG.1 (2022-11-09)
    • DH.1 (2022-11-09)
    • BR.2.1 (2022-11-09)
    • BN.1.7 (2022-11-10)
    • CM.8.1 (2022-11-10)
    • CM.9 (2022-11-10)
    • CM.6.1 (2022-11-10)
    • BE.9 (2022-11-12)
    • BQ.1.26 (2022-11-12)
    • BF.7.5.1 (2022-11-13)
    • BA.5.2.41 (2022-11-13)
    • CK.3 (2022-11-14)

2022-11-03

15 Nov 16:21
f931826
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All monkeypox datasets

New dataset version (tag 2022-11-03T12:00:00Z)

2022-10-27

31 Oct 12:02
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All SARS-CoV-2 datasets

New dataset version (tag 2022-10-27T12:00:00Z)

  • Phase 1 of migration of clade labels started: We will migrate clade labels from being a composite of Nextstrain clade, WHO name and legacy names (e.g. 20J (Gamma, V3)) to a set of independent clade labels.
    Phase 1 does not make braking changes. clade remains composite as in the past. However, 3 new clade columns are introduced (in the TSV/CSV only so far): clade_nextstrain (e.g. 20J) and clade_who (e.g. Gamma) and clade_legacy (e.g. 20J (Gamma, V3).
    If you don't want to change your code, you can future proof it by starting to use clade_legacy instead of clade, which is identical at the moment, but in the mid-term (earliest a month) clade may change. However, clade_legacy will remain part of the dataset for much longer.
    If you want to start using new split clades, you can start using clade_nextstrain and clade_who from now on.
    Phase 2 which will happen at the earliest in a month (2022-12-01) will involve changing clade from being composite and identical with clade_legacy to being identical with clade_nextstrain.
    Phase 3 which will happen at the earliest in 6 months (2023-04-01) may involve dropping clade_legacy and clade_nextstrain.

  • New clade 22F (Omicron) (XBB) added, see nextstrain/ncov#1020 for details, e.g. on the reasons for elevation

  • virus_properties.json has been updated with mutations characteristic of clades 22E (BQ.1) and 22F (XBB) to enable detection of contamination/recombination involving these clades

  • qc.json has been updated with common frameshifts and stop codons that appear in hundreds of sequences and plausibly occur in viable virus

  • Data update: New Pango lineages, with designation date between 2022-09-20 and 2022-10-27 are now included, unfold below to see all the lineages:

    New Pango lineages included in this release
    • XBB.4 (2022-10-20)
    • XBB.3.1 (2022-10-20)
    • XBB.5 (2022-10-20)
    • BQ.1.1.3 (2022-10-20)
    • BQ.1.1.4 (2022-10-20)
    • BQ.1.1.5 (2022-10-20)
    • BQ.1.1.6 (2022-10-20)
    • BQ.1.1.7 (2022-10-20)
    • BQ.1.1.8 (2022-10-20)
    • BQ.1.1.9 (2022-10-20)
    • BQ.1.1.10 (2022-10-20)
    • BN.1.2.1 (2022-10-20)
    • BN.1.4 (2022-10-20)
    • BN.1.5 (2022-10-20)
    • BN.1.6 (2022-10-20)
    • CK.2 (2022-10-20)
    • CK.2.1 (2022-10-20)
    • CK.2.1.1 (2022-10-20)
    • CQ.2 (2022-10-20)
    • BQ.1.1.11 (2022-10-21)
    • BQ.1.1.12 (2022-10-21)
    • BY.1.1 (2022-10-21)
    • BY.1.1.1 (2022-10-21)
    • BY.1.2 (2022-10-21)
    • BY.1.2.1 (2022-10-21)
    • CM.4 (2022-10-21)
    • CM.5 (2022-10-21)
    • CM.6 (2022-10-21)
    • XBE (2022-10-22)
    • BU.3 (2022-10-23)
    • BA.5.1.30 (2022-10-23)
    • CV.1 (2022-10-23)
    • XBB.1.3 (2022-10-23)
    • BQ.1.1.13 (2022-10-23)
    • CA.7 (2022-10-24)

2022-10-19

20 Oct 11:02
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New dataset version (tag 2022-10-19T12:00:00Z)

  • New clade 22E (Omicron) (BQ.1*) added, see nextstrain/ncov#1012 for details

  • The SARS-CoV-2 trees are now purely based on Pango consensus sequences, and no longer contain any actual sequences. This makes builds more stable and helps mitigate issues with sequence artefacts. For the Omicron part of the tree, no actual sequences were ever included, so this change only affects the pre-Omicron part of the reference tree.

  • This release contains the first recombinant sublineages. These work in the same way as the other sublineages.

  • Data update: New Pango lineages, with designation date between 2022-09-25 and 2022-10-19 are now included, unfold below to see all the lineages:

    New Pango lineages included in this release
    • BA.5.2.26 (designation date: 2022-09-29)
    • BA.5.2.27 (designation date: 2022-09-29)
    • BA.5.2.28 (designation date: 2022-09-29)
    • BA.5.1.22 (designation date: 2022-09-29)
    • BA.5.1.23 (designation date: 2022-09-29)
    • BA.5.1.24 (designation date: 2022-09-29)
    • BA.5.1.25 (designation date: 2022-09-29)
    • BF.26 (designation date: 2022-09-29)
    • BF.27 (designation date: 2022-09-29)
    • BF.28 (designation date: 2022-09-29)
    • CA.2 (designation date: 2022-09-30)
    • BA.2.75.9 (designation date: 2022-09-30)
    • CB.1 (designation date: 2022-09-30)
    • BL.1.3 (designation date: 2022-09-30)
    • BS.1.1 (designation date: 2022-09-30)
    • BA.2.85 (designation date: 2022-09-30)
    • BA.5.2.29 (designation date: 2022-09-30)
    • BE.4 (designation date: 2022-09-30)
    • BE.4.1 (designation date: 2022-09-30)
    • BE.4.1.1 (designation date: 2022-09-30)
    • BE.1.1.2 (designation date: 2022-09-30)
    • CC.1 (designation date: 2022-09-30)
    • BA.5.2.30 (designation date: 2022-09-30)
    • BA.5.2.31 (designation date: 2022-09-30)
    • CD.1 (designation date: 2022-09-30)
    • CD.2 (designation date: 2022-09-30)
    • BA.5.2.32 (designation date: 2022-09-30)
    • BA.5.2.33 (designation date: 2022-09-30)
    • CE.1 (designation date: 2022-09-30)
    • BA.5.1.26 (designation date: 2022-09-30)
    • BA.5.1.27 (designation date: 2022-09-30)
    • BA.5.1.28 (designation date: 2022-09-30)
    • CF.1 (designation date: 2022-09-30)
    • CG.1 (designation date: 2022-10-03)
    • XBB.1 (designation date: 2022-10-03)
    • BQ.1.4 (designation date: 2022-10-03)
    • XBC.1 (designation date: 2022-10-03)
    • BF.7.1 (designation date: 2022-10-05)
    • BA.5.3.5 (designation date: 2022-10-07)
    • BA.5.1.29 (designation date: 2022-10-07)
    • BQ.1.5 (designation date: 2022-10-11)
    • BQ.1.6 (designation date: 2022-10-11)
    • BQ.1.7 (designation date: 2022-10-11)
    • BQ.1.8 (designation date: 2022-10-11)
    • BQ.1.9 (designation date: 2022-10-11)
    • BA.5.6.3 (designation date: 2022-10-11)
    • BG.7 (designation date: 2022-10-11)
    • BA.4.6.2 (designation date: 2022-10-11)
    • BE.4.2 (designation date: 2022-10-11)
    • BA.4.6.3 (designation date: 2022-10-11)
    • CH.1 (designation date: 2022-10-11)
    • CH.2 (designation date: 2022-10-11)
    • CJ.1 (designation date: 2022-10-11)
    • CK.1 (designation date: 2022-10-11)
    • CL.1 (designation date: 2022-10-11)
    • CM.1 (designation date: 2022-10-11)
    • BR.4 (designation date: 2022-10-12)
    • CN.1 (designation date: 2022-10-12)
    • BA.5.2.34 (designation date: 2022-10-12)
    • XBD (designation date: 2022-10-12)
    • BA.2.38.4 (designation date: 2022-10-12)
    • BF.29 (designation date: 2022-10-12)
    • CH.1.1 (designation date: 2022-10-13)
    • BQ.1.10 (designation date: 2022-10-13)
    • BQ.1.11 (designation date: 2022-10-13)
    • BQ.1.12 (designation date: 2022-10-13)
    • BQ.1.13 (designation date: 2022-10-13)
    • BQ.1.14 (designation date: 2022-10-13)
    • BQ.1.15 (designation date: 2022-10-13)
    • BQ.1.16 (designation date: 2022-10-13)
    • XAY.1 (designation date: 2022-10-13)
    • XAY.2 (designation date: 2022-10-13)
    • BA.2.3.21 (designation date: 2022-10-13)
    • CM.2 (designation date: 2022-10-13)
    • BQ.2 (designation date: 2022-10-13)
    • BQ.1.17 (designation date: 2022-10-13)
    • CP.1 (designation date: 2022-10-13)
    • CP.1.1 (designation date: 2022-10-13)
    • BA.5.2.35 (designation date: 2022-10-13)
    • BE.5 (designation date: 2022-10-13)
    • CQ.1 (designation date: 2022-10-13)
    • BF.7.2 (designation date: 2022-10-13)
    • BN.1.1 (designation date: 2022-10-13)
    • CR.1 (designation date: 2022-10-13)
    • CR.2 (designation date: 2022-10-13)
    • CS.1 (designation date: 2022-10-14)
    • BL.2.1 (designation date: 2022-10-14)
    • BF.7.3 (designation date: 2022-10-14)
    • BF.30 (designation date: 2022-10-14)
    • BM.2.1 (designation date: 2022-10-14)
    • BM.2.2 (designation date: 2022-10-14)
    • BM.2.3 (designation date: 2022-10-14)
    • BM.6 (designation date: 2022-10-14)
    • BA.4.6.4 (designation date: 2022-10-14)
    • XBC.2 (designation date: 2022-10-14)
    • BN.1.2 (designation date: 2022-10-15)
    • BN.1.1.1 (designation date: 2022-10-15)
    • BN.1.3 (designation date: 2022-10-15)
    • BN.3 (designation date: 2022-10-15)
    • BR.1.1 (designation date: 2022-10-15)
    • BR.1.2 (designation date: 2022-10-15)
    • BA.2.75.10 (designation date: 2022-10-15)
    • BM.1.1.2 (designation date: 2022-10-15)
    • BQ.1.1.1 (designation date: 2022-10-15)
    • BQ.1.18 (designation date: 2022-10-15)
    • BQ.1.8.1 (designation date: 2022-10-15)
    • BQ.1.8.2 (designation date: 2022-10-15)
    • BQ.1.10.1 (designation date: 2022-10-15)
    • XBB.2 (designation date: 2022-10-15)
    • XBB.3 (designation date: 2022-10-15)
    • XBB.1.1 (designation date: 2022-10-15)
    • BA.5.2.36 (designation date: 2022-10-15)
    • CT.1 (designation date: 2022-10-15)
    • BN.3.1 (designation date: 2022-10-15)
    • BN.4 (designation date: 2022-10-15)
    • BN.5 (designation date: 2022-10-15)
    • BN.6 (designation date: 2022-10-15)
    • CA.3 (designation date: 2022-10-15)
    • CA.4 (designation date: 2022-10-15)
    • CA.5 (designation date: 2022-10-15)
    • BM.1.1.3 (designation date: 2022-10-15)
    • CM.3 (designation date: 2022-10-15)
    • BQ.1.19 (designation date: 2022-10-15)
    • BU.2 (designation date: 2022-10-15)
    • BL.1.4 (designation date: 2022-10-16)
    • BQ.1.20 (designation date: 2022-10-16)
    • CA.6 (designation date: 2022-10-16)
    • BF.11.1 (designation date: 2022-10-16)
    • BF.11.3 (designation date: 2022-10-16)
    • BF.11.2 (designation date: 2022-10-16)
    • BF.11.4 (designation date: 2022-10-16)
    • BF.11.5 (designation date: 2022-10-16)
    • BF.7.4 (designation date: 2022-10-16)
    • BF.7.5 (designation date: 2022-10-16)
    • BF.7.6 (designation date: 2022-10-16)
    • BF.7.8 (designation date: 2022-10-16)
    • BF.7.7 (designation date: 2022-10-16)
    • BF.7.9 (designation date: 2022-10-16)
    • BF.7.10 (designation date: 2022-10-16)
    • BF.7.11 (designation date: 2022-10-16)
    • BF.7.12 (designation date: 2022-10-16)
    • BE.1.4 (designation date: 2022-10-16)
    • BE.1.4.2 (designation date: 2022-10-16)
    • BE.1.4.1 (designation date: 2022-10-16)
    • BE.1.4.3 (designation date: 2022-10-16)
    • BE.1.4.4 (designation date: 2022-10-16)
    • CU.1 (designation date: 2022-10-16)
    • XBB.1.2 (designation date: 2022-10-17)
    • BT.2 (designation date: 2022-10-17)
    • BA.5.6.4 (designation date: 2022-10-17)
    • BA.5.2.37 (designation date: 2022-10-17)
    • BQ.1.1.2 (designation date: 2022-10-19)