Releases: nextstrain/nextclade_data
2023-01-27
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
)
- New monkeypox lineages B.1.15, B.1.16, and B.1.17 were added to the datasets, see mpxv-lineages/lineage-designation#31 for details on these lineages.
2023-01-19
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
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
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
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
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
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
All monkeypox datasets
New dataset version (tag 2022-11-03T12:00:00Z
)
- New monkeypox lineages A.2.3, A.3, B.1.13 and B.1.14 were added to the dataset, see mpxv-lineages/lineage-designation#28 for details on these lineages.
2022-10-27
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
) andclade_who
(e.g.Gamma
) andclade_legacy
(e.g.20J (Gamma, V3
).
If you don't want to change your code, you can future proof it by starting to useclade_legacy
instead ofclade
, 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 usingclade_nextstrain
andclade_who
from now on.
Phase 2 which will happen at the earliest in a month (2022-12-01) will involve changingclade
from being composite and identical withclade_legacy
to being identical withclade_nextstrain
.
Phase 3 which will happen at the earliest in 6 months (2023-04-01) may involve droppingclade_legacy
andclade_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 clades22E
(BQ.1) and22F
(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
All SARS-CoV-2 datasets
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)