Releases · nextstrain/nextclade_data

15 Nov 19:31

corneliusroemer

2022-11-15--19-26-01--UTC

dd103bf

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)

Assets 2

15 Nov 16:21

corneliusroemer

2022-11-03--17-22-38--UTC

f931826

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.

Assets 2

31 Oct 12:02

corneliusroemer

2022-10-31--11-48-49--UTC

5fc0093

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) 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)

Assets 2

20 Oct 11:02

corneliusroemer

2022-10-19

2949a27

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)

Assets 2

28 Sep 18:12

corneliusroemer

2022-09-28--16-01-10--UTC

1090966

2022-09-27

New dataset version (tag `2022-09-27T12:00:00Z`)

All SARS-CoV-2 datasets

Data update: New Pango lineages are included, see cov-lineages/pango-designation@efabcb6...cfe736 for new desigantions that are included
Identical sequences have been removed from B.1* lineages to reduce size of that part of the tree from ~1.6k to ~800.

BA.2 dataset (experimental)

Reversions to wild type (Wuhan-Hu-1) are now labelled as rev to make it easier to spot problematic sequences
The dataset now contains antibody escape and ACE2 binding data from two repositories of Jesse Bloom's group on Github: https://jbloomlab.github.io/SARS-CoV-2-RBD_DMS_Omicron/epistatic-shifts/ and https://jbloomlab.github.io/SARS2_RBD_Ab_escape_maps/escape-calc/. For more information, please refer to: https://doi.org/10.1093/ve/veac021, https://doi.org/10.1101/2022.09.15.507787 and https://doi.org/10.1101/2022.09.20.508745.

Monkeypox datasets

New lineages A.2.2 and B.1.10-B.1.12 have been added, see here for details: https://github.com/mpxv-lineages/lineage-designation/blob/master/designation_records/B.1.10-A.2.2_2022-09-26.md

hMPXV B.1 dataset

Mutations to a genotype found in MPXV-UK_P2 or MPXV-M5312_HM12_Rivers are now "labelled" as rev (reversion to reference). This should help identify wrong calls to reference when using the B.1 dataset. Until now, these artefacts were only visible as reversions when using the hMPXV or all-clades datasets.

MPXV (All clades)

Frame shifts and stop codons that are encountered in a majority of sequences from clades IIa or I are now annotated as "known" mutations, which means that they do not influence the quality score. This should help increase the signal to noise ratio when uploading sequences from either of the clades.

Assets 2

27 Sep 16:44

corneliusroemer

2022-09-14--18-25-04--UTC

d9cc43c

2022-09-13

New dataset version (tag `2022-09-13T12:00:00Z`)

All monkeypox datasets

New lineages A.2.1 and B.1.9 have been added, see here for details: https://github.com/mpxv-lineages/lineage-designation/blob/master/designation_records/B.1.9-A.2.1_2022-09-13.md

Assets 2

09 Sep 16:48

corneliusroemer

2022-09-09--16-35-58--UTC

41cda4c

2022-09-09

New dataset version (tag `2022-09-09T12:00:00Z`)

All SARS-CoV-2 datasets

Data update: New pango lineages are included, see cov-lineages/pango-designation@fcad365...efabcb6 for new desigantions that are included
Added 5 sample sequences from recently designated Pango lineages

Click to see all new lineages

BP.1        Alias of B.1.1.529.2.3.16.1, Oceania/South East Asia lineage, from pango-designation issue #1009
BA.2.3.20   Alias of B.1.1.529.2.3.20, found globally, unclear origin, from pango-designation issue #1013
BL.2        Alias of B.1.1.529.2.75.1.2, mainly found in India, defined by S:R346T on A26612T branch 
BL.3        Alias of B.1.1.529.2.75.1.3, mainly found in India, defined by ORF1a:P2685S on A26612T branch 
BL.4        Alias of B.1.1.529.2.75.1.4, mainly found in India, defined by ORF7a:P45L with 11224T and 22720G branch 
BM.1        Alias of B.1.1.529.2.75.3.1, mainly found in India, pango-designation issue #965
BM.1.1      Alias of B.1.1.529.2.75.3.1.1, mainly found in India (West Bengal), defined by S:346T
BM.2        Alias of B.1.1.529.2.75.3.2, mainly found in India (Telangana), defined by S:346T
BM.3        Alias of B.1.1.529.2.75.3.3, found in Nepal and globally, defined by ORF1b:P1652S
BM.4        Alias of B.1.1.529.2.75.3.4, mainly found in India, defined by ORF1a:Q1198K, from pango-designation issue #957
BM.4.1      Alias of B.1.1.529.2.75.3.4.1, mainly found in India, defined by S:F486S, from pango-designation issue #957
BR.1        Alias of B.1.1.529.2.75.4.1, mainly found in India (Karnataka), defined by S:K444M
BN.1        Alias of B.1.1.529.2.75.5.1, mainly found in India, pango-designation issue #994
BN.2        Alias of B.1.1.529.2.75.5.2, mainly found in India, pango-designation issue #1021
BN.2.1      Alias of B.1.1.529.2.75.5.2.1, mainly USA and Canada lineage, defined by S:H49Y and S:F490S
BA.2.75.6   Alias of B.1.1.529.2.75.6, mainly found in India, defined by S:R346T on the BA.2.75 polytomy
BA.2.75.7   Alias of B.1.1.529.2.75.7, mainly found in India, defined by S:F486S on the BA.2.75 polytomy
BA.4.1.9    Alias of B.1.1.529.4.1.9, mainly found in USA, England and Mexico, from pango-designation issue #926
BA.4.6.1    Alias of B.1.1.529.4.6.1, mainly found in UK, USA and Germany, from pango-designation issue #900
BA.5.1.15   Alias of B.1.1.529.5.1.15, Peru and Brazil lineage
BA.5.1.16   Alias of B.1.1.529.5.1.16, Japan lineage
BA.5.1.17   Alias of B.1.1.529.5.1.17, France lineage
BA.5.1.18   Alias of B.1.1.529.5.1.18, mainly found in USA, from pango-designation issue #930
BA.5.1.19   Alias of B.1.1.529.5.1.19, mainly found in Netherlands, Germany, USA, and England, from pango-designation issue #999
BF.16       Alias of B.1.1.529.5.2.1.16, found in USA, from pango-designation issue #942
BF.17       Alias of B.1.1.529.5.2.1.17, Australia lineage
BF.18       Alias of B.1.1.529.5.2.1.18, Australia lineage
BF.19       Alias of B.1.1.529.5.2.1.19, Greece lineage
BF.20       Alias of B.1.1.529.5.2.1.20, lineage in Kenya and other countries
BF.21       Alias of B.1.1.529.5.2.1.21, USA lineage
BF.22       Alias of B.1.1.529.5.2.1.22, mainly found in Japan, from pango-designation issue #1010
BA.5.2.8    Alias of B.1.1.529.5.2.8, Israel lineage
BA.5.2.9    Alias of B.1.1.529.5.2.9, USA lineage
BA.5.2.10   Alias of B.1.1.529.5.2.10, Brazil lineage
BA.5.2.11   Alias of B.1.1.529.5.2.11, Philippines lineage
BA.5.2.12   Alias of B.1.1.529.5.2.12, Japan lineage
BA.5.2.13   Alias of B.1.1.529.5.2.13, mainly found in England, from pango-designation issue #959
BE.1.1.1    Alias of B.1.1.529.5.3.1.1.1.1, found globally, from pango-designation issue #931
BQ.1        Alias of B.1.1.529.5.3.1.1.1.1.1, Nigeria lineage, from pango-designation issue #993
BE.1.3      Alias of B.1.1.529.5.3.1.1.3, Finland and Estonia lineage
BA.5.5.2    Alias of B.1.1.529.5.5.2, mainly found in USA, Canada, England and Ireland, from pango-designation issue #938
BA.5.5.3    Alias of B.1.1.529.5.5.3, USA lineage, from pango-designation issue #1015
XAU         Recombinant lineage of BA.1.1* and BA.2.9*, predominantly in Spain, England and France, from pango-designation issue #894
XAV         Recombinant lineage of BA.2* and BA.5*, mainly France, USA, and Scotland lineage, from pango-designation issue #911
XAW         Recombinant lineage of BA.2* and AY.122, Russia lineage, from pango-designation issue #895
XAY         Recombinant lineage of BA.2 and AY.45, South Africa lineage, from pango-designation issue #844
XAZ         Recombinant lineage of BA.2.5, BA.5. and BA.2.5, predominantly found in France, Germany, Croatia, Denmark and USA, from pango-designation issue #797
*BA.5.1.13  Withdrawn: Defined solely by Artic v3 artefacts, see issue #1029

Experimental BA.2 dataset (sars-cov-2-21L)

(Use this dataset via web as it is not guaranteed to be continued as the other datasets)

Unaliased column: To help sort Nextclade web results by Pango lineage in a way that respects the meaning of aliases, there is now an unaliased column included, that writes out full lineage names as if there were no alias, e.g. BA.5.2 becomes B.1.1.529.5.2 and so forth. This has the additional advantage that you can learn what new aliases stand for.

Assets 2

29 Aug 19:17

corneliusroemer

2022-08-26--16-47-36--UTC

200c0fa

2022-08-26

New dataset version (tag 2022-08-26T12:00:00Z)

All Monkeypox datasets

New lineages B.1.6-B.1.8 have been added, see this PR for details: https://github.com/mpxv-lineages/lineage-designation/pull/13/files.
Lineages are now colored using color ordering, making it easier to spot lineages that are closely related on the Auspice tree.

Assets 2

23 Aug 14:07

corneliusroemer

2022-08-23--14-06-34--UTC

ef4cfe5

2022-08-23

New dataset version (tag `2022-08-23T12:00:00Z`)

All SARS-CoV-2 datasets

Data update: New pango lineages are included up to commit cov-lineages/pango-designation@4213460...fcad365)

Assets 2

19 Aug 15:01

corneliusroemer

2022-08-19--15-00-21--UTC

b557ec8

2022-08-19

Monkeypox datasets

New dataset version (tag `2022-08-19T12:00:00Z`)

All monkeypox datasets

Clade names now follow the convention agreed during WHO consultation:

Clade 1 -> Clade I
Clade 2 -> Clade IIa
Clade 3 -> Clade IIb

The common ancestor of clade IIa and clade IIb is called clade II.

The clade/lineage hierarchy now has a middle level called outbreak. For now there is just one outbreak called hMPXV-1 but in the future other clusters that may be worth naming may get an outbreak name - even if they don't get lineages of their own.

This middle level is output into Nextclade web and TSV/CSV files in the same way as lineages. The field is called outbreak. If a sequence does not belong to an outbreak, the field will be empty.

Sequences released by Genbank up to 2022-08-18 are included in the new dataset.

MPXV (All clades)

The reconstructed ancestor is now assigned clade outgroup - until now the clade field was empty.

The reference.fasta ID has been renamed to reconstructed_ancestral_mpox_in_NC_063383_coordinates as requested in issue #35. This should not impact most users - the change only affects the name of the reference sequence as output to the alignment if you use Nextclade-CLI and include the --include-reference flag.

hMPXV-1 B.1 dataset

The reference.fasta ID has been renamed to MPXV_USA_2022_MA001_in_NC_063383_coordinates, see above for a description of the impact (for most people none).

Assets 2

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