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Releases: nextstrain/nextclade_data

2024-01-16--20-31-02Z

16 Jan 20:31
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2024-01-16--20-31-02Z
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2024-01-16--20-31-02Z

This release contains changes for datasets:

  • nextstrain/sars-cov-2/wuhan-hu-1/orfs (SARS-CoV-2)
  • nextstrain/sars-cov-2/wuhan-hu-1/proteins (SARS-CoV-2 (Mature proteins))
  • nextstrain/sars-cov-2/BA.2 (SARS-CoV-2 (BA.2))
  • nextstrain/sars-cov-2/XBB (SARS-CoV-2 (XBB))
  • nextstrain/sars-cov-2/BA.2.86 (SARS-CoV-2 (BA.2.86))
  • nextstrain/flu/h1n1pdm/ha/CY121680 (Influenza A H1N1pdm HA)
  • nextstrain/flu/h1n1pdm/ha/MW626062 (Influenza A H1N1pdm HA)
  • nextstrain/flu/h1n1pdm/na/MW626056 (Influenza A H1N1pdm NA)
  • nextstrain/flu/h3n2/ha/CY163680 (Influenza A H3N2 HA)
  • nextstrain/flu/h3n2/ha/EPI1857216 (Influenza A H3N2 HA)
  • nextstrain/flu/h3n2/na/EPI1857215 (Influenza A H3N2 NA)
  • nextstrain/flu/vic/ha/KX058884 (Influenza B Victoria HA)
  • nextstrain/flu/vic/na/CY073894 (Influenza B Victoria NA)
  • nextstrain/flu/yam/ha/JN993010 (Influenza B Yamagata HA)
  • nextstrain/rsv/a/EPI_ISL_412866 (RSV-A)
  • nextstrain/rsv/b/EPI_ISL_1653999 (RSV-B)
  • nextstrain/mpox/all-clades (Mpox virus (All clades))
  • nextstrain/mpox/clade-iib (Mpox virus (Clade IIb))
  • nextstrain/mpox/lineage-b.1 (Mpox virus (Lineage B.1))
  • nextstrain/flu/h3n2/pb1 (Influenza A H3N2 PB1 (segment 2))
  • nextstrain/flu/h3n2/np (Influenza A H3N2 NP (segment 5))
  • nextstrain/flu/h1n1pdm/pa (Influenza A H1N1pdm PA (segment 3))
  • nextstrain/flu/h3n2/ns (Influenza A H3N2 NS (segment 8))
  • nextstrain/flu/h1n1pdm/mp (Influenza A H1N1pdm MP (segment 7))
  • nextstrain/flu/h1n1pdm/np (Influenza A H1N1pdm NP (segment 5))
  • nextstrain/flu/h1n1pdm/ns (Influenza A H1N1pdm NS (segment 8))
  • nextstrain/flu/h3n2/mp (Influenza A H3N2 MP (segment 7))
  • nextstrain/flu/h3n2/pa (Influenza A H3N2 PA (segment 3))
  • nextstrain/flu/h1n1pdm/pb2 (Influenza A H1N1pdm PB2 (segment 1))
  • nextstrain/flu/h1n1pdm/pb1 (Influenza A H1N1pdm PB1 (segment 2))
  • nextstrain/flu/h3n2/pb2 (Influenza A H3N2 PB2 (segment 1))

SARS-CoV-2 (nextstrain/sars-cov-2/wuhan-hu-1/orfs)

Initial release of this v3 dataset.

This dataset is very similar to the v2 dataset sars-cov-2.

SARS-CoV-2 (Mature proteins) (nextstrain/sars-cov-2/wuhan-hu-1/proteins)

Initial release of this v3 dataset.

This dataset is similar to the v2 dataset sars-cov-2 but translating mature proteins (nsp1-16) instead of ORF1a/b.

SARS-CoV-2 (BA.2) (nextstrain/sars-cov-2/BA.2)

Initial release of this v3 dataset.

This dataset is very similar to the v2 dataset sars-cov-2-21L. Immune escape scores are informed by some additional DMS data.

SARS-CoV-2 (XBB) (nextstrain/sars-cov-2/XBB)

Initial release of this v3 dataset.

This dataset is new to v3 and does not have a v2 equivalent.

SARS-CoV-2 (BA.2.86) (nextstrain/sars-cov-2/BA.2.86)

Initial release of this v3 dataset.

This dataset is new to v3 and does not have a v2 equivalent.

Influenza A H1N1pdm HA (nextstrain/flu/h1n1pdm/ha/CY121680)

Initial release for Nextclade v3!

  • addition of subclade C.1.7

Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

Influenza A H1N1pdm HA (nextstrain/flu/h1n1pdm/ha/MW626062)

Initial release for Nextclade v3!

  • addition of subclade C.1.7

Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

Influenza A H1N1pdm NA (nextstrain/flu/h1n1pdm/na/MW626056)

Initial release for Nextclade v3!

Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

Influenza A H3N2 HA (nextstrain/flu/h3n2/ha/CY163680)

Initial release for Nextclade v3!

  • Addition of subclade H.1, H.2, H.3, and H.4
  • Aliasing of G.1.3.1.1 as subclade H

Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

Influenza A H3N2 HA (nextstrain/flu/h3n2/ha/EPI1857216)

Initial release for Nextclade v3!

  • Addition of subclade H.1, H.2, H.3, and H.4
  • Aliasing of G.1.3.1.1 as subclade H

Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

Influenza A H3N2 NA (nextstrain/flu/h3n2/na/EPI1857215)

Initial release for Nextclade v3!

Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

Influenza B Victoria HA (nextstrain/flu/vic/ha/KX058884)

  • fix subclade definition of C.2 and C.4

Influenza B Victoria NA (nextstrain/flu/vic/na/CY073894)

Initial release for Nextclade v3!

  • addition of subclade B.7.1
  • addition of subclade B.7.2
  • addition of subclade B.7.3
  • addition of subclade B.8

Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

Influenza B Yamagata HA (nextstrain/flu/yam/ha/JN993010)

Initial release for Nextclade v3!

Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

RSV-A (nextstrain/rsv/a/EPI_ISL_412866)

first release of v3 dataset.

Updated consortium nomenclature.

RSV-B (nextstrain/rsv/b/EPI_ISL_1653999)

first release of v3 dataset.

Updated consortium nomenclature.

Mpox virus (All clades) (nextstrain/mpox/all-clades)

Initial release of this dataset. This dataset is similar to the v2 dataset MPXV/ancestral with some differences.

New and changed gene names

Some genes have been renamed and one has been added. The new annotation is based on NCBI refseq annotations that were released in November 2022. The v2 dataset predates this refseq:

  • The 4 genes in the inverted terminal repeat segment (ITR) on both ends of the genome (OPG001, OPG002, OPG003,OPG015) are now all included. The genes on the 3' end (~positions 190000-197000) now have an _dup appended to distinguish them.
  • The gene previously named NBT03_gp052 is now called OPG073
  • The gene previously named NBT03_gp174 is now called OPG016
  • The gene previously named NBT03_gp175 is now called OPG015_dup
  • Gene OPG166 has been added

Mpox virus (Clade IIb) (nextstrain/mpox/clade-iib)

Initial release of this dataset. This dataset is similar to the v2 dataset hMPXV/NC_063383.1 with some differences.

New and changed gene names

Some genes have been renamed and one has been added. The new annotation is based on NCBI refseq annotations that were released in November 2022. The v2 dataset predates this refseq:

  • The 4 genes in the inverted terminal repeat segment (ITR) on both ends of the genome (OPG001, OPG002, OPG003,OPG015) are now all included. The genes on the 3' end (~positions 190000-197000) now have an _dup appended to distinguish them.
  • The gene previously named NBT03_gp052 is now called OPG073
  • The gene previously named NBT03_gp174 is now called OPG016
  • The gene previously named NBT03_gp175 is now called OPG015_dup
  • Gene OPG166 has been added

Mpox virus (Lineage B.1) (nextstrain/mpox/lineage-b.1)

Initial release of this dataset. This dataset is similar to the v2 dataset hMPXV_B.1/pseudo_ON563414 with some differences.

New and changed gene names

Some genes have been renamed and one has been added. The new annotation is based on NCBI refseq annotations that were released in November 2022. The v2 dataset predates this refseq:

  • The 4 genes in the inverted terminal repeat segment (ITR) on both ends of the genome (OPG001, OPG002, OPG003,OPG015) are now all included. The genes on the 3' end (~positions 190000-197000) now have an _dup appended to distinguish them.
  • The gene previously named NBT03_gp052 is now called OPG073
  • The gene previously named NBT03_gp174 is now called OPG016
  • The gene previously named NBT03_gp175 is now called OPG015_dup
  • Gene OPG166 has been added

Influenza A H3N2 PB1 (segment 2) (nextstrain/flu/h3n2/pb1)

Initial release of for non-HA/NA segments of Influenza A viruses based on genome in RefSeq.

Influenza A H3N2 NP (segment 5) (nextstrain/flu/h3n2/np)

Initial release of for non-HA/NA segments of Influenza A viruses based on genome in RefSeq.

Influenza A H1N1pdm PA (segment 3) (nextstrain/flu/h1n1pdm/pa)

Initial release of for non-HA/NA segments of Influenza A viruses based on genome in RefSeq.

Influenza A H3N2 NS (segment 8) (nextstrain/flu/h3n2/ns)

Initial release of for non-HA/NA segments of Influenza A viruses based on genome in RefSeq.

Influenza A H1N1pdm MP (segment 7) (nextstrain/flu/h1n1pdm/mp)

Initial release of for non-HA/NA segments of Influenza A viruses based on genome in RefSeq.

Influenza A H1N1pdm NP (segment 5) (nextstrain/flu/h1n1pdm/np)

Initial release of for non-HA/NA segments of Influenza A viruses based on genome in RefSeq.

Influenza A H1N1pdm NS (segment 8) (nex...

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2024-01-15

15 Jan 20:53
@corneliusroemer corneliusroemer
2024-01-15--20-23-55--UTC
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2024-01-15

New SARS-CoV-2 dataset version (tag 2024-01-15T12:00:00Z)

  • Important: This is the last release of SARS-CoV-2 datasets for nextclade v2. All v2 datasets will remain usable with nextclade v2. However, there will be no more dataset updates as future dataset releases will be for nextclade v3 only. Nextclade v3 has corresponding versions for each current v2 dataset. Read more about migrating from v2 to v3 in the v3 migration guide, specifically, CLI dataset paths may need to be updated, see Dataset path changes. As the first v3-only dataset is expected to be released mid February 2024, you have a month to migrate to v3 without any interruption in dataset updates.
  • Pango lineages designated between 2023-12-03 and 2024-01-14 are now included, unfold below to see a list with designation dates:
Newly included lineages, with designation date in parentheses
  • HV.2 (2023-12-17)
  • JD.1.1.7 (2023-12-17)
  • JD.1.1.8 (2023-12-17)
  • JD.2.2 (2023-12-17)
  • FY.1.2.1 (2023-12-17)
  • FY.1.2.2 (2023-12-17)
  • FY.1.2.3 (2023-12-17)
  • XBB.1.16.28 (2023-12-17)
  • JF.3 (2023-12-17)
  • XBB.1.16.29 (2023-12-17)
  • XBB.1.16.30 (2023-12-17)
  • XBB.1.16.31 (2023-12-17)
  • XDJ (2023-12-17)
  • XBB.1.5.108 (2023-12-17)
  • XCF.3 (2023-12-17)
  • XBB.1.5.109 (2023-12-17)
  • XBB.1.5.110 (2023-12-17)
  • XDA.1 (2023-12-17)
  • XBB.2.3.21 (2023-12-17)
  • XBB.2.3.22 (2023-12-17)
  • JD.1.2.2 (2023-12-17)
  • HN.7 (2023-12-17)
  • XDK (2023-12-17)
  • DV.7.1.8 (2023-12-17)
  • KG.1 (2023-12-17)
  • KG.2 (2023-12-17)
  • DV.7.1.9 (2023-12-17)
  • GE.1.2.1 (2023-12-17)
  • JG.3.4 (2023-12-17)
  • FL.38 (2023-12-17)
  • HN.4.1 (2023-12-17)
  • HN.4.1.1 (2023-12-17)
  • HN.4.2 (2023-12-17)
  • FL.39 (2023-12-17)
  • FL.39.1 (2023-12-17)
  • FL.40 (2023-12-17)
  • FL.24.1 (2023-12-17)
  • FL.1.8 (2023-12-17)
  • JE.1.1.1 (2023-12-20)
  • KH.1 (2023-12-20)
  • JF.1.1 (2023-12-20)
  • JF.1.1.1 (2023-12-20)
  • JF.1.1.2 (2023-12-20)
  • JF.4 (2023-12-20)
  • JN.1.3 (2023-12-20)
  • GK.1.8.1 (2023-12-21)
  • GK.1.11 (2023-12-21)
  • GK.1.11.1 (2023-12-21)
  • JW.1.1 (2023-12-21)
  • JC.5.1 (2023-12-21)
  • GN.1.4 (2023-12-21)
  • XBB.1.16.32 (2023-12-21)
  • KJ.1 (2023-12-21)
  • FL.2.7 (2023-12-21)
  • FL.2.7.1 (2023-12-21)
  • JN.1.4 (2024-01-08)
  • XDL (2024-01-08)
  • HV.1.8 (2024-01-09)
  • HV.1.9 (2024-01-09)
  • HV.1.10 (2024-01-09)
  • JN.1.5 (2024-01-09)
  • XDD.1 (2024-01-09)
  • XDD.1.1 (2024-01-09)
  • XDD.2 (2024-01-09)
  • JN.2.2 (2024-01-09)
  • JN.2.3 (2024-01-09)
  • JN.2.4 (2024-01-09)
  • JN.2.5 (2024-01-09)
  • JN.1.1.2 (2024-01-09)
  • HN.8 (2024-01-09)
  • JN.1.1.3 (2024-01-09)
  • JN.1.6 (2024-01-09)
  • JN.1.6.1 (2024-01-09)
  • JN.1.7 (2024-01-09)
  • JN.1.8 (2024-01-09)
  • JN.1.8.1 (2024-01-09)
  • JN.1.9 (2024-01-09)
  • FW.1.1.1 (2024-01-10)
  • HK.3.14 (2024-01-10)
  • XDM (2024-01-10)
  • KK.1 (2024-01-10)
  • KK.2 (2024-01-10)
  • KL.1 (2024-01-10)
  • KL.1.1 (2024-01-10)
  • HV.1.11 (2024-01-10)
  • JN.1.10 (2024-01-11)
  • JN.1.11 (2024-01-11)
Assets 2
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2023-12-20

15 Jan 20:53
@corneliusroemer corneliusroemer
2023-12-20--14-21-29--UTC
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2023-12-20

New Influenza virus A/H3N2 HA dataset version (tag 2023-12-20T12:00:00Z)

  • New A/H3N2 HA subclades H.1 - H.4
Assets 2
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2023-12-03

04 Dec 10:31
@corneliusroemer corneliusroemer
2023-12-04--10-17-19--UTC
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2023-12-03

New SARS-CoV-2 dataset version (tag 2023-12-03T12:00:00Z)

  • New Nextstrain clades 23G (XBB.1.5.70), 23H (HK.3=EG.5.1.1.3), 23I (BA.2.86) are added. See ncov PR for a detailed discussion of the clades.
  • Pango lineages designated between 2023-10-25 and 2023-12-03 are now included, unfold below to see a list with designation dates:
Newly included lineages, with designation date in parentheses
  • HK.20 (2023-11-02)
  • HK.20.1 (2023-11-02)
  • JN.4 (2023-11-12)
  • JD.1.2.1 (2023-11-12)
  • HK.21 (2023-11-12)
  • XCT.1 (2023-11-12)
  • HK.22 (2023-11-12)
  • XBB.1.16.26 (2023-11-12)
  • JN.5 (2023-11-14)
  • JN.6 (2023-11-14)
  • JG.3.2 (2023-11-17)
  • JG.3.3 (2023-11-17)
  • GK.1.10 (2023-11-17)
  • JN.7 (2023-11-17)
  • JN.8 (2023-11-17)
  • JN.9 (2023-11-17)
  • JN.3.1 (2023-11-17)
  • HR.1.1 (2023-11-17)
  • XDD (2023-11-17)
  • JN.2.1 (2023-11-21)
  • JN.10 (2023-11-21)
  • BA.2.86.4 (2023-11-21)
  • JN.5.1 (2023-11-21)
  • JD.1.1.4 (2023-11-21)
  • HK.3.8 (2023-11-21)
  • HK.3.2.1 (2023-11-21)
  • FL.15.4 (2023-11-21)
  • HK.8.1 (2023-11-21)
  • XDE (2023-11-21)
  • KB.1 (2023-11-21)
  • XBB.1.16.27 (2023-11-21)
  • XDF (2023-11-24)
  • EG.5.2.4 (2023-11-24)
  • FL.37 (2023-11-24)
  • XDG (2023-11-24)
  • HK.3.2.2 (2023-11-24)
  • HK.3.9 (2023-11-24)
  • HK.23 (2023-11-24)
  • HK.23.1 (2023-11-24)
  • HK.23.1.1 (2023-11-24)
  • HK.24 (2023-11-24)
  • HK.24.1 (2023-11-24)
  • HK.3.10 (2023-11-24)
  • HK.3.11 (2023-11-24)
  • HK.25 (2023-11-27)
  • KC.1 (2023-11-28)
  • KC.1.1 (2023-11-28)
  • HK.26 (2023-11-28)
  • HK.26.1 (2023-11-28)
  • HK.27 (2023-11-28)
  • HK.27.1 (2023-11-28)
  • HK.27.1.1 (2023-11-28)
  • HK.28 (2023-11-28)
  • HK.29 (2023-11-28)
  • HK.30 (2023-11-28)
  • HK.31 (2023-11-28)
  • HK.32 (2023-11-28)
  • HK.32.1 (2023-11-28)
  • EG.5.1.12 (2023-11-28)
  • EG.5.1.13 (2023-11-28)
  • EG.5.1.14 (2023-11-28)
  • EG.5.1.15 (2023-11-28)
  • EG.5.1.16 (2023-11-28)
  • EG.5.1.17 (2023-11-28)
  • EG.5.1.18 (2023-11-28)
  • EG.5.1.19 (2023-11-28)
  • KB.2 (2023-11-28)
  • KB.3 (2023-11-28)
  • KB.4 (2023-11-28)
  • BA.2.86.5 (2023-11-28)
  • JN.1.1 (2023-11-28)
  • DV.7.1.6 (2023-11-28)
  • DV.7.1.7 (2023-11-28)
  • JB.1.1 (2023-11-28)
  • JR.1.1.1 (2023-11-29)
  • GY.1.1 (2023-11-30)
  • GY.1.1.1 (2023-11-30)
  • FY.8.1 (2023-11-30)
  • EG.10.1.1 (2023-11-30)
  • BN.1.2.8 (2023-12-01)
  • XDH (2023-12-01)
  • XBC.1.3.1 (2023-12-01)
  • KD.1 (2023-12-01)
  • KD.2 (2023-12-01)
  • KD.3 (2023-12-01)
  • KD.4 (2023-12-01)
  • KD.5 (2023-12-01)
  • JP.1.1 (2023-12-01)
  • JN.1.1.1 (2023-12-02)
  • JN.1.2 (2023-12-02)
  • HV.1.5 (2023-12-02)
  • HV.1.6 (2023-12-02)
  • HV.1.6.1 (2023-12-02)
  • HV.1.7 (2023-12-02)
  • JD.1.1.5 (2023-12-02)
  • JD.1.1.6 (2023-12-02)
  • FY.5.2 (2023-12-02)
  • FY.5.3 (2023-12-02)
  • KE.1 (2023-12-02)
  • KE.2 (2023-12-02)
  • KE.3 (2023-12-02)
  • GY.9 (2023-12-02)
  • HK.3.12 (2023-12-02)
  • HK.3.13 (2023-12-02)
  • HK.34 (2023-12-02)
  • HK.33 (2023-12-02)
  • FY.5.4 (2023-12-02)
  • FY.5.5 (2023-12-02)
  • FY.5.5.1 (2023-12-02)
  • FY.8.1.1 (2023-12-02)
  • HK.34.1 (2023-12-02)
  • KF.1 (2023-12-02)
  • KF.2 (2023-12-02)
  • GA.10.1 (2023-12-03)
Assets 2
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2023-10-26

26 Oct 16:20
@corneliusroemer corneliusroemer
2023-10-26--14-46-43--UTC
049af87
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2023-10-26

New SARS-CoV-2 dataset version (tag 2023-10-26T12:00:00Z)

  • Fixed a bug in consensus sequence algorithm that treated ambiguous nucleotides as reference as opposed to unknowns. This only affected a few lineages with few designated sequences where the consensus was wrongly reference when it should have been mutated.
  • Pango lineages designated between 2023-09-20 and 2023-10-25 are now included, unfold below to see a list with designation dates:
Newly included lineages, with designation date in parentheses
  • XCN (2023-09-21)
  • FL.31 (2023-09-21)
  • FL.31.1 (2023-09-21)
  • FL.20.2 (2023-09-21)
  • FL.32 (2023-09-21)
  • FL.32.1 (2023-09-21)
  • FL.10.3 (2023-09-21)
  • FL.33 (2023-09-21)
  • FL.33.1 (2023-09-21)
  • FL.34 (2023-09-21)
  • FL.35 (2023-09-21)
  • JM.1 (2023-09-22)
  • JM.2 (2023-09-22)
  • GS.5 (2023-09-22)
  • GK.2.1.1 (2023-09-24)
  • EG.4.5 (2023-09-24)
  • CH.1.1.31 (2023-09-24)
  • JP.1 (2023-09-24)
  • CH.1.1.32 (2023-09-24)
  • JD.1.1.1 (2023-09-26)
  • JD.1.1.2 (2023-09-26)
  • XCP (2023-09-26)
  • EG.5.1.10 (2023-09-26)
  • GA.4.1.1 (2023-09-26)
  • FR.1.5 (2023-09-26)
  • EP.1.1 (2023-09-26)
  • EP.1.1.1 (2023-09-26)
  • HC.3 (2023-09-26)
  • FL.36 (2023-09-26)
  • HC.4 (2023-09-26)
  • FL.15.1 (2023-09-27)
  • FL.15.1.1 (2023-09-27)
  • FL.15.2 (2023-09-27)
  • FL.15.3 (2023-09-27)
  • JN.1 (2023-09-29)
  • JD.1.1.3 (2023-10-04)
  • JD.2 (2023-10-04)
  • GJ.1.2.6 (2023-10-04)
  • GJ.1.2.7 (2023-10-04)
  • JE.1.1 (2023-10-04)
  • GJ.1.2.8 (2023-10-04)
  • GJ.5 (2023-10-04)
  • GJ.5.1 (2023-10-04)
  • BA.2.86.2 (2023-10-12)
  • BA.2.86.3 (2023-10-12)
  • JQ.1 (2023-10-12)
  • JN.2 (2023-10-12)
  • JN.3 (2023-10-12)
  • GK.2.4 (2023-10-12)
  • HK.12 (2023-10-12)
  • EG.6.1.2 (2023-10-12)
  • HV.1.1 (2023-10-13)
  • HV.1.2 (2023-10-13)
  • HV.1.3 (2023-10-13)
  • HV.1.4 (2023-10-13)
  • HK.13 (2023-10-13)
  • HK.13.1 (2023-10-13)
  • HK.13.2 (2023-10-13)
  • HK.1.1 (2023-10-13)
  • HK.1.2 (2023-10-13)
  • HK.14 (2023-10-13)
  • HK.15 (2023-10-13)
  • EG.5.1.11 (2023-10-13)
  • JR.1 (2023-10-13)
  • JR.1.1 (2023-10-13)
  • GA.2.1 (2023-10-13)
  • GA.2.1.1 (2023-10-13)
  • GA.4.2 (2023-10-13)
  • GA.4.3 (2023-10-13)
  • GA.4.1.2 (2023-10-13)
  • HK.16 (2023-10-13)
  • HK.17 (2023-10-13)
  • HK.18 (2023-10-13)
  • HK.19 (2023-10-13)
  • XBB.2.3.15 (2023-10-13)
  • JS.1 (2023-10-13)
  • JS.2 (2023-10-13)
  • XCQ (2023-10-13)
  • XBB.2.3.16 (2023-10-13)
  • XBB.2.3.17 (2023-10-13)
  • JD.2.1 (2023-10-13)
  • GW.5.2 (2023-10-13)
  • GW.5.3 (2023-10-13)
  • GW.5.3.1 (2023-10-13)
  • HW.1.2 (2023-10-13)
  • HW.1.3 (2023-10-13)
  • XBC.1.6.5 (2023-10-13)
  • JT.1 (2023-10-13)
  • XBC.1.6.6 (2023-10-13)
  • GL.2 (2023-10-13)
  • GL.3 (2023-10-13)
  • XCR (2023-10-13)
  • GK.5 (2023-10-15)
  • GK.5.1 (2023-10-15)
  • GK.6 (2023-10-15)
  • GK.7 (2023-10-15)
  • GK.8 (2023-10-15)
  • GK.8.1 (2023-10-15)
  • GK.9 (2023-10-15)
  • GK.10 (2023-10-15)
  • GK.11 (2023-10-15)
  • GK.1.5 (2023-10-15)
  • GK.1.6 (2023-10-15)
  • GK.1.6.1 (2023-10-15)
  • GK.1.2.1 (2023-10-15)
  • GK.1.7 (2023-10-15)
  • GK.1.8 (2023-10-15)
  • GK.12 (2023-10-15)
  • GK.1.9 (2023-10-15)
  • XBB.1.16.25 (2023-10-15)
  • XCS (2023-10-15)
  • GK.1.1.1 (2023-10-15)
  • FU.1.1 (2023-10-15)
  • FU.1.1.1 (2023-10-15)
  • HG.3 (2023-10-15)
  • HG.1.1 (2023-10-15)
  • XBB.2.3.18 (2023-10-15)
  • GS.6 (2023-10-15)
  • GS.4.1.1 (2023-10-15)
  • GS.7 (2023-10-15)
  • GS.7.1 (2023-10-15)
  • GS.8 (2023-10-15)
  • GJ.6 (2023-10-15)
  • GJ.7 (2023-10-15)
  • JU.1 (2023-10-15)
  • JV.1 (2023-10-15)
  • JV.2 (2023-10-15)
  • JC.2 (2023-10-15)
  • JC.3 (2023-10-15)
  • JC.4 (2023-10-15)
  • JC.5 (2023-10-15)
  • JC.6 (2023-10-15)
  • XBB.1.41.3 (2023-10-15)
  • JW.1 (2023-10-15)
  • FL.30.1 (2023-10-15)
  • FL.13.2.1 (2023-10-15)
  • FL.13.4 (2023-10-15)
  • FL.13.4.1 (2023-10-15)
  • FL.13.5 (2023-10-15)
  • JG.4 (2023-10-15)
  • DV.7.1.3 (2023-10-15)
  • DV.7.1.4 (2023-10-15)
  • DV.7.1.5 (2023-10-15)
  • XCT (2023-10-15)
  • XBC.1.7.2 (2023-10-15)
  • XBC.1.7.1 (2023-10-15)
  • FL.23.2.1 (2023-10-15)
  • FL.23.2 (2023-10-15)
  • XCU (2023-10-15)
  • HH.2.1 (2023-10-15)
  • HH.3 (2023-10-15)
  • HH.4 (2023-10-15)
  • HH.5 (2023-10-15)
  • HH.6 (2023-10-15)
  • HH.7 (2023-10-15)
  • HH.8 (2023-10-15)
  • HH.8.1 (2023-10-15)
  • GE.1.4 (2023-10-15)
  • GE.1.5 (2023-10-15)
  • GE.1.6 (2023-10-15)
  • XBB.2.3.19 (2023-10-15)
  • JY.1 (2023-10-15)
  • JY.1.1 (2023-10-15)
  • JG.3.1 (2023-10-15)
  • HK.2.1 (2023-10-15)
  • HK.3.4 (2023-10-15)
  • HK.3.5 (2023-10-15)
  • HK.3.6 (2023-10-15)
  • HK.3.7 (2023-10-15)
  • HK.11.1 (2023-10-15)
  • FL.35.1 (2023-10-15)
  • GA.7 (2023-10-15)
  • GA.7.1 (2023-10-15)
  • GA.7.2 (2023-10-15)
  • GA.8 (2023-10-15)
  • GA.8.1 (2023-10-15)
  • GA.9 (2023-10-15)
  • GA.10 (2023-10-15)
  • XCV (2023-10-15)
  • XBB.2.3.20 (2023-10-15)
  • XCW (2023-10-15)
  • XBB.1.5.107 (2023-10-16)
  • JZ.1 (2023-10-16)
  • FD.5 (2023-10-16)
  • FD.5.1 (2023-10-16)
  • HE.2 (2023-10-16)
  • FE.1.1.5 (2023-10-16)
  • KA.1 (2023-10-16)
  • GN.1.2 (2023-10-16)
  • GN.1.3 (2023-10-16)
  • XCY (2023-10-16)
  • XCZ (2023-10-16)
  • FY.8 (2023-10-16)
  • FY.6.2 (2023-10-16)
  • FY.6.1 (2023-10-16)
  • FY.9 (2023-10-16)
  • FY.1.4 (2023-10-16)
  • FY.1.4.1 (2023-10-16)
  • FY.5.1 (2023-10-16)
  • FY.5.1.1 (2023-10-16)
  • HN.2 (2023-10-17)
  • HN.2.1 (2023-10-17)
  • HN.3 (2023-10-17)
  • HN.3.1 (2023-10-17)
  • HN.4 (2023-10-17)
  • HN.5 (2023-10-17)
  • HN.6 (2023-10-17)
  • GA.4.1.3 (2023-10-17)
  • XDA (2023-10-18)
  • XDB (2023-10-18)
  • XDC (2023-10-18)
Assets 2
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2023-10-03

26 Oct 14:26
@corneliusroemer corneliusroemer
2023-10-03--17-34-18--UTC
4356f0e
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2023-10-03

New RSV datasets with consortium nomenclature (tag 2023-10-02T12:00:00Z)

  • this adds a new developed nomenclature for RSV-A and RSV-B by the international RSV nomenclature consortium
  • the old G_clade nomenclature is kept for backwards compatibility
Assets 2
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2023-09-21

21 Sep 16:55
@corneliusroemer corneliusroemer
2023-09-21--16-39-25--UTC
ada2e5a
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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)
Assets 2
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2023-08-22

21 Sep 16:54
@corneliusroemer corneliusroemer
2023-08-22--21-25-46--UTC
67fcbeb
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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.

Assets 2
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2023-08-17

18 Aug 14:32
@rneher rneher
2023-08-17--15-51-24--UTC
25153e5
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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.

Assets 2
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2023-08-09

09 Aug 12:36
@corneliusroemer corneliusroemer
2023-08-09--12-06-38--UTC
89ad5e0
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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)
Assets 2
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