Skip to content

Releases: nextstrain/nextclade_data

2024-06-07--06-48-19Z

07 Jun 06:48
@github-actions github-actions
2024-06-07--06-48-19Z
ba4c1fa
Compare
Choose a tag to compare
2024-06-07--06-48-19Z

This release contains changes for datasets:

  • Measles N450 (WHO-2012) (nextstrain/measles/N450/WHO-2012)

Measles N450 (WHO-2012) (nextstrain/measles/N450/WHO-2012)

Initial release.

Assets 3
Loading

2024-06-04--16-27-23Z

04 Jun 16:27
@github-actions github-actions
2024-06-04--16-27-23Z
c0149e7
Compare
Choose a tag to compare
2024-06-04--16-27-23Z

This release contains changes for datasets:

  • Influenza A H3N2 PB1 (segment 2) (nextstrain/flu/h3n2/pb1)
  • Influenza A H3N2 NP (segment 5) (nextstrain/flu/h3n2/np)
  • Influenza A H1N1pdm PA (segment 3) (nextstrain/flu/h1n1pdm/pa)
  • Influenza A H3N2 NS (segment 8) (nextstrain/flu/h3n2/ns)
  • Influenza A H1N1pdm MP (segment 7) (nextstrain/flu/h1n1pdm/mp)
  • Influenza A H1N1pdm NP (segment 5) (nextstrain/flu/h1n1pdm/np)
  • Influenza A H1N1pdm NS (segment 8) (nextstrain/flu/h1n1pdm/ns)
  • Influenza A H3N2 MP (segment 7) (nextstrain/flu/h3n2/mp)
  • Influenza A H3N2 PA (segment 3) (nextstrain/flu/h3n2/pa)
  • Influenza A H1N1pdm PB2 (segment 1) (nextstrain/flu/h1n1pdm/pb2)
  • Influenza A H1N1pdm PB1 (segment 2) (nextstrain/flu/h1n1pdm/pb1)
  • Influenza A H3N2 PB2 (segment 1) (nextstrain/flu/h3n2/pb2)

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

Removes redundant fields from pathogen.json. This is a technical cleanup and does not involve any changes to the actual data.

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

Removes redundant fields from pathogen.json. This is a technical cleanup and does not involve any changes to the actual data.

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

Removes redundant fields from pathogen.json. This is a technical cleanup and does not involve any changes to the actual data.

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

Removes redundant fields from pathogen.json. This is a technical cleanup and does not involve any changes to the actual data.

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

Removes redundant fields from pathogen.json. This is a technical cleanup and does not involve any changes to the actual data.

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

Removes redundant fields from pathogen.json. This is a technical cleanup and does not involve any changes to the actual data.

Influenza A H1N1pdm NS (segment 8) (nextstrain/flu/h1n1pdm/ns)

Removes redundant fields from pathogen.json. This is a technical cleanup and does not involve any changes to the actual data.

Influenza A H3N2 MP (segment 7) (nextstrain/flu/h3n2/mp)

Removes redundant fields from pathogen.json. This is a technical cleanup and does not involve any changes to the actual data.

Influenza A H3N2 PA (segment 3) (nextstrain/flu/h3n2/pa)

Removes redundant fields from pathogen.json. This is a technical cleanup and does not involve any changes to the actual data.

Influenza A H1N1pdm PB2 (segment 1) (nextstrain/flu/h1n1pdm/pb2)

Removes redundant fields from pathogen.json. This is a technical cleanup and does not involve any changes to the actual data.

Influenza A H1N1pdm PB1 (segment 2) (nextstrain/flu/h1n1pdm/pb1)

Removes redundant fields from pathogen.json. This is a technical cleanup and does not involve any changes to the actual data.

Influenza A H3N2 PB2 (segment 1) (nextstrain/flu/h3n2/pb2)

Removes redundant fields from pathogen.json. This is a technical cleanup and does not involve any changes to the actual data.

Assets 14
Loading

2024-05-08--11-39-52Z

08 May 11:40
@github-actions github-actions
2024-05-08--11-39-52Z
c617d50
Compare
Choose a tag to compare
2024-05-08--11-39-52Z

This release contains changes for datasets:

  • HIV-1 (HXB2) (community/neherlab/hiv-1/hxb2)
  • H5Nx clade 2.3.4.4 (community/moncla-lab/iav-h5/ha/2.3.4.4)
  • H5Nx (all clades) (community/moncla-lab/iav-h5/ha/all-clades)
  • H5Nx clade 2.3.2.1 (community/moncla-lab/iav-h5/ha/2.3.2.1)

HIV-1 (HXB2) (community/neherlab/hiv-1/hxb2)

Initial release of an HIV-1 dataset for subtype classification.

H5Nx clade 2.3.4.4 (community/moncla-lab/iav-h5/ha/2.3.4.4)

Initial release for Nextclade v3!

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

H5Nx (all clades) (community/moncla-lab/iav-h5/ha/all-clades)

Initial release for Nextclade v3!

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

H5Nx clade 2.3.2.1 (community/moncla-lab/iav-h5/ha/2.3.2.1)

Initial release for Nextclade v3!

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

Assets 6
Loading

2024-04-25--01-03-07Z

25 Apr 01:03
@github-actions github-actions
2024-04-25--01-03-07Z
577696e
Compare
Choose a tag to compare
2024-04-25--01-03-07Z

This release contains changes for datasets:

  • SARS-CoV-2 (nextstrain/sars-cov-2/wuhan-hu-1/orfs)
  • SARS-CoV-2 (Mature proteins) (nextstrain/sars-cov-2/wuhan-hu-1/proteins)
  • SARS-CoV-2 (BA.2) (nextstrain/sars-cov-2/BA.2)
  • SARS-CoV-2 (XBB) (nextstrain/sars-cov-2/XBB)
  • SARS-CoV-2 (BA.2.86) (nextstrain/sars-cov-2/BA.2.86)

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

  • fix: Increase Nextclade alignment parameter "excessBandwidth" from 9 to 12 to correctly align complex series of indels that has arisen in Spike NTD with the occurrence of S:31- in some JN.1. The bandwidth is chosen to be as small as possible (to ensure fast runtime) but as large as necessary for correct alignment. As a result, occasional adjustments like here are required. Nothing else is changed in this SARS-CoV-2 dataset update.

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

  • fix: Increase Nextclade alignment parameter "excessBandwidth" from 9 to 12 to correctly align complex series of indels that has arisen in Spike NTD with the occurrence of S:31- in some JN.1. The bandwidth is chosen to be as small as possible (to ensure fast runtime) but as large as necessary for correct alignment. As a result, occasional adjustments like here are required. Nothing else is changed in this SARS-CoV-2 dataset update.

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

  • fix: Increase Nextclade alignment parameter "excessBandwidth" from 9 to 12 to correctly align complex series of indels that has arisen in Spike NTD with the occurrence of S:31- in some JN.1. The bandwidth is chosen to be as small as possible (to ensure fast runtime) but as large as necessary for correct alignment. As a result, occasional adjustments like here are required. Nothing else is changed in this SARS-CoV-2 dataset update.

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

  • fix: Increase Nextclade alignment parameter "excessBandwidth" from 9 to 12 to correctly align complex series of indels that has arisen in Spike NTD with the occurrence of S:31- in some JN.1. The bandwidth is chosen to be as small as possible (to ensure fast runtime) but as large as necessary for correct alignment. As a result, occasional adjustments like here are required. Nothing else is changed in this SARS-CoV-2 dataset update.

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

  • fix: Increase Nextclade alignment parameter "excessBandwidth" from 9 to 12 to correctly align complex series of indels that has arisen in Spike NTD with the occurrence of S:31- in some JN.1. The bandwidth is chosen to be as small as possible (to ensure fast runtime) but as large as necessary for correct alignment. As a result, occasional adjustments like here are required. Nothing else is changed in this SARS-CoV-2 dataset update.
Assets 7
Loading

2024-04-19--07-50-39Z

19 Apr 07:50
@github-actions github-actions
2024-04-19--07-50-39Z
30b4ee2
Compare
Choose a tag to compare
2024-04-19--07-50-39Z

This release contains changes for datasets:

  • Influenza A H1N1pdm HA (nextstrain/flu/h1n1pdm/ha/CY121680)
  • Influenza A H1N1pdm HA (nextstrain/flu/h1n1pdm/ha/MW626062)
  • Influenza A H1N1pdm NA (nextstrain/flu/h1n1pdm/na/MW626056)
  • Influenza A H3N2 HA (nextstrain/flu/h3n2/ha/CY163680)
  • Influenza A H3N2 HA (nextstrain/flu/h3n2/ha/EPI1857216)
  • Influenza A H3N2 NA (nextstrain/flu/h3n2/na/EPI1857215)
  • Influenza B Victoria HA (nextstrain/flu/vic/ha/KX058884)
  • Influenza B Victoria NA (nextstrain/flu/vic/na/CY073894)
  • Mpox virus (All clades) (nextstrain/mpox/all-clades)
  • Mpox virus (Clade IIb) (nextstrain/mpox/clade-iib)
  • Mpox virus (Lineage B.1) (nextstrain/mpox/lineage-b.1)

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

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

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

  • addition of subclade C.5.3.1
  • addition of subclade C.5.3.2
  • addition of subclade C.5.3.3
  • adjustment of definition of C.5.3

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

Update of the datasets with more recent data. No new clades were added on this occasion.

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

Update of the datasets with more recent data. No new clades were added on this occasion.

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

  • addition of subclade B.4.1
  • addition of subclade B.4.2
  • addition of subclade B.4.3

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

Update of the datasets with more recent data. No new clades were added on this occasion.

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

  • revision of definitions of B.7.2 and B.7.3
  • addition of subclade B.7.4

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

  • New hMPXV-1 lineages B.1.21, B.1.22, and C.1.1 are now included in the dataset. For more information on these lineages, see the hMPXV-1 lineage definitions PR
  • The sequences used in the reference trees have been updated to include the latest sequences available in Genbank as of 2024-04-16

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

  • New hMPXV-1 lineages B.1.21, B.1.22, and C.1.1 are now included in the dataset. For more information on these lineages, see the hMPXV-1 lineage definitions PR
  • The sequences used in the reference trees have been updated to include the latest sequences available in Genbank as of 2024-04-16

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

  • New hMPXV-1 lineages B.1.21, B.1.22, and C.1.1 are now included in the dataset. For more information on these lineages, see the hMPXV-1 lineage definitions PR
  • The sequences used in the reference trees have been updated to include the latest sequences available in Genbank as of 2024-04-16
Assets 13
Loading

2024-04-15--15-08-22Z

15 Apr 15:08
@github-actions github-actions
2024-04-15--15-08-22Z
fb4a856
Compare
Choose a tag to compare
2024-04-15--15-08-22Z

This release contains changes for datasets:

  • SARS-CoV-2 (nextstrain/sars-cov-2/wuhan-hu-1/orfs)
  • SARS-CoV-2 (Mature proteins) (nextstrain/sars-cov-2/wuhan-hu-1/proteins)
  • SARS-CoV-2 (BA.2) (nextstrain/sars-cov-2/BA.2)
  • SARS-CoV-2 (XBB) (nextstrain/sars-cov-2/XBB)
  • SARS-CoV-2 (BA.2.86) (nextstrain/sars-cov-2/BA.2.86)

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

  • Nextstrain clades 24A (JN.1) and 24B (JN.1.11.1) are now included.
  • All 83 Pango lineages designated between 2024-02-13 and 2024-04-12 are now included, unfold below to see a list of all newly included lineages with their designation dates:
Newly included lineages, with designation date in parentheses
  • JN.1.23 (2024-02-20)
  • KP.1 (2024-02-22)
  • JN.1.7.1 (2024-03-01)
  • JN.1.7.2 (2024-03-01)
  • KQ.1 (2024-03-01)
  • JN.1.13.1 (2024-03-01)
  • JN.1.1.5 (2024-03-01)
  • KR.1 (2024-03-04)
  • KP.1.1 (2024-03-04)
  • KP.2 (2024-03-04)
  • JN.1.24 (2024-03-04)
  • XDK.1 (2024-03-04)
  • JN.1.25 (2024-03-04)
  • JN.1.25.1 (2024-03-04)
  • XDQ.1 (2024-03-04)
  • JQ.2 (2024-03-05)
  • JN.13 (2024-03-06)
  • JN.13.1 (2024-03-06)
  • JN.1.1.6 (2024-03-09)
  • JN.1.26 (2024-03-09)
  • JN.1.27 (2024-03-09)
  • JN.1.4.4 (2024-03-09)
  • JN.1.8.2 (2024-03-09)
  • JN.1.28 (2024-03-09)
  • JN.1.1.7 (2024-03-09)
  • JN.1.29 (2024-03-09)
  • JN.1.4.5 (2024-03-14)
  • JN.1.18.1 (2024-03-14)
  • JN.1.30 (2024-03-14)
  • JN.1.31 (2024-03-14)
  • JN.1.16.1 (2024-03-14)
  • KS.1 (2024-03-14)
  • JN.1.4.6 (2024-03-14)
  • JN.1.32 (2024-03-14)
  • GE.1.2.2 (2024-03-17)
  • KT.1 (2024-03-17)
  • KT.1.1 (2024-03-17)
  • KT.1.2 (2024-03-17)
  • KP.3 (2024-03-17)
  • JN.1.33 (2024-03-17)
  • JN.1.34 (2024-03-17)
  • JN.1.35 (2024-03-17)
  • JN.1.36 (2024-03-17)
  • KP.2.1 (2024-03-19)
  • KP.2.2 (2024-03-19)
  • JN.1.30.1 (2024-03-19)
  • JQ.2.1 (2024-03-20)
  • XDD.1.1.1 (2024-03-25)
  • KU.1 (2024-03-25)
  • KU.2 (2024-03-25)
  • JN.1.18.2 (2024-03-25)
  • JN.1.36.1 (2024-03-25)
  • KV.1 (2024-03-25)
  • JN.1.37 (2024-03-25)
  • JN.1.28.1 (2024-03-25)
  • KW.1 (2024-03-25)
  • JN.1.38 (2024-03-25)
  • JN.1.39 (2024-03-25)
  • JN.1.40 (2024-03-25)
  • JN.1.41 (2024-03-25)
  • JN.1.42 (2024-03-25)
  • JN.1.43 (2024-03-25)
  • JN.1.43.1 (2024-03-25)
  • KP.1.1.1 (2024-03-25)
  • JN.1.44 (2024-03-25)
  • XDU (2024-03-26)
  • XDP.1 (2024-03-26)
  • JN.2.2.1 (2024-03-26)
  • JN.1.8.3 (2024-03-29)
  • KY.1 (2024-03-29)
  • JN.14 (2024-03-29)
  • JN.1.45 (2024-03-29)
  • XDV (2024-04-02)
  • XDV.1 (2024-04-02)
  • JN.1.42.1 (2024-04-02)
  • JN.1.46 (2024-04-02)
  • JN.1.4.7 (2024-04-02)
  • KV.2 (2024-04-02)
  • KW.1.1 (2024-04-03)
  • KZ.1 (2024-04-04)
  • KZ.1.1 (2024-04-04)
  • KZ.1.1.1 (2024-04-04)
  • JN.1.7.3 (2024-04-04)

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

  • Nextstrain clades 24A (JN.1) and 24B (JN.1.11.1) are now included.
  • All 83 Pango lineages designated between 2024-02-13 and 2024-04-12 are now included, unfold below to see a list of all newly included lineages with their designation dates:
Newly included lineages, with designation date in parentheses
  • JN.1.23 (2024-02-20)
  • KP.1 (2024-02-22)
  • JN.1.7.1 (2024-03-01)
  • JN.1.7.2 (2024-03-01)
  • KQ.1 (2024-03-01)
  • JN.1.13.1 (2024-03-01)
  • JN.1.1.5 (2024-03-01)
  • KR.1 (2024-03-04)
  • KP.1.1 (2024-03-04)
  • KP.2 (2024-03-04)
  • JN.1.24 (2024-03-04)
  • XDK.1 (2024-03-04)
  • JN.1.25 (2024-03-04)
  • JN.1.25.1 (2024-03-04)
  • XDQ.1 (2024-03-04)
  • JQ.2 (2024-03-05)
  • JN.13 (2024-03-06)
  • JN.13.1 (2024-03-06)
  • JN.1.1.6 (2024-03-09)
  • JN.1.26 (2024-03-09)
  • JN.1.27 (2024-03-09)
  • JN.1.4.4 (2024-03-09)
  • JN.1.8.2 (2024-03-09)
  • JN.1.28 (2024-03-09)
  • JN.1.1.7 (2024-03-09)
  • JN.1.29 (2024-03-09)
  • JN.1.4.5 (2024-03-14)
  • JN.1.18.1 (2024-03-14)
  • JN.1.30 (2024-03-14)
  • JN.1.31 (2024-03-14)
  • JN.1.16.1 (2024-03-14)
  • KS.1 (2024-03-14)
  • JN.1.4.6 (2024-03-14)
  • JN.1.32 (2024-03-14)
  • GE.1.2.2 (2024-03-17)
  • KT.1 (2024-03-17)
  • KT.1.1 (2024-03-17)
  • KT.1.2 (2024-03-17)
  • KP.3 (2024-03-17)
  • JN.1.33 (2024-03-17)
  • JN.1.34 (2024-03-17)
  • JN.1.35 (2024-03-17)
  • JN.1.36 (2024-03-17)
  • KP.2.1 (2024-03-19)
  • KP.2.2 (2024-03-19)
  • JN.1.30.1 (2024-03-19)
  • JQ.2.1 (2024-03-20)
  • XDD.1.1.1 (2024-03-25)
  • KU.1 (2024-03-25)
  • KU.2 (2024-03-25)
  • JN.1.18.2 (2024-03-25)
  • JN.1.36.1 (2024-03-25)
  • KV.1 (2024-03-25)
  • JN.1.37 (2024-03-25)
  • JN.1.28.1 (2024-03-25)
  • KW.1 (2024-03-25)
  • JN.1.38 (2024-03-25)
  • JN.1.39 (2024-03-25)
  • JN.1.40 (2024-03-25)
  • JN.1.41 (2024-03-25)
  • JN.1.42 (2024-03-25)
  • JN.1.43 (2024-03-25)
  • JN.1.43.1 (2024-03-25)
  • KP.1.1.1 (2024-03-25)
  • JN.1.44 (2024-03-25)
  • XDU (2024-03-26)
  • XDP.1 (2024-03-26)
  • JN.2.2.1 (2024-03-26)
  • JN.1.8.3 (2024-03-29)
  • KY.1 (2024-03-29)
  • JN.14 (2024-03-29)
  • JN.1.45 (2024-03-29)
  • XDV (2024-04-02)
  • XDV.1 (2024-04-02)
  • JN.1.42.1 (2024-04-02)
  • JN.1.46 (2024-04-02)
  • JN.1.4.7 (2024-04-02)
  • KV.2 (2024-04-02)
  • KW.1.1 (2024-04-03)
  • KZ.1 (2024-04-04)
  • KZ.1.1 (2024-04-04)
  • KZ.1.1.1 (2024-04-04)
  • JN.1.7.3 (2024-04-04)

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

  • Nextstrain clades 24A (JN.1) and 24B (JN.1.11.1) are now included.
  • All 83 Pango lineages designated between 2024-02-13 and 2024-04-12 are now included, unfold below to see a list of all newly included lineages with their designation dates:
Newly included lineages, with designation date in parentheses
  • JN.1.23 (2024-02-20)
  • KP.1 (2024-02-22)
  • JN.1.7.1 (2024-03-01)
  • JN.1.7.2 (2024-03-01)
  • KQ.1 (2024-03-01)
  • JN.1.13.1 (2024-03-01)
  • JN.1.1.5 (2024-03-01)
  • KR.1 (2024-03-04)
  • KP.1.1 (2024-03-04)
  • KP.2 (2024-03-04)
  • JN.1.24 (2024-03-04)
  • XDK.1 (2024-03-04)
  • JN.1.25 (2024-03-04)
  • JN.1.25.1 (2024-03-04)
  • XDQ.1 (2024-03-04)
  • JQ.2 (2024-03-05)
  • JN.13 (2024-03-06)
  • JN.13.1 (2024-03-06)
  • JN.1.1.6 (2024-03-09)
  • JN.1.26 (2024-03-09)
  • JN.1.27 (2024-03-09)
  • JN.1.4.4 (2024-03-09)
  • JN.1.8.2 (2024-03-09)
  • JN.1.28 (2024-03-09)
  • JN.1.1.7 (2024-03-09)
  • JN.1.29 (2024-03-09)
  • JN.1.4.5 (2024-03-14)
  • JN.1.18.1 (2024-03-14)
  • JN.1.30 (2024-03-14)
  • JN.1.31 (2024-03-14)
  • JN.1.16.1 (2024-03-14)
  • KS.1 (2024-03-14)
  • JN.1.4.6 (2024-03-14)
  • JN.1.32 (2024-03-14)
  • GE.1.2.2 (2024-03-17)
  • KT.1 (2024-03-17)
  • KT.1.1 (2024-03-17)
  • KT.1.2 (2024-03-17)
  • KP.3 (2024-03-17)
  • JN.1.33 (2024-03-17)
  • JN.1.34 (2024-03-17)
  • JN.1.35 (2024-03-17)
  • JN.1.36 (2024-03-17)
  • KP.2.1 (2024-03-19)
  • KP.2.2 (2024-03-19)
  • JN.1.30.1 (2024-03-19)
  • JQ.2.1 (2024-03-20)
  • XDD.1.1.1 (2024-03-25)
  • KU.1 (2024-03-25)
  • KU.2 (2024-03-25)
  • JN.1.18.2 (2024-03-25)
  • JN.1.36.1 (2024-03-25)
  • KV.1 (2024-03-25)
  • JN.1.37 (2024-03-25)
  • JN.1.28.1 (2024-03-25)
  • KW.1 (2024-03-25)
  • JN.1.38 (2024-03-25)
  • JN.1.39 (2024-03-25)
  • JN.1.40 (2024-03-25)
  • JN.1.41 (2024-03-25)
  • JN.1.42 (2024-03-25)
  • JN.1.43 (2024-03-25)
  • JN.1.43.1 (2024-03-25)
  • KP.1.1.1 (2024-03-25)
  • JN.1.44 (2024-03-25)
  • XDU (2024-03-26)
  • XDP.1 (2024-03-26)
  • JN.2.2.1 (2024-03-26)
  • JN.1.8.3 (2024-03-29)
  • KY.1 (2024-03-29)
  • JN.14 (2024-03-29)
  • JN.1.45 (2024-03-29)
  • XDV (2024-04-02)
  • XDV.1 (2024-04-02)
  • JN.1.42.1 (2024-04-02)
  • JN.1.46 (2024-04-02)
  • JN.1.4.7 (2024-04-02)
  • KV.2 (2024-04-02)
  • KW.1.1 (2024-04-03)
  • KZ.1 (2024-04-04)
  • KZ.1.1 (2024-04-04)
  • KZ.1.1.1 (2024-04-04)
  • JN.1.7.3 (2024-04-04)

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

  • Nextstrain clades 24A (JN.1) and 24B (JN.1.11.1) are now included.
  • All 83 Pango lineages designated between 2024-02-13 and 2024-04-12 are now included, unfold below to see a list of all newly included lineages with their designation dates:
Newly included lineages, with designation date in parentheses
  • JN.1.23 (2024-02-20)
  • KP.1 (2024-02-22)
  • JN.1.7.1 (2024-03-01)
  • JN.1.7.2 (2024-03-01)
  • KQ.1 (2024-03-01)
  • JN.1.13.1 (2024-03-01)
  • JN.1.1.5 (2024-03-01)
  • KR.1 (2024-03-04)
  • KP.1.1 (2024-03-04)
  • KP.2 (2024-03-04)
  • JN.1.24 (2024-03-04)
  • XDK.1 (2024-03-04)
  • JN.1.25 (2024-03-04)
  • JN.1.25.1 (2024-03-04)
  • XDQ.1 (2024-03-04)
  • JQ.2 (2024-03-05)
  • JN.13 (2024-03-06)
  • JN.13.1 (2024-03-06)
  • JN.1.1.6 (2024-03-09)
  • JN.1.26 (2024-03-09)
  • JN.1.27 (2024-03-09)
  • JN.1.4.4 (2024-03-09)
  • JN.1.8.2 (2024-03-09)
  • JN.1.28 (2024-03-09)
  • JN.1.1.7 (2024-03-09)
  • JN.1.29 (2024-03-09)
  • JN.1.4.5 (2024-03-14)
  • JN.1.18.1 (2024-03-14)
  • JN.1.30 (2024-03-14)
  • JN.1.31 (2024-03-14)
  • JN.1.16.1 (2024-03-14)
  • KS.1 (2024-03-14)
  • JN.1.4.6 (2024-03-14)
  • JN.1.32 (2024-03-14)
  • GE.1.2.2 (2024-03-17)
  • KT.1 (2024-03-17)
  • KT.1.1 (2024-03-17)
  • KT.1.2 (2024-03-17)
  • KP.3 (2024-03-17)
  • JN.1.33 (2024-03-17)
  • JN.1.34 (2024-03-17)
  • JN.1.35 (2024-03-17)
  • JN.1.36 (2024-03-17)
  • KP.2.1 (2024-03-19)
  • KP.2.2 (2024-03-19)
  • JN.1.30.1 (2024-03-19)
  • JQ.2.1 (2024-03-20)
  • XDD.1.1.1 (2024-03-25)
  • KU.1 (2024-03-25)
  • KU.2 (2024-03-25)
  • JN.1.18.2 (2024-03-25)
  • JN.1.36.1 (2024-03-25)
  • KV.1 (2024-03-25)
  • JN.1.37 (2024-03-25)
  • JN.1.28.1 (2024-03-25)
  • KW.1 (2024-03-25)
  • JN.1.38 (2024-03-25)
  • JN.1.39 (2024-03-25)
  • JN.1.40 (2024-03-25)
  • JN.1.41 (2024-03-25)
  • JN.1.42 (2024-03-25)
  • JN.1.43 (2024-03-25)
  • JN.1.43.1 (2024-03-25)
  • KP.1.1.1 (2024-03-25)
  • JN.1.44 (2024-03-25)
  • XDU (2024-03-26)
  • XDP.1 (2024-03-26)
  • JN.2.2.1 (2024-03-26)
  • JN.1.8.3 (2024-03-29)
  • KY.1 (2024-03-29)
  • JN.14 (2024-03-29)
  • JN.1.45 (2024-03-29)
  • XDV (2024-04-02)
  • XDV.1 (2024-04-02)
  • JN.1.42.1 (2024-04-02)
  • JN.1.46 (2024-04-02)
  • JN.1.4.7 (2024-04-02)
  • KV.2 (2024-04-02)
  • KW.1.1 (2024-04-03)
  • KZ.1 (2024-04-04)
  • KZ.1.1 (2024-04-04)
  • KZ.1.1.1 (2024-04-04)
  • JN.1.7.3 (2024-04-04)

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

  • Nextstrain clades 24A (JN.1) and 24B (JN.1.11.1) are now included.
  • All 83 Pango lineages designated between 2024-02-13 and 2024-04-12 are now included, unfold below to see a list of all newly included lineages with their designation dates:
Newly included lineages, with designation date in parentheses
  • JN.1.23 (2024-02-20)
  • KP.1 (2024-02-22)
  • JN.1.7.1 (2024-03-01)
  • JN.1.7.2 (2024-03-01)
  • KQ.1 (2024-03-01)
  • JN.1.13....
Read more
Assets 7
Loading

2024-02-22--16-12-03Z

22 Feb 16:12
@github-actions github-actions
2024-02-22--16-12-03Z
949bad2
Compare
Choose a tag to compare
2024-02-22--16-12-03Z

This release contains changes for datasets:

  • Influenza A H3N2 HA (nextstrain/flu/h3n2/ha/CY163680)
  • Influenza A H3N2 HA (nextstrain/flu/h3n2/ha/EPI1857216)
  • PRRSV-2 ORF5 Lineages, Yim-im & Zhang 2023 Microbiol Spectr (community/isuvdl/mazeller/prrsv2/orf5/yimim2023)

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

After discussion with various members of the seasonal influenza virus surveillance community, it was decided that subclade names starting with H have the potential to be confused with major influenza hemagglutinin subtypes. These subclades where therefore renamed to start with the alias J.

  • H --> J
  • H.1 --> J.1
  • H.2 --> J.2
  • H.3 --> J.3
  • H.4 --> J.4

The subclades H and H.* were revoked, and a comment was added to explain the reason. No subclade definitions were changed.

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

After discussion with various members of the seasonal influenza virus surveillance community, it was decided that subclade names starting with H have the potential to be confused with major influenza hemagglutinin subtypes. These subclades where therefore renamed to start with the alias J.

  • H --> J
  • H.1 --> J.1
  • H.2 --> J.2
  • H.3 --> J.3
  • H.4 --> J.4

The subclades H and H.* were revoked, and a comment was added to explain the reason. No subclade definitions were changed.

PRRSV-2 ORF5 Lineages, Yim-im & Zhang 2023 Microbiol Spectr (community/isuvdl/mazeller/prrsv2/orf5/yimim2023)

Fix(metadata): Swap reference name and reference accession fields in pathogen.json attributes. This is a metadata-only change with no impact on analysis results.

Assets 5
Loading

2024-02-16--04-00-32Z

16 Feb 04:00
@github-actions github-actions
2024-02-16--04-00-32Z
954d829
Compare
Choose a tag to compare
2024-02-16--04-00-32Z

This release contains changes for datasets:

  • SARS-CoV-2 (nextstrain/sars-cov-2/wuhan-hu-1/orfs)
  • SARS-CoV-2 (Mature proteins) (nextstrain/sars-cov-2/wuhan-hu-1/proteins)
  • SARS-CoV-2 (BA.2) (nextstrain/sars-cov-2/BA.2)
  • SARS-CoV-2 (XBB) (nextstrain/sars-cov-2/XBB)
  • SARS-CoV-2 (BA.2.86) (nextstrain/sars-cov-2/BA.2.86)
  • PRRSV-2 ORF5 Lineages, Yim-im & Zhang 2023 Microbiol Spectr (community/isuvdl/mazeller/prrsv2/orf5/yimim2023)

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

  • All 35 Pango lineages designated between 2024-01-16 and 2024-02-12 are now included, unfold below to see a list of all newly included lineages with their designation dates:
Newly included lineages, with designation date in parentheses
  • XDN (2024-01-16)
  • XDP (2024-01-16)
  • JN.3.2 (2024-01-16)
  • JN.3.2.1 (2024-01-16)
  • JN.11 (2024-01-21)
  • JN.1.12 (2024-01-21)
  • JN.12 (2024-01-22)
  • JN.1.11.1 (2024-01-22)
  • KM.1 (2024-01-31)
  • BA.2.87 (2024-02-01)
  • BA.2.87.1 (2024-02-01)
  • XDQ (2024-02-01)
  • GK.1.10.1 (2024-02-01)
  • XDR (2024-02-01)
  • JN.1.13 (2024-02-01)
  • JN.1.14 (2024-02-01)
  • JN.1.15 (2024-02-01)
  • JN.1.4.1 (2024-02-01)
  • JN.1.2.1 (2024-02-01)
  • JN.1.16 (2024-02-01)
  • JN.1.17 (2024-02-01)
  • JN.1.4.2 (2024-02-02)
  • JN.1.18 (2024-02-04)
  • JN.1.19 (2024-02-04)
  • JN.1.20 (2024-02-04)
  • XDS (2024-02-04)
  • JN.1.9.1 (2024-02-04)
  • JN.1.21 (2024-02-04)
  • JN.1.22 (2024-02-04)
  • JN.1.4.3 (2024-02-12)
  • XDT (2024-02-12)
  • HK.13.2.1 (2024-02-12)
  • KN.1 (2024-02-12)
  • KN.1.1 (2024-02-12)
  • JN.1.1.4 (2024-02-12)

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

  • All 35 Pango lineages designated between 2024-01-16 and 2024-02-12 are now included, unfold below to see a list of all newly included lineages with their designation dates:
Newly included lineages, with designation date in parentheses
  • XDN (2024-01-16)
  • XDP (2024-01-16)
  • JN.3.2 (2024-01-16)
  • JN.3.2.1 (2024-01-16)
  • JN.11 (2024-01-21)
  • JN.1.12 (2024-01-21)
  • JN.12 (2024-01-22)
  • JN.1.11.1 (2024-01-22)
  • KM.1 (2024-01-31)
  • BA.2.87 (2024-02-01)
  • BA.2.87.1 (2024-02-01)
  • XDQ (2024-02-01)
  • GK.1.10.1 (2024-02-01)
  • XDR (2024-02-01)
  • JN.1.13 (2024-02-01)
  • JN.1.14 (2024-02-01)
  • JN.1.15 (2024-02-01)
  • JN.1.4.1 (2024-02-01)
  • JN.1.2.1 (2024-02-01)
  • JN.1.16 (2024-02-01)
  • JN.1.17 (2024-02-01)
  • JN.1.4.2 (2024-02-02)
  • JN.1.18 (2024-02-04)
  • JN.1.19 (2024-02-04)
  • JN.1.20 (2024-02-04)
  • XDS (2024-02-04)
  • JN.1.9.1 (2024-02-04)
  • JN.1.21 (2024-02-04)
  • JN.1.22 (2024-02-04)
  • JN.1.4.3 (2024-02-12)
  • XDT (2024-02-12)
  • HK.13.2.1 (2024-02-12)
  • KN.1 (2024-02-12)
  • KN.1.1 (2024-02-12)
  • JN.1.1.4 (2024-02-12)

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

  • All 35 Pango lineages designated between 2024-01-16 and 2024-02-12 are now included, unfold below to see a list of all newly included lineages with their designation dates:
Newly included lineages, with designation date in parentheses
  • XDN (2024-01-16)
  • XDP (2024-01-16)
  • JN.3.2 (2024-01-16)
  • JN.3.2.1 (2024-01-16)
  • JN.11 (2024-01-21)
  • JN.1.12 (2024-01-21)
  • JN.12 (2024-01-22)
  • JN.1.11.1 (2024-01-22)
  • KM.1 (2024-01-31)
  • BA.2.87 (2024-02-01)
  • BA.2.87.1 (2024-02-01)
  • XDQ (2024-02-01)
  • GK.1.10.1 (2024-02-01)
  • XDR (2024-02-01)
  • JN.1.13 (2024-02-01)
  • JN.1.14 (2024-02-01)
  • JN.1.15 (2024-02-01)
  • JN.1.4.1 (2024-02-01)
  • JN.1.2.1 (2024-02-01)
  • JN.1.16 (2024-02-01)
  • JN.1.17 (2024-02-01)
  • JN.1.4.2 (2024-02-02)
  • JN.1.18 (2024-02-04)
  • JN.1.19 (2024-02-04)
  • JN.1.20 (2024-02-04)
  • XDS (2024-02-04)
  • JN.1.9.1 (2024-02-04)
  • JN.1.21 (2024-02-04)
  • JN.1.22 (2024-02-04)
  • JN.1.4.3 (2024-02-12)
  • XDT (2024-02-12)
  • HK.13.2.1 (2024-02-12)
  • KN.1 (2024-02-12)
  • KN.1.1 (2024-02-12)
  • JN.1.1.4 (2024-02-12)

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

  • All 35 Pango lineages designated between 2024-01-16 and 2024-02-12 are now included, unfold below to see a list of all newly included lineages with their designation dates:
Newly included lineages, with designation date in parentheses
  • XDN (2024-01-16)
  • XDP (2024-01-16)
  • JN.3.2 (2024-01-16)
  • JN.3.2.1 (2024-01-16)
  • JN.11 (2024-01-21)
  • JN.1.12 (2024-01-21)
  • JN.12 (2024-01-22)
  • JN.1.11.1 (2024-01-22)
  • KM.1 (2024-01-31)
  • BA.2.87 (2024-02-01)
  • BA.2.87.1 (2024-02-01)
  • XDQ (2024-02-01)
  • GK.1.10.1 (2024-02-01)
  • XDR (2024-02-01)
  • JN.1.13 (2024-02-01)
  • JN.1.14 (2024-02-01)
  • JN.1.15 (2024-02-01)
  • JN.1.4.1 (2024-02-01)
  • JN.1.2.1 (2024-02-01)
  • JN.1.16 (2024-02-01)
  • JN.1.17 (2024-02-01)
  • JN.1.4.2 (2024-02-02)
  • JN.1.18 (2024-02-04)
  • JN.1.19 (2024-02-04)
  • JN.1.20 (2024-02-04)
  • XDS (2024-02-04)
  • JN.1.9.1 (2024-02-04)
  • JN.1.21 (2024-02-04)
  • JN.1.22 (2024-02-04)
  • JN.1.4.3 (2024-02-12)
  • XDT (2024-02-12)
  • HK.13.2.1 (2024-02-12)
  • KN.1 (2024-02-12)
  • KN.1.1 (2024-02-12)
  • JN.1.1.4 (2024-02-12)

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

  • All 35 Pango lineages designated between 2024-01-16 and 2024-02-12 are now included, unfold below to see a list of all newly included lineages with their designation dates:
Newly included lineages, with designation date in parentheses
  • XDN (2024-01-16)
  • XDP (2024-01-16)
  • JN.3.2 (2024-01-16)
  • JN.3.2.1 (2024-01-16)
  • JN.11 (2024-01-21)
  • JN.1.12 (2024-01-21)
  • JN.12 (2024-01-22)
  • JN.1.11.1 (2024-01-22)
  • KM.1 (2024-01-31)
  • BA.2.87 (2024-02-01)
  • BA.2.87.1 (2024-02-01)
  • XDQ (2024-02-01)
  • GK.1.10.1 (2024-02-01)
  • XDR (2024-02-01)
  • JN.1.13 (2024-02-01)
  • JN.1.14 (2024-02-01)
  • JN.1.15 (2024-02-01)
  • JN.1.4.1 (2024-02-01)
  • JN.1.2.1 (2024-02-01)
  • JN.1.16 (2024-02-01)
  • JN.1.17 (2024-02-01)
  • JN.1.4.2 (2024-02-02)
  • JN.1.18 (2024-02-04)
  • JN.1.19 (2024-02-04)
  • JN.1.20 (2024-02-04)
  • XDS (2024-02-04)
  • JN.1.9.1 (2024-02-04)
  • JN.1.21 (2024-02-04)
  • JN.1.22 (2024-02-04)
  • JN.1.4.3 (2024-02-12)
  • XDT (2024-02-12)
  • HK.13.2.1 (2024-02-12)
  • KN.1 (2024-02-12)
  • KN.1.1 (2024-02-12)
  • JN.1.1.4 (2024-02-12)

PRRSV-2 ORF5 Lineages, Yim-im & Zhang 2023 Microbiol Spectr (community/isuvdl/mazeller/prrsv2/orf5/yimim2023)

Initial release for Nextclade v3!

Proposed dataset for PRRSV2 nomenclature from Yimim et al. 2023. Dataset includes clades, dates, geographic locations,
RFLPs, and vaccines.

Assets 8
Loading

2024-01-30--16-34-55Z

30 Jan 16:35
@github-actions github-actions
2024-01-30--16-34-55Z
7d2b75e
Compare
Choose a tag to compare
2024-01-30--16-34-55Z

This release contains changes for datasets:

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

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

Fix: Add shortcut paths to maintain backwards compatibility: i.e. one can request the dataset via nextclade dataset get --name flu_yam_ha --output-dir dataset, using the v2 path flu_yam_ha, instead of requiring the full v3 path nextstrain/flu/yam/ha/JN993010.

Assets 3
Loading

2024-01-29--10-29-43Z

29 Jan 10:29
@github-actions github-actions
2024-01-29--10-29-43Z
c3a8485
Compare
Choose a tag to compare
2024-01-29--10-29-43Z

This release contains changes for datasets:

  • nextstrain/rsv/a/EPI_ISL_412866 (RSV-A)
  • nextstrain/rsv/b/EPI_ISL_1653999 (RSV-B)

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

  • fix definitions of G_clades (legacy) for RSV-A and RSV-B

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

  • fix definitions of G_clades (legacy) for RSV-A and RSV-B
Assets 4
Loading