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Releases: nextstrain/nextclade_data

2024-08-01--22-31-31Z

01 Aug 22:31
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2024-08-01--22-31-31Z
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2024-08-01--22-31-31Z

This release contains changes for datasets:

  • RSV-A (nextstrain/rsv/a/EPI_ISL_412866)
  • RSV-B (nextstrain/rsv/b/EPI_ISL_1653999)
  • Mpox virus (Clade I) (nextstrain/mpox/clade-i)

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

  • add subclades A.D.1.4-8
  • add subclades A.D.3.2-6, add representatives to A.D.3.1
  • add subclade A.D.5.4, adjust definition of A.D.5.3 to make it a clear sibling

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

  • update of reference tree with additional data. No new clades.

Mpox virus (Clade I) (nextstrain/mpox/clade-i)

Initial release of this dataset.

Assets 5
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2024-07-17--12-57-03Z

17 Jul 12:57
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2024-07-17--12-57-03Z
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2024-07-17--12-57-03Z

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)

  • Include newly designated Nextstrain clade 24C (KP.3)
  • All 84 Pango lineages designated between 2024-06-11 and 2024-07-14 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
  • BA.2.86.7 (2024-06-13)
  • XDZ (2024-06-14)
  • JN.1.1.10 (2024-06-14)
  • JN.1.63 (2024-06-14)
  • JN.1.63.1 (2024-06-14)
  • XEA (2024-06-14)
  • XEB (2024-06-14)
  • XDP.2 (2024-06-14)
  • XDP.3 (2024-06-14)
  • LV.1 (2024-06-14)
  • LV.2 (2024-06-14)
  • LE.1.3 (2024-06-14)
  • LE.1.3.1 (2024-06-14)
  • JN.1.58.3 (2024-06-14)
  • KP.4.1.1 (2024-06-17)
  • KP.4.1.2 (2024-06-17)
  • KP.4.1.3 (2024-06-17)
  • LW.1 (2024-06-17)
  • LP.3 (2024-06-17)
  • KP.3.1.5 (2024-06-17)
  • KP.1.1.5 (2024-06-17)
  • XDD.3 (2024-06-29)
  • LF.3.1.1 (2024-06-29)
  • LB.1.3.1 (2024-06-29)
  • KP.2.3.4 (2024-06-29)
  • JN.1.18.6 (2024-06-29)
  • LY.2 (2024-06-29)
  • LY.1 (2024-06-29)
  • JN.1.18.7 (2024-06-29)
  • LZ.1 (2024-06-29)
  • LZ.1.1 (2024-06-29)
  • MA.1 (2024-06-29)
  • MB.1 (2024-06-29)
  • MB.1.1 (2024-06-29)
  • LP.1.1 (2024-06-29)
  • LF.4 (2024-06-29)
  • LF.4.1 (2024-06-29)
  • KP.3.3.1 (2024-06-29)
  • MC.1 (2024-06-29)
  • LU.2 (2024-07-01)
  • JN.1.64 (2024-07-01)
  • JN.1.64.1 (2024-07-01)
  • MD.1 (2024-07-01)
  • MD.1.1 (2024-07-01)
  • MD.2 (2024-07-01)
  • MD.3 (2024-07-01)
  • MD.3.1 (2024-07-01)
  • LK.2 (2024-07-03)
  • LK.2.1 (2024-07-03)
  • JN.1.7.8 (2024-07-03)
  • JN.1.50.2 (2024-07-03)
  • ME.1 (2024-07-03)
  • LF.5 (2024-07-10)
  • JN.1.48.3 (2024-07-10)
  • KS.1.3 (2024-07-10)
  • JN.1.65 (2024-07-10)
  • JN.1.65.1 (2024-07-10)
  • MF.1 (2024-07-10)
  • MF.2 (2024-07-10)
  • KP.3.3.2 (2024-07-10)
  • MG.1 (2024-07-10)
  • KP.4.2.3 (2024-07-10)
  • KP.2.17 (2024-07-10)
  • LB.1.3.2 (2024-07-10)
  • MH.1 (2024-07-10)
  • LB.1.8 (2024-07-10)
  • JN.1.7.9 (2024-07-10)
  • MJ.1 (2024-07-10)
  • KP.3.1.6 (2024-07-12)
  • MK.1 (2024-07-12)
  • MK.2 (2024-07-12)
  • KP.3.4.1 (2024-07-12)
  • KP.3.3.3 (2024-07-12)
  • ML.1 (2024-07-12)
  • ML.2 (2024-07-12)
  • MM.1 (2024-07-12)
  • MM.2 (2024-07-12)
  • JN.1.66 (2024-07-12)
  • MN.1 (2024-07-12)
  • KP.3.5 (2024-07-12)
  • LB.1.4.1 (2024-07-13)
  • LB.1.7.1 (2024-07-13)
  • LB.1.7.2 (2024-07-13)
  • LB.1.7.3 (2024-07-13)

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

  • Include newly designated Nextstrain clade 24C (KP.3)
  • All 84 Pango lineages designated between 2024-06-11 and 2024-07-14 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
  • BA.2.86.7 (2024-06-13)
  • XDZ (2024-06-14)
  • JN.1.1.10 (2024-06-14)
  • JN.1.63 (2024-06-14)
  • JN.1.63.1 (2024-06-14)
  • XEA (2024-06-14)
  • XEB (2024-06-14)
  • XDP.2 (2024-06-14)
  • XDP.3 (2024-06-14)
  • LV.1 (2024-06-14)
  • LV.2 (2024-06-14)
  • LE.1.3 (2024-06-14)
  • LE.1.3.1 (2024-06-14)
  • JN.1.58.3 (2024-06-14)
  • KP.4.1.1 (2024-06-17)
  • KP.4.1.2 (2024-06-17)
  • KP.4.1.3 (2024-06-17)
  • LW.1 (2024-06-17)
  • LP.3 (2024-06-17)
  • KP.3.1.5 (2024-06-17)
  • KP.1.1.5 (2024-06-17)
  • XDD.3 (2024-06-29)
  • LF.3.1.1 (2024-06-29)
  • LB.1.3.1 (2024-06-29)
  • KP.2.3.4 (2024-06-29)
  • JN.1.18.6 (2024-06-29)
  • LY.2 (2024-06-29)
  • LY.1 (2024-06-29)
  • JN.1.18.7 (2024-06-29)
  • LZ.1 (2024-06-29)
  • LZ.1.1 (2024-06-29)
  • MA.1 (2024-06-29)
  • MB.1 (2024-06-29)
  • MB.1.1 (2024-06-29)
  • LP.1.1 (2024-06-29)
  • LF.4 (2024-06-29)
  • LF.4.1 (2024-06-29)
  • KP.3.3.1 (2024-06-29)
  • MC.1 (2024-06-29)
  • LU.2 (2024-07-01)
  • JN.1.64 (2024-07-01)
  • JN.1.64.1 (2024-07-01)
  • MD.1 (2024-07-01)
  • MD.1.1 (2024-07-01)
  • MD.2 (2024-07-01)
  • MD.3 (2024-07-01)
  • MD.3.1 (2024-07-01)
  • LK.2 (2024-07-03)
  • LK.2.1 (2024-07-03)
  • JN.1.7.8 (2024-07-03)
  • JN.1.50.2 (2024-07-03)
  • ME.1 (2024-07-03)
  • LF.5 (2024-07-10)
  • JN.1.48.3 (2024-07-10)
  • KS.1.3 (2024-07-10)
  • JN.1.65 (2024-07-10)
  • JN.1.65.1 (2024-07-10)
  • MF.1 (2024-07-10)
  • MF.2 (2024-07-10)
  • KP.3.3.2 (2024-07-10)
  • MG.1 (2024-07-10)
  • KP.4.2.3 (2024-07-10)
  • KP.2.17 (2024-07-10)
  • LB.1.3.2 (2024-07-10)
  • MH.1 (2024-07-10)
  • LB.1.8 (2024-07-10)
  • JN.1.7.9 (2024-07-10)
  • MJ.1 (2024-07-10)
  • KP.3.1.6 (2024-07-12)
  • MK.1 (2024-07-12)
  • MK.2 (2024-07-12)
  • KP.3.4.1 (2024-07-12)
  • KP.3.3.3 (2024-07-12)
  • ML.1 (2024-07-12)
  • ML.2 (2024-07-12)
  • MM.1 (2024-07-12)
  • MM.2 (2024-07-12)
  • JN.1.66 (2024-07-12)
  • MN.1 (2024-07-12)
  • KP.3.5 (2024-07-12)
  • LB.1.4.1 (2024-07-13)
  • LB.1.7.1 (2024-07-13)
  • LB.1.7.2 (2024-07-13)
  • LB.1.7.3 (2024-07-13)

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

  • Include newly designated Nextstrain clade 24C (KP.3)
  • All 84 Pango lineages designated between 2024-06-11 and 2024-07-14 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
  • BA.2.86.7 (2024-06-13)
  • XDZ (2024-06-14)
  • JN.1.1.10 (2024-06-14)
  • JN.1.63 (2024-06-14)
  • JN.1.63.1 (2024-06-14)
  • XEA (2024-06-14)
  • XEB (2024-06-14)
  • XDP.2 (2024-06-14)
  • XDP.3 (2024-06-14)
  • LV.1 (2024-06-14)
  • LV.2 (2024-06-14)
  • LE.1.3 (2024-06-14)
  • LE.1.3.1 (2024-06-14)
  • JN.1.58.3 (2024-06-14)
  • KP.4.1.1 (2024-06-17)
  • KP.4.1.2 (2024-06-17)
  • KP.4.1.3 (2024-06-17)
  • LW.1 (2024-06-17)
  • LP.3 (2024-06-17)
  • KP.3.1.5 (2024-06-17)
  • KP.1.1.5 (2024-06-17)
  • XDD.3 (2024-06-29)
  • LF.3.1.1 (2024-06-29)
  • LB.1.3.1 (2024-06-29)
  • KP.2.3.4 (2024-06-29)
  • JN.1.18.6 (2024-06-29)
  • LY.2 (2024-06-29)
  • LY.1 (2024-06-29)
  • JN.1.18.7 (2024-06-29)
  • LZ.1 (2024-06-29)
  • LZ.1.1 (2024-06-29)
  • MA.1 (2024-06-29)
  • MB.1 (2024-06-29)
  • MB.1.1 (2024-06-29)
  • LP.1.1 (2024-06-29)
  • LF.4 (2024-06-29)
  • LF.4.1 (2024-06-29)
  • KP.3.3.1 (2024-06-29)
  • MC.1 (2024-06-29)
  • LU.2 (2024-07-01)
  • JN.1.64 (2024-07-01)
  • JN.1.64.1 (2024-07-01)
  • MD.1 (2024-07-01)
  • MD.1.1 (2024-07-01)
  • MD.2 (2024-07-01)
  • MD.3 (2024-07-01)
  • MD.3.1 (2024-07-01)
  • LK.2 (2024-07-03)
  • LK.2.1 (2024-07-03)
  • JN.1.7.8 (2024-07-03)
  • JN.1.50.2 (2024-07-03)
  • ME.1 (2024-07-03)
  • LF.5 (2024-07-10)
  • JN.1.48.3 (2024-07-10)
  • KS.1.3 (2024-07-10)
  • JN.1.65 (2024-07-10)
  • JN.1.65.1 (2024-07-10)
  • MF.1 (2024-07-10)
  • MF.2 (2024-07-10)
  • KP.3.3.2 (2024-07-10)
  • MG.1 (2024-07-10)
  • KP.4.2.3 (2024-07-10)
  • KP.2.17 (2024-07-10)
  • LB.1.3.2 (2024-07-10)
  • MH.1 (2024-07-10)
  • LB.1.8 (2024-07-10)
  • JN.1.7.9 (2024-07-10)
  • MJ.1 (2024-07-10)
  • KP.3.1.6 (2024-07-12)
  • MK.1 (2024-07-12)
  • MK.2 (2024-07-12)
  • KP.3.4.1 (2024-07-12)
  • KP.3.3.3 (2024-07-12)
  • ML.1 (2024-07-12)
  • ML.2 (2024-07-12)
  • MM.1 (2024-07-12)
  • MM.2 (2024-07-12)
  • JN.1.66 (2024-07-12)
  • MN.1 (2024-07-12)
  • KP.3.5 (2024-07-12)
  • LB.1.4.1 (2024-07-13)
  • LB.1.7.1 (2024-07-13)
  • LB.1.7.2 (2024-07-13)
  • LB.1.7.3 (2024-07-13)

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

  • Include newly designated Nextstrain clade 24C (KP.3)
  • All 84 Pango lineages designated between 2024-06-11 and 2024-07-14 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
  • BA.2.86.7 (2024-06-13)
  • XDZ (2024-06-14)
  • JN.1.1.10 (2024-06-14)
  • JN.1.63 (2024-06-14)
  • JN.1.63.1 (2024-06-14)
  • XEA (2024-06-14)
  • XEB (2024-06-14)
  • XDP.2 (2024-06-14)
  • XDP.3 (2024-06-14)
  • LV.1 (2024-06-14)
  • LV.2 (2024-06-14)
  • LE.1.3 (2024-06-14)
  • LE.1.3.1 (2024-06-14)
  • JN.1.58.3 (2024-06-14)
  • KP.4.1.1 (2024-06-17)
  • KP.4.1.2 (2024-06-17)
  • KP.4.1.3 (2024-06-17)
  • LW.1 (2024-06-17)
  • LP.3 (2024-06-17)
  • KP.3.1.5 (2024-06-17)
  • KP.1.1.5 (2024-06-17)
  • XDD.3 (2024-06-29)
  • LF.3.1.1 (2024-06-29)
  • LB.1.3.1 (2024-06-29)
  • KP.2.3.4 (2024-06-29)
  • JN.1.18.6 (2024-06-29)
  • LY.2 (2024-06-29)
  • LY.1 (2024-06-29)
  • JN.1.18.7 (2024-06-29)
  • LZ.1 (2024-06-29)
  • LZ.1.1 (2024-06-29)
  • MA.1 (2024-06-29)
  • MB.1 (2024-06-29)
  • MB.1.1 (2024-06-29)
  • LP.1.1 (2024-06-29)
  • LF.4 (2024-06-29)
  • LF.4.1 (2024-06-29)
  • KP.3.3.1 (2024-06-29)
  • MC.1 (2024-06-29)
  • LU.2 (2024-07-01)
  • JN.1.64 (2024-07-01)
  • JN.1.64.1 (2024-07-01)
  • MD.1 (2024-07-01)
  • MD.1.1 (2024-07-01)
  • MD.2 (2024-07-01)
  • MD.3 (2024-07-01)
  • MD.3.1 (2024-07-01)
  • LK.2 (2024-07-03)
  • LK.2.1 (2024-07-03)
  • JN.1.7.8 (2024-07-03)
  • JN.1.50.2 (2024-07-03)
  • ME.1 (2024-07-03)
  • LF.5 (2024-07-10)
  • JN.1.48.3 (2024-07-10)
  • KS.1.3 (2024-07-10)
  • JN.1.65 (2024-07-10)
  • JN.1.65.1 (2024-07-10)
  • MF.1 (2024-07-10)
  • MF.2 (2024-07-10)
  • KP.3.3.2 (2024-07-10)
  • MG.1 (2024-07-10)
  • KP.4.2.3 (2024-07-10)
  • KP.2.17 (2024-07-10)
  • LB.1.3.2 (2024-07-10)
  • MH.1 (2024-07-10)
  • LB.1.8 (2024-07-10)
  • JN.1.7.9 (2024-07-10)
  • MJ.1 (2024-07-10)
  • KP.3.1.6 (2024-07-12)
  • MK.1 (2024-07-12)
  • MK.2 (2024-07-12)
  • KP.3.4.1 (2024-07-12)
  • KP.3.3.3 (2024-07-12)
  • ML.1 (2024-07-12)
  • ML.2 (2024-07-12)
  • MM.1 (2024-07-12)
  • MM.2 (2024-07-12)
  • JN.1.66 (2024-07-12)
  • MN.1 (2024-07-12)
  • KP.3.5 (2024-07-12)
  • LB.1.4.1 (2024-07-13)
  • LB.1.7.1 (2024-07-13)
  • LB.1.7.2 (2024-07-13)
  • LB.1.7.3 (2024-07-13)

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

  • Include newly designated Nextstrain clade 24C (KP.3)
  • All 84 Pango lineages designated between 2024-06-11 and 2024-07-14 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
  • BA.2.86.7 (2024-06-13)
  • XDZ (2024-06-14)
  • JN.1.1.10 (2024-06-14)
  • JN.1.63 (2024-06-14)
  • JN.1.63.1 (2024-06-14)
  • XEA (2024-06-14)
  • XEB (2024-06-14)
  • XDP.2 (2024-06-14)
  • XDP.3 (2024-06-14)
  • LV.1 (2024-06-14)
  • LV.2 (2024-06-14)
  • LE.1.3 (2024-06-14)
  • LE.1.3.1 (2...
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Assets 7
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2024-07-03--08-29-55Z

03 Jul 08:30
@github-actions github-actions
2024-07-03--08-29-55Z
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Compare
Choose a tag to compare
2024-07-03--08-29-55Z

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

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

Added configuration of current and recent vaccine strains as 'reference nodes' on the reference tree, against which query sequences can be compared. This feature is in addition to the new 'compare to clade founder' feature, allowing to compare each query sequence to the most ancestral node of a clade or lineage.

The datasets themselves remain unchanged.

See Nextclade documentation for more details about 'relative mutations' functionality.

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

Added configuration of current and recent vaccine strains as 'reference nodes' on the reference tree, against which query sequences can be compared. This feature is in addition to the new 'compare to clade founder' feature, allowing to compare each query sequence to the most ancestral node of a clade or lineage.

The datasets themselves remain unchanged.

See Nextclade documentation for more details about 'relative mutations' functionality.

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

Added configuration of current and recent vaccine strains as 'reference nodes' on the reference tree, against which query sequences can be compared. This feature is in addition to the new 'compare to clade founder' feature, allowing to compare each query sequence to the most ancestral node of a clade or lineage.

The datasets themselves remain unchanged.

See Nextclade documentation for more details about 'relative mutations' functionality.

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

Added configuration of current and recent vaccine strains as 'reference nodes' on the reference tree, against which query sequences can be compared. This feature is in addition to the new 'compare to clade founder' feature, allowing to compare each query sequence to the most ancestral node of a clade or lineage.

The datasets themselves remain unchanged.

See Nextclade documentation for more details about 'relative mutations' functionality.

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

Added configuration of current and recent vaccine strains as 'reference nodes' on the reference tree, against which query sequences can be compared. This feature is in addition to the new 'compare to clade founder' feature, allowing to compare each query sequence to the most ancestral node of a clade or lineage.

The datasets themselves remain unchanged.

See Nextclade documentation for more details about 'relative mutations' functionality.

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

  • add representative samples from early pandemic-era clades including 1, 2, 3, 4, 6C, 7, and 8 to improve clade label annotations for older sequences

  • added configuration of current and recent vaccine strains as 'reference nodes' on the reference tree, against which query sequences can be compared. This feature is in addition to the new 'compare to clade founder' feature, allowing to compare each query sequence to the most ancestral node of a clade or lineage. See Nextclade documentation for more details about 'relative mutations' functionality.

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

Added configuration of current and recent vaccine strains as 'reference nodes' on the reference tree, against which query sequences can be compared. This feature is in addition to the new 'compare to clade founder' feature, allowing to compare each query sequence to the most ancestral node of a clade or lineage.

The datasets themselves remain unchanged.

See Nextclade documentation for more details about 'relative mutations' functionality.

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

Added configuration of current and recent vaccine strains as 'reference nodes' on the reference tree, against which query sequences can be compared. This feature is in addition to the new 'compare to clade founder' feature, allowing to compare each query sequence to the most ancestral node of a clade or lineage.

The datasets themselves remain unchanged.

See Nextclade documentation for more details about 'relative mutations' functionality.

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

Added configuration of current and recent vaccine strains as 'reference nodes' on the reference tree, against which query sequences can be compared. This feature is in addition to the new 'compare to clade founder' feature, allowing to compare each query sequence to the most ancestral node of a clade or lineage.

The datasets themselves remain unchanged.

See Nextclade documentation for more details about 'relative mutations' functionality.

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

Added configuration of current and recent vaccine strains as 'reference nodes' on the reference tree, against which query sequences can be compared. This feature is in addition to the new 'compare to clade founder' feature, allowing to compare each query sequence to the most ancestral node of a clade or lineage.

The datasets themselves remain unchanged.

See Nextclade documentation for more details about 'relative mutations' functionality.

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

Added configuration of current and recent vaccine strains as 'reference nodes' on the reference tree, against which query sequences can be compared. This feature is in addition to the new 'compare to clade founder' feature, allowing to compare each query sequence to the most ancestral node of a clade or lineage.

The datasets themselves remain unchanged.

See Nextclade documentation for more details about 'relative mutations' functionality.

Assets 13
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2024-06-18--19-09-40Z

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This release contains changes for datasets:

  • Dengue virus All serotypes (nextstrain/dengue/all)

Dengue virus All serotypes (nextstrain/dengue/all)

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 3
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2024-06-13--23-42-47Z

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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)

  • Labelled mutations added for Nextstrain clades 24A (JN.1) and 24B (JN.1.11.1)
  • All 172 Pango lineages designated between 2024-04-13 and 2024-06-10 are now included, unfold below to see a list of all newly included lineages with their designation dates:
  • Fixed a bug that made amino acid gaps on the reference tree be left-aligned instead of right-aligned. This only affected the display of mutations on branches in tree view. The bug existed since switching the default gap alignment from right to left in nextclade v2.
Newly included lineages, with designation date in parentheses
  • KP.4 (2024-04-15)
  • KP.4.1 (2024-04-15)
  • KP.4.2 (2024-04-15)
  • KP.1.2 (2024-04-15)
  • KP.2.3 (2024-04-15)
  • JN.1.47 (2024-04-15)
  • JN.1.47.1 (2024-04-15)
  • JN.1.47.2 (2024-04-15)
  • JN.1.16.2 (2024-04-15)
  • LA.1 (2024-04-15)
  • LA.2 (2024-04-15)
  • JN.1.9.2 (2024-04-15)
  • LB.2 (2024-04-15)
  • JN.1.7.4 (2024-04-15)
  • JN.1.24.1 (2024-04-15)
  • LC.1 (2024-04-15)
  • JN.1.32.1 (2024-04-15)
  • KW.1.2 (2024-04-15)
  • JN.1.8.4 (2024-04-15)
  • JN.1.48 (2024-04-15)
  • JN.1.48.1 (2024-04-15)
  • LB.1 (2024-04-16)
  • XDW (2024-04-18)
  • XDQ.2 (2024-04-18)
  • XDQ.3 (2024-04-18)
  • XDQ.1.1 (2024-05-15)
  • XDK.1.1 (2024-05-15)
  • XDK.1.2 (2024-05-15)
  • XDK.2 (2024-05-15)
  • XDK.3 (2024-05-15)
  • XDR.1 (2024-05-15)
  • KP.2.4 (2024-05-15)
  • KP.2.5 (2024-05-15)
  • KP.2.6 (2024-05-15)
  • KP.2.7 (2024-05-15)
  • KP.2.3.1 (2024-05-15)
  • KP.4.2.1 (2024-05-15)
  • KP.2.8 (2024-05-15)
  • KP.2.9 (2024-05-15)
  • KP.2.10 (2024-05-15)
  • KP.2.11 (2024-05-15)
  • KP.2.12 (2024-05-15)
  • LD.1 (2024-05-15)
  • JN.1.48.2 (2024-05-15)
  • KP.1.1.2 (2024-05-15)
  • LE.1 (2024-05-15)
  • LE.1.1 (2024-05-15)
  • LE.1.2 (2024-05-15)
  • LE.2 (2024-05-15)
  • LF.1 (2024-05-15)
  • LF.1.1 (2024-05-15)
  • JN.1.42.2 (2024-05-15)
  • JN.1.49 (2024-05-15)
  • JN.1.49.1 (2024-05-15)
  • JN.1.49.2 (2024-05-15)
  • KW.1.1.1 (2024-05-15)
  • LG.1 (2024-05-15)
  • JN.1.39.1 (2024-05-15)
  • JN.1.39.2 (2024-05-16)
  • KP.5 (2024-05-16)
  • KP.3.1 (2024-05-16)
  • KP.3.2 (2024-05-16)
  • KP.3.3 (2024-05-16)
  • JN.1.39.3 (2024-05-16)
  • JN.15 (2024-05-16)
  • JN.3.3 (2024-05-16)
  • JN.16 (2024-05-16)
  • JN.17 (2024-05-16)
  • JN.11.1 (2024-05-16)
  • BA.2.86.6 (2024-05-16)
  • JN.18 (2024-05-16)
  • JQ.2.1.1 (2024-05-16)
  • JN.19 (2024-05-16)
  • JN.1.1.8 (2024-05-17)
  • KP.2.13 (2024-05-17)
  • JN.1.50 (2024-05-18)
  • JN.1.23.1 (2024-05-28)
  • JN.1.29.1 (2024-05-28)
  • JN.1.18.3 (2024-05-28)
  • JN.1.18.4 (2024-05-28)
  • LH.1 (2024-05-28)
  • LH.2 (2024-05-28)
  • KP.1.1.3 (2024-05-28)
  • KP.3.1.1 (2024-05-28)
  • KP.2.14 (2024-05-28)
  • JN.1.51 (2024-05-28)
  • JN.1.51.1 (2024-05-28)
  • LJ.1 (2024-05-28)
  • LF.2 (2024-05-28)
  • JN.1.52 (2024-05-28)
  • JN.1.7.5 (2024-05-28)
  • LK.1 (2024-05-28)
  • JN.1.50.1 (2024-05-28)
  • LF.3 (2024-05-28)
  • KP.4.2.2 (2024-05-28)
  • XDK.4 (2024-05-28)
  • XDK.4.1 (2024-05-28)
  • XDK.5 (2024-05-28)
  • XDK.6 (2024-05-28)
  • LL.1 (2024-05-28)
  • LM.1 (2024-05-28)
  • KS.1.1 (2024-05-28)
  • JN.1.53 (2024-05-28)
  • JN.1.53.1 (2024-05-28)
  • LN.1 (2024-05-28)
  • LN.1.1 (2024-05-28)
  • JN.1.54 (2024-05-28)
  • JN.1.54.1 (2024-05-28)
  • LP.1 (2024-05-28)
  • KP.3.4 (2024-05-29)
  • KP.3.2.1 (2024-05-29)
  • KP.2.15 (2024-05-30)
  • KR.1.1 (2024-05-30)
  • KR.1.2 (2024-05-30)
  • KR.3 (2024-05-30)
  • KR.4 (2024-05-30)
  • KR.5 (2024-05-30)
  • KS.1.2 (2024-05-30)
  • JN.1.55 (2024-05-30)
  • JN.1.55.1 (2024-05-30)
  • JN.1.55.2 (2024-05-30)
  • KP.3.2.2 (2024-05-30)
  • JN.1.56 (2024-05-31)
  • JN.1.56.1 (2024-05-31)
  • JN.1.44.1 (2024-05-31)
  • LB.1.1 (2024-06-04)
  • LB.1.2 (2024-06-04)
  • LB.1.2.1 (2024-06-04)
  • LB.1.3 (2024-06-04)
  • LB.1.4 (2024-06-04)
  • LB.1.5 (2024-06-04)
  • LB.1.6 (2024-06-04)
  • KP.2.3.2 (2024-06-04)
  • KP.2.16 (2024-06-04)
  • LF.3.1 (2024-06-04)
  • KP.3.1.2 (2024-06-04)
  • KP.3.1.3 (2024-06-04)
  • KP.3.1.4 (2024-06-04)
  • KP.3.2.3 (2024-06-04)
  • KP.3.2.4 (2024-06-04)
  • LB.1.7 (2024-06-04)
  • LF.1.1.1 (2024-06-04)
  • KP.1.1.4 (2024-06-04)
  • LP.2 (2024-06-04)
  • XDY (2024-06-04)
  • LQ.1 (2024-06-04)
  • LQ.1.1 (2024-06-04)
  • LQ.2 (2024-06-04)
  • LQ.3 (2024-06-04)
  • JN.1.4.8 (2024-06-04)
  • JN.1.7.6 (2024-06-04)
  • JN.1.57 (2024-06-04)
  • JN.1.57.1 (2024-06-04)
  • JN.1.58 (2024-06-04)
  • JN.1.58.1 (2024-06-04)
  • JN.1.58.2 (2024-06-04)
  • LR.1 (2024-06-04)
  • LR.2 (2024-06-04)
  • JN.1.59 (2024-06-05)
  • JN.1.7.7 (2024-06-05)
  • JN.1.60 (2024-06-05)
  • JN.1.61 (2024-06-05)
  • JN.1.18.5 (2024-06-07)
  • LS.1 (2024-06-07)
  • KP.2.3.3 (2024-06-07)
  • JN.1.62 (2024-06-08)
  • KP.3.2.5 (2024-06-09)
  • LT.1 (2024-06-10)
  • JN.1.1.9 (2024-06-10)
  • JN.1.16.3 (2024-06-10)
  • JN.1.15.1 (2024-06-10)
  • LU.1 (2024-06-10)

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

  • Labelled mutations added for Nextstrain clades 24A (JN.1) and 24B (JN.1.11.1)
  • All 172 Pango lineages designated between 2024-04-13 and 2024-06-10 are now included, unfold below to see a list of all newly included lineages with their designation dates:
  • Fixed a bug that made amino acid gaps on the reference tree be left-aligned instead of right-aligned. This only affected the display of mutations on branches in tree view. The bug existed since switching the default gap alignment from right to left in nextclade v2.
Newly included lineages, with designation date in parentheses
  • KP.4 (2024-04-15)
  • KP.4.1 (2024-04-15)
  • KP.4.2 (2024-04-15)
  • KP.1.2 (2024-04-15)
  • KP.2.3 (2024-04-15)
  • JN.1.47 (2024-04-15)
  • JN.1.47.1 (2024-04-15)
  • JN.1.47.2 (2024-04-15)
  • JN.1.16.2 (2024-04-15)
  • LA.1 (2024-04-15)
  • LA.2 (2024-04-15)
  • JN.1.9.2 (2024-04-15)
  • LB.2 (2024-04-15)
  • JN.1.7.4 (2024-04-15)
  • JN.1.24.1 (2024-04-15)
  • LC.1 (2024-04-15)
  • JN.1.32.1 (2024-04-15)
  • KW.1.2 (2024-04-15)
  • JN.1.8.4 (2024-04-15)
  • JN.1.48 (2024-04-15)
  • JN.1.48.1 (2024-04-15)
  • LB.1 (2024-04-16)
  • XDW (2024-04-18)
  • XDQ.2 (2024-04-18)
  • XDQ.3 (2024-04-18)
  • XDQ.1.1 (2024-05-15)
  • XDK.1.1 (2024-05-15)
  • XDK.1.2 (2024-05-15)
  • XDK.2 (2024-05-15)
  • XDK.3 (2024-05-15)
  • XDR.1 (2024-05-15)
  • KP.2.4 (2024-05-15)
  • KP.2.5 (2024-05-15)
  • KP.2.6 (2024-05-15)
  • KP.2.7 (2024-05-15)
  • KP.2.3.1 (2024-05-15)
  • KP.4.2.1 (2024-05-15)
  • KP.2.8 (2024-05-15)
  • KP.2.9 (2024-05-15)
  • KP.2.10 (2024-05-15)
  • KP.2.11 (2024-05-15)
  • KP.2.12 (2024-05-15)
  • LD.1 (2024-05-15)
  • JN.1.48.2 (2024-05-15)
  • KP.1.1.2 (2024-05-15)
  • LE.1 (2024-05-15)
  • LE.1.1 (2024-05-15)
  • LE.1.2 (2024-05-15)
  • LE.2 (2024-05-15)
  • LF.1 (2024-05-15)
  • LF.1.1 (2024-05-15)
  • JN.1.42.2 (2024-05-15)
  • JN.1.49 (2024-05-15)
  • JN.1.49.1 (2024-05-15)
  • JN.1.49.2 (2024-05-15)
  • KW.1.1.1 (2024-05-15)
  • LG.1 (2024-05-15)
  • JN.1.39.1 (2024-05-15)
  • JN.1.39.2 (2024-05-16)
  • KP.5 (2024-05-16)
  • KP.3.1 (2024-05-16)
  • KP.3.2 (2024-05-16)
  • KP.3.3 (2024-05-16)
  • JN.1.39.3 (2024-05-16)
  • JN.15 (2024-05-16)
  • JN.3.3 (2024-05-16)
  • JN.16 (2024-05-16)
  • JN.17 (2024-05-16)
  • JN.11.1 (2024-05-16)
  • BA.2.86.6 (2024-05-16)
  • JN.18 (2024-05-16)
  • JQ.2.1.1 (2024-05-16)
  • JN.19 (2024-05-16)
  • JN.1.1.8 (2024-05-17)
  • KP.2.13 (2024-05-17)
  • JN.1.50 (2024-05-18)
  • JN.1.23.1 (2024-05-28)
  • JN.1.29.1 (2024-05-28)
  • JN.1.18.3 (2024-05-28)
  • JN.1.18.4 (2024-05-28)
  • LH.1 (2024-05-28)
  • LH.2 (2024-05-28)
  • KP.1.1.3 (2024-05-28)
  • KP.3.1.1 (2024-05-28)
  • KP.2.14 (2024-05-28)
  • JN.1.51 (2024-05-28)
  • JN.1.51.1 (2024-05-28)
  • LJ.1 (2024-05-28)
  • LF.2 (2024-05-28)
  • JN.1.52 (2024-05-28)
  • JN.1.7.5 (2024-05-28)
  • LK.1 (2024-05-28)
  • JN.1.50.1 (2024-05-28)
  • LF.3 (2024-05-28)
  • KP.4.2.2 (2024-05-28)
  • XDK.4 (2024-05-28)
  • XDK.4.1 (2024-05-28)
  • XDK.5 (2024-05-28)
  • XDK.6 (2024-05-28)
  • LL.1 (2024-05-28)
  • LM.1 (2024-05-28)
  • KS.1.1 (2024-05-28)
  • JN.1.53 (2024-05-28)
  • JN.1.53.1 (2024-05-28)
  • LN.1 (2024-05-28)
  • LN.1.1 (2024-05-28)
  • JN.1.54 (2024-05-28)
  • JN.1.54.1 (2024-05-28)
  • LP.1 (2024-05-28)
  • KP.3.4 (2024-05-29)
  • KP.3.2.1 (2024-05-29)
  • KP.2.15 (2024-05-30)
  • KR.1.1 (2024-05-30)
  • KR.1.2 (2024-05-30)
  • KR.3 (2024-05-30)
  • KR.4 (2024-05-30)
  • KR.5 (2024-05-30)
  • KS.1.2 (2024-05-30)
  • JN.1.55 (2024-05-30)
  • JN.1.55.1 (2024-05-30)
  • JN.1.55.2 (2024-05-30)
  • KP.3.2.2 (2024-05-30)
  • JN.1.56 (2024-05-31)
  • JN.1.56.1 (2024-05-31)
  • JN.1.44.1 (2024-05-31)
  • LB.1.1 (2024-06-04)
  • LB.1.2 (2024-06-04)
  • LB.1.2.1 (2024-06-04)
  • LB.1.3 (2024-06-04)
  • LB.1.4 (2024-06-04)
  • LB.1.5 (2024-06-04)
  • LB.1.6 (2024-06-04)
  • KP.2.3.2 (2024-06-04)
  • KP.2.16 (2024-06-04)
  • LF.3.1 (2024-06-04)
  • KP.3.1.2 (2024-06-04)
  • KP.3.1.3 (2024-06-04)
  • KP.3.1.4 (2024-06-04)
  • KP.3.2.3 (2024-06-04)
  • KP.3.2.4 (2024-06-04)
  • LB.1.7 (2024-06-04)
  • LF.1.1.1 (2024-06-04)
  • KP.1.1.4 (2024-06-04)
  • LP.2 (2024-06-04)
  • XDY (2024-06-04)
  • LQ.1 (2024-06-04)
  • LQ.1.1 (2024-06-04)
  • LQ.2 (2024-06-04)
  • LQ.3 (2024-06-04)
  • JN.1.4.8 (2024-06-04)
  • JN.1.7.6 (2024-06-04)
  • JN.1.57 (2024-06-04)
  • JN.1.57.1 (2024-06-04)
  • JN.1.58 (2024-06-04)
  • JN.1.58.1 (2024-06-04)
  • JN.1.58.2 (2024-06-04)
  • LR.1 (2024-06-04)
  • LR.2 (2024-06-04)
  • JN.1.59 (2024-06-05)
  • JN.1.7.7 (2024-06-05)
  • JN.1.60 (2024-06-05)
  • JN.1.61 (2024-06-05)
  • JN.1.18.5 (2024-06-07)
  • LS.1 (2024-06-07)
  • KP.2.3.3 (2024-06-07)
  • JN.1.62 (2024-06-08)
  • KP.3.2.5 (2024-06-09)
  • LT.1 (2024-06-10)
  • JN.1.1.9 (2024-06-10)
  • JN.1.16.3 (2024-06-10)
  • JN.1.15.1 (2024-06-10)
  • LU.1 (2024-06-10)

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

  • Labelled mutations added for Nextstrain clades 24A (JN.1) and 24B (JN.1.11.1)
  • All 172 Pango lineages designated between 2024-04-13 and 2024-06-10 are now included, unfold below to see a list of all newly included lineages with their designation dates:
  • Fixed a bug that made amino acid gaps on the reference tree be left-aligned instead of right-aligned. This only affected the display of mutations on branches in tree view. The bug existed since s...
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Assets 7
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2024-06-07--06-48-19Z

07 Jun 06:48
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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
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2024-06-04--16-27-23Z

04 Jun 16:27
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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
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2024-05-08--11-39-52Z

08 May 11:40
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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
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2024-04-25--01-03-07Z

25 Apr 01:03
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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
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2024-04-19--07-50-39Z

19 Apr 07:50
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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
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