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Releases: nextstrain/nextclade_data

2024-10-17--16-48-48Z

17 Oct 16:49
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2024-10-17--16-48-48Z
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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)
  • DENV-1 (community/v-gen-lab/dengue/denv1)
  • DENV-2 (community/v-gen-lab/dengue/denv2)
  • DENV-3 (community/v-gen-lab/dengue/denv3)
  • DENV-4 (community/v-gen-lab/dengue/denv4)

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

  • Add newly designated Nextstrain clades 24F (XEC) and 24G (KP.2.3)
  • Add all 4 Pango lineages designated between 2024-09-26 and 2024-10-14. Unfold below to see a list of all newly included lineages with their designation dates:
Newly included lineages, with designation date in parentheses
  • XEH (2024-09-28)
  • XEJ (2024-09-28)
  • XEC.2 (2024-09-28)
  • XEK (2024-09-28)

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

  • Add newly designated Nextstrain clades 24F (XEC) and 24G (KP.2.3)
  • Add all 4 Pango lineages designated between 2024-09-26 and 2024-10-14. Unfold below to see a list of all newly included lineages with their designation dates:
Newly included lineages, with designation date in parentheses
  • XEH (2024-09-28)
  • XEJ (2024-09-28)
  • XEC.2 (2024-09-28)
  • XEK (2024-09-28)

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

  • Add newly designated Nextstrain clades 24F (XEC) and 24G (KP.2.3)
  • Add all 4 Pango lineages designated between 2024-09-26 and 2024-10-14. Unfold below to see a list of all newly included lineages with their designation dates:
Newly included lineages, with designation date in parentheses
  • XEH (2024-09-28)
  • XEJ (2024-09-28)
  • XEC.2 (2024-09-28)
  • XEK (2024-09-28)

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

  • Add newly designated Nextstrain clades 24F (XEC) and 24G (KP.2.3)
  • Add all 4 Pango lineages designated between 2024-09-26 and 2024-10-14. Unfold below to see a list of all newly included lineages with their designation dates:
Newly included lineages, with designation date in parentheses
  • XEH (2024-09-28)
  • XEJ (2024-09-28)
  • XEC.2 (2024-09-28)
  • XEK (2024-09-28)

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

  • Add newly designated Nextstrain clades 24F (XEC) and 24G (KP.2.3)
  • Add all 4 Pango lineages designated between 2024-09-26 and 2024-10-14. Unfold below to see a list of all newly included lineages with their designation dates:
Newly included lineages, with designation date in parentheses
  • XEH (2024-09-28)
  • XEJ (2024-09-28)
  • XEC.2 (2024-09-28)
  • XEK (2024-09-28)

DENV-1 (community/v-gen-lab/dengue/denv1)

  • Update of the reference tree to avoid subclassification errors detected in other tools; We have added more representative sequences to some of the lineages.

DENV-2 (community/v-gen-lab/dengue/denv2)

  • Update of the reference tree to avoid subclassification errors detected in other tools; We have added more representative sequences to some of the lineages.

DENV-3 (community/v-gen-lab/dengue/denv3)

  • Update of the reference tree to avoid subclassification errors detected in other tools; We have added more representative sequences to some of the lineages.

DENV-4 (community/v-gen-lab/dengue/denv4)

  • Update of the reference tree to avoid subclassification errors detected in other tools; We have added more representative sequences to some of the lineages.
Assets 11
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2024-09-25--21-50-30Z

25 Sep 21:50
@github-actions github-actions
2024-09-25--21-50-30Z
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2024-09-25--21-50-30Z

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 clades 24D (XDV.1) and 24E (KP.3.1.1)
  • All 113 Pango lineages designated between 2024-07-15 and 2024-09-25 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
  • XEC (2024-08-07)
  • KP.2.3.5 (2024-08-07)
  • KP.2.3.6 (2024-08-07)
  • LP.4 (2024-08-07)
  • LP.1.2 (2024-08-07)
  • LB.1.2.2 (2024-08-07)
  • LB.1.2.3 (2024-08-07)
  • KP.2.18 (2024-08-07)
  • KP.2.14.1 (2024-08-07)
  • MC.2 (2024-08-08)
  • MC.2.1 (2024-08-08)
  • KR.1.3 (2024-08-08)
  • MP.1 (2024-08-08)
  • MP.1.1 (2024-08-08)
  • JQ.2.1.2 (2024-08-08)
  • MC.4 (2024-08-08)
  • MC.3 (2024-08-08)
  • LB.1.3.3 (2024-08-08)
  • KP.2.15.1 (2024-08-08)
  • KP.3.1.7 (2024-08-08)
  • MQ.1 (2024-08-08)
  • MQ.2 (2024-08-08)
  • KP.3.3.4 (2024-08-08)
  • MR.1 (2024-08-08)
  • MK.3 (2024-08-08)
  • XED (2024-08-08)
  • LZ.2 (2024-08-12)
  • XEC.1 (2024-08-14)
  • MS.1 (2024-08-15)
  • KU.2.1 (2024-08-15)
  • KU.2.2 (2024-08-15)
  • MA.1.1 (2024-08-15)
  • MA.1.1.1 (2024-08-15)
  • JN.1.18.8 (2024-08-15)
  • JN.1.59.1 (2024-08-15)
  • JN.1.16.4 (2024-08-15)
  • LU.2.1 (2024-08-15)
  • LU.2.1.1 (2024-08-15)
  • MT.1 (2024-08-15)
  • KP.2.19 (2024-08-15)
  • LF.6 (2024-08-15)
  • LR.3 (2024-08-15)
  • XDV.1.1 (2024-08-15)
  • XDV.1.2 (2024-08-15)
  • XDV.1.2.1 (2024-08-15)
  • XDV.1.3 (2024-08-15)
  • XDV.1.4 (2024-08-15)
  • XDV.1.5 (2024-08-15)
  • XDV.1.6 (2024-08-15)
  • LF.7 (2024-08-15)
  • MU.1 (2024-08-15)
  • JN.1.4.9 (2024-08-15)
  • JN.1.38.1 (2024-08-15)
  • MC.5 (2024-08-15)
  • MC.6 (2024-08-15)
  • MC.7 (2024-08-15)
  • MC.8 (2024-08-15)
  • MC.8.1 (2024-08-15)
  • MC.9 (2024-08-15)
  • MC.10 (2024-08-15)
  • MC.11 (2024-08-15)
  • MC.11.1 (2024-08-15)
  • MC.12 (2024-08-15)
  • MC.13 (2024-08-15)
  • MC.13.1 (2024-08-15)
  • MC.14 (2024-08-15)
  • MC.15 (2024-08-15)
  • MC.16 (2024-08-15)
  • MB.1.1.1 (2024-08-15)
  • MV.1 (2024-08-15)
  • KP.2.20 (2024-08-15)
  • KP.2.20.1 (2024-08-15)
  • JN.1.67 (2024-08-15)
  • JN.1.67.1 (2024-08-15)
  • XEF (2024-08-15)
  • KP.2.22 (2024-08-16)
  • KP.2.24 (2024-08-16)
  • KP.2.25 (2024-08-16)
  • KP.2.26 (2024-08-16)
  • KR.4.1 (2024-08-16)
  • KP.6 (2024-08-16)
  • XEG (2024-08-16)
  • KP.2.3.7 (2024-08-16)
  • MW.1 (2024-08-16)
  • KP.2.23 (2024-08-16)
  • JN.1.68 (2024-08-16)
  • LF.8 (2024-08-16)
  • LF.8.1 (2024-08-16)
  • LF.8.1.1 (2024-08-16)
  • XEE (2024-08-16)
  • MC.17 (2024-08-16)
  • JN.1.16.5 (2024-08-16)
  • LW.1.1 (2024-08-16)
  • LW.1.2 (2024-08-16)
  • KP.3.6 (2024-08-16)
  • LB.1.9 (2024-08-16)
  • KP.3.1.8 (2024-08-16)
  • MY.1 (2024-08-16)
  • XDV.1.7 (2024-08-17)
  • XDV.1.8 (2024-08-17)
  • XDV.1.9 (2024-08-17)
  • XDR.1.1 (2024-08-17)
  • XDR.1.2 (2024-08-17)
  • XDV.1.10 (2024-08-17)
  • XDV.1.11 (2024-08-17)
  • LU.2.2 (2024-08-20)
  • LB.1.4.3 (2024-08-24)
  • LF.9 (2024-08-27)
  • LF.9.1 (2024-08-27)
  • XDV.1.7.1 (2024-09-05)
  • XDV.1.9.1 (2024-09-05)
  • LZ.2.1 (2024-09-05)
  • MZ.1 (2024-09-05)

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

  • Include newly designated Nextstrain clades 24D (XDV.1) and 24E (KP.3.1.1)
  • All 113 Pango lineages designated between 2024-07-15 and 2024-09-25 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
  • XEC (2024-08-07)
  • KP.2.3.5 (2024-08-07)
  • KP.2.3.6 (2024-08-07)
  • LP.4 (2024-08-07)
  • LP.1.2 (2024-08-07)
  • LB.1.2.2 (2024-08-07)
  • LB.1.2.3 (2024-08-07)
  • KP.2.18 (2024-08-07)
  • KP.2.14.1 (2024-08-07)
  • MC.2 (2024-08-08)
  • MC.2.1 (2024-08-08)
  • KR.1.3 (2024-08-08)
  • MP.1 (2024-08-08)
  • MP.1.1 (2024-08-08)
  • JQ.2.1.2 (2024-08-08)
  • MC.4 (2024-08-08)
  • MC.3 (2024-08-08)
  • LB.1.3.3 (2024-08-08)
  • KP.2.15.1 (2024-08-08)
  • KP.3.1.7 (2024-08-08)
  • MQ.1 (2024-08-08)
  • MQ.2 (2024-08-08)
  • KP.3.3.4 (2024-08-08)
  • MR.1 (2024-08-08)
  • MK.3 (2024-08-08)
  • XED (2024-08-08)
  • LZ.2 (2024-08-12)
  • XEC.1 (2024-08-14)
  • MS.1 (2024-08-15)
  • KU.2.1 (2024-08-15)
  • KU.2.2 (2024-08-15)
  • MA.1.1 (2024-08-15)
  • MA.1.1.1 (2024-08-15)
  • JN.1.18.8 (2024-08-15)
  • JN.1.59.1 (2024-08-15)
  • JN.1.16.4 (2024-08-15)
  • LU.2.1 (2024-08-15)
  • LU.2.1.1 (2024-08-15)
  • MT.1 (2024-08-15)
  • KP.2.19 (2024-08-15)
  • LF.6 (2024-08-15)
  • LR.3 (2024-08-15)
  • XDV.1.1 (2024-08-15)
  • XDV.1.2 (2024-08-15)
  • XDV.1.2.1 (2024-08-15)
  • XDV.1.3 (2024-08-15)
  • XDV.1.4 (2024-08-15)
  • XDV.1.5 (2024-08-15)
  • XDV.1.6 (2024-08-15)
  • LF.7 (2024-08-15)
  • MU.1 (2024-08-15)
  • JN.1.4.9 (2024-08-15)
  • JN.1.38.1 (2024-08-15)
  • MC.5 (2024-08-15)
  • MC.6 (2024-08-15)
  • MC.7 (2024-08-15)
  • MC.8 (2024-08-15)
  • MC.8.1 (2024-08-15)
  • MC.9 (2024-08-15)
  • MC.10 (2024-08-15)
  • MC.11 (2024-08-15)
  • MC.11.1 (2024-08-15)
  • MC.12 (2024-08-15)
  • MC.13 (2024-08-15)
  • MC.13.1 (2024-08-15)
  • MC.14 (2024-08-15)
  • MC.15 (2024-08-15)
  • MC.16 (2024-08-15)
  • MB.1.1.1 (2024-08-15)
  • MV.1 (2024-08-15)
  • KP.2.20 (2024-08-15)
  • KP.2.20.1 (2024-08-15)
  • JN.1.67 (2024-08-15)
  • JN.1.67.1 (2024-08-15)
  • XEF (2024-08-15)
  • KP.2.22 (2024-08-16)
  • KP.2.24 (2024-08-16)
  • KP.2.25 (2024-08-16)
  • KP.2.26 (2024-08-16)
  • KR.4.1 (2024-08-16)
  • KP.6 (2024-08-16)
  • XEG (2024-08-16)
  • KP.2.3.7 (2024-08-16)
  • MW.1 (2024-08-16)
  • KP.2.23 (2024-08-16)
  • JN.1.68 (2024-08-16)
  • LF.8 (2024-08-16)
  • LF.8.1 (2024-08-16)
  • LF.8.1.1 (2024-08-16)
  • XEE (2024-08-16)
  • MC.17 (2024-08-16)
  • JN.1.16.5 (2024-08-16)
  • LW.1.1 (2024-08-16)
  • LW.1.2 (2024-08-16)
  • KP.3.6 (2024-08-16)
  • LB.1.9 (2024-08-16)
  • KP.3.1.8 (2024-08-16)
  • MY.1 (2024-08-16)
  • XDV.1.7 (2024-08-17)
  • XDV.1.8 (2024-08-17)
  • XDV.1.9 (2024-08-17)
  • XDR.1.1 (2024-08-17)
  • XDR.1.2 (2024-08-17)
  • XDV.1.10 (2024-08-17)
  • XDV.1.11 (2024-08-17)
  • LU.2.2 (2024-08-20)
  • LB.1.4.3 (2024-08-24)
  • LF.9 (2024-08-27)
  • LF.9.1 (2024-08-27)
  • XDV.1.7.1 (2024-09-05)
  • XDV.1.9.1 (2024-09-05)
  • LZ.2.1 (2024-09-05)
  • MZ.1 (2024-09-05)

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

  • Include newly designated Nextstrain clades 24D (XDV.1) and 24E (KP.3.1.1)
  • All 113 Pango lineages designated between 2024-07-15 and 2024-09-25 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
  • XEC (2024-08-07)
  • KP.2.3.5 (2024-08-07)
  • KP.2.3.6 (2024-08-07)
  • LP.4 (2024-08-07)
  • LP.1.2 (2024-08-07)
  • LB.1.2.2 (2024-08-07)
  • LB.1.2.3 (2024-08-07)
  • KP.2.18 (2024-08-07)
  • KP.2.14.1 (2024-08-07)
  • MC.2 (2024-08-08)
  • MC.2.1 (2024-08-08)
  • KR.1.3 (2024-08-08)
  • MP.1 (2024-08-08)
  • MP.1.1 (2024-08-08)
  • JQ.2.1.2 (2024-08-08)
  • MC.4 (2024-08-08)
  • MC.3 (2024-08-08)
  • LB.1.3.3 (2024-08-08)
  • KP.2.15.1 (2024-08-08)
  • KP.3.1.7 (2024-08-08)
  • MQ.1 (2024-08-08)
  • MQ.2 (2024-08-08)
  • KP.3.3.4 (2024-08-08)
  • MR.1 (2024-08-08)
  • MK.3 (2024-08-08)
  • XED (2024-08-08)
  • LZ.2 (2024-08-12)
  • XEC.1 (2024-08-14)
  • MS.1 (2024-08-15)
  • KU.2.1 (2024-08-15)
  • KU.2.2 (2024-08-15)
  • MA.1.1 (2024-08-15)
  • MA.1.1.1 (2024-08-15)
  • JN.1.18.8 (2024-08-15)
  • JN.1.59.1 (2024-08-15)
  • JN.1.16.4 (2024-08-15)
  • LU.2.1 (2024-08-15)
  • LU.2.1.1 (2024-08-15)
  • MT.1 (2024-08-15)
  • KP.2.19 (2024-08-15)
  • LF.6 (2024-08-15)
  • LR.3 (2024-08-15)
  • XDV.1.1 (2024-08-15)
  • XDV.1.2 (2024-08-15)
  • XDV.1.2.1 (2024-08-15)
  • XDV.1.3 (2024-08-15)
  • XDV.1.4 (2024-08-15)
  • XDV.1.5 (2024-08-15)
  • XDV.1.6 (2024-08-15)
  • LF.7 (2024-08-15)
  • MU.1 (2024-08-15)
  • JN.1.4.9 (2024-08-15)
  • JN.1.38.1 (2024-08-15)
  • MC.5 (2024-08-15)
  • MC.6 (2024-08-15)
  • MC.7 (2024-08-15)
  • MC.8 (2024-08-15)
  • MC.8.1 (2024-08-15)
  • MC.9 (2024-08-15)
  • MC.10 (2024-08-15)
  • MC.11 (2024-08-15)
  • MC.11.1 (2024-08-15)
  • MC.12 (2024-08-15)
  • MC.13 (2024-08-15)
  • MC.13.1 (2024-08-15)
  • MC.14 (2024-08-15)
  • MC.15 (2024-08-15)
  • MC.16 (2024-08-15)
  • MB.1.1.1 (2024-08-15)
  • MV.1 (2024-08-15)
  • KP.2.20 (2024-08-15)
  • KP.2.20.1 (2024-08-15)
  • JN.1.67 (2024-08-15)
  • JN.1.67.1 (2024-08-15)
  • XEF (2024-08-15)
  • KP.2.22 (2024-08-16)
  • KP.2.24 (2024-08-16)
  • KP.2.25 (2024-08-16)
  • KP.2.26 (2024-08-16)
  • KR.4.1 (2024-08-16)
  • KP.6 (2024-08-16)
  • XEG (2024-08-16)
  • KP.2.3.7 (2024-08-16)
  • MW.1 (2024-08-16)
  • KP.2.23 (2024-08-16)
  • JN.1.68 (2024-08-16)
  • LF.8 (2024-08-16)
  • LF.8.1 (2024-08-16)
  • LF.8.1.1 (2024-08-16)
  • XEE (2024-08-16)
  • MC.17 (2024-08-16)
  • JN.1.16.5 (2024-08-16)
  • LW.1.1 (2024-08-16)
  • LW.1.2 (2024-08-16)
  • KP.3.6 (2024-08-16)
  • LB.1.9 (2024-08-16)
  • KP.3.1.8 (2024-08-16)
  • MY.1 (2024-08-16)
  • XDV.1.7 (2024-08-17)
  • XDV.1.8 (2024-08-17)
  • XDV.1.9 (2024-08-17)
  • XDR.1.1 (2024-08-17)
  • XDR.1.2 (2024-08-17)
  • XDV.1.10 (2024-08-17)
  • XDV.1.11 (2024-08-17)
  • LU.2.2 (2024-08-20)
  • LB.1.4.3 (2024-08-24)
  • LF.9 (2024-08-27)
  • LF.9.1 (2024-08-27)
  • XDV.1.7.1 (2024-09-05)
  • XDV.1.9.1 (2024-09-05)
  • LZ.2.1 (2024-09-05)
  • MZ.1 (2024-09-05)

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

  • Include newly designated Nextstrain clades 24D (XDV.1) and 24E (KP.3.1.1)
  • All 113 Pango lineages designated between 2024-07-15 and 2024-09-25 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
  • XEC (2024-08-07)
  • KP.2.3.5 (2024-08-07)
  • KP.2.3.6 (2024-08-07)
  • LP.4 (2024-08-07)
  • LP.1.2 (2024-08-07)
  • LB.1.2.2 (2024-08-07)
  • LB.1.2.3 (2024-08-07)
  • KP.2.18 (2024-08-07)
  • KP.2.14.1 (2024-08-07)
  • MC.2 (2024-08-08)
  • MC.2.1 (2024-08-08)
  • KR.1.3 (2024-08-08)
  • MP.1 (2024-08-08)
  • MP.1.1 (2024-08-08)
  • JQ.2.1.2 (2024-08-08)
  • MC.4 (2024-08-08)
  • MC.3 (2024-08-08)
  • LB.1.3.3 (2024-08-08)
  • KP.2.15.1 (2024-08-08)
  • KP.3.1.7 (2024-08-08)
  • MQ.1 (2024-08-08)
  • MQ.2 (2024-08-08)
  • KP.3.3.4 ...
Read more
Assets 7
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2024-08-31--20-44-06Z

31 Aug 20:44
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This release contains changes for datasets:

  • DENV-1 (community/v-gen-lab/dengue/denv1)
  • DENV-2 (community/v-gen-lab/dengue/denv2)
  • DENV-3 (community/v-gen-lab/dengue/denv3)
  • DENV-4 (community/v-gen-lab/dengue/denv4)

DENV-1 (community/v-gen-lab/dengue/denv1)

Initial release of a DENV-1 dataset for Lineage classification!

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

DENV-2 (community/v-gen-lab/dengue/denv2)

Initial release of a DENV-2 dataset for Lineage classification!

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

DENV-3 (community/v-gen-lab/dengue/denv3)

Initial release of a DENV-3 dataset for Lineage classification!

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

DENV-4 (community/v-gen-lab/dengue/denv4)

Initial release of a DENV-4 dataset for Lineage classification!

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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2024-08-27--21-28-04Z

27 Aug 21:28
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This release contains changes for datasets:

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

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

  • Clade Ia and clade Ib are now distinguished
  • Sequences shared via Genbank since 2024 have been added
Assets 3
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2024-08-08--05-08-21Z

08 Aug 05:08
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This release contains changes for datasets:

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

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

Fix numbering of RBD sites it the pathogen.json. The relevant positions were indexed 1-based, when they should have been indexed 0-based.

Assets 3
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2024-08-01--22-31-31Z

01 Aug 22:31
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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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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...
Read more
Assets 7
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2024-07-03--08-29-55Z

03 Jul 08:30
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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

18 Jun 19:09
@github-actions github-actions
2024-06-18--19-09-40Z
ed9e048
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2024-06-18--19-09-40Z

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

13 Jun 23:43
@github-actions github-actions
2024-06-13--23-42-47Z
03703e0
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2024-06-13--23-42-47Z

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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