github nextstrain/nextclade_data 2026-04-14--11-55-23Z
on GitHub

13 hours ago

This release contains changes for datasets:

  • 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/EPI1857216)
  • Influenza A H3N2 NA (nextstrain/flu/h3n2/na/EPI1857215)
  • Influenza B (all) HA (nextstrain/flu/b/ha/KX058884)
  • Influenza B (all) NA (nextstrain/flu/b/na/CY073894)
  • Influenza B Victoria HA (nextstrain/flu/vic/ha/KX058884)
  • Influenza B Victoria NA (nextstrain/flu/vic/na/CY073894)
  • Influenza B Yamagata HA (nextstrain/flu/yam/ha/JN993010)
  • RSV-A (nextstrain/rsv/a/EPI_ISL_412866)
  • RSV-B (nextstrain/rsv/b/EPI_ISL_1653999)
  • Mpox virus (All clades) (nextstrain/mpox/all-clades)
  • Mpox virus (Clade I) (nextstrain/mpox/clade-i)
  • Mpox virus (Clade IIb) (nextstrain/mpox/clade-iib)
  • Mpox virus (Lineage B.1) (nextstrain/mpox/lineage-b.1)
  • Ebola virus (nextstrain/orthoebolavirus/ebov)
  • Sudan virus (nextstrain/orthoebolavirus/sudv)
  • Measles morbillivirus -- complete genome (nextstrain/measles/genome/WHO-2012)
  • Dengue virus All serotypes (nextstrain/dengue/all)
  • Human Metapneumovirus (nextstrain/hmpv/all-clades/NC_039199)
  • Varicella-Zoster Virus (VZV) (nextstrain/herpes/vzv/NC_001348)
  • Rubella virus E1 region (nextstrain/rubella/E1)
  • Mumps MuV Genotypes (SH gene 315nt region) (nextstrain/mumps/sh)
  • Mumps MuV Genotypes (Full genome) (nextstrain/mumps/genome)
  • Rubella (nextstrain/rubella/genome)
  • Influenza A H3N2 PB2 (nextstrain/flu/h3n2/pb2)
  • Influenza A H3N2 PB1 (nextstrain/flu/h3n2/pb1)
  • Influenza A H3N2 PA (nextstrain/flu/h3n2/pa)
  • Influenza A H3N2 HA (nextstrain/flu/h3n2/ha/CY163680)
  • Influenza A H3N2 NP (nextstrain/flu/h3n2/np)
  • Influenza A H3N2 MP (nextstrain/flu/h3n2/mp)
  • Influenza A H3N2 NS (nextstrain/flu/h3n2/ns)
  • Influenza A H1N1pdm PB2 (nextstrain/flu/h1n1pdm/pb2)
  • Influenza A H1N1pdm PB1 (nextstrain/flu/h1n1pdm/pb1)
  • Influenza A H1N1pdm PA (nextstrain/flu/h1n1pdm/pa)
  • Influenza A H1N1pdm HA (nextstrain/flu/h1n1pdm/ha/CY121680)
  • Influenza A H1N1pdm MP (nextstrain/flu/h1n1pdm/mp)
  • Influenza A H1N1pdm NP (nextstrain/flu/h1n1pdm/np)
  • Influenza A H1N1pdm NS (nextstrain/flu/h1n1pdm/ns)
  • West Nile Virus (nextstrain/wnv/all-lineages)
  • Enterovirus D68 (enpen/enterovirus/ev-d68)
  • PRRSV-1 ORF5 (community/isuvdl/mazeller/prrsv1/orf5/yimim2025)
  • PRRSV-2 ORF5 Lineages, Yim-im & Zhang 2023 Microbiol Spectr (community/isuvdl/mazeller/prrsv2/orf5/yimim2023)
  • 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)
  • 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)
  • chikV (community/v-gen-lab/chikV/genotypes)
  • Zika virus (community/itps/zikav)

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

  • Remove empty nucMutLabelMap and legacy nucMutLabelMapReverse
  • add NA clade annotations to tree

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

  • add subclade D.3
  • add HA clade annotations to tree

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

  • Remove empty nucMutLabelMap and legacy nucMutLabelMapReverse

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

  • Move aaMutLabelMap (NAI resistance markers) into mutLabels section
  • Remove legacy nucMutLabelMapReverse

Influenza B (all) HA (nextstrain/flu/b/ha/KX058884)

  • Remove empty nucMutLabelMap and legacy nucMutLabelMapReverse
  • addition of subclade C.3.3
  • inclusion of older sequences that precede the current subclade system

Influenza B (all) NA (nextstrain/flu/b/na/CY073894)

  • Remove empty nucMutLabelMap and legacy nucMutLabelMapReverse
  • inclusion of older sequences that precede the current subclade system

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

  • Remove empty nucMutLabelMap and legacy nucMutLabelMapReverse
  • addition of subclade C.3.3
  • inclusion of older sequences that precede the current subclade system

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

  • Remove empty nucMutLabelMap and legacy nucMutLabelMapReverse
  • Move aaMutLabelMap (NAI resistance markers) into mutLabels section
  • inclusion of older sequences that precede the current subclade system

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

  • Remove empty nucMutLabelMap and legacy nucMutLabelMapReverse

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

  • Remove redundant geneOrderPreference (superseded by cdsOrderPreference)

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

  • Remove redundant geneOrderPreference (superseded by cdsOrderPreference)

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

  • Align pathogen.json metadata with the current Nextclade schema layout.

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

  • Align pathogen.json metadata with the current Nextclade schema layout.

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

  • Align pathogen.json metadata with the current Nextclade schema layout.

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

  • Align pathogen.json metadata with the current Nextclade schema layout.

Ebola virus (nextstrain/orthoebolavirus/ebov)

  • Align pathogen.json metadata with the current Nextclade schema layout.

Sudan virus (nextstrain/orthoebolavirus/sudv)

  • Align pathogen.json metadata with the current Nextclade schema layout.

Measles morbillivirus -- complete genome (nextstrain/measles/genome/WHO-2012)

  • Remove obsolete QC score-weight fields from pathogen.json.

Dengue virus All serotypes (nextstrain/dengue/all)

  • Align pathogen.json metadata with the current Nextclade schema layout.

Human Metapneumovirus (nextstrain/hmpv/all-clades/NC_039199)

  • Rename qc.frameShifts.ignoreFrameShifts to ignoredFrameShifts
  • Rename geneOrderPreference to cdsOrderPreference

Varicella-Zoster Virus (VZV) (nextstrain/herpes/vzv/NC_001348)

  • Remove obsolete QC score-weight fields from pathogen.json.

Rubella virus E1 region (nextstrain/rubella/E1)

  • Fix typo: excessBandwith to excessBandwidth

Mumps MuV Genotypes (SH gene 315nt region) (nextstrain/mumps/sh)

  • Align pathogen.json metadata with the current Nextclade schema layout.
  • Move includeReference and includeNearestNodeInfo from alignmentParams to generalParams

Mumps MuV Genotypes (Full genome) (nextstrain/mumps/genome)

  • Align pathogen.json metadata with the current Nextclade schema layout.
  • Move includeNearestNodeInfo from alignmentParams to generalParams

Rubella (nextstrain/rubella/genome)

  • Remove obsolete QC score-weight fields from pathogen.json.

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

  • updates to reference trees
  • added coloring by HA and NA clades by isolate

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

  • updates to reference trees
  • added coloring by HA and NA clades by isolate

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

  • updates to reference trees
  • added coloring by HA and NA clades by isolate

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

  • Remove empty nucMutLabelMap and legacy nucMutLabelMapReverse

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

  • updates to reference trees
  • added coloring by HA and NA clades by isolate

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

  • updates to reference trees
  • added coloring by HA and NA clades by isolate

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

  • updates to reference trees
  • added coloring by HA and NA clades by isolate

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

  • updates to reference trees
  • added coloring by HA and NA clades by isolate

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

  • updates to reference trees
  • added coloring by HA and NA clades by isolate

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

  • updates to reference trees
  • added coloring by HA and NA clades by isolate

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

  • Remove empty nucMutLabelMap and legacy nucMutLabelMapReverse

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

  • updates to reference trees
  • added coloring by HA and NA clades by isolate

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

  • updates to reference trees
  • added coloring by HA and NA clades by isolate

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

  • updates to reference trees
  • added coloring by HA and NA clades by isolate

West Nile Virus (nextstrain/wnv/all-lineages)

  • Align pathogen.json metadata with the current Nextclade schema layout.

Enterovirus D68 (enpen/enterovirus/ev-d68)

  • Remove deprecated nucMutLabelMapReverse field (computed at runtime in v3)
  • Remove invalid qc.divergence rule (not a configurable parameter)

PRRSV-1 ORF5 (community/isuvdl/mazeller/prrsv1/orf5/yimim2025)

  • Remove invalid qc.missingData.scoreWeight and qc.mixedSites.scoreWeight

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

  • Unify attributes per schema update

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

  • Move placementMaskRanges to tree.json
  • Unify attributes per schema update

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

  • Remove obsolete deprecated and experimental fields

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

  • Remove obsolete deprecated and experimental fields

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

  • Remove obsolete deprecated and experimental fields

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

  • Move placementMaskRanges to tree.json
  • Unify attributes per schema update

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

  • Move placementMaskRanges to tree.json
  • Unify attributes per schema update

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

  • Move placementMaskRanges to tree.json
  • Unify attributes per schema update

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

  • Move placementMaskRanges to tree.json
  • Unify attributes per schema update

chikV (community/v-gen-lab/chikV/genotypes)

  • Move placementMaskRanges to tree.json
  • Unify attributes per schema update

Zika virus (community/itps/zikav)

  • Move placementMaskRanges to tree.json
  • Unify attributes per schema update
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