2026-07-07--14-07-11Z

This release contains changes for datasets:

• 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)

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

• Breaking change: Clade Ib outbreak sh2023 now has lineages defined. Those lineages follow the same scheme as the existing clade IIb outbreak sh2017 lineage system. The root lineage is A, B might become an alias for another lineage than in IIb/sh2017. Hence, to unambiguously refer to a lineage, the outbreak must be included as well. To faciliate this, a new outbreakLineage field has been added that concatenates outbreak and lineage separated by a slash, e.g. sh2017/B.1. Existing clade, outbreak, and lineage fields remain unchanged - except that lineage A is now assigned to both clade Ib/sh2023 lineage A and clade IIb/sh2017 lineage A. The new outbreakLineage field is the way to unambiguously refer to a lineage.
• New sequences that have become available on Pathoplexus between December 2025 and June 2026 are now included in the dataset.

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

• Breaking change: Clade Ib outbreak sh2023 now has lineages defined. Those lineages follow the same scheme as the existing clade IIb outbreak sh2017 lineage system. The root lineage is A, and B might become an alias for another lineage than in IIb/sh2017. Hence, to unambiguously refer to a lineage, the outbreak must be included as well. To facilitate this, a new outbreakLineage field has been added that concatenates outbreak and lineage separated by a slash, e.g. sh2023/A.1. Existing clade, outbreak, and lineage fields remain unchanged - except that lineage A is now assigned to both clade Ib/sh2023 lineage A and (in datasets that contain it) clade IIb/sh2017 lineage A. The new outbreakLineage field is the way to unambiguously refer to a lineage.
• New sequences that have become available on Pathoplexus between December 2025 and June 2026 are now included in the dataset.
• The range 185990-186092 is no longer masked for placement. It is informative, reliable and relevant for assignment sh2023/A.1.

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

• A new outbreakLineage field has been added that concatenates outbreak and lineage separated by a slash, e.g. sh2017/B.1. It unambiguously identifies a lineage across outbreaks: clade Ib outbreak sh2023 now also has a lineage system that reuses the same lineage names (e.g. root lineage A) as clade IIb outbreak sh2017. Existing clade, outbreak, and lineage fields remain unchanged. Clade Ib sequences are not part of this clade IIb dataset; use nextstrain/mpox/all-clades or nextstrain/mpox/clade-i for those.
• New sequences that have become available on Pathoplexus between December 2025 and June 2026 are now included in the dataset.

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

• A new outbreakLineage field has been added that concatenates outbreak and lineage separated by a slash, e.g. sh2017/B.1. It unambiguously identifies a lineage across outbreaks: clade Ib outbreak sh2023 now also has a lineage system that reuses the same lineage names (e.g. root lineage A) as clade IIb outbreak sh2017. Existing clade, outbreak, and lineage fields remain unchanged.
• New sequences that have become available on Pathoplexus between December 2025 and June 2026 are now included in the dataset.

2026-07-03--09-35-04Z

This release contains changes for datasets:

• Bundibugyo ebolavirus (nextstrain/orthoebolavirus/bdbv)

Bundibugyo ebolavirus (nextstrain/orthoebolavirus/bdbv)

• Include open 2026 Outbreak sequences as examples;
• squash zero length branches
• change display defaults to show mutations relative to reference tree

2026-06-16--14-30-45Z

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

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

• Add all 36 Pango lineages newly designated between 2026-04-16 and 2026-06-08. Unfold below to see a list of all newly included lineages with their designation dates:

Newly included lineages, with designation date in parentheses

• XGY (2026-04-24)
• SS.1 (2026-04-24)
• RS.1.5 (2026-04-24)
• RS.1.1.1 (2026-04-24)
• ST.1 (2026-04-27)
• PQ.2.5.6 (2026-04-27)
• XFG.40 (2026-05-04)
• XFG.3.8.2 (2026-05-04)
• SU.1 (2026-05-04)
• RV.1.1 (2026-05-04)
• RV.1.2 (2026-05-04)
• RV.1.3 (2026-05-04)
• RV.1.4 (2026-05-04)
• SV.1 (2026-05-04)
• SV.1.1 (2026-05-04)
• RK.1.1 (2026-05-04)
• RK.1.2 (2026-05-04)
• RK.1.3 (2026-05-04)
• PQ.2.15 (2026-05-04)
• SW.1 (2026-05-04)
• XFG.6.14 (2026-05-04)
• RF.5.1 (2026-05-04)
• RF.5.2 (2026-05-04)
• RF.5.3 (2026-05-04)
• RC.11 (2026-05-06)
• RS.6 (2026-05-07)
• SS.2 (2026-05-07)
• XGZ (2026-05-08)
• PQ.2.7.2 (2026-05-08)
• XFG.6.14.1 (2026-05-15)
• SW.2 (2026-05-15)
• QF.3.1 (2026-05-15)
• SV.2 (2026-05-15)
• SV.2.1 (2026-05-15)
• SE.2.1.1 (2026-05-21)
• SY.1 (2026-05-21)

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

• Add all 36 Pango lineages newly designated between 2026-04-16 and 2026-06-08. Unfold below to see a list of all newly included lineages with their designation dates:

Newly included lineages, with designation date in parentheses

• XGY (2026-04-24)
• SS.1 (2026-04-24)
• RS.1.5 (2026-04-24)
• RS.1.1.1 (2026-04-24)
• ST.1 (2026-04-27)
• PQ.2.5.6 (2026-04-27)
• XFG.40 (2026-05-04)
• XFG.3.8.2 (2026-05-04)
• SU.1 (2026-05-04)
• RV.1.1 (2026-05-04)
• RV.1.2 (2026-05-04)
• RV.1.3 (2026-05-04)
• RV.1.4 (2026-05-04)
• SV.1 (2026-05-04)
• SV.1.1 (2026-05-04)
• RK.1.1 (2026-05-04)
• RK.1.2 (2026-05-04)
• RK.1.3 (2026-05-04)
• PQ.2.15 (2026-05-04)
• SW.1 (2026-05-04)
• XFG.6.14 (2026-05-04)
• RF.5.1 (2026-05-04)
• RF.5.2 (2026-05-04)
• RF.5.3 (2026-05-04)
• RC.11 (2026-05-06)
• RS.6 (2026-05-07)
• SS.2 (2026-05-07)
• XGZ (2026-05-08)
• PQ.2.7.2 (2026-05-08)
• XFG.6.14.1 (2026-05-15)
• SW.2 (2026-05-15)
• QF.3.1 (2026-05-15)
• SV.2 (2026-05-15)
• SV.2.1 (2026-05-15)
• SE.2.1.1 (2026-05-21)
• SY.1 (2026-05-21)

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

• Add all 36 Pango lineages newly designated between 2026-04-16 and 2026-06-08. Unfold below to see a list of all newly included lineages with their designation dates:

Newly included lineages, with designation date in parentheses

• XGY (2026-04-24)
• SS.1 (2026-04-24)
• RS.1.5 (2026-04-24)
• RS.1.1.1 (2026-04-24)
• ST.1 (2026-04-27)
• PQ.2.5.6 (2026-04-27)
• XFG.40 (2026-05-04)
• XFG.3.8.2 (2026-05-04)
• SU.1 (2026-05-04)
• RV.1.1 (2026-05-04)
• RV.1.2 (2026-05-04)
• RV.1.3 (2026-05-04)
• RV.1.4 (2026-05-04)
• SV.1 (2026-05-04)
• SV.1.1 (2026-05-04)
• RK.1.1 (2026-05-04)
• RK.1.2 (2026-05-04)
• RK.1.3 (2026-05-04)
• PQ.2.15 (2026-05-04)
• SW.1 (2026-05-04)
• XFG.6.14 (2026-05-04)
• RF.5.1 (2026-05-04)
• RF.5.2 (2026-05-04)
• RF.5.3 (2026-05-04)
• RC.11 (2026-05-06)
• RS.6 (2026-05-07)
• SS.2 (2026-05-07)
• XGZ (2026-05-08)
• PQ.2.7.2 (2026-05-08)
• XFG.6.14.1 (2026-05-15)
• SW.2 (2026-05-15)
• QF.3.1 (2026-05-15)
• SV.2 (2026-05-15)
• SV.2.1 (2026-05-15)
• SE.2.1.1 (2026-05-21)
• SY.1 (2026-05-21)

2026-05-29--13-46-38Z

This release contains changes for datasets:

• Andesvirus (segment L) (nextstrain/orthohantavirus/andv/l)
• Andesvirus (segment M) (nextstrain/orthohantavirus/andv/m)
• Andesvirus (segment S) (nextstrain/orthohantavirus/andv/s)

Andesvirus (segment L) (nextstrain/orthohantavirus/andv/l)

• Update tree with the latest sequences submitted to Pathoplexus

Andesvirus (segment M) (nextstrain/orthohantavirus/andv/m)

• Update tree with the latest sequences submitted to Pathoplexus

Andesvirus (segment S) (nextstrain/orthohantavirus/andv/s)

• Update tree with the latest sequences submitted to Pathoplexus

2026-05-22--16-04-17Z

This release contains changes for datasets:

• Bundibugyo ebolavirus (nextstrain/orthoebolavirus/bdbv)

Bundibugyo ebolavirus (nextstrain/orthoebolavirus/bdbv)

• adjust QC param settings to reudce private mutation threshold (outbreak genomes should be very similar)
• add SNP cluster QC rule to trigger on stretches of high private mutation density
• update tree

2026-05-18--20-09-34Z

This release contains changes for datasets:

• Bundibugyo ebolavirus (nextstrain/orthoebolavirus/bdbv)

Bundibugyo ebolavirus (nextstrain/orthoebolavirus/bdbv)

• Add outbreak annotation
• add GP_003:367 to known stop codons
• Include 2026 genomes

2026-05-15--16-16-45Z

This release contains changes for datasets:

• Bundibugyo ebolavirus (nextstrain/orthoebolavirus/bdbv)

Bundibugyo ebolavirus (nextstrain/orthoebolavirus/bdbv)

2026-05-12--16-39-06Z

This release contains changes for datasets:

• Andesvirus (segment L) (nextstrain/orthohantavirus/andv/l)
• Andesvirus (segment M) (nextstrain/orthohantavirus/andv/m)
• Andesvirus (segment S) (nextstrain/orthohantavirus/andv/s)
• orov/L/refseq (community/itps/orov/L/refseq)
• orov/M/refseq (community/itps/orov/M/refseq)
• orov/M/tefe (community/itps/orov/M/tefe)
• orov/L/tefe (community/itps/orov/L/tefe)
• orov/S/tefe (community/itps/orov/S/tefe)
• orov/S/refseq (community/itps/orov/S/refseq)

Andesvirus (segment L) (nextstrain/orthohantavirus/andv/l)

• update outbreak name to 2026-Hondius
• make nucleotide default sequence view.
• add GPC amino acid substitutions

Andesvirus (segment M) (nextstrain/orthohantavirus/andv/m)

• update outbreak name to 2026-Hondius
• make nucleotide default sequence view.
• add GPC amino acid substitutions

Andesvirus (segment S) (nextstrain/orthohantavirus/andv/s)

• update outbreak name to 2026-Hondius
• make nucleotide default sequence view.
• add GPC amino acid substitutions

orov/L/refseq (community/itps/orov/L/refseq)

Initial release of a Oropouche Virus (OROV) dataset for segment L based on NCBI refseq reference genome.

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

orov/M/refseq (community/itps/orov/M/refseq)

Initial release of a Oropouche Virus (OROV) dataset for segment M based on NCBI refseq reference genome.

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

orov/M/tefe (community/itps/orov/M/tefe)

Initial release of a Oropouche Virus (OROV) dataset for segment M based on Tefe outbreak reference genome (ILMD_TF29).

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

orov/L/tefe (community/itps/orov/L/tefe)

Initial release of a Oropouche Virus (OROV) dataset for segment L based on Tefe outbreak reference genome (ILMD_TF29).

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

orov/S/tefe (community/itps/orov/S/tefe)

Initial release of a Oropouche Virus (OROV) dataset for segment S based on Tefe outbreak reference genome (ILMD_TF29).

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

orov/S/refseq (community/itps/orov/S/refseq)

Initial release of a Oropouche Virus (OROV) dataset for segment S based on NCBI refseq reference genome.

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

2026-05-11--18-59-50Z

This release contains changes for datasets:

• Andesvirus (segment L) (nextstrain/orthohantavirus/andv/l)
• Andesvirus (segment M) (nextstrain/orthohantavirus/andv/m)
• Andesvirus (segment S) (nextstrain/orthohantavirus/andv/s)

Andesvirus (segment L) (nextstrain/orthohantavirus/andv/l)

• Updating Nextclade dataset with the latest sequences and metadata from Pathoplexus
• Include 2026 outbreak sequences
• add 2026 outbreak annotation

Andesvirus (segment M) (nextstrain/orthohantavirus/andv/m)

• Updating Nextclade dataset with the latest sequences and metadata from Pathoplexus
• Include 2026 outbreak sequences
• add 2026 outbreak annotation

Andesvirus (segment S) (nextstrain/orthohantavirus/andv/s)

• Updating Nextclade dataset with the latest sequences and metadata from Pathoplexus
• Include 2026 outbreak sequences
• add 2026 outbreak annotation

2026-05-08--21-17-05Z

This release contains changes for datasets:

• Andesvirus (segment L) (nextstrain/orthohantavirus/andv/l)
• Andesvirus (segment M) (nextstrain/orthohantavirus/andv/m)
• Andesvirus (segment S) (nextstrain/orthohantavirus/andv/s)

Andesvirus (segment L) (nextstrain/orthohantavirus/andv/l)

• initial release

Andesvirus (segment M) (nextstrain/orthohantavirus/andv/m)

• initial release

Andesvirus (segment S) (nextstrain/orthohantavirus/andv/s)

• initial release