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

This release contains changes for datasets:

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

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

• All 35 Pango lineages designated between 2024-01-16 and 2024-02-12 are now included, unfold below to see a list of all newly included lineages with their designation dates:

Newly included lineages, with designation date in parentheses

• XDN (2024-01-16)
• XDP (2024-01-16)
• JN.3.2 (2024-01-16)
• JN.3.2.1 (2024-01-16)
• JN.11 (2024-01-21)
• JN.1.12 (2024-01-21)
• JN.12 (2024-01-22)
• JN.1.11.1 (2024-01-22)
• KM.1 (2024-01-31)
• BA.2.87 (2024-02-01)
• BA.2.87.1 (2024-02-01)
• XDQ (2024-02-01)
• GK.1.10.1 (2024-02-01)
• XDR (2024-02-01)
• JN.1.13 (2024-02-01)
• JN.1.14 (2024-02-01)
• JN.1.15 (2024-02-01)
• JN.1.4.1 (2024-02-01)
• JN.1.2.1 (2024-02-01)
• JN.1.16 (2024-02-01)
• JN.1.17 (2024-02-01)
• JN.1.4.2 (2024-02-02)
• JN.1.18 (2024-02-04)
• JN.1.19 (2024-02-04)
• JN.1.20 (2024-02-04)
• XDS (2024-02-04)
• JN.1.9.1 (2024-02-04)
• JN.1.21 (2024-02-04)
• JN.1.22 (2024-02-04)
• JN.1.4.3 (2024-02-12)
• XDT (2024-02-12)
• HK.13.2.1 (2024-02-12)
• KN.1 (2024-02-12)
• KN.1.1 (2024-02-12)
• JN.1.1.4 (2024-02-12)

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

• All 35 Pango lineages designated between 2024-01-16 and 2024-02-12 are now included, unfold below to see a list of all newly included lineages with their designation dates:

Newly included lineages, with designation date in parentheses

• XDN (2024-01-16)
• XDP (2024-01-16)
• JN.3.2 (2024-01-16)
• JN.3.2.1 (2024-01-16)
• JN.11 (2024-01-21)
• JN.1.12 (2024-01-21)
• JN.12 (2024-01-22)
• JN.1.11.1 (2024-01-22)
• KM.1 (2024-01-31)
• BA.2.87 (2024-02-01)
• BA.2.87.1 (2024-02-01)
• XDQ (2024-02-01)
• GK.1.10.1 (2024-02-01)
• XDR (2024-02-01)
• JN.1.13 (2024-02-01)
• JN.1.14 (2024-02-01)
• JN.1.15 (2024-02-01)
• JN.1.4.1 (2024-02-01)
• JN.1.2.1 (2024-02-01)
• JN.1.16 (2024-02-01)
• JN.1.17 (2024-02-01)
• JN.1.4.2 (2024-02-02)
• JN.1.18 (2024-02-04)
• JN.1.19 (2024-02-04)
• JN.1.20 (2024-02-04)
• XDS (2024-02-04)
• JN.1.9.1 (2024-02-04)
• JN.1.21 (2024-02-04)
• JN.1.22 (2024-02-04)
• JN.1.4.3 (2024-02-12)
• XDT (2024-02-12)
• HK.13.2.1 (2024-02-12)
• KN.1 (2024-02-12)
• KN.1.1 (2024-02-12)
• JN.1.1.4 (2024-02-12)

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

• All 35 Pango lineages designated between 2024-01-16 and 2024-02-12 are now included, unfold below to see a list of all newly included lineages with their designation dates:

Newly included lineages, with designation date in parentheses

• XDN (2024-01-16)
• XDP (2024-01-16)
• JN.3.2 (2024-01-16)
• JN.3.2.1 (2024-01-16)
• JN.11 (2024-01-21)
• JN.1.12 (2024-01-21)
• JN.12 (2024-01-22)
• JN.1.11.1 (2024-01-22)
• KM.1 (2024-01-31)
• BA.2.87 (2024-02-01)
• BA.2.87.1 (2024-02-01)
• XDQ (2024-02-01)
• GK.1.10.1 (2024-02-01)
• XDR (2024-02-01)
• JN.1.13 (2024-02-01)
• JN.1.14 (2024-02-01)
• JN.1.15 (2024-02-01)
• JN.1.4.1 (2024-02-01)
• JN.1.2.1 (2024-02-01)
• JN.1.16 (2024-02-01)
• JN.1.17 (2024-02-01)
• JN.1.4.2 (2024-02-02)
• JN.1.18 (2024-02-04)
• JN.1.19 (2024-02-04)
• JN.1.20 (2024-02-04)
• XDS (2024-02-04)
• JN.1.9.1 (2024-02-04)
• JN.1.21 (2024-02-04)
• JN.1.22 (2024-02-04)
• JN.1.4.3 (2024-02-12)
• XDT (2024-02-12)
• HK.13.2.1 (2024-02-12)
• KN.1 (2024-02-12)
• KN.1.1 (2024-02-12)
• JN.1.1.4 (2024-02-12)

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

• All 35 Pango lineages designated between 2024-01-16 and 2024-02-12 are now included, unfold below to see a list of all newly included lineages with their designation dates:

Newly included lineages, with designation date in parentheses

• XDN (2024-01-16)
• XDP (2024-01-16)
• JN.3.2 (2024-01-16)
• JN.3.2.1 (2024-01-16)
• JN.11 (2024-01-21)
• JN.1.12 (2024-01-21)
• JN.12 (2024-01-22)
• JN.1.11.1 (2024-01-22)
• KM.1 (2024-01-31)
• BA.2.87 (2024-02-01)
• BA.2.87.1 (2024-02-01)
• XDQ (2024-02-01)
• GK.1.10.1 (2024-02-01)
• XDR (2024-02-01)
• JN.1.13 (2024-02-01)
• JN.1.14 (2024-02-01)
• JN.1.15 (2024-02-01)
• JN.1.4.1 (2024-02-01)
• JN.1.2.1 (2024-02-01)
• JN.1.16 (2024-02-01)
• JN.1.17 (2024-02-01)
• JN.1.4.2 (2024-02-02)
• JN.1.18 (2024-02-04)
• JN.1.19 (2024-02-04)
• JN.1.20 (2024-02-04)
• XDS (2024-02-04)
• JN.1.9.1 (2024-02-04)
• JN.1.21 (2024-02-04)
• JN.1.22 (2024-02-04)
• JN.1.4.3 (2024-02-12)
• XDT (2024-02-12)
• HK.13.2.1 (2024-02-12)
• KN.1 (2024-02-12)
• KN.1.1 (2024-02-12)
• JN.1.1.4 (2024-02-12)

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

• All 35 Pango lineages designated between 2024-01-16 and 2024-02-12 are now included, unfold below to see a list of all newly included lineages with their designation dates:

Newly included lineages, with designation date in parentheses

• XDN (2024-01-16)
• XDP (2024-01-16)
• JN.3.2 (2024-01-16)
• JN.3.2.1 (2024-01-16)
• JN.11 (2024-01-21)
• JN.1.12 (2024-01-21)
• JN.12 (2024-01-22)
• JN.1.11.1 (2024-01-22)
• KM.1 (2024-01-31)
• BA.2.87 (2024-02-01)
• BA.2.87.1 (2024-02-01)
• XDQ (2024-02-01)
• GK.1.10.1 (2024-02-01)
• XDR (2024-02-01)
• JN.1.13 (2024-02-01)
• JN.1.14 (2024-02-01)
• JN.1.15 (2024-02-01)
• JN.1.4.1 (2024-02-01)
• JN.1.2.1 (2024-02-01)
• JN.1.16 (2024-02-01)
• JN.1.17 (2024-02-01)
• JN.1.4.2 (2024-02-02)
• JN.1.18 (2024-02-04)
• JN.1.19 (2024-02-04)
• JN.1.20 (2024-02-04)
• XDS (2024-02-04)
• JN.1.9.1 (2024-02-04)
• JN.1.21 (2024-02-04)
• JN.1.22 (2024-02-04)
• JN.1.4.3 (2024-02-12)
• XDT (2024-02-12)
• HK.13.2.1 (2024-02-12)
• KN.1 (2024-02-12)
• KN.1.1 (2024-02-12)
• JN.1.1.4 (2024-02-12)

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

Initial release for Nextclade v3!

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

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

This release contains changes for datasets:

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

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

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

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

This release contains changes for datasets:

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

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

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

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

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

2024-01-16--20-31-02Z

This release contains changes for datasets:

• nextstrain/sars-cov-2/wuhan-hu-1/orfs (SARS-CoV-2)
• nextstrain/sars-cov-2/wuhan-hu-1/proteins (SARS-CoV-2 (Mature proteins))
• nextstrain/sars-cov-2/BA.2 (SARS-CoV-2 (BA.2))
• nextstrain/sars-cov-2/XBB (SARS-CoV-2 (XBB))
• nextstrain/sars-cov-2/BA.2.86 (SARS-CoV-2 (BA.2.86))
• nextstrain/flu/h1n1pdm/ha/CY121680 (Influenza A H1N1pdm HA)
• nextstrain/flu/h1n1pdm/ha/MW626062 (Influenza A H1N1pdm HA)
• nextstrain/flu/h1n1pdm/na/MW626056 (Influenza A H1N1pdm NA)
• nextstrain/flu/h3n2/ha/CY163680 (Influenza A H3N2 HA)
• nextstrain/flu/h3n2/ha/EPI1857216 (Influenza A H3N2 HA)
• nextstrain/flu/h3n2/na/EPI1857215 (Influenza A H3N2 NA)
• nextstrain/flu/vic/ha/KX058884 (Influenza B Victoria HA)
• nextstrain/flu/vic/na/CY073894 (Influenza B Victoria NA)
• nextstrain/flu/yam/ha/JN993010 (Influenza B Yamagata HA)
• nextstrain/rsv/a/EPI_ISL_412866 (RSV-A)
• nextstrain/rsv/b/EPI_ISL_1653999 (RSV-B)
• nextstrain/mpox/all-clades (Mpox virus (All clades))
• nextstrain/mpox/clade-iib (Mpox virus (Clade IIb))
• nextstrain/mpox/lineage-b.1 (Mpox virus (Lineage B.1))
• nextstrain/flu/h3n2/pb1 (Influenza A H3N2 PB1 (segment 2))
• nextstrain/flu/h3n2/np (Influenza A H3N2 NP (segment 5))
• nextstrain/flu/h1n1pdm/pa (Influenza A H1N1pdm PA (segment 3))
• nextstrain/flu/h3n2/ns (Influenza A H3N2 NS (segment 8))
• nextstrain/flu/h1n1pdm/mp (Influenza A H1N1pdm MP (segment 7))
• nextstrain/flu/h1n1pdm/np (Influenza A H1N1pdm NP (segment 5))
• nextstrain/flu/h1n1pdm/ns (Influenza A H1N1pdm NS (segment 8))
• nextstrain/flu/h3n2/mp (Influenza A H3N2 MP (segment 7))
• nextstrain/flu/h3n2/pa (Influenza A H3N2 PA (segment 3))
• nextstrain/flu/h1n1pdm/pb2 (Influenza A H1N1pdm PB2 (segment 1))
• nextstrain/flu/h1n1pdm/pb1 (Influenza A H1N1pdm PB1 (segment 2))
• nextstrain/flu/h3n2/pb2 (Influenza A H3N2 PB2 (segment 1))

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

Initial release of this v3 dataset.

This dataset is very similar to the v2 dataset sars-cov-2.

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

Initial release of this v3 dataset.

This dataset is similar to the v2 dataset sars-cov-2 but translating mature proteins (nsp1-16) instead of ORF1a/b.

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

Initial release of this v3 dataset.

This dataset is very similar to the v2 dataset sars-cov-2-21L. Immune escape scores are informed by some additional DMS data.

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

Initial release of this v3 dataset.

This dataset is new to v3 and does not have a v2 equivalent.

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

Initial release of this v3 dataset.

This dataset is new to v3 and does not have a v2 equivalent.

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

Initial release for Nextclade v3!

• addition of subclade C.1.7

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

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

Initial release for Nextclade v3!

• addition of subclade C.1.7

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

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

Initial release for Nextclade v3!

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

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

Initial release for Nextclade v3!

• Addition of subclade H.1, H.2, H.3, and H.4
• Aliasing of G.1.3.1.1 as subclade H

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

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

Initial release for Nextclade v3!

• Addition of subclade H.1, H.2, H.3, and H.4
• Aliasing of G.1.3.1.1 as subclade H

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

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

Initial release for Nextclade v3!

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

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

• fix subclade definition of C.2 and C.4

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

Initial release for Nextclade v3!

• addition of subclade B.7.1
• addition of subclade B.7.2
• addition of subclade B.7.3
• addition of subclade B.8

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

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

Initial release for Nextclade v3!

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

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

first release of v3 dataset.

Updated consortium nomenclature.

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

first release of v3 dataset.

Updated consortium nomenclature.

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

Initial release of this dataset. This dataset is similar to the v2 dataset MPXV/ancestral with some differences.

New and changed gene names

Some genes have been renamed and one has been added. The new annotation is based on NCBI refseq annotations that were released in November 2022. The v2 dataset predates this refseq:

• The 4 genes in the inverted terminal repeat segment (ITR) on both ends of the genome (OPG001, OPG002, OPG003,OPG015) are now all included. The genes on the 3' end (~positions 190000-197000) now have an _dup appended to distinguish them.
• The gene previously named NBT03_gp052 is now called OPG073
• The gene previously named NBT03_gp174 is now called OPG016
• The gene previously named NBT03_gp175 is now called OPG015_dup
• Gene OPG166 has been added

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

Initial release of this dataset. This dataset is similar to the v2 dataset hMPXV/NC_063383.1 with some differences.

New and changed gene names

Some genes have been renamed and one has been added. The new annotation is based on NCBI refseq annotations that were released in November 2022. The v2 dataset predates this refseq:

• The 4 genes in the inverted terminal repeat segment (ITR) on both ends of the genome (OPG001, OPG002, OPG003,OPG015) are now all included. The genes on the 3' end (~positions 190000-197000) now have an _dup appended to distinguish them.
• The gene previously named NBT03_gp052 is now called OPG073
• The gene previously named NBT03_gp174 is now called OPG016
• The gene previously named NBT03_gp175 is now called OPG015_dup
• Gene OPG166 has been added

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

Initial release of this dataset. This dataset is similar to the v2 dataset hMPXV_B.1/pseudo_ON563414 with some differences.

New and changed gene names

Some genes have been renamed and one has been added. The new annotation is based on NCBI refseq annotations that were released in November 2022. The v2 dataset predates this refseq:

• The 4 genes in the inverted terminal repeat segment (ITR) on both ends of the genome (OPG001, OPG002, OPG003,OPG015) are now all included. The genes on the 3' end (~positions 190000-197000) now have an _dup appended to distinguish them.
• The gene previously named NBT03_gp052 is now called OPG073
• The gene previously named NBT03_gp174 is now called OPG016
• The gene previously named NBT03_gp175 is now called OPG015_dup
• Gene OPG166 has been added

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

Initial release of for non-HA/NA segments of Influenza A viruses based on genome in RefSeq.

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

Initial release of for non-HA/NA segments of Influenza A viruses based on genome in RefSeq.

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

Initial release of for non-HA/NA segments of Influenza A viruses based on genome in RefSeq.

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

Initial release of for non-HA/NA segments of Influenza A viruses based on genome in RefSeq.

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

Initial release of for non-HA/NA segments of Influenza A viruses based on genome in RefSeq.

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

Initial release of for non-HA/NA segments of Influenza A viruses based on genome in RefSeq.

Influenza A H1N1pdm NS (segment 8) (nex...

2024-01-15

New SARS-CoV-2 dataset version (tag 2024-01-15T12:00:00Z)

• Important: This is the last release of SARS-CoV-2 datasets for nextclade v2. All v2 datasets will remain usable with nextclade v2. However, there will be no more dataset updates as future dataset releases will be for nextclade v3 only. Nextclade v3 has corresponding versions for each current v2 dataset. Read more about migrating from v2 to v3 in the v3 migration guide, specifically, CLI dataset paths may need to be updated, see Dataset path changes. As the first v3-only dataset is expected to be released mid February 2024, you have a month to migrate to v3 without any interruption in dataset updates.
• Pango lineages designated between 2023-12-03 and 2024-01-14 are now included, unfold below to see a list with designation dates:

Newly included lineages, with designation date in parentheses

• HV.2 (2023-12-17)
• JD.1.1.7 (2023-12-17)
• JD.1.1.8 (2023-12-17)
• JD.2.2 (2023-12-17)
• FY.1.2.1 (2023-12-17)
• FY.1.2.2 (2023-12-17)
• FY.1.2.3 (2023-12-17)
• XBB.1.16.28 (2023-12-17)
• JF.3 (2023-12-17)
• XBB.1.16.29 (2023-12-17)
• XBB.1.16.30 (2023-12-17)
• XBB.1.16.31 (2023-12-17)
• XDJ (2023-12-17)
• XBB.1.5.108 (2023-12-17)
• XCF.3 (2023-12-17)
• XBB.1.5.109 (2023-12-17)
• XBB.1.5.110 (2023-12-17)
• XDA.1 (2023-12-17)
• XBB.2.3.21 (2023-12-17)
• XBB.2.3.22 (2023-12-17)
• JD.1.2.2 (2023-12-17)
• HN.7 (2023-12-17)
• XDK (2023-12-17)
• DV.7.1.8 (2023-12-17)
• KG.1 (2023-12-17)
• KG.2 (2023-12-17)
• DV.7.1.9 (2023-12-17)
• GE.1.2.1 (2023-12-17)
• JG.3.4 (2023-12-17)
• FL.38 (2023-12-17)
• HN.4.1 (2023-12-17)
• HN.4.1.1 (2023-12-17)
• HN.4.2 (2023-12-17)
• FL.39 (2023-12-17)
• FL.39.1 (2023-12-17)
• FL.40 (2023-12-17)
• FL.24.1 (2023-12-17)
• FL.1.8 (2023-12-17)
• JE.1.1.1 (2023-12-20)
• KH.1 (2023-12-20)
• JF.1.1 (2023-12-20)
• JF.1.1.1 (2023-12-20)
• JF.1.1.2 (2023-12-20)
• JF.4 (2023-12-20)
• JN.1.3 (2023-12-20)
• GK.1.8.1 (2023-12-21)
• GK.1.11 (2023-12-21)
• GK.1.11.1 (2023-12-21)
• JW.1.1 (2023-12-21)
• JC.5.1 (2023-12-21)
• GN.1.4 (2023-12-21)
• XBB.1.16.32 (2023-12-21)
• KJ.1 (2023-12-21)
• FL.2.7 (2023-12-21)
• FL.2.7.1 (2023-12-21)
• JN.1.4 (2024-01-08)
• XDL (2024-01-08)
• HV.1.8 (2024-01-09)
• HV.1.9 (2024-01-09)
• HV.1.10 (2024-01-09)
• JN.1.5 (2024-01-09)
• XDD.1 (2024-01-09)
• XDD.1.1 (2024-01-09)
• XDD.2 (2024-01-09)
• JN.2.2 (2024-01-09)
• JN.2.3 (2024-01-09)
• JN.2.4 (2024-01-09)
• JN.2.5 (2024-01-09)
• JN.1.1.2 (2024-01-09)
• HN.8 (2024-01-09)
• JN.1.1.3 (2024-01-09)
• JN.1.6 (2024-01-09)
• JN.1.6.1 (2024-01-09)
• JN.1.7 (2024-01-09)
• JN.1.8 (2024-01-09)
• JN.1.8.1 (2024-01-09)
• JN.1.9 (2024-01-09)
• FW.1.1.1 (2024-01-10)
• HK.3.14 (2024-01-10)
• XDM (2024-01-10)
• KK.1 (2024-01-10)
• KK.2 (2024-01-10)
• KL.1 (2024-01-10)
• KL.1.1 (2024-01-10)
• HV.1.11 (2024-01-10)
• JN.1.10 (2024-01-11)
• JN.1.11 (2024-01-11)

2023-12-20

New Influenza virus A/H3N2 HA dataset version (tag 2023-12-20T12:00:00Z)

• New A/H3N2 HA subclades H.1 - H.4

2023-12-03

New SARS-CoV-2 dataset version (tag 2023-12-03T12:00:00Z)

• New Nextstrain clades 23G (XBB.1.5.70), 23H (HK.3=EG.5.1.1.3), 23I (BA.2.86) are added. See ncov PR for a detailed discussion of the clades.
• Pango lineages designated between 2023-10-25 and 2023-12-03 are now included, unfold below to see a list with designation dates:

Newly included lineages, with designation date in parentheses

• HK.20 (2023-11-02)
• HK.20.1 (2023-11-02)
• JN.4 (2023-11-12)
• JD.1.2.1 (2023-11-12)
• HK.21 (2023-11-12)
• XCT.1 (2023-11-12)
• HK.22 (2023-11-12)
• XBB.1.16.26 (2023-11-12)
• JN.5 (2023-11-14)
• JN.6 (2023-11-14)
• JG.3.2 (2023-11-17)
• JG.3.3 (2023-11-17)
• GK.1.10 (2023-11-17)
• JN.7 (2023-11-17)
• JN.8 (2023-11-17)
• JN.9 (2023-11-17)
• JN.3.1 (2023-11-17)
• HR.1.1 (2023-11-17)
• XDD (2023-11-17)
• JN.2.1 (2023-11-21)
• JN.10 (2023-11-21)
• BA.2.86.4 (2023-11-21)
• JN.5.1 (2023-11-21)
• JD.1.1.4 (2023-11-21)
• HK.3.8 (2023-11-21)
• HK.3.2.1 (2023-11-21)
• FL.15.4 (2023-11-21)
• HK.8.1 (2023-11-21)
• XDE (2023-11-21)
• KB.1 (2023-11-21)
• XBB.1.16.27 (2023-11-21)
• XDF (2023-11-24)
• EG.5.2.4 (2023-11-24)
• FL.37 (2023-11-24)
• XDG (2023-11-24)
• HK.3.2.2 (2023-11-24)
• HK.3.9 (2023-11-24)
• HK.23 (2023-11-24)
• HK.23.1 (2023-11-24)
• HK.23.1.1 (2023-11-24)
• HK.24 (2023-11-24)
• HK.24.1 (2023-11-24)
• HK.3.10 (2023-11-24)
• HK.3.11 (2023-11-24)
• HK.25 (2023-11-27)
• KC.1 (2023-11-28)
• KC.1.1 (2023-11-28)
• HK.26 (2023-11-28)
• HK.26.1 (2023-11-28)
• HK.27 (2023-11-28)
• HK.27.1 (2023-11-28)
• HK.27.1.1 (2023-11-28)
• HK.28 (2023-11-28)
• HK.29 (2023-11-28)
• HK.30 (2023-11-28)
• HK.31 (2023-11-28)
• HK.32 (2023-11-28)
• HK.32.1 (2023-11-28)
• EG.5.1.12 (2023-11-28)
• EG.5.1.13 (2023-11-28)
• EG.5.1.14 (2023-11-28)
• EG.5.1.15 (2023-11-28)
• EG.5.1.16 (2023-11-28)
• EG.5.1.17 (2023-11-28)
• EG.5.1.18 (2023-11-28)
• EG.5.1.19 (2023-11-28)
• KB.2 (2023-11-28)
• KB.3 (2023-11-28)
• KB.4 (2023-11-28)
• BA.2.86.5 (2023-11-28)
• JN.1.1 (2023-11-28)
• DV.7.1.6 (2023-11-28)
• DV.7.1.7 (2023-11-28)
• JB.1.1 (2023-11-28)
• JR.1.1.1 (2023-11-29)
• GY.1.1 (2023-11-30)
• GY.1.1.1 (2023-11-30)
• FY.8.1 (2023-11-30)
• EG.10.1.1 (2023-11-30)
• BN.1.2.8 (2023-12-01)
• XDH (2023-12-01)
• XBC.1.3.1 (2023-12-01)
• KD.1 (2023-12-01)
• KD.2 (2023-12-01)
• KD.3 (2023-12-01)
• KD.4 (2023-12-01)
• KD.5 (2023-12-01)
• JP.1.1 (2023-12-01)
• JN.1.1.1 (2023-12-02)
• JN.1.2 (2023-12-02)
• HV.1.5 (2023-12-02)
• HV.1.6 (2023-12-02)
• HV.1.6.1 (2023-12-02)
• HV.1.7 (2023-12-02)
• JD.1.1.5 (2023-12-02)
• JD.1.1.6 (2023-12-02)
• FY.5.2 (2023-12-02)
• FY.5.3 (2023-12-02)
• KE.1 (2023-12-02)
• KE.2 (2023-12-02)
• KE.3 (2023-12-02)
• GY.9 (2023-12-02)
• HK.3.12 (2023-12-02)
• HK.3.13 (2023-12-02)
• HK.34 (2023-12-02)
• HK.33 (2023-12-02)
• FY.5.4 (2023-12-02)
• FY.5.5 (2023-12-02)
• FY.5.5.1 (2023-12-02)
• FY.8.1.1 (2023-12-02)
• HK.34.1 (2023-12-02)
• KF.1 (2023-12-02)
• KF.2 (2023-12-02)
• GA.10.1 (2023-12-03)

2023-10-26

New SARS-CoV-2 dataset version (tag 2023-10-26T12:00:00Z)

• Fixed a bug in consensus sequence algorithm that treated ambiguous nucleotides as reference as opposed to unknowns. This only affected a few lineages with few designated sequences where the consensus was wrongly reference when it should have been mutated.
• Pango lineages designated between 2023-09-20 and 2023-10-25 are now included, unfold below to see a list with designation dates:

Newly included lineages, with designation date in parentheses

• XCN (2023-09-21)
• FL.31 (2023-09-21)
• FL.31.1 (2023-09-21)
• FL.20.2 (2023-09-21)
• FL.32 (2023-09-21)
• FL.32.1 (2023-09-21)
• FL.10.3 (2023-09-21)
• FL.33 (2023-09-21)
• FL.33.1 (2023-09-21)
• FL.34 (2023-09-21)
• FL.35 (2023-09-21)
• JM.1 (2023-09-22)
• JM.2 (2023-09-22)
• GS.5 (2023-09-22)
• GK.2.1.1 (2023-09-24)
• EG.4.5 (2023-09-24)
• CH.1.1.31 (2023-09-24)
• JP.1 (2023-09-24)
• CH.1.1.32 (2023-09-24)
• JD.1.1.1 (2023-09-26)
• JD.1.1.2 (2023-09-26)
• XCP (2023-09-26)
• EG.5.1.10 (2023-09-26)
• GA.4.1.1 (2023-09-26)
• FR.1.5 (2023-09-26)
• EP.1.1 (2023-09-26)
• EP.1.1.1 (2023-09-26)
• HC.3 (2023-09-26)
• FL.36 (2023-09-26)
• HC.4 (2023-09-26)
• FL.15.1 (2023-09-27)
• FL.15.1.1 (2023-09-27)
• FL.15.2 (2023-09-27)
• FL.15.3 (2023-09-27)
• JN.1 (2023-09-29)
• JD.1.1.3 (2023-10-04)
• JD.2 (2023-10-04)
• GJ.1.2.6 (2023-10-04)
• GJ.1.2.7 (2023-10-04)
• JE.1.1 (2023-10-04)
• GJ.1.2.8 (2023-10-04)
• GJ.5 (2023-10-04)
• GJ.5.1 (2023-10-04)
• BA.2.86.2 (2023-10-12)
• BA.2.86.3 (2023-10-12)
• JQ.1 (2023-10-12)
• JN.2 (2023-10-12)
• JN.3 (2023-10-12)
• GK.2.4 (2023-10-12)
• HK.12 (2023-10-12)
• EG.6.1.2 (2023-10-12)
• HV.1.1 (2023-10-13)
• HV.1.2 (2023-10-13)
• HV.1.3 (2023-10-13)
• HV.1.4 (2023-10-13)
• HK.13 (2023-10-13)
• HK.13.1 (2023-10-13)
• HK.13.2 (2023-10-13)
• HK.1.1 (2023-10-13)
• HK.1.2 (2023-10-13)
• HK.14 (2023-10-13)
• HK.15 (2023-10-13)
• EG.5.1.11 (2023-10-13)
• JR.1 (2023-10-13)
• JR.1.1 (2023-10-13)
• GA.2.1 (2023-10-13)
• GA.2.1.1 (2023-10-13)
• GA.4.2 (2023-10-13)
• GA.4.3 (2023-10-13)
• GA.4.1.2 (2023-10-13)
• HK.16 (2023-10-13)
• HK.17 (2023-10-13)
• HK.18 (2023-10-13)
• HK.19 (2023-10-13)
• XBB.2.3.15 (2023-10-13)
• JS.1 (2023-10-13)
• JS.2 (2023-10-13)
• XCQ (2023-10-13)
• XBB.2.3.16 (2023-10-13)
• XBB.2.3.17 (2023-10-13)
• JD.2.1 (2023-10-13)
• GW.5.2 (2023-10-13)
• GW.5.3 (2023-10-13)
• GW.5.3.1 (2023-10-13)
• HW.1.2 (2023-10-13)
• HW.1.3 (2023-10-13)
• XBC.1.6.5 (2023-10-13)
• JT.1 (2023-10-13)
• XBC.1.6.6 (2023-10-13)
• GL.2 (2023-10-13)
• GL.3 (2023-10-13)
• XCR (2023-10-13)
• GK.5 (2023-10-15)
• GK.5.1 (2023-10-15)
• GK.6 (2023-10-15)
• GK.7 (2023-10-15)
• GK.8 (2023-10-15)
• GK.8.1 (2023-10-15)
• GK.9 (2023-10-15)
• GK.10 (2023-10-15)
• GK.11 (2023-10-15)
• GK.1.5 (2023-10-15)
• GK.1.6 (2023-10-15)
• GK.1.6.1 (2023-10-15)
• GK.1.2.1 (2023-10-15)
• GK.1.7 (2023-10-15)
• GK.1.8 (2023-10-15)
• GK.12 (2023-10-15)
• GK.1.9 (2023-10-15)
• XBB.1.16.25 (2023-10-15)
• XCS (2023-10-15)
• GK.1.1.1 (2023-10-15)
• FU.1.1 (2023-10-15)
• FU.1.1.1 (2023-10-15)
• HG.3 (2023-10-15)
• HG.1.1 (2023-10-15)
• XBB.2.3.18 (2023-10-15)
• GS.6 (2023-10-15)
• GS.4.1.1 (2023-10-15)
• GS.7 (2023-10-15)
• GS.7.1 (2023-10-15)
• GS.8 (2023-10-15)
• GJ.6 (2023-10-15)
• GJ.7 (2023-10-15)
• JU.1 (2023-10-15)
• JV.1 (2023-10-15)
• JV.2 (2023-10-15)
• JC.2 (2023-10-15)
• JC.3 (2023-10-15)
• JC.4 (2023-10-15)
• JC.5 (2023-10-15)
• JC.6 (2023-10-15)
• XBB.1.41.3 (2023-10-15)
• JW.1 (2023-10-15)
• FL.30.1 (2023-10-15)
• FL.13.2.1 (2023-10-15)
• FL.13.4 (2023-10-15)
• FL.13.4.1 (2023-10-15)
• FL.13.5 (2023-10-15)
• JG.4 (2023-10-15)
• DV.7.1.3 (2023-10-15)
• DV.7.1.4 (2023-10-15)
• DV.7.1.5 (2023-10-15)
• XCT (2023-10-15)
• XBC.1.7.2 (2023-10-15)
• XBC.1.7.1 (2023-10-15)
• FL.23.2.1 (2023-10-15)
• FL.23.2 (2023-10-15)
• XCU (2023-10-15)
• HH.2.1 (2023-10-15)
• HH.3 (2023-10-15)
• HH.4 (2023-10-15)
• HH.5 (2023-10-15)
• HH.6 (2023-10-15)
• HH.7 (2023-10-15)
• HH.8 (2023-10-15)
• HH.8.1 (2023-10-15)
• GE.1.4 (2023-10-15)
• GE.1.5 (2023-10-15)
• GE.1.6 (2023-10-15)
• XBB.2.3.19 (2023-10-15)
• JY.1 (2023-10-15)
• JY.1.1 (2023-10-15)
• JG.3.1 (2023-10-15)
• HK.2.1 (2023-10-15)
• HK.3.4 (2023-10-15)
• HK.3.5 (2023-10-15)
• HK.3.6 (2023-10-15)
• HK.3.7 (2023-10-15)
• HK.11.1 (2023-10-15)
• FL.35.1 (2023-10-15)
• GA.7 (2023-10-15)
• GA.7.1 (2023-10-15)
• GA.7.2 (2023-10-15)
• GA.8 (2023-10-15)
• GA.8.1 (2023-10-15)
• GA.9 (2023-10-15)
• GA.10 (2023-10-15)
• XCV (2023-10-15)
• XBB.2.3.20 (2023-10-15)
• XCW (2023-10-15)
• XBB.1.5.107 (2023-10-16)
• JZ.1 (2023-10-16)
• FD.5 (2023-10-16)
• FD.5.1 (2023-10-16)
• HE.2 (2023-10-16)
• FE.1.1.5 (2023-10-16)
• KA.1 (2023-10-16)
• GN.1.2 (2023-10-16)
• GN.1.3 (2023-10-16)
• XCY (2023-10-16)
• XCZ (2023-10-16)
• FY.8 (2023-10-16)
• FY.6.2 (2023-10-16)
• FY.6.1 (2023-10-16)
• FY.9 (2023-10-16)
• FY.1.4 (2023-10-16)
• FY.1.4.1 (2023-10-16)
• FY.5.1 (2023-10-16)
• FY.5.1.1 (2023-10-16)
• HN.2 (2023-10-17)
• HN.2.1 (2023-10-17)
• HN.3 (2023-10-17)
• HN.3.1 (2023-10-17)
• HN.4 (2023-10-17)
• HN.5 (2023-10-17)
• HN.6 (2023-10-17)
• GA.4.1.3 (2023-10-17)
• XDA (2023-10-18)
• XDB (2023-10-18)
• XDC (2023-10-18)

2023-10-03

New RSV datasets with consortium nomenclature (tag 2023-10-02T12:00:00Z)

• this adds a new developed nomenclature for RSV-A and RSV-B by the international RSV nomenclature consortium
• the old G_clade nomenclature is kept for backwards compatibility

2023-09-21

New SARS-CoV-2 dataset version (tag 2023-09-21T12:00:00Z)

• Add extra example sequences (GL.1, FL.1.5.1, EG.5.1, HV.1, DV.7.1, GK.2, BA.2.86)
• Add new frame shifts and stop codons to be ignored by QC
• Pango lineages designated between 2023-08-09 and 2023-09-20 are now included, unfold below to see a list with designation dates:

Newly included lineages, with designation date in parentheses

• JA.1 (2023-08-10)
• JB.1 (2023-08-10)
• JB.2 (2023-08-10)
• FW.1.1 (2023-08-22)
• JC.1 (2023-08-22)
• XBB.1.41.2 (2023-08-22)
• GA.4.1 (2023-08-22)
• GE.1.1 (2023-08-22)
• GE.1.2 (2023-08-22)
• XBB.1.5.102 (2023-08-22)
• JD.1 (2023-08-22)
• FL.1.5.2 (2023-08-23)
• JB.2.1 (2023-08-24)
• HK.6 (2023-08-24)
• GS.2 (2023-08-24)
• GS.3 (2023-08-24)
• GS.4 (2023-08-24)
• GS.4.1 (2023-08-24)
• GE.1.3 (2023-08-24)
• JE.1 (2023-08-24)
• HG.2 (2023-08-24)
• JF.1 (2023-08-24)
• JF.2 (2023-08-24)
• GK.1.4 (2023-08-24)
• GK.2.1 (2023-08-24)
• HK.3.1 (2023-08-24)
• XCH (2023-08-24)
• XCJ (2023-08-24)
• GM.3 (2023-08-24)
• GM.3.1 (2023-08-24)
• HC.2 (2023-08-25)
• EG.5.1.7 (2023-08-25)
• JD.1.1 (2023-08-25)
• JD.1.2 (2023-08-25)
• XBB.1.5.103 (2023-08-30)
• XCH.1 (2023-08-30)
• JG.1 (2023-08-30)
• HK.7 (2023-08-30)
• EG.2.2 (2023-08-30)
• EG.2.3 (2023-08-30)
• EG.2.4 (2023-08-30)
• EG.2.5 (2023-08-30)
• EG.13 (2023-08-31)
• FL.4.8 (2023-08-31)
• FL.4.9 (2023-08-31)
• FL.4.10 (2023-08-31)
• FY.3.2 (2023-08-31)
• FY.3.3 (2023-08-31)
• JH.1 (2023-08-31)
• JH.2 (2023-08-31)
• FL.2.6 (2023-08-31)
• XCK (2023-08-31)
• FL.10.2 (2023-08-31)
• XCL (2023-09-01)
• FL.30 (2023-09-01)
• GW.1.1 (2023-09-01)
• GK.2.2 (2023-09-01)
• HF.1.1 (2023-09-01)
• HF.1.2 (2023-09-01)
• XBB.1.5.104 (2023-09-01)
• XBB.1.16.23 (2023-09-01)
• XBB.1.5.105 (2023-09-01)
• HK.8 (2023-09-01)
• HK.9 (2023-09-01)
• JJ.1 (2023-09-01)
• HK.10 (2023-09-01)
• JK.1 (2023-09-01)
• HS.1.1 (2023-09-01)
• HK.11 (2023-09-04)
• JG.2 (2023-09-04)
• XBB.1.16.24 (2023-09-04)
• JL.1 (2023-09-04)
• BA.2.86.1 (2023-09-05)
• XCM (2023-09-05)
• FY.4.1.2 (2023-09-06)
• EG.6.1.1 (2023-09-07)
• GJ.1.2.2 (2023-09-10)
• GJ.1.2.3 (2023-09-10)
• GJ.1.2.4 (2023-09-10)
• GJ.1.2.5 (2023-09-10)
• FL.4.11 (2023-09-10)
• HK.3.2 (2023-09-10)
• HK.3.3 (2023-09-10)
• EG.14 (2023-09-10)
• GK.3.2 (2023-09-10)
• CK.1.1.2 (2023-09-10)
• EF.3 (2023-09-10)
• GW.5.1 (2023-09-11)
• GW.5.1.1 (2023-09-11)
• DV.7.1.1 (2023-09-11)
• DV.7.1.2 (2023-09-11)
• EG.5.1.8 (2023-09-11)
• GK.2.3 (2023-09-17)
• GK.4 (2023-09-17)
• EG.5.1.9 (2023-09-17)
• JG.3 (2023-09-17)
• XBB.1.5.106 (2023-09-17)