nextstrain/nextclade_data 2024-01-16--20-31-02Z

on GitHub

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) (nextstrain/flu/h1n1pdm/ns)

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

Influenza A H3N2 MP (segment 7) (nextstrain/flu/h3n2/mp)

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

Influenza A H3N2 PA (segment 3) (nextstrain/flu/h3n2/pa)

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

Influenza A H1N1pdm PB2 (segment 1) (nextstrain/flu/h1n1pdm/pb2)

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

Influenza A H1N1pdm PB1 (segment 2) (nextstrain/flu/h1n1pdm/pb1)

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

Influenza A H3N2 PB2 (segment 1) (nextstrain/flu/h3n2/pb2)

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