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Merge pull request #131 from nextstrain/2024-01-15-sc2-v2
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Update v2 SC2 datasets
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corneliusroemer authored Jan 15, 2024
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102 changes: 101 additions & 1 deletion CHANGELOG.md
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# CHANGELOG

## 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](https://docs.nextstrain.org/projects/nextclade/en/latest/user/migration-v3.html), specifically, CLI dataset paths may need to be updated, see [Dataset path changes](https://docs.nextstrain.org/projects/nextclade/en/latest/user/migration-v3.html#migration-paths-for-nextclade-cli). 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:

<details>
<summary> Newly included lineages, with designation date in parentheses</summary>

- 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)

</details>

## 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
- New A/H3N2 HA subclades H.1 - H.4

## 2023-12-03

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18 changes: 18 additions & 0 deletions data/datasets/sars-cov-2-21L/references/BA.2/versions/2024-01-15T12:00:00Z/files/genemap.gff
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##gff-version 3
##sequence-region MN908947 1 29903
# Gene map (genome annotation) of SARS-CoV-2 in GFF format.
# For gene map purpses we only need some of the columns. We substitute unused values with "." as per GFF spec.
# See GFF format reference at https://www.ensembl.org/info/website/upload/gff.html
# seqname source feature start end score strand frame attribute
MN908947 GenBank gene 266 13468 . + . gene_name=ORF1a
MN908947 GenBank gene 13468 21555 . + . gene_name=ORF1b
MN908947 GenBank gene 25393 26220 . + . gene_name=ORF3a
MN908947 GenBank gene 21563 25384 . + . gene_name=S
MN908947 GenBank gene 26245 26472 . + . gene_name=E
MN908947 GenBank gene 26523 27191 . + . gene_name=M
MN908947 GenBank gene 27202 27387 . + . gene_name=ORF6
MN908947 GenBank gene 27394 27759 . + . gene_name=ORF7a
MN908947 GenBank gene 27756 27887 . + . gene_name=ORF7b
MN908947 GenBank gene 27894 28259 . + . gene_name=ORF8
MN908947 GenBank gene 28274 29533 . + . gene_name=N
MN908947 GenBank gene 28284 28577 . + . gene_name=ORF9b
1 change: 1 addition & 0 deletions data/datasets/sars-cov-2-21L/references/BA.2/versions/2024-01-15T12:00:00Z/files/primers.csv
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Country (Institute),Target,Oligonucleotide,Sequence
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