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Merge pull request #113 from nextstrain/sc2-2023-12-03
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Update SC2 dataset, new clades 23G/H/I
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@corneliusroemer
corneliusroemer authored Dec 4, 2023
2 parents 7b5ffc1 + b523288 commit 8070204
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134 changes: 131 additions & 3 deletions CHANGELOG.md
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# CHANGELOG

## 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](https://github.com/nextstrain/ncov/pull/1087) 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:

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

- 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)

</details>

## 2023-11-25

### RSV-A and RSV-B nomenclature revision (tag `2023-11-25T12:00:00Z`)

Update RSV-A and RSV-B datasets with the revised consortium nomenclature. This update slightly reduces the number of lineages and renames some lineages. The lineage definitions are now available on https://github.com/rsv-lineages.

## 2023-11-22

### Fix for influenza B/Vic dataset version (tag `2023-11-22T12:00:00Z`)

- the previous dataset was missing two subclades C.2 and C.4.
- the previous dataset was missing two subclades C.2 and C.4.

## 2023-11-18

### New Influenza datasets version (tag `2023-11-18T12:00:00Z`)

- new subclades for several lineages
- new alias for A/H3N2 HA
- new subclades for several lineages
- new alias for A/H3N2 HA

## 2023-10-26

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18 changes: 18 additions & 0 deletions data/datasets/sars-cov-2-21L/references/BA.2/versions/2023-12-03T12:00:00Z/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/2023-12-03T12:00:00Z/files/primers.csv
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Country (Institute),Target,Oligonucleotide,Sequence
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