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Merge pull request #75 from nextstrain/sc2-2023-05
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SC2 2023-05-10 update
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@corneliusroemer
corneliusroemer authored May 10, 2023
2 parents 46e43a2 + 5a56ad6 commit 594fe34
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158 changes: 158 additions & 0 deletions CHANGELOG.md
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# CHANGELOG

## 2023-05-10

### New SARS-CoV-2 dataset version (tag `2023-05-10T12:00:00Z`)

- The most terminal 50bp are now ignored/masked for reference tree placement purposes, see the [Nextclade changelog](https://github.com/nextstrain/nextclade/blob/master/CHANGELOG.md#algorithm--datasets-enable-masked-sites-for-distance-calculation) for details. This feature requires Nextclade v2.14.0 or later. Most sequences will be unaffected. As the only mutation appearing in this range in the reference tree is C44T in some BA.2/4/5 and XBB sequences.
- Labeled mutations have been updated. Criteria for inclusion have been relaxed to show slightly more non-clade defining mutations that commonly occurred within a clade, e.g. BN.1 and CH.1.1 defining mutations are now included under clade 22D (BA.2.75). This potentially worsens quality score for some sequences with such mutations.
- Pango lineages designated between 2023-04-18 and 2023-05-09 are now included, unfold below to see a list with designation dates:

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

- XBL.1 (2023-04-19)
- XBL.2 (2023-04-19)
- XBL.3 (2023-04-19)
- XBB.2.3.6 (2023-04-19)
- XBB.2.3.7 (2023-04-19)
- XBB.1.34 (2023-04-20)
- FR.1 (2023-04-21)
- FS.1 (2023-04-21)
- XCC (2023-04-22)
- EG.3 (2023-04-22)
- EG.1.2 (2023-04-22)
- EG.1.3 (2023-04-22)
- EG.1.4 (2023-04-22)
- EG.4 (2023-04-22)
- EG.5 (2023-04-22)
- FL.3 (2023-04-22)
- FL.4 (2023-04-22)
- FL.5 (2023-04-22)
- FK.1.2 (2023-04-22)
- FT.1 (2023-04-22)
- XAY.2.3 (2023-04-22)
- XAY.1.1.2 (2023-04-22)
- XAY.1.1.3 (2023-04-22)
- XBB.1.16.2 (2023-04-22)
- XBB.1.16.3 (2023-04-22)
- FU.1 (2023-04-22)
- FU.2 (2023-04-22)
- XBB.1.5.41 (2023-04-22)
- XBB.1.5.42 (2023-04-22)
- FL.2.1 (2023-04-22)
- FL.2.2 (2023-04-22)
- XBC.1.6.1 (2023-04-23)
- XBC.1.6.2 (2023-04-23)
- XBC.1.6.3 (2023-04-23)
- XBC.1.5.43 (2023-04-23)
- XBB.1.35 (2023-04-23)
- XBB.1.5.44 (2023-04-23)
- XBB.1.5.45 (2023-04-23)
- XBB.1.5.46 (2023-04-23)
- XBB.1.6.1 (2023-04-23)
- XBB.1.5.43 (2023-04-24)
- XBB.1.36 (2023-04-24)
- XBB.8.1 (2023-04-24)
- XBB.9 (2023-04-24)
- XBB.3.4 (2023-04-24)
- XBB.1.5.47 (2023-04-25)
- XBB.1.5.48 (2023-04-25)
- XBB.1.5.49 (2023-04-25)
- EU.1.1.1 (2023-04-26)
- XBB.1.5.50 (2023-04-26)
- XBB.1.5.51 (2023-04-26)
- XBB.1.5.52 (2023-04-26)
- FV.1 (2023-04-26)
- XBB.1.5.53 (2023-04-26)
- XBB.1.9.6 (2023-04-26)
- BQ.1.2.2 (2023-04-28)
- FW.1 (2023-05-01)
- FW.2 (2023-05-01)
- XBB.1.5.54 (2023-05-01)
- EK.4 (2023-05-01)
- XBB.2.3.8 (2023-05-01)
- FD.3 (2023-05-03)
- XBB.1.5.55 (2023-05-03)
- FL.6 (2023-05-03)
- XBB.2.3.9 (2023-05-04)
- XBB.2.3.10 (2023-05-04)
- FY.1 (2023-05-04)
- FY.2 (2023-05-04)
- FY.3 (2023-05-04)
- FY.4 (2023-05-04)
- FZ.1 (2023-05-05)
- FZ.1.1 (2023-05-05)
- FZ.2 (2023-05-05)
- XBB.1.5.56 (2023-05-05)
- XBB.1.16.4 (2023-05-05)
- XBB.1.5.57 (2023-05-05)
- FE.1.1 (2023-05-05)
- FE.1.2 (2023-05-05)
- GA.1 (2023-05-06)
- GA.2 (2023-05-06)
- GA.3 (2023-05-06)
- CH.1.1.24 (2023-05-06)
- CH.1.1.25 (2023-05-06)
- CH.1.1.26 (2023-05-06)
- DV.6 (2023-05-06)
- CH.1.1.27 (2023-05-06)
- XBB.1.5.58 (2023-05-06)
- XBB.1.5.59 (2023-05-06)
- XBB.1.5.60 (2023-05-06)
- XBB.1.5.61 (2023-05-06)
- XBB.1.5.62 (2023-05-06)
- XBB.1.5.63 (2023-05-06)
- XBB.1.5.64 (2023-05-06)
- XBB.1.5.65 (2023-05-06)
- XBB.1.5.66 (2023-05-06)
- XBB.1.5.67 (2023-05-06)
- GB.1 (2023-05-06)
- XBB.1.16.5 (2023-05-06)
- FD.4 (2023-05-06)
- FL.7 (2023-05-06)
- XBB.1.5.68 (2023-05-06)
- XBB.1.37 (2023-05-06)
- XBB.1.37.1 (2023-05-06)
- XBB.1.5.69 (2023-05-07)
- XBB.1.16.6 (2023-05-07)
- EG.5.1 (2023-05-07)
- GC.1 (2023-05-07)
- GC.2 (2023-05-07)
- FL.8 (2023-05-07)
- FL.9 (2023-05-07)
- FL.10 (2023-05-07)
- FL.11 (2023-05-07)
- CH.1.1.28 (2023-05-07)
- FL.3.1 (2023-05-07)
- FL.3.2 (2023-05-07)
- FL.3.3 (2023-05-07)
- FL.3.4 (2023-05-07)
- XBB.1.24.1 (2023-05-07)
- XBB.1.24.2 (2023-05-07)
- XBB.1.24.3 (2023-05-07)
- XBB.1.38 (2023-05-07)
- GD.1 (2023-05-07)
- XBB.1.39 (2023-05-07)
- XBB.1.40 (2023-05-07)
- GE.1 (2023-05-07)
- XBB.2.3.11 (2023-05-07)
- FL.1.1 (2023-05-07)
- FL.1.2 (2023-05-07)
- FL.1.3 (2023-05-07)
- XBB.3.5 (2023-05-07)
- BN.1.2.5 (2023-05-07)
- FR.2 (2023-05-07)
- BN.1.2.6 (2023-05-07)
- EJ.3 (2023-05-07)
- BN.1.3.11 (2023-05-07)
- BQ.1.2.3 (2023-05-07)
- BQ.1.3.1 (2023-05-07)
- BQ.1.3.2 (2023-05-07)
- BQ.1.33 (2023-05-07)
- DN.2 (2023-05-07)
- DN.3 (2023-05-07)
- DN.3.1 (2023-05-07)
- XBB.1.32.1 (2023-05-08)
- FL.12 (2023-05-08)

</details>

## 2023-04-18

### New SARS-CoV-2 dataset version (tag `2023-04-18T12:00:00Z`)
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18 changes: 18 additions & 0 deletions data/datasets/sars-cov-2-21L/references/BA.2/versions/2023-05-10T12:00:00Z/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/2023-05-10T12:00:00Z/files/primers.csv
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Country (Institute),Target,Oligonucleotide,Sequence
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