Merge pull request #73 from nextstrain/sc2-update-2022-04-18

SC2 update 2023-04-18

CHANGELOG.md

@@ -1,5 +1,165 @@
 # CHANGELOG
 
+## 2023-04-18
+
+### New SARS-CoV-2 dataset version (tag `2023-04-18T12:00:00Z`)
+
+#### `SARS-CoV-2` and `SARS-CoV-2-21L`
+
+- New Nextstrain clade 23B (XBB.1.16) was added, see this [ncov PR](https://github.com/nextstrain/ncov/pull/1059) for a detailed discussion of this clade
+- The `SARS-CoV-2` dataset now shows WHO variant name in the web results table instead of unaliased Pango lineage. This is a web-display-only change: All output files (web/CLI) are unchanged. Unaliased Pango lineage is still available in the `SARS-CoV-2-21L` dataset.
+- Pango lineages designated between 2023-03-15 and 2023-04-17 are now included, unfold below to see a list with designation dates:
+
+<details>
+  <summary> Newly included lineages, with designation date in parentheses</summary>
+
+- ET.1 (2023-03-16)
+- XBC.1.6 (2023-03-16)
+- XBB.1.17 (2023-03-18)
+- XBB.1.17.1 (2023-03-18)
+- XBB.1.17.2 (2023-03-18)
+- XBB.1.5.22 (2023-03-18)
+- XBB.1.5.23 (2023-03-18)
+- XBB.1.18 (2023-03-18)
+- XBB.1.18.1 (2023-03-18)
+- XBB.1.5.24 (2023-03-18)
+- XBB.1.5.25 (2023-03-18)
+- XBU (2023-03-19)
+- XBB.1.19 (2023-03-19)
+- XBB.1.19.1 (2023-03-19)
+- XBB.1.20 (2023-03-19)
+- XBV (2023-03-19)
+- DV.1.1 (2023-03-19)
+- CP.8 (2023-03-19)
+- XBW (2023-03-19)
+- XBY (2023-03-19)
+- XBB.1.5.26 (2023-03-19)
+- EU.1 (2023-03-19)
+- EU.1.1 (2023-03-19)
+- XBF.8.1 (2023-03-19)
+- XBB.1.21 (2023-03-19)
+- XBC.2.1 (2023-03-19)
+- XBB.1.22 (2023-03-19)
+- XBB.1.22.1 (2023-03-19)
+- XBB.1.22.2 (2023-03-19)
+- XBB.1.9.5 (2023-03-19)
+- XBB.1.9.4 (2023-03-19)
+- XBB.1.23 (2023-03-19)
+- XBJ.1 (2023-03-19)
+- XBJ.1.1 (2023-03-19)
+- XBJ.2 (2023-03-19)
+- XBJ.3 (2023-03-19)
+- XBJ.4 (2023-03-19)
+- XBB.2.7 (2023-03-19)
+- XBB.1.27 (2023-03-19)
+- XBB.1.24 (2023-03-20)
+- XBB.1.25 (2023-03-20)
+- XBB.1.26 (2023-03-20)
+- CH.1.1.16 (2023-03-20)
+- CH.1.1.17 (2023-03-20)
+- DV.5 (2023-03-20)
+- EV.1 (2023-03-21)
+- EW.1 (2023-03-21)
+- EW.2 (2023-03-21)
+- EW.3 (2023-03-21)
+- EY.1 (2023-03-21)
+- EZ.1 (2023-03-21)
+- XBB.1.16.1 (2023-03-22)
+- XBB.1.5.27 (2023-03-22)
+- EK.3 (2023-03-22)
+- EK.2.1 (2023-03-22)
+- XBB.1.5.28 (2023-03-22)
+- BE.11 (2023-03-22)
+- BE.12 (2023-03-22)
+- BE.13 (2023-03-22)
+- FA.1 (2023-03-22)
+- FA.2 (2023-03-22)
+- DR.2 (2023-03-22)
+- FB.1 (2023-03-22)
+- FB.2 (2023-03-22)
+- BQ.1.1.72 (2023-03-22)
+- FC.1 (2023-03-22)
+- FD.1 (2023-03-22)
+- FD.1.1 (2023-03-22)
+- FE.1 (2023-03-22)
+- XBB.1.5.29 (2023-03-22)
+- XBB.1.5.30 (2023-03-22)
+- FF.1 (2023-03-22)
+- CP.8.1 (2023-03-23)
+- BN.1.3.9 (2023-03-23)
+- XBB.1.5.31 (2023-03-24)
+- XBB.1.5.32 (2023-03-24)
+- XBB.1.5.33 (2023-03-24)
+- XBB.2.3.1 (2023-03-24)
+- XBB.2.3.2 (2023-03-24)
+- CH.1.1.18 (2023-03-24)
+- XBB.1.28 (2023-03-24)
+- XBB.1.29 (2023-03-24)
+- XBB.1.5.34 (2023-03-24)
+- XBB.1.30 (2023-03-24)
+- XBB.1.5.35 (2023-03-24)
+- XBB.1.5.36 (2023-03-24)
+- BL.1.5 (2023-03-24)
+- BQ.1.26.2 (2023-03-24)
+- XBF.9 (2023-03-24)
+- FG.1 (2023-03-24)
+- FG.2 (2023-03-24)
+- FG.3 (2023-03-24)
+- CH.1.1.19 (2023-03-24)
+- CH.1.1.20 (2023-03-24)
+- CM.8.1.3 (2023-03-24)
+- CM.8.1.4 (2023-03-24)
+- DN.1.1.3 (2023-03-24)
+- DN.1.1.4 (2023-03-24)
+- XBB.2.8 (2023-03-24)
+- XBB.2.7.1 (2023-03-24)
+- BF.5.5 (2023-03-24)
+- XBB.1.5.37 (2023-03-27)
+- FD.2 (2023-03-27)
+- XBB.1.5.38 (2023-03-27)
+- FH.1 (2023-03-27)
+- XBB.1.5.39 (2023-03-27)
+- XBZ (2023-03-28)
+- CH.1.1.21 (2023-03-29)
+- CH.1.1.22 (2023-03-29)
+- FJ.1 (2023-03-29)
+- BN.1.3.10 (2023-03-30)
+- FK.1 (2023-03-31)
+- BQ.1.1.73 (2023-04-03)
+- XCA (2023-04-03)
+- EG.2 (2023-04-04)
+- XBB.1.31 (2023-04-04)
+- XBB.1.32 (2023-04-04)
+- FL.1 (2023-04-04)
+- XBB.2.3.3 (2023-04-04)
+- XBB.2.3.4 (2023-04-04)
+- XBB.1.5.40 (2023-04-04)
+- FM.1 (2023-04-04)
+- FM.2 (2023-04-04)
+- FL.2 (2023-04-04)
+- BQ.1.1.74 (2023-04-05)
+- FN.1 (2023-04-05)
+- EG.1.1 (2023-04-07)
+- XBB.1.28.1 (2023-04-07)
+- CJ.1.2 (2023-04-07)
+- CJ.1.3 (2023-04-07)
+- XBF.1.1 (2023-04-08)
+- XBF.10 (2023-04-08)
+- FP.1 (2023-04-11)
+- BF.42 (2023-04-11)
+- CH.1.1.23 (2023-04-11)
+- XBB.2.3.5 (2023-04-12)
+- FK.1.1 (2023-04-13)
+- XCB (2023-04-14)
+- FQ.1 (2023-04-17)
+- XBB.1.33 (2023-04-18)
+
+</details>
+
+#### `SARS-CoV-2-no-recomb` will no longer be updated
+
+Starting with this update, the `SARS-CoV-2-no-recomb` dataset - an auxiliary dataset with niche usage - will no longer be updated. This dataset was created to mitigate bias Nextclade had in previous versions to attach incomplete sequences to recombinants. This bias has been fixed in Nextclade version 2.13.0 (see this [CHANGELOG entry](https://github.com/nextstrain/nextclade/blob/master/CHANGELOG.md#attach-sequences-to-a-priori-most-likely-node-if-reference-tree-contains-placement_prior) for a detailed discussion). Furthermore, with the majority of current circulation being recombinant (mostly XBB), this dataset is no longer adequate. Users should simply use the main `SARS-CoV-2` dataset instead.
+
 ## 2023-04-02
 
 ### New dataset version (tag `2023-04-02T12:00:00Z`)
@@ -23,7 +183,7 @@ The B/Vic annotation of the HA segment was fixed -- it was previously off by 3 n
 #### SARS-CoV-2 datasets
 
 - Placement priors: Every tree node is now annotated with a `placement_prior`, an approximate probability (on log10 scale) that a random sequence is attached to this node. For this dataset, the prior was caluclated after placing 300k sequences on the tree. A value of `-10` is chosen when no sequence in the sample attached to a node. The placement priors will improve placement accuracy of incomplete sequences (such as Spike only) - but only with a recent version of Nextclade (probably 2.13.0 and above). In that release, we will introduce a new placement tie-breaking feature: when a query sequence can attach to multiple nodes with equal number of mismatches, the sequence will be attached to the reference tree node with the highest prior. This is in contrast to the previous naive tie breaking logic which always chose the node with the fewest number of parent nodes. This lead to a bias towards attaching to recombinants. See <https://github.com/neherlab/nextclade_data_workflows/pull/38> for the code calculating the placement priors, and <https://github.com/nextstrain/nextclade/pull/1119> to see how the priors are used in Nextclade.
-- Pango lineages desiganted between 2023-02-24 and 2023-03-15 are now included, unfold below to see a list of them:
+- Pango lineages designated between 2023-02-24 and 2023-03-15 are now included, unfold below to see a list of them:
 
 <details>
   <summary> Newly included lineages, with designation date in parentheses</summary>

data/datasets/sars-cov-2-21L/references/BA.2/versions/2023-04-18T12:00:00Z/files/genemap.gff

@@ -0,0 +1,18 @@
+##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

data/datasets/sars-cov-2-21L/references/BA.2/versions/2023-04-18T12:00:00Z/files/primers.csv

@@ -0,0 +1 @@
+Country (Institute),Target,Oligonucleotide,Sequence