Merge pull request #209 from nextstrain/sc2-june-2024

Update SC2 datasets
nextstrain · Jun 11, 2024 · 655cab4 · 655cab4
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diff --git a/data/nextstrain/sars-cov-2/BA.2.86/CHANGELOG.md b/data/nextstrain/sars-cov-2/BA.2.86/CHANGELOG.md
@@ -1,3 +1,186 @@
+## Unreleased
+
+- Labelled mutations added for Nextstrain clades 24A (JN.1) and 24B (JN.1.11.1)
+- All 172 Pango lineages designated between 2024-04-13 and 2024-06-10 are now included, unfold below to see a list of all newly included lineages with their designation dates:
+
+<details>
+  <summary> Newly included lineages, with designation date in parentheses</summary>
+
+- KP.4 (2024-04-15)
+- KP.4.1 (2024-04-15)
+- KP.4.2 (2024-04-15)
+- KP.1.2 (2024-04-15)
+- KP.2.3 (2024-04-15)
+- JN.1.47 (2024-04-15)
+- JN.1.47.1 (2024-04-15)
+- JN.1.47.2 (2024-04-15)
+- JN.1.16.2 (2024-04-15)
+- LA.1 (2024-04-15)
+- LA.2 (2024-04-15)
+- JN.1.9.2 (2024-04-15)
+- LB.2 (2024-04-15)
+- JN.1.7.4 (2024-04-15)
+- JN.1.24.1 (2024-04-15)
+- LC.1 (2024-04-15)
+- JN.1.32.1 (2024-04-15)
+- KW.1.2 (2024-04-15)
+- JN.1.8.4 (2024-04-15)
+- JN.1.48 (2024-04-15)
+- JN.1.48.1 (2024-04-15)
+- LB.1 (2024-04-16)
+- XDW (2024-04-18)
+- XDQ.2 (2024-04-18)
+- XDQ.3 (2024-04-18)
+- XDQ.1.1 (2024-05-15)
+- XDK.1.1 (2024-05-15)
+- XDK.1.2 (2024-05-15)
+- XDK.2 (2024-05-15)
+- XDK.3 (2024-05-15)
+- XDR.1 (2024-05-15)
+- KP.2.4 (2024-05-15)
+- KP.2.5 (2024-05-15)
+- KP.2.6 (2024-05-15)
+- KP.2.7 (2024-05-15)
+- KP.2.3.1 (2024-05-15)
+- KP.4.2.1 (2024-05-15)
+- KP.2.8 (2024-05-15)
+- KP.2.9 (2024-05-15)
+- KP.2.10 (2024-05-15)
+- KP.2.11 (2024-05-15)
+- KP.2.12 (2024-05-15)
+- LD.1 (2024-05-15)
+- JN.1.48.2 (2024-05-15)
+- KP.1.1.2 (2024-05-15)
+- LE.1 (2024-05-15)
+- LE.1.1 (2024-05-15)
+- LE.1.2 (2024-05-15)
+- LE.2 (2024-05-15)
+- LF.1 (2024-05-15)
+- LF.1.1 (2024-05-15)
+- JN.1.42.2 (2024-05-15)
+- JN.1.49 (2024-05-15)
+- JN.1.49.1 (2024-05-15)
+- JN.1.49.2 (2024-05-15)
+- KW.1.1.1 (2024-05-15)
+- LG.1 (2024-05-15)
+- JN.1.39.1 (2024-05-15)
+- JN.1.39.2 (2024-05-16)
+- KP.5 (2024-05-16)
+- KP.3.1 (2024-05-16)
+- KP.3.2 (2024-05-16)
+- KP.3.3 (2024-05-16)
+- JN.1.39.3 (2024-05-16)
+- JN.15 (2024-05-16)
+- JN.3.3 (2024-05-16)
+- JN.16 (2024-05-16)
+- JN.17 (2024-05-16)
+- JN.11.1 (2024-05-16)
+- BA.2.86.6 (2024-05-16)
+- JN.18 (2024-05-16)
+- JQ.2.1.1 (2024-05-16)
+- JN.19 (2024-05-16)
+- JN.1.1.8 (2024-05-17)
+- KP.2.13 (2024-05-17)
+- JN.1.50 (2024-05-18)
+- JN.1.23.1 (2024-05-28)
+- JN.1.29.1 (2024-05-28)
+- JN.1.18.3 (2024-05-28)
+- JN.1.18.4 (2024-05-28)
+- LH.1 (2024-05-28)
+- LH.2 (2024-05-28)
+- KP.1.1.3 (2024-05-28)
+- KP.3.1.1 (2024-05-28)
+- KP.2.14 (2024-05-28)
+- JN.1.51 (2024-05-28)
+- JN.1.51.1 (2024-05-28)
+- LJ.1 (2024-05-28)
+- LF.2 (2024-05-28)
+- JN.1.52 (2024-05-28)
+- JN.1.7.5 (2024-05-28)
+- LK.1 (2024-05-28)
+- JN.1.50.1 (2024-05-28)
+- LF.3 (2024-05-28)
+- KP.4.2.2 (2024-05-28)
+- XDK.4 (2024-05-28)
+- XDK.4.1 (2024-05-28)
+- XDK.5 (2024-05-28)
+- XDK.6 (2024-05-28)
+- LL.1 (2024-05-28)
+- LM.1 (2024-05-28)
+- KS.1.1 (2024-05-28)
+- JN.1.53 (2024-05-28)
+- JN.1.53.1 (2024-05-28)
+- LN.1 (2024-05-28)
+- LN.1.1 (2024-05-28)
+- JN.1.54 (2024-05-28)
+- JN.1.54.1 (2024-05-28)
+- LP.1 (2024-05-28)
+- KP.3.4 (2024-05-29)
+- KP.3.2.1 (2024-05-29)
+- KP.2.15 (2024-05-30)
+- KR.1.1 (2024-05-30)
+- KR.1.2 (2024-05-30)
+- KR.3 (2024-05-30)
+- KR.4 (2024-05-30)
+- KR.5 (2024-05-30)
+- KS.1.2 (2024-05-30)
+- JN.1.55 (2024-05-30)
+- JN.1.55.1 (2024-05-30)
+- JN.1.55.2 (2024-05-30)
+- KP.3.2.2 (2024-05-30)
+- JN.1.56 (2024-05-31)
+- JN.1.56.1 (2024-05-31)
+- JN.1.44.1 (2024-05-31)
+- LB.1.1 (2024-06-04)
+- LB.1.2 (2024-06-04)
+- LB.1.2.1 (2024-06-04)
+- LB.1.3 (2024-06-04)
+- LB.1.4 (2024-06-04)
+- LB.1.5 (2024-06-04)
+- LB.1.6 (2024-06-04)
+- KP.2.3.2 (2024-06-04)
+- KP.2.16 (2024-06-04)
+- LF.3.1 (2024-06-04)
+- KP.3.1.2 (2024-06-04)
+- KP.3.1.3 (2024-06-04)
+- KP.3.1.4 (2024-06-04)
+- KP.3.2.3 (2024-06-04)
+- KP.3.2.4 (2024-06-04)
+- LB.1.7 (2024-06-04)
+- LF.1.1.1 (2024-06-04)
+- KP.1.1.4 (2024-06-04)
+- LP.2 (2024-06-04)
+- XDY (2024-06-04)
+- LQ.1 (2024-06-04)
+- LQ.1.1 (2024-06-04)
+- LQ.2 (2024-06-04)
+- LQ.3 (2024-06-04)
+- JN.1.4.8 (2024-06-04)
+- JN.1.7.6 (2024-06-04)
+- JN.1.57 (2024-06-04)
+- JN.1.57.1 (2024-06-04)
+- JN.1.58 (2024-06-04)
+- JN.1.58.1 (2024-06-04)
+- JN.1.58.2 (2024-06-04)
+- LR.1 (2024-06-04)
+- LR.2 (2024-06-04)
+- JN.1.59 (2024-06-05)
+- JN.1.7.7 (2024-06-05)
+- JN.1.60 (2024-06-05)
+- JN.1.61 (2024-06-05)
+- JN.1.18.5 (2024-06-07)
+- LS.1 (2024-06-07)
+- KP.2.3.3 (2024-06-07)
+- JN.1.62 (2024-06-08)
+- KP.3.2.5 (2024-06-09)
+- LT.1 (2024-06-10)
+- JN.1.1.9 (2024-06-10)
+- JN.1.16.3 (2024-06-10)
+- JN.1.15.1 (2024-06-10)
+- LU.1 (2024-06-10)
+
+</details>
+
 ## 2024-04-25T01:03:07Z
 
 - fix: Increase Nextclade alignment parameter "excessBandwidth" from 9 to 12 to correctly align complex series of indels that has arisen in Spike NTD with the occurrence of S:31- in some JN.1. The bandwidth is chosen to be as small as possible (to ensure fast runtime) but as large as necessary for correct alignment. As a result, occasional adjustments like here are required. Nothing else is changed in this SARS-CoV-2 dataset update.