diff --git a/data/nextstrain/sars-cov-2/wuhan-hu-1/orfs/CHANGELOG.md b/data/nextstrain/sars-cov-2/wuhan-hu-1/orfs/CHANGELOG.md
index 8860eec46..7161bb523 100644
--- a/data/nextstrain/sars-cov-2/wuhan-hu-1/orfs/CHANGELOG.md
+++ b/data/nextstrain/sars-cov-2/wuhan-hu-1/orfs/CHANGELOG.md
@@ -1,3 +1,7 @@
+## Unreleased
+
+Add "recombinant" QC metric
+
## 2025-09-19T14:53:06Z
- Add all 172 Pango lineages newly designated between 2025-08-01 and 2025-09-18. Unfold below to see a list of all newly included lineages with their designation dates:
diff --git a/data/nextstrain/sars-cov-2/wuhan-hu-1/orfs/pathogen.json b/data/nextstrain/sars-cov-2/wuhan-hu-1/orfs/pathogen.json
index e97bbe448..3bb31f72f 100644
--- a/data/nextstrain/sars-cov-2/wuhan-hu-1/orfs/pathogen.json
+++ b/data/nextstrain/sars-cov-2/wuhan-hu-1/orfs/pathogen.json
@@ -2691,6 +2691,11 @@
"cdsName": "ORF9b"
}
]
+ },
+ "recombinants": {
+ "enabled": true,
+ "mutationsThreshold": 3,
+ "scoreWeight": 100.0
}
},
"schemaVersion": "3.0.0",
diff --git a/data_output/index.json b/data_output/index.json
index 6e0f52ab0..ac512d4a8 100644
--- a/data_output/index.json
+++ b/data_output/index.json
@@ -88,13 +88,21 @@
"mixedSites",
"privateMutations",
"snpClusters",
- "stopCodons"
+ "stopCodons",
+ "recombinants"
],
"other": [
"mutLabels"
]
},
"versions": [
+ {
+ "tag": "unreleased",
+ "compatibility": {
+ "cli": "3.0.0-alpha.0",
+ "web": "3.0.0-alpha.0"
+ }
+ },
{
"updatedAt": "2025-09-19T14:53:06Z",
"tag": "2025-09-19--14-53-06Z",
@@ -257,8 +265,7 @@
}
],
"version": {
- "updatedAt": "2025-09-19T14:53:06Z",
- "tag": "2025-09-19--14-53-06Z",
+ "tag": "unreleased",
"compatibility": {
"cli": "3.0.0-alpha.0",
"web": "3.0.0-alpha.0"
diff --git a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/CHANGELOG.md b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/CHANGELOG.md
new file mode 100644
index 000000000..7161bb523
--- /dev/null
+++ b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/CHANGELOG.md
@@ -0,0 +1,1460 @@
+## Unreleased
+
+Add "recombinant" QC metric
+
+## 2025-09-19T14:53:06Z
+
+- Add all 172 Pango lineages newly designated between 2025-08-01 and 2025-09-18. Unfold below to see a list of all newly included lineages with their designation dates:
+
+
+ Newly included lineages, with designation date in parentheses
+
+- XFG.5.1 (2025-08-02)
+- XFG.5.2 (2025-08-02)
+- XFG.5.3 (2025-08-02)
+- XFG.7.1 (2025-08-02)
+- MC.44 (2025-08-02)
+- MC.45 (2025-08-02)
+- MC.46 (2025-08-02)
+- MC.46.1 (2025-08-02)
+- XFG.23 (2025-08-03)
+- XFG.23.1 (2025-08-03)
+- XFG.18.1 (2025-08-03)
+- QK.1 (2025-08-03)
+- PQ.2.3 (2025-08-03)
+- PQ.2.4 (2025-08-03)
+- XFG.3.4.4 (2025-08-17)
+- XFG.3.8 (2025-08-17)
+- XFG.3.8.1 (2025-08-17)
+- NY.15.2 (2025-08-17)
+- NY.15.1 (2025-08-17)
+- PQ.9.1.1 (2025-08-17)
+- XFG.2.3 (2025-08-17)
+- XFG.2.3.1 (2025-08-17)
+- QL.1 (2025-08-17)
+- QL.1.1 (2025-08-17)
+- NW.1.2.1 (2025-08-17)
+- QM.1 (2025-08-17)
+- NW.1.2.2 (2025-08-17)
+- NW.1.2.3 (2025-08-17)
+- PY.1.5 (2025-08-17)
+- PY.1.6 (2025-08-17)
+- PY.1.7 (2025-08-17)
+- PY.1.8 (2025-08-17)
+- NY.13.1 (2025-08-17)
+- NY.13.2 (2025-08-17)
+- NY.13.2.1 (2025-08-17)
+- NY.13.3.1 (2025-08-17)
+- XFG.24 (2025-08-17)
+- XFG.25 (2025-08-17)
+- NB.1.9 (2025-08-18)
+- NB.1.5.1 (2025-08-18)
+- QN.1 (2025-08-18)
+- NB.1.5.2 (2025-08-18)
+- NB.1.10 (2025-08-18)
+- NB.1.11 (2025-08-18)
+- NB.1.5.3 (2025-08-18)
+- NB.1.12 (2025-08-18)
+- NB.1.13 (2025-08-18)
+- PQ.29 (2025-08-18)
+- XFW (2025-08-20)
+- XFW.1 (2025-08-20)
+- XDY.3.1 (2025-08-20)
+- XDY.3.2 (2025-08-20)
+- XDY.3.3 (2025-08-20)
+- XFG.17.1 (2025-08-20)
+- XFG.17.2 (2025-08-20)
+- XFG.17.3 (2025-08-20)
+- LF.7.2.2 (2025-08-20)
+- XFG.3.9 (2025-08-20)
+- XFG.3.10 (2025-08-20)
+- XFG.3.11 (2025-08-20)
+- XFG.3.12 (2025-08-20)
+- XFG.3.12.1 (2025-08-20)
+- PQ.31 (2025-08-22)
+- XFG.3.13 (2025-08-22)
+- XFG.6.1 (2025-08-22)
+- XFJ.2.1 (2025-08-22)
+- XFV.1 (2025-08-22)
+- NY.13.3 (2025-08-22)
+- PQ.30 (2025-08-24)
+- XFY (2025-08-24)
+- XFZ (2025-08-24)
+- PG.3.2 (2025-08-24)
+- XFG.26 (2025-08-26)
+- XFG.27 (2025-08-26)
+- XFG.28 (2025-08-26)
+- XFG.29 (2025-08-26)
+- XFG.30 (2025-08-26)
+- XFG.31 (2025-08-26)
+- XFG.3.14 (2025-08-26)
+- XFG.3.16 (2025-08-26)
+- XFG.32 (2025-08-26)
+- XFG.10.1 (2025-08-26)
+- QK.2 (2025-08-26)
+- XFG.3.1.4 (2025-08-26)
+- XFG.17.2.1 (2025-08-26)
+- XFG.3.15 (2025-08-26)
+- LH.3 (2025-08-27)
+- XFG.3.5.2 (2025-08-30)
+- XFG.22.1 (2025-08-30)
+- XFG.17.4 (2025-09-04)
+- XFT.1 (2025-09-06)
+- XFG.3.1.5 (2025-09-06)
+- XFG.7.1.1 (2025-09-06)
+- PG.6.1 (2025-09-06)
+- NB.1.1.1 (2025-09-06)
+- PQ.17.1 (2025-09-07)
+- PQ.1.5 (2025-09-07)
+- PQ.1.6 (2025-09-07)
+- PQ.1.6.1 (2025-09-07)
+- PQ.17.2 (2025-09-07)
+- PQ.2.5 (2025-09-07)
+- XFC.1.7 (2025-09-07)
+- NW.3.1 (2025-09-07)
+- NW.3.2 (2025-09-07)
+- XFG.1.1 (2025-09-11)
+- NY.3.7 (2025-09-11)
+- XFG.4.1.1 (2025-09-12)
+- XFG.4.2 (2025-09-12)
+- PQ.4.2 (2025-09-12)
+- PQ.4.3 (2025-09-12)
+- PQ.4.4 (2025-09-12)
+- PQ.4.5 (2025-09-12)
+- XEC.42 (2025-09-13)
+- XEC.43 (2025-09-13)
+- PE.1.2 (2025-09-13)
+- PE.1.1.1 (2025-09-13)
+- PE.1.6 (2025-09-13)
+- PE.1.7 (2025-09-13)
+- PE.1.4.1 (2025-09-13)
+- PE.1.4.2 (2025-09-13)
+- PE.2 (2025-09-13)
+- PE.3 (2025-09-13)
+- QP.1 (2025-09-13)
+- NY.20 (2025-09-13)
+- NY.20.1 (2025-09-13)
+- NY.22 (2025-09-13)
+- NY.23 (2025-09-13)
+- NY.25 (2025-09-13)
+- NY.25.1 (2025-09-13)
+- NY.24 (2025-09-13)
+- XGA (2025-09-13)
+- NW.1.2.5 (2025-09-13)
+- NW.1.2.4 (2025-09-13)
+- XFG.3.17 (2025-09-13)
+- QK.3 (2025-09-13)
+- XFG.9.2 (2025-09-13)
+- PQ.32 (2025-09-13)
+- PQ.13.2 (2025-09-13)
+- PQ.33 (2025-09-13)
+- PQ.2.6 (2025-09-13)
+- PQ.25.1 (2025-09-13)
+- PQ.25.2 (2025-09-13)
+- PQ.31.1 (2025-09-13)
+- PQ.34 (2025-09-13)
+- QR.1 (2025-09-14)
+- QR.2 (2025-09-14)
+- PC.3.3 (2025-09-14)
+- PC.3.4 (2025-09-14)
+- LF.7.11.1 (2025-09-14)
+- LF.7.11.2 (2025-09-14)
+- LF.7.11.3 (2025-09-14)
+- PL.1.2 (2025-09-14)
+- PL.4 (2025-09-14)
+- PL.5 (2025-09-14)
+- XEK.7.1 (2025-09-14)
+- KP.7 (2025-09-14)
+- KP.7.1 (2025-09-14)
+- XFG.33 (2025-09-14)
+- XFG.6.2 (2025-09-14)
+- KP.3.18 (2025-09-14)
+- XFG.14.3 (2025-09-14)
+- QS.1 (2025-09-14)
+- NW.1.7.1 (2025-09-14)
+- NW.1.7.2 (2025-09-14)
+- NW.1.7.3 (2025-09-14)
+- NW.1.7.4 (2025-09-14)
+- XFG.3.18 (2025-09-14)
+- XGB (2025-09-14)
+- QS.2 (2025-09-14)
+- XFG.9.3 (2025-09-14)
+- XFG.9.4 (2025-09-14)
+- XFG.9.5 (2025-09-14)
+
+
+
+## 2025-09-09T12:13:13Z
+
+Add schema definition url to `pathogen.json`. This is a purely technical change, for convenience of dataset authors. The data itself is not modified.
+
+## 2025-08-02T08:55:17Z
+
+- Add all 185 Pango lineages newly designated between 2025-06-09 and 2025-07-30. Unfold below to see a list of all newly included lineages with their designation dates:
+
+
+ Newly included lineages, with designation date in parentheses
+
+- PE.1.1 (2025-06-12)
+- PE.1.3 (2025-06-12)
+- PE.1.4 (2025-06-12)
+- PE.1.5 (2025-06-12)
+- MC.10.2.3 (2025-06-12)
+- XEC.27.1 (2025-06-12)
+- XEC.27.2 (2025-06-12)
+- NY.16.2 (2025-06-12)
+- XEC.23.1 (2025-06-12)
+- MC.9.3 (2025-06-12)
+- XEC.2.7 (2025-06-12)
+- XEC.2.8 (2025-06-12)
+- XEC.2.9 (2025-06-12)
+- XEC.2.10 (2025-06-12)
+- XEC.41 (2025-06-12)
+- PZ.1 (2025-06-13)
+- QA.1 (2025-06-13)
+- QA.2 (2025-06-13)
+- QA.3 (2025-06-13)
+- QA.4 (2025-06-13)
+- QA.5 (2025-06-13)
+- QA.6 (2025-06-13)
+- QA.7 (2025-06-13)
+- NT.3 (2025-06-13)
+- NT.2.1 (2025-06-13)
+- NT.4 (2025-06-13)
+- NT.5 (2025-06-13)
+- NT.6 (2025-06-13)
+- LF.7.1.12 (2025-06-13)
+- LF.7.1.13 (2025-06-13)
+- QB.1 (2025-06-13)
+- XFP.1 (2025-06-14)
+- XFG.4 (2025-06-14)
+- XFG.5 (2025-06-14)
+- XFG.6 (2025-06-14)
+- NY.18 (2025-06-14)
+- NY.18.1 (2025-06-14)
+- XDY.8 (2025-06-15)
+- XDY.9 (2025-06-15)
+- XDY.10 (2025-06-15)
+- XDY.11 (2025-06-15)
+- XDY.12 (2025-06-15)
+- XDY.12.1 (2025-06-15)
+- XDY.12.1.1 (2025-06-15)
+- XFG.7 (2025-06-16)
+- PY.1.1 (2025-06-16)
+- QC.1 (2025-06-17)
+- QC.2 (2025-06-17)
+- QC.3 (2025-06-17)
+- QC.4 (2025-06-17)
+- QC.5 (2025-06-19)
+- PQ.17 (2025-06-28)
+- PQ.10.1 (2025-06-28)
+- PQ.2.1 (2025-06-28)
+- PQ.13.1 (2025-06-28)
+- PY.4.1 (2025-07-02)
+- PY.1.1.1 (2025-07-02)
+- PY.1.2 (2025-07-03)
+- PY.1.3 (2025-07-03)
+- PY.1.4 (2025-07-03)
+- PY.1.4.1 (2025-07-03)
+- XFP.2 (2025-07-08)
+- XFP.1.1 (2025-07-08)
+- XFG.8 (2025-07-08)
+- XFG.9 (2025-07-08)
+- XFG.10 (2025-07-08)
+- XFQ (2025-07-08)
+- XFG.11 (2025-07-08)
+- XFG.12 (2025-07-08)
+- XFG.13 (2025-07-08)
+- XFG.3.2 (2025-07-08)
+- XFG.3.3 (2025-07-08)
+- XFG.3.4 (2025-07-08)
+- XFG.3.4.1 (2025-07-08)
+- XFG.14 (2025-07-08)
+- PQ.2.2 (2025-07-14)
+- PQ.1.2 (2025-07-14)
+- PQ.1.3 (2025-07-14)
+- PQ.1.4 (2025-07-14)
+- PQ.18 (2025-07-14)
+- PQ.19 (2025-07-14)
+- PQ.20 (2025-07-14)
+- PQ.21 (2025-07-14)
+- PQ.22 (2025-07-14)
+- XFG.15 (2025-07-14)
+- PQ.23 (2025-07-14)
+- PQ.9.1 (2025-07-14)
+- PQ.8.1 (2025-07-14)
+- LF.7.11 (2025-07-14)
+- PQ.24 (2025-07-14)
+- XFG.4.1 (2025-07-14)
+- QD.1 (2025-07-14)
+- XFG.9.1 (2025-07-18)
+- XFG.3.4.2 (2025-07-18)
+- XFC.1.3 (2025-07-18)
+- XFC.1.4 (2025-07-18)
+- XFC.3 (2025-07-18)
+- LF.7.9.4 (2025-07-18)
+- LF.7.9.5 (2025-07-18)
+- MC.18.1 (2025-07-18)
+- MC.18.2 (2025-07-18)
+- NY.1.1 (2025-07-18)
+- NY.1.2 (2025-07-18)
+- NY.1.2.1 (2025-07-18)
+- LP.8.1.16 (2025-07-18)
+- QE.1 (2025-07-18)
+- QF.1 (2025-07-18)
+- PQ.25 (2025-07-18)
+- NY.3.3 (2025-07-18)
+- NY.3.3.1 (2025-07-18)
+- NY.3.4 (2025-07-18)
+- NY.3.5 (2025-07-18)
+- NY.3.6 (2025-07-18)
+- NY.19 (2025-07-19)
+- XFG.14.1 (2025-07-21)
+- XFG.14.2 (2025-07-21)
+- XFG.16 (2025-07-21)
+- XFG.17 (2025-07-21)
+- XFG.18 (2025-07-21)
+- XFG.19 (2025-07-21)
+- PW.3 (2025-07-22)
+- LF.7.10.2 (2025-07-22)
+- PL.3 (2025-07-22)
+- PP.1.1 (2025-07-22)
+- PP.1.1.1 (2025-07-22)
+- NW.3 (2025-07-22)
+- NW.1.4 (2025-07-22)
+- NW.1.5 (2025-07-22)
+- NW.1.6 (2025-07-22)
+- NW.1.7 (2025-07-22)
+- XES.1 (2025-07-22)
+- XES.1.1 (2025-07-22)
+- XFC.1.5 (2025-07-22)
+- XFC.1.6 (2025-07-22)
+- XFC.1.8 (2025-07-22)
+- XFC.1.9 (2025-07-22)
+- XFN.1 (2025-07-24)
+- XFN.2 (2025-07-24)
+- PG.3.1 (2025-07-25)
+- XFG.2.1 (2025-07-25)
+- XFG.2.2 (2025-07-25)
+- XFG.3.4.3 (2025-07-25)
+- XFG.21 (2025-07-25)
+- XFG.22 (2025-07-25)
+- LF.7.12 (2025-07-28)
+- LF.7.12.1 (2025-07-28)
+- PQ.26 (2025-07-29)
+- PQ.4.1 (2025-07-29)
+- PQ.5.1 (2025-07-29)
+- PQ.5.1.1 (2025-07-29)
+- PQ.5.1.2 (2025-07-29)
+- PQ.27 (2025-07-29)
+- PQ.28 (2025-07-29)
+- XFG.3.5 (2025-07-29)
+- XFG.3.5.1 (2025-07-29)
+- XFG.3.6 (2025-07-29)
+- XFG.3.7 (2025-07-29)
+- XFG.3.1.1 (2025-07-29)
+- XFG.3.1.2 (2025-07-29)
+- XFG.3.1.3 (2025-07-29)
+- NL.23 (2025-07-29)
+- NL.5.2.1 (2025-07-29)
+- LB.1.7.4 (2025-07-29)
+- LB.1.11 (2025-07-29)
+- LB.1.11.1 (2025-07-29)
+- LB.1.11.2 (2025-07-29)
+- XFR (2025-07-29)
+- XFS (2025-07-29)
+- QG.1 (2025-07-29)
+- QH.1 (2025-07-29)
+- XFT (2025-07-29)
+- XFU (2025-07-29)
+- QC.2.1 (2025-07-29)
+- QC.2.2 (2025-07-29)
+- QC.2.3 (2025-07-29)
+- QC.4.1 (2025-07-29)
+- QC.6 (2025-07-29)
+- LF.7.6.3 (2025-07-29)
+- LF.7.6.4 (2025-07-29)
+- LF.7.6.5 (2025-07-29)
+- LF.7.1.14 (2025-07-29)
+- XFG.3.3.1 (2025-07-29)
+- XFV (2025-07-29)
+- QJ.1 (2025-07-29)
+- QJ.2 (2025-07-29)
+
+
+
+## 2025-06-09T15:42:38Z
+
+- Add newly designated Nextstrain clade 25C (XFG)
+- Add labeled mutations for clades 25B (NB.1.8.1) and 25C (XFG) to help identify recombinants
+- Add all 241 Pango lineages newly designated between 2025-05-04 and 2025-06-08. Unfold below to see a list of all newly included lineages with their designation dates:
+
+
+ Newly included lineages, with designation date in parentheses
+
+- NL.3.1 (2025-05-04)
+- NL.10 (2025-05-04)
+- NL.11 (2025-05-04)
+- NL.12 (2025-05-04)
+- NL.13 (2025-05-04)
+- XFG.1 (2025-05-04)
+- XFG.2 (2025-05-04)
+- XFJ.1 (2025-05-14)
+- LF.7.9.1 (2025-05-14)
+- LF.7.9.2 (2025-05-14)
+- NL.15 (2025-05-14)
+- NL.14 (2025-05-14)
+- NL.2.1 (2025-05-14)
+- NL.16 (2025-05-14)
+- NL.6.1 (2025-05-14)
+- LF.7.1.8 (2025-05-15)
+- LF.7.1.9 (2025-05-15)
+- LF.7.1.10 (2025-05-15)
+- PC.2.3 (2025-05-15)
+- PC.2.2 (2025-05-15)
+- PC.2.1 (2025-05-15)
+- PC.3.1 (2025-05-15)
+- PC.3.2 (2025-05-15)
+- PC.4.1 (2025-05-15)
+- LF.7.10 (2025-05-15)
+- LF.7.10.1 (2025-05-15)
+- XEC.33 (2025-05-15)
+- XEC.34 (2025-05-15)
+- XEC.35 (2025-05-15)
+- XEC.35.1 (2025-05-15)
+- XEC.36 (2025-05-15)
+- XEC.37 (2025-05-15)
+- NB.1.2.1 (2025-05-15)
+- PH.1 (2025-05-15)
+- MC.10.1.8 (2025-05-15)
+- PJ.1 (2025-05-15)
+- PA.1.3 (2025-05-15)
+- PA.2 (2025-05-15)
+- PA.3 (2025-05-15)
+- PK.1 (2025-05-15)
+- PK.1.1 (2025-05-15)
+- XEC.38 (2025-05-15)
+- XEC.2.4 (2025-05-15)
+- PL.1 (2025-05-15)
+- XFJ.2 (2025-05-16)
+- XEC.4.1.1 (2025-05-16)
+- XEC.4.1.2 (2025-05-16)
+- XEC.4.1.3 (2025-05-16)
+- XEC.4.1.4 (2025-05-16)
+- XEC.4.1.5 (2025-05-16)
+- XEC.4.1.6 (2025-05-16)
+- XEC.4.2 (2025-05-16)
+- XEC.4.3 (2025-05-16)
+- XEC.4.4 (2025-05-16)
+- XEC.4.5 (2025-05-16)
+- XEC.4.6 (2025-05-16)
+- XEC.18.1 (2025-05-16)
+- XEC.39 (2025-05-16)
+- XEC.32.1 (2025-05-16)
+- XEC.14.1 (2025-05-16)
+- XEC.14.1.1 (2025-05-16)
+- NY.13 (2025-05-16)
+- XEC.2.5 (2025-05-16)
+- XEC.2.6 (2025-05-16)
+- XEK.1.2 (2025-05-16)
+- XEK.1.2.1 (2025-05-16)
+- MC.11.2 (2025-05-16)
+- MC.11.3 (2025-05-16)
+- MC.11.3.1 (2025-05-16)
+- XFB.1 (2025-05-16)
+- XFB.2 (2025-05-16)
+- XFB.3 (2025-05-16)
+- MC.41 (2025-05-16)
+- PD.1.1 (2025-05-16)
+- PD.1.2 (2025-05-16)
+- PD.2 (2025-05-16)
+- PD.2.1 (2025-05-16)
+- PD.3 (2025-05-16)
+- KP.3.3.10 (2025-05-16)
+- NY.4.1 (2025-05-16)
+- NY.11.1 (2025-05-16)
+- MC.10.2.2 (2025-05-16)
+- PG.4 (2025-05-18)
+- PG.4.1 (2025-05-18)
+- PG.5 (2025-05-18)
+- PG.6 (2025-05-18)
+- PM.1 (2025-05-18)
+- PM.1.2 (2025-05-18)
+- PM.1.1 (2025-05-18)
+- PM.2 (2025-05-18)
+- PM.3 (2025-05-18)
+- XDV.1.7.2 (2025-05-18)
+- XDV.1.7.3 (2025-05-18)
+- PN.1 (2025-05-18)
+- XDV.1.7.4 (2025-05-18)
+- XDV.1.12 (2025-05-18)
+- XDV.1.7.5 (2025-05-18)
+- NY.14 (2025-05-18)
+- LP.8.1.10 (2025-05-20)
+- LP.8.1.11 (2025-05-20)
+- LP.8.1.12 (2025-05-20)
+- LP.8.1.13 (2025-05-20)
+- LP.8.1.14 (2025-05-20)
+- PP.2 (2025-05-20)
+- PP.2.1 (2025-05-20)
+- PP.1 (2025-05-20)
+- PF.2 (2025-05-20)
+- PF.2.1 (2025-05-20)
+- PF.2.2 (2025-05-20)
+- PF.2.2.1 (2025-05-20)
+- PF.2.3 (2025-05-20)
+- NY.7.1 (2025-05-20)
+- MC.32.1.1 (2025-05-20)
+- PQ.1 (2025-05-20)
+- PQ.2 (2025-05-20)
+- XEP.1 (2025-05-20)
+- XEP.1.1 (2025-05-20)
+- XEP.2 (2025-05-20)
+- XEP.3 (2025-05-20)
+- XFH.1 (2025-05-20)
+- XFH.2 (2025-05-20)
+- XFC.1 (2025-05-20)
+- XFC.1.1 (2025-05-20)
+- NY.15 (2025-05-29)
+- NY.3.1 (2025-05-29)
+- NY.3.1.1 (2025-05-29)
+- NY.3.2 (2025-05-29)
+- NW.2 (2025-05-29)
+- NW.1.1 (2025-05-29)
+- NW.1.1.1 (2025-05-29)
+- NW.1.2 (2025-05-29)
+- NW.1.3 (2025-05-29)
+- PR.1 (2025-05-29)
+- PR.2 (2025-05-29)
+- PR.3 (2025-05-29)
+- PA.1.4 (2025-05-29)
+- MC.13.2.3 (2025-05-29)
+- MC.13.2.4 (2025-05-29)
+- PL.1.1 (2025-05-29)
+- PL.2 (2025-05-29)
+- XEC.24.1 (2025-05-29)
+- MC.9.2 (2025-05-29)
+- MV.1.5 (2025-05-29)
+- MV.1.6 (2025-05-29)
+- PS.1 (2025-05-29)
+- PS.2 (2025-05-29)
+- PT.1 (2025-05-29)
+- PU.1 (2025-05-29)
+- XEC.25.1.1 (2025-05-29)
+- XEC.25.1.2 (2025-05-29)
+- XEC.25.1.3 (2025-05-29)
+- XFN (2025-05-29)
+- XEC.4.6.1 (2025-05-29)
+- XEC.4.5.1 (2025-05-29)
+- XEC.4.7 (2025-05-29)
+- XEC.4.8 (2025-05-29)
+- XEC.4.9 (2025-05-29)
+- XEC.32.2 (2025-05-29)
+- XEC.32.3 (2025-05-29)
+- XFJ.3 (2025-05-29)
+- XFP (2025-05-29)
+- XFC.1.1.1 (2025-05-29)
+- XFC.1.2 (2025-05-29)
+- XFC.2 (2025-05-29)
+- XFG.3 (2025-05-29)
+- XFG.3.1 (2025-05-29)
+- NY.16 (2025-05-29)
+- NY.16.1 (2025-05-29)
+- XEC.40 (2025-05-29)
+- NY.12.1 (2025-05-29)
+- LF.7.1.11 (2025-05-29)
+- PV.1 (2025-05-29)
+- PV.2 (2025-05-29)
+- PV.3 (2025-05-29)
+- PV.3.1 (2025-05-29)
+- NL.8.1 (2025-05-29)
+- NL.17 (2025-05-30)
+- NL.18 (2025-05-30)
+- NL.19 (2025-05-30)
+- NL.20 (2025-05-30)
+- NL.21 (2025-05-30)
+- NL.22 (2025-05-30)
+- NL.22.1 (2025-05-30)
+- NM.3 (2025-05-30)
+- XEK.5.1 (2025-05-30)
+- XEK.5.2 (2025-05-30)
+- XEK.7 (2025-05-30)
+- XEK.8 (2025-05-30)
+- NL.16.1 (2025-06-06)
+- BA.3.2.1 (2025-06-06)
+- BA.3.2.2 (2025-06-06)
+- XFJ.4 (2025-06-06)
+- LS.2.1 (2025-06-06)
+- LS.2.1.1 (2025-06-06)
+- XEK.2.1 (2025-06-07)
+- PQ.3 (2025-06-07)
+- PQ.4 (2025-06-07)
+- PQ.5 (2025-06-07)
+- PQ.6 (2025-06-07)
+- PQ.7 (2025-06-07)
+- PQ.1.1 (2025-06-07)
+- PA.4 (2025-06-07)
+- PA.4.1 (2025-06-07)
+- PA.4.2 (2025-06-07)
+- MC.42 (2025-06-07)
+- XEC.18.2 (2025-06-07)
+- XEC.18.3 (2025-06-07)
+- XEC.18.4 (2025-06-07)
+- MC.43 (2025-06-07)
+- MC.19.1.1 (2025-06-07)
+- PW.1 (2025-06-07)
+- PW.2 (2025-06-07)
+- LF.7.9.3 (2025-06-07)
+- PY.1 (2025-06-07)
+- PY.2 (2025-06-07)
+- PY.3 (2025-06-07)
+- PY.4 (2025-06-07)
+- PY.5 (2025-06-07)
+- PY.6 (2025-06-07)
+- PC.2.1.1 (2025-06-07)
+- PC.2.1.2 (2025-06-07)
+- PC.4.1.1 (2025-06-07)
+- NY.7.2 (2025-06-07)
+- NY.7.1.1 (2025-06-07)
+- PF.2.4 (2025-06-07)
+- LP.8.1.15 (2025-06-07)
+- NY.17 (2025-06-07)
+- NY.17.1 (2025-06-07)
+- NY.17.2 (2025-06-07)
+- XFF.1 (2025-06-07)
+- NB.1.6.1 (2025-06-07)
+- NB.1.7.1 (2025-06-07)
+- PQ.8 (2025-06-08)
+- PQ.9 (2025-06-08)
+- PQ.10 (2025-06-08)
+- PQ.11 (2025-06-08)
+- PQ.12 (2025-06-08)
+- PQ.13 (2025-06-08)
+- PQ.14 (2025-06-08)
+- PQ.15 (2025-06-08)
+- PQ.16 (2025-06-08)
+
+
+
+## 2025-05-05T13:15:29Z
+
+- Newly designated Nextstrain clade 25B (Pango lineage NB.1.8.1 = XDV.1.5.1.1.8.1) is now included.
+
+## 2025-04-01T08:20:12Z
+
+Automated update
+
+## 2025-03-26T11:47:13Z
+
+Fix GFF3 format issues in genome annotation
+
+## 2025-03-04T17:31:25Z
+
+Automated update
+
+## 2025-01-28T16:39:09Z
+
+- Add newly designated Nextstrain clade 25A (LP.8.1)
+- Add all 78 Pango lineages newly designated between 2024-11-14 and 2025-01-27. Unfold below to see a list of all newly included lineages with their designation dates:
+
+
+ Newly included lineages, with designation date in parentheses
+
+- XEK.1 (2024-12-10)
+- XEK.1.1 (2024-12-10)
+- XEK.2 (2024-12-10)
+- XEK.3 (2024-12-10)
+- XEQ (2024-12-10)
+- LP.11 (2024-12-10)
+- LP.8.2.1 (2024-12-10)
+- LP.8.1.1 (2024-12-10)
+- XEC.8 (2024-12-10)
+- XEC.9 (2024-12-10)
+- XEC.10 (2024-12-10)
+- XEC.11 (2024-12-10)
+- XEC.2.1 (2024-12-10)
+- XEC.2.2 (2024-12-10)
+- XEC.2.3 (2024-12-10)
+- XEC.2.3.1 (2024-12-10)
+- XEC.12 (2024-12-10)
+- LF.7.3.1 (2024-12-10)
+- MV.1.1 (2024-12-10)
+- MU.2.1.1 (2024-12-10)
+- MU.1.1 (2024-12-10)
+- MU.4 (2024-12-10)
+- MU.5 (2024-12-10)
+- MC.23 (2024-12-10)
+- XEC.13 (2024-12-11)
+- MC.24 (2024-12-11)
+- MC.25 (2024-12-11)
+- MC.26 (2024-12-11)
+- MC.26.1 (2024-12-11)
+- MC.27 (2024-12-11)
+- MC.28 (2024-12-11)
+- MC.28.1 (2024-12-11)
+- MC.1.2 (2024-12-11)
+- XEC.14 (2024-12-11)
+- MC.13.3 (2024-12-11)
+- LB.1.3.4 (2024-12-11)
+- LP.10.1.1 (2024-12-18)
+- KP.2.3.14 (2024-12-18)
+- JN.1.68.1 (2024-12-18)
+- LP.8.1.2 (2024-12-18)
+- KP.3.1.11 (2024-12-18)
+- KP.3.1.12 (2024-12-18)
+- NR.1 (2024-12-18)
+- NS.1 (2024-12-18)
+- NS.1.1 (2024-12-18)
+- NS.1.2 (2024-12-18)
+- NS.2 (2024-12-18)
+- MT.1.1 (2024-12-18)
+- NF.1.1 (2024-12-18)
+- NS.3 (2024-12-18)
+- ND.2.1 (2024-12-18)
+- ND.1.1.1 (2024-12-18)
+- ND.1.1.2 (2024-12-18)
+- XEJ.1 (2024-12-18)
+- XEJ.2 (2024-12-18)
+- XEJ.3 (2024-12-18)
+- XEK.4 (2024-12-18)
+- NT.1 (2024-12-18)
+- LF.7.5 (2024-12-18)
+- XEC.15 (2024-12-18)
+- KS.2 (2024-12-18)
+- XER (2024-12-18)
+- XEC.16 (2024-12-18)
+- NU.1 (2024-12-18)
+- XES (2024-12-18)
+- MC.1.3 (2024-12-18)
+- MC.1.3.1 (2024-12-18)
+- KP.2.3.15 (2024-12-18)
+- KP.2.6.2 (2024-12-18)
+- KP.2.6.3 (2024-12-18)
+- NB.1.1 (2024-12-18)
+- LF.7.6 (2024-12-18)
+- LF.7.6.1 (2024-12-18)
+- MC.19.1 (2024-12-19)
+- KP.3.3.5 (2024-12-20)
+- NV.1 (2024-12-20)
+- XET (2024-12-20)
+- XEU (2024-12-20)
+
+
+
+## 2024-11-19T14:18:53Z
+
+Fix duplicate changelog entry, nothing else changed.
+
+## 2024-11-14T17:22:16Z
+
+- Add newly designated Nextstrain clades 24H (LF.7) and 24I (MV.1)
+- Add all 128 Pango lineages newly designated between 2024-10-19 and 2024-11-14. Unfold below to see a list of all newly included lineages with their designation dates:
+
+
+ Newly included lineages, with designation date in parentheses
+
+- LF.7.1 (2024-10-19)
+- LF.7.1.1 (2024-10-19)
+- LF.7.2 (2024-10-19)
+- LF.7.2.1 (2024-10-19)
+- LF.7.3 (2024-10-19)
+- LF.7.4 (2024-10-19)
+- JN.1.49.3 (2024-10-20)
+- MV.2 (2024-10-20)
+- MB.1.1.2 (2024-10-20)
+- MB.1.1.3 (2024-10-20)
+- NA.1 (2024-10-20)
+- NA.1.1 (2024-10-20)
+- XDV.1.5.1 (2024-10-20)
+- NB.1 (2024-10-20)
+- KS.1.1.1 (2024-10-20)
+- KS.1.1.2 (2024-10-20)
+- LF.3.1.2 (2024-10-20)
+- XEL (2024-10-20)
+- NC.1 (2024-10-20)
+- ND.1 (2024-10-20)
+- ND.1.1 (2024-10-20)
+- ND.2 (2024-10-20)
+- ND.3 (2024-10-20)
+- MC.10.1 (2024-10-20)
+- KP.2.2.1 (2024-10-20)
+- KP.2.25.1 (2024-10-20)
+- KP.2.25.2 (2024-10-20)
+- KP.2.25.3 (2024-10-20)
+- MD.3.1.1 (2024-10-20)
+- MD.3.1.2 (2024-10-20)
+- MD.3.1.3 (2024-10-20)
+- MD.3.1.4 (2024-10-20)
+- MD.1.2 (2024-10-20)
+- MD.1.1.1 (2024-10-20)
+- KP.3.2.6 (2024-10-21)
+- MC.1.1 (2024-10-21)
+- MC.18 (2024-10-21)
+- KP.2.27 (2024-10-22)
+- KP.2.3.8 (2024-10-22)
+- KP.2.2.2 (2024-10-22)
+- XEM (2024-10-22)
+- KP.3.1.9 (2024-10-22)
+- KP.1.1.6 (2024-10-23)
+- NE.1 (2024-10-23)
+- XEN (2024-10-23)
+- NF.1 (2024-10-24)
+- KP.2.3.9 (2024-10-24)
+- NG.1 (2024-10-24)
+- NH.1 (2024-10-24)
+- NH.2 (2024-10-24)
+- NH.3 (2024-10-24)
+- JN.1.11.2 (2024-10-25)
+- NJ.1 (2024-10-25)
+- KP.2.3.10 (2024-10-25)
+- NK.1 (2024-10-25)
+- LP.5 (2024-10-25)
+- LP.6 (2024-10-25)
+- LP.7 (2024-10-25)
+- KP.2.3.11 (2024-10-25)
+- LD.2 (2024-10-25)
+- KP.3.1.10 (2024-10-25)
+- NL.1 (2024-10-25)
+- MU.2 (2024-10-25)
+- MU.2.1 (2024-10-25)
+- KP.3.7 (2024-10-25)
+- LZ.2.1.2 (2024-10-27)
+- LZ.2.1.1 (2024-10-27)
+- KR.1.4 (2024-10-27)
+- KP.2.3.12 (2024-10-27)
+- NM.1 (2024-10-27)
+- LP.8 (2024-10-27)
+- LP.7.1.2 (2024-10-27)
+- KP.4.2.5 (2024-10-27)
+- KP.4.2.4 (2024-10-27)
+- LF.7.1.2 (2024-10-27)
+- MC.19 (2024-11-01)
+- KP.2.6.1 (2024-11-01)
+- MC.20 (2024-11-01)
+- MC.10.2 (2024-11-01)
+- KP.3.2.7 (2024-11-01)
+- KP.3.2.8 (2024-11-01)
+- KP.3.2.9 (2024-11-01)
+- XEC.3 (2024-11-01)
+- XEC.4 (2024-11-01)
+- XEC.5 (2024-11-01)
+- XEC.6 (2024-11-01)
+- XEC.7 (2024-11-01)
+- MJ.2 (2024-11-05)
+- MJ.2.1 (2024-11-05)
+- MJ.2.1.1 (2024-11-05)
+- MJ.1.1 (2024-11-05)
+- LF.10 (2024-11-05)
+- LP.8.1 (2024-11-08)
+- LP.8.2 (2024-11-08)
+- LF.7.1.3 (2024-11-08)
+- NL.2 (2024-11-08)
+- NL.3 (2024-11-08)
+- NL.4 (2024-11-08)
+- NL.5 (2024-11-08)
+- NL.6 (2024-11-08)
+- NL.7 (2024-11-08)
+- NM.2 (2024-11-12)
+- LP.9 (2024-11-12)
+- LP.9.1 (2024-11-12)
+- NN.1 (2024-11-12)
+- NN.1.1 (2024-11-12)
+- NN.2 (2024-11-12)
+- LP.1.2.1 (2024-11-12)
+- NC.1.1 (2024-11-12)
+- NC.1.2 (2024-11-12)
+- LB.1.10 (2024-11-12)
+- NP.1 (2024-11-12)
+- NP.2 (2024-11-12)
+- XEP (2024-11-12)
+- MC.13.2 (2024-11-12)
+- MC.21 (2024-11-12)
+- MC.21.1 (2024-11-12)
+- MC.22 (2024-11-12)
+- XDY.1 (2024-11-12)
+- LP.10 (2024-11-12)
+- LP.10.1 (2024-11-12)
+- NQ.1 (2024-11-12)
+- NH.4 (2024-11-12)
+- MU.3 (2024-11-12)
+- KP.2.3.13 (2024-11-13)
+- MG.2 (2024-11-13)
+- MG.3 (2024-11-13)
+- MG.4 (2024-11-14)
+
+
+
+## 2024-10-17T16:48:48Z
+
+- Add newly designated Nextstrain clades 24F (XEC) and 24G (KP.2.3)
+- Add all 4 Pango lineages designated between 2024-09-26 and 2024-10-14. Unfold below to see a list of all newly included lineages with their designation dates:
+
+
+ Newly included lineages, with designation date in parentheses
+
+- XEH (2024-09-28)
+- XEJ (2024-09-28)
+- XEC.2 (2024-09-28)
+- XEK (2024-09-28)
+
+
+
+## 2024-09-25T21:50:30Z
+
+- Include newly designated Nextstrain clades 24D (XDV.1) and 24E (KP.3.1.1)
+- All 113 Pango lineages designated between 2024-07-15 and 2024-09-25 are now included, unfold below to see a list of all newly included lineages with their designation dates
+
+
+ Newly included lineages, with designation date in parentheses
+
+- XEC (2024-08-07)
+- KP.2.3.5 (2024-08-07)
+- KP.2.3.6 (2024-08-07)
+- LP.4 (2024-08-07)
+- LP.1.2 (2024-08-07)
+- LB.1.2.2 (2024-08-07)
+- LB.1.2.3 (2024-08-07)
+- KP.2.18 (2024-08-07)
+- KP.2.14.1 (2024-08-07)
+- MC.2 (2024-08-08)
+- MC.2.1 (2024-08-08)
+- KR.1.3 (2024-08-08)
+- MP.1 (2024-08-08)
+- MP.1.1 (2024-08-08)
+- JQ.2.1.2 (2024-08-08)
+- MC.4 (2024-08-08)
+- MC.3 (2024-08-08)
+- LB.1.3.3 (2024-08-08)
+- KP.2.15.1 (2024-08-08)
+- KP.3.1.7 (2024-08-08)
+- MQ.1 (2024-08-08)
+- MQ.2 (2024-08-08)
+- KP.3.3.4 (2024-08-08)
+- MR.1 (2024-08-08)
+- MK.3 (2024-08-08)
+- XED (2024-08-08)
+- LZ.2 (2024-08-12)
+- XEC.1 (2024-08-14)
+- MS.1 (2024-08-15)
+- KU.2.1 (2024-08-15)
+- KU.2.2 (2024-08-15)
+- MA.1.1 (2024-08-15)
+- MA.1.1.1 (2024-08-15)
+- JN.1.18.8 (2024-08-15)
+- JN.1.59.1 (2024-08-15)
+- JN.1.16.4 (2024-08-15)
+- LU.2.1 (2024-08-15)
+- LU.2.1.1 (2024-08-15)
+- MT.1 (2024-08-15)
+- KP.2.19 (2024-08-15)
+- LF.6 (2024-08-15)
+- LR.3 (2024-08-15)
+- XDV.1.1 (2024-08-15)
+- XDV.1.2 (2024-08-15)
+- XDV.1.2.1 (2024-08-15)
+- XDV.1.3 (2024-08-15)
+- XDV.1.4 (2024-08-15)
+- XDV.1.5 (2024-08-15)
+- XDV.1.6 (2024-08-15)
+- LF.7 (2024-08-15)
+- MU.1 (2024-08-15)
+- JN.1.4.9 (2024-08-15)
+- JN.1.38.1 (2024-08-15)
+- MC.5 (2024-08-15)
+- MC.6 (2024-08-15)
+- MC.7 (2024-08-15)
+- MC.8 (2024-08-15)
+- MC.8.1 (2024-08-15)
+- MC.9 (2024-08-15)
+- MC.10 (2024-08-15)
+- MC.11 (2024-08-15)
+- MC.11.1 (2024-08-15)
+- MC.12 (2024-08-15)
+- MC.13 (2024-08-15)
+- MC.13.1 (2024-08-15)
+- MC.14 (2024-08-15)
+- MC.15 (2024-08-15)
+- MC.16 (2024-08-15)
+- MB.1.1.1 (2024-08-15)
+- MV.1 (2024-08-15)
+- KP.2.20 (2024-08-15)
+- KP.2.20.1 (2024-08-15)
+- JN.1.67 (2024-08-15)
+- JN.1.67.1 (2024-08-15)
+- XEF (2024-08-15)
+- KP.2.22 (2024-08-16)
+- KP.2.24 (2024-08-16)
+- KP.2.25 (2024-08-16)
+- KP.2.26 (2024-08-16)
+- KR.4.1 (2024-08-16)
+- KP.6 (2024-08-16)
+- XEG (2024-08-16)
+- KP.2.3.7 (2024-08-16)
+- MW.1 (2024-08-16)
+- KP.2.23 (2024-08-16)
+- JN.1.68 (2024-08-16)
+- LF.8 (2024-08-16)
+- LF.8.1 (2024-08-16)
+- LF.8.1.1 (2024-08-16)
+- XEE (2024-08-16)
+- MC.17 (2024-08-16)
+- JN.1.16.5 (2024-08-16)
+- LW.1.1 (2024-08-16)
+- LW.1.2 (2024-08-16)
+- KP.3.6 (2024-08-16)
+- LB.1.9 (2024-08-16)
+- KP.3.1.8 (2024-08-16)
+- MY.1 (2024-08-16)
+- XDV.1.7 (2024-08-17)
+- XDV.1.8 (2024-08-17)
+- XDV.1.9 (2024-08-17)
+- XDR.1.1 (2024-08-17)
+- XDR.1.2 (2024-08-17)
+- XDV.1.10 (2024-08-17)
+- XDV.1.11 (2024-08-17)
+- LU.2.2 (2024-08-20)
+- LB.1.4.3 (2024-08-24)
+- LF.9 (2024-08-27)
+- LF.9.1 (2024-08-27)
+- XDV.1.7.1 (2024-09-05)
+- XDV.1.9.1 (2024-09-05)
+- LZ.2.1 (2024-09-05)
+- MZ.1 (2024-09-05)
+
+
+
+## 2024-07-17T12:57:03Z
+
+- Include newly designated Nextstrain clade 24C (KP.3)
+- All 84 Pango lineages designated between 2024-06-11 and 2024-07-14 are now included, unfold below to see a list of all newly included lineages with their designation dates
+
+
+ Newly included lineages, with designation date in parentheses
+
+- BA.2.86.7 (2024-06-13)
+- XDZ (2024-06-14)
+- JN.1.1.10 (2024-06-14)
+- JN.1.63 (2024-06-14)
+- JN.1.63.1 (2024-06-14)
+- XEA (2024-06-14)
+- XEB (2024-06-14)
+- XDP.2 (2024-06-14)
+- XDP.3 (2024-06-14)
+- LV.1 (2024-06-14)
+- LV.2 (2024-06-14)
+- LE.1.3 (2024-06-14)
+- LE.1.3.1 (2024-06-14)
+- JN.1.58.3 (2024-06-14)
+- KP.4.1.1 (2024-06-17)
+- KP.4.1.2 (2024-06-17)
+- KP.4.1.3 (2024-06-17)
+- LW.1 (2024-06-17)
+- LP.3 (2024-06-17)
+- KP.3.1.5 (2024-06-17)
+- KP.1.1.5 (2024-06-17)
+- XDD.3 (2024-06-29)
+- LF.3.1.1 (2024-06-29)
+- LB.1.3.1 (2024-06-29)
+- KP.2.3.4 (2024-06-29)
+- JN.1.18.6 (2024-06-29)
+- LY.2 (2024-06-29)
+- LY.1 (2024-06-29)
+- JN.1.18.7 (2024-06-29)
+- LZ.1 (2024-06-29)
+- LZ.1.1 (2024-06-29)
+- MA.1 (2024-06-29)
+- MB.1 (2024-06-29)
+- MB.1.1 (2024-06-29)
+- LP.1.1 (2024-06-29)
+- LF.4 (2024-06-29)
+- LF.4.1 (2024-06-29)
+- KP.3.3.1 (2024-06-29)
+- MC.1 (2024-06-29)
+- LU.2 (2024-07-01)
+- JN.1.64 (2024-07-01)
+- JN.1.64.1 (2024-07-01)
+- MD.1 (2024-07-01)
+- MD.1.1 (2024-07-01)
+- MD.2 (2024-07-01)
+- MD.3 (2024-07-01)
+- MD.3.1 (2024-07-01)
+- LK.2 (2024-07-03)
+- LK.2.1 (2024-07-03)
+- JN.1.7.8 (2024-07-03)
+- JN.1.50.2 (2024-07-03)
+- ME.1 (2024-07-03)
+- LF.5 (2024-07-10)
+- JN.1.48.3 (2024-07-10)
+- KS.1.3 (2024-07-10)
+- JN.1.65 (2024-07-10)
+- JN.1.65.1 (2024-07-10)
+- MF.1 (2024-07-10)
+- MF.2 (2024-07-10)
+- KP.3.3.2 (2024-07-10)
+- MG.1 (2024-07-10)
+- KP.4.2.3 (2024-07-10)
+- KP.2.17 (2024-07-10)
+- LB.1.3.2 (2024-07-10)
+- MH.1 (2024-07-10)
+- LB.1.8 (2024-07-10)
+- JN.1.7.9 (2024-07-10)
+- MJ.1 (2024-07-10)
+- KP.3.1.6 (2024-07-12)
+- MK.1 (2024-07-12)
+- MK.2 (2024-07-12)
+- KP.3.4.1 (2024-07-12)
+- KP.3.3.3 (2024-07-12)
+- ML.1 (2024-07-12)
+- ML.2 (2024-07-12)
+- MM.1 (2024-07-12)
+- MM.2 (2024-07-12)
+- JN.1.66 (2024-07-12)
+- MN.1 (2024-07-12)
+- KP.3.5 (2024-07-12)
+- LB.1.4.1 (2024-07-13)
+- LB.1.7.1 (2024-07-13)
+- LB.1.7.2 (2024-07-13)
+- LB.1.7.3 (2024-07-13)
+
+
+
+## 2024-07-03T08:29:55Z
+
+Added configuration of current and recent vaccine strains as 'reference nodes' on the reference tree, against which query sequences can be compared. This feature is in addition to the new 'compare to clade founder' feature, allowing to compare each query sequence to the most ancestral node of a clade or lineage.
+
+The datasets themselves remain unchanged.
+
+See Nextclade documentation for more details about 'relative mutations' functionality.
+
+## 2024-06-13T23:42:47Z
+
+- 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:
+- Fixed a bug that made amino acid gaps on the reference tree be left-aligned instead of right-aligned. This only affected the display of mutations on branches in tree view. The bug existed since switching the default gap alignment from right to left in nextclade v2.
+
+
+ Newly included lineages, with designation date in parentheses
+
+- 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)
+
+
+
+## 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.
+
+## 2024-04-15T15:08:22Z
+
+- Nextstrain clades 24A (JN.1) and 24B (JN.1.11.1) are now included.
+- All 83 Pango lineages designated between 2024-02-13 and 2024-04-12 are now included, unfold below to see a list of all newly included lineages with their designation dates:
+
+
+ Newly included lineages, with designation date in parentheses
+
+- JN.1.23 (2024-02-20)
+- KP.1 (2024-02-22)
+- JN.1.7.1 (2024-03-01)
+- JN.1.7.2 (2024-03-01)
+- KQ.1 (2024-03-01)
+- JN.1.13.1 (2024-03-01)
+- JN.1.1.5 (2024-03-01)
+- KR.1 (2024-03-04)
+- KP.1.1 (2024-03-04)
+- KP.2 (2024-03-04)
+- JN.1.24 (2024-03-04)
+- XDK.1 (2024-03-04)
+- JN.1.25 (2024-03-04)
+- JN.1.25.1 (2024-03-04)
+- XDQ.1 (2024-03-04)
+- JQ.2 (2024-03-05)
+- JN.13 (2024-03-06)
+- JN.13.1 (2024-03-06)
+- JN.1.1.6 (2024-03-09)
+- JN.1.26 (2024-03-09)
+- JN.1.27 (2024-03-09)
+- JN.1.4.4 (2024-03-09)
+- JN.1.8.2 (2024-03-09)
+- JN.1.28 (2024-03-09)
+- JN.1.1.7 (2024-03-09)
+- JN.1.29 (2024-03-09)
+- JN.1.4.5 (2024-03-14)
+- JN.1.18.1 (2024-03-14)
+- JN.1.30 (2024-03-14)
+- JN.1.31 (2024-03-14)
+- JN.1.16.1 (2024-03-14)
+- KS.1 (2024-03-14)
+- JN.1.4.6 (2024-03-14)
+- JN.1.32 (2024-03-14)
+- GE.1.2.2 (2024-03-17)
+- KT.1 (2024-03-17)
+- KT.1.1 (2024-03-17)
+- KT.1.2 (2024-03-17)
+- KP.3 (2024-03-17)
+- JN.1.33 (2024-03-17)
+- JN.1.34 (2024-03-17)
+- JN.1.35 (2024-03-17)
+- JN.1.36 (2024-03-17)
+- KP.2.1 (2024-03-19)
+- KP.2.2 (2024-03-19)
+- JN.1.30.1 (2024-03-19)
+- JQ.2.1 (2024-03-20)
+- XDD.1.1.1 (2024-03-25)
+- KU.1 (2024-03-25)
+- KU.2 (2024-03-25)
+- JN.1.18.2 (2024-03-25)
+- JN.1.36.1 (2024-03-25)
+- KV.1 (2024-03-25)
+- JN.1.37 (2024-03-25)
+- JN.1.28.1 (2024-03-25)
+- KW.1 (2024-03-25)
+- JN.1.38 (2024-03-25)
+- JN.1.39 (2024-03-25)
+- JN.1.40 (2024-03-25)
+- JN.1.41 (2024-03-25)
+- JN.1.42 (2024-03-25)
+- JN.1.43 (2024-03-25)
+- JN.1.43.1 (2024-03-25)
+- KP.1.1.1 (2024-03-25)
+- JN.1.44 (2024-03-25)
+- XDU (2024-03-26)
+- XDP.1 (2024-03-26)
+- JN.2.2.1 (2024-03-26)
+- JN.1.8.3 (2024-03-29)
+- KY.1 (2024-03-29)
+- JN.14 (2024-03-29)
+- JN.1.45 (2024-03-29)
+- XDV (2024-04-02)
+- XDV.1 (2024-04-02)
+- JN.1.42.1 (2024-04-02)
+- JN.1.46 (2024-04-02)
+- JN.1.4.7 (2024-04-02)
+- KV.2 (2024-04-02)
+- KW.1.1 (2024-04-03)
+- KZ.1 (2024-04-04)
+- KZ.1.1 (2024-04-04)
+- KZ.1.1.1 (2024-04-04)
+- JN.1.7.3 (2024-04-04)
+
+
+
+## 2024-02-16T04:00:32Z
+
+- All 35 Pango lineages designated between 2024-01-16 and 2024-02-12 are now included, unfold below to see a list of all newly included lineages with their designation dates:
+
+
+ Newly included lineages, with designation date in parentheses
+
+- XDN (2024-01-16)
+- XDP (2024-01-16)
+- JN.3.2 (2024-01-16)
+- JN.3.2.1 (2024-01-16)
+- JN.11 (2024-01-21)
+- JN.1.12 (2024-01-21)
+- JN.12 (2024-01-22)
+- JN.1.11.1 (2024-01-22)
+- KM.1 (2024-01-31)
+- BA.2.87 (2024-02-01)
+- BA.2.87.1 (2024-02-01)
+- XDQ (2024-02-01)
+- GK.1.10.1 (2024-02-01)
+- XDR (2024-02-01)
+- JN.1.13 (2024-02-01)
+- JN.1.14 (2024-02-01)
+- JN.1.15 (2024-02-01)
+- JN.1.4.1 (2024-02-01)
+- JN.1.2.1 (2024-02-01)
+- JN.1.16 (2024-02-01)
+- JN.1.17 (2024-02-01)
+- JN.1.4.2 (2024-02-02)
+- JN.1.18 (2024-02-04)
+- JN.1.19 (2024-02-04)
+- JN.1.20 (2024-02-04)
+- XDS (2024-02-04)
+- JN.1.9.1 (2024-02-04)
+- JN.1.21 (2024-02-04)
+- JN.1.22 (2024-02-04)
+- JN.1.4.3 (2024-02-12)
+- XDT (2024-02-12)
+- HK.13.2.1 (2024-02-12)
+- KN.1 (2024-02-12)
+- KN.1.1 (2024-02-12)
+- JN.1.1.4 (2024-02-12)
+
+
+
+## 2024-01-16T20:31:02Z
+
+Initial release of this v3 dataset.
+
+This dataset is very similar to the v2 dataset `sars-cov-2`.
diff --git a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/README.md b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/README.md
new file mode 100644
index 000000000..3d8580c1e
--- /dev/null
+++ b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/README.md
@@ -0,0 +1,48 @@
+# SARS-CoV-2 dataset with reference Wuhan-Hu-1/2019
+
+| Key | Value |
+| ----------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| authors | [Cornelius Roemer](https://neherlab.org), [Richard Neher](https://neherlab.org), [Nextstrain](https://nextstrain.org) |
+| reference | `Wuhan-Hu-1/2019` |
+| workflow | https://github.com/neherlab/nextclade_data_workflows/tree/v3-sc2/sars-cov-2 |
+| path | `nextstrain/sars-cov-2/orfs` |
+| clade definitions | [Nextstrain clades](https://nextstrain.org/blog/2022-04-29-SARS-CoV-2-clade-naming-2022) and [Pango lineages](https://www.nature.com/articles/s41564-020-0770-5) |
+
+## Scope of this dataset
+
+This dataset shows mutations relative to `Wuhan-Hu-1/2019` and is particularly useful for the analysis of SARS-CoV-2 sequences spanning the entire pandemic.
+
+For the analysis of more recent sequences, the BA.2, XBB and BA.2.86 datasets may be more appropriate, as they show mutations relative to the respective variants. The related `wuhan-hu-1/proteins` dataset shows amino acid mutations in coordinates of mature proteins (nsp1-16) instead of ORF1a/ORF1b coordinates.
+
+## Reference sequence and reference tree
+
+The reference sequence in this dataset is `Wuhan-Hu-1/2019`. Amino acids in the polyprotein ORF1ab are annotated relative to ORF1a and ORF1b.
+
+The reference tree contains one sequence for each Pango lineage designated since mid-2021 and most lineages designated before that.
+
+## Features
+
+This dataset supports:
+
+- Assignment of Nextstrain clades
+- Assignment of Pango lineages
+- Sequence QC
+- Phylogenetic placement
+
+## Nextstrain clades
+
+Since its emergence in late 2019, SARS-CoV-2 has evolved into many co-circulating variants. To facilitate discussion of these variants, we have grouped them into clades which are defined by specific signature mutations.
+
+Nextstrain clade names consist of two numbers representing a year and then a single letter representing the clade within that year. For example, 21A is the first clade we named in 2021.
+
+We define each clade by a combination of signature mutations. You can find the exact clade definition on Github in this [file](https://github.com/nextstrain/ncov/blob/master/defaults/clades.tsv).
+
+Below is an illustration of the phylogenetic relationships of Nextstrain clades ([source](https://github.com/nextstrain/ncov-clades-schema/)):
+
+
+
+Learn more about how Nextclade assigns clades in the [documentation](https://docs.nextstrain.org/projects/nextclade/en/stable/user/algorithm/).
+
+## What are Nextclade datasets
+
+Read more about Nextclade datasets in the Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html
diff --git a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/dataset.zip b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/dataset.zip
new file mode 100644
index 000000000..7efaff5bc
Binary files /dev/null and b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/dataset.zip differ
diff --git a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/genome_annotation.gff3 b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/genome_annotation.gff3
new file mode 100644
index 000000000..2b3bd9f8c
--- /dev/null
+++ b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/genome_annotation.gff3
@@ -0,0 +1,14 @@
+##gff-version 3
+##sequence-region . 266 29533
+. . gene 26245 26472 . + . gene_name=E
+. . gene 26523 27191 . + . gene_name=M
+. . gene 28274 29533 . + . gene_name=N
+. . gene 266 13468 . + . gene_name=ORF1a
+. . gene 13468 21555 . + . gene_name=ORF1b
+. . gene 25393 26220 . + . gene_name=ORF3a
+. . gene 27202 27387 . + . gene_name=ORF6
+. . gene 27394 27759 . + . gene_name=ORF7a
+. . gene 27756 27887 . + . gene_name=ORF7b
+. . gene 27894 28259 . + . gene_name=ORF8
+. . gene 28284 28577 . + . gene_name=ORF9b
+. . gene 21563 25384 . + . gene_name=S
diff --git a/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/pathogen.json b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/pathogen.json
new file mode 100644
index 000000000..98228a272
--- /dev/null
+++ b/data_output/nextstrain/sars-cov-2/wuhan-hu-1/orfs/unreleased/pathogen.json
@@ -0,0 +1,7449 @@
+{
+ "$schema": "https://raw.githubusercontent.com/nextstrain/nextclade/refs/heads/release/packages/nextclade-schemas/input-pathogen-json.schema.json",
+ "alignmentParams": {
+ "excessBandwidth": 12,
+ "terminalBandwidth": 100,
+ "allowedMismatches": 4,
+ "gapAlignmentSide": "right",
+ "minSeedCover": 0.1
+ },
+ "compatibility": {
+ "cli": "3.0.0-alpha.0",
+ "web": "3.0.0-alpha.0"
+ },
+ "defaultCds": "S",
+ "files": {
+ "changelog": "CHANGELOG.md",
+ "examples": "sequences.fasta",
+ "genomeAnnotation": "genome_annotation.gff3",
+ "pathogenJson": "pathogen.json",
+ "readme": "README.md",
+ "reference": "reference.fasta",
+ "treeJson": "tree.json"
+ },
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