diff --git a/docs/CHANGELOG.old.md b/docs/CHANGELOG.old.md index 3bdaa506..df1ff22e 100644 --- a/docs/CHANGELOG.old.md +++ b/docs/CHANGELOG.old.md @@ -2,6 +2,600 @@ This file contains a summary of changes for Nextclade v2 datasets. This is deprecated after Nextclade v3 is released. +## 2024-01-15 + +### New SARS-CoV-2 dataset version (tag `2024-01-15T12:00:00Z`) + +- Important: This is the last release of SARS-CoV-2 datasets for nextclade v2. All v2 datasets will remain usable with nextclade v2. However, there will be no more dataset updates as future dataset releases will be for nextclade v3 only. Nextclade v3 has corresponding versions for each current v2 dataset. Read more about migrating from v2 to v3 in the [v3 migration guide](https://docs.nextstrain.org/projects/nextclade/en/latest/user/migration-v3.html), specifically, CLI dataset paths may need to be updated, see [Dataset path changes](https://docs.nextstrain.org/projects/nextclade/en/latest/user/migration-v3.html#migration-paths-for-nextclade-cli). As the first v3-only dataset is expected to be released mid February 2024, you have a month to migrate to v3 without any interruption in dataset updates. +- Pango lineages designated between 2023-12-03 and 2024-01-14 are now included, unfold below to see a list with designation dates: + +
+ Newly included lineages, with designation date in parentheses + +- HV.2 (2023-12-17) +- JD.1.1.7 (2023-12-17) +- JD.1.1.8 (2023-12-17) +- JD.2.2 (2023-12-17) +- FY.1.2.1 (2023-12-17) +- FY.1.2.2 (2023-12-17) +- FY.1.2.3 (2023-12-17) +- XBB.1.16.28 (2023-12-17) +- JF.3 (2023-12-17) +- XBB.1.16.29 (2023-12-17) +- XBB.1.16.30 (2023-12-17) +- XBB.1.16.31 (2023-12-17) +- XDJ (2023-12-17) +- XBB.1.5.108 (2023-12-17) +- XCF.3 (2023-12-17) +- XBB.1.5.109 (2023-12-17) +- XBB.1.5.110 (2023-12-17) +- XDA.1 (2023-12-17) +- XBB.2.3.21 (2023-12-17) +- XBB.2.3.22 (2023-12-17) +- JD.1.2.2 (2023-12-17) +- HN.7 (2023-12-17) +- XDK (2023-12-17) +- DV.7.1.8 (2023-12-17) +- KG.1 (2023-12-17) +- KG.2 (2023-12-17) +- DV.7.1.9 (2023-12-17) +- GE.1.2.1 (2023-12-17) +- JG.3.4 (2023-12-17) +- FL.38 (2023-12-17) +- HN.4.1 (2023-12-17) +- HN.4.1.1 (2023-12-17) +- HN.4.2 (2023-12-17) +- FL.39 (2023-12-17) +- FL.39.1 (2023-12-17) +- FL.40 (2023-12-17) +- FL.24.1 (2023-12-17) +- FL.1.8 (2023-12-17) +- JE.1.1.1 (2023-12-20) +- KH.1 (2023-12-20) +- JF.1.1 (2023-12-20) +- JF.1.1.1 (2023-12-20) +- JF.1.1.2 (2023-12-20) +- JF.4 (2023-12-20) +- JN.1.3 (2023-12-20) +- GK.1.8.1 (2023-12-21) +- GK.1.11 (2023-12-21) +- GK.1.11.1 (2023-12-21) +- JW.1.1 (2023-12-21) +- JC.5.1 (2023-12-21) +- GN.1.4 (2023-12-21) +- XBB.1.16.32 (2023-12-21) +- KJ.1 (2023-12-21) +- FL.2.7 (2023-12-21) +- FL.2.7.1 (2023-12-21) +- JN.1.4 (2024-01-08) +- XDL (2024-01-08) +- HV.1.8 (2024-01-09) +- HV.1.9 (2024-01-09) +- HV.1.10 (2024-01-09) +- JN.1.5 (2024-01-09) +- XDD.1 (2024-01-09) +- XDD.1.1 (2024-01-09) +- XDD.2 (2024-01-09) +- JN.2.2 (2024-01-09) +- JN.2.3 (2024-01-09) +- JN.2.4 (2024-01-09) +- JN.2.5 (2024-01-09) +- JN.1.1.2 (2024-01-09) +- HN.8 (2024-01-09) +- JN.1.1.3 (2024-01-09) +- JN.1.6 (2024-01-09) +- JN.1.6.1 (2024-01-09) +- JN.1.7 (2024-01-09) +- JN.1.8 (2024-01-09) +- JN.1.8.1 (2024-01-09) +- JN.1.9 (2024-01-09) +- FW.1.1.1 (2024-01-10) +- HK.3.14 (2024-01-10) +- XDM (2024-01-10) +- KK.1 (2024-01-10) +- KK.2 (2024-01-10) +- KL.1 (2024-01-10) +- KL.1.1 (2024-01-10) +- HV.1.11 (2024-01-10) +- JN.1.10 (2024-01-11) +- JN.1.11 (2024-01-11) + +
+ +## 2023-12-20 + +### New Influenza virus A/H3N2 HA dataset version (tag `2023-12-20T12:00:00Z`) + +- New A/H3N2 HA subclades H.1 - H.4 + +## 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: + +
+ Newly included lineages, with designation date in parentheses + +- 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) + +
+ +## 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. + +## 2023-11-18 + +### New Influenza datasets version (tag `2023-11-18T12:00:00Z`) + +- new subclades for several lineages +- new alias for A/H3N2 HA + +## 2023-10-26 + +### New SARS-CoV-2 dataset version (tag `2023-10-26T12:00:00Z`) + +- Fixed a bug in consensus sequence algorithm that treated ambiguous nucleotides as reference as opposed to unknowns. This only affected a few lineages with few designated sequences where the consensus was wrongly reference when it should have been mutated. +- Pango lineages designated between 2023-09-20 and 2023-10-25 are now included, unfold below to see a list with designation dates: + +
+ Newly included lineages, with designation date in parentheses + +- XCN (2023-09-21) +- FL.31 (2023-09-21) +- FL.31.1 (2023-09-21) +- FL.20.2 (2023-09-21) +- FL.32 (2023-09-21) +- FL.32.1 (2023-09-21) +- FL.10.3 (2023-09-21) +- FL.33 (2023-09-21) +- FL.33.1 (2023-09-21) +- FL.34 (2023-09-21) +- FL.35 (2023-09-21) +- JM.1 (2023-09-22) +- JM.2 (2023-09-22) +- GS.5 (2023-09-22) +- GK.2.1.1 (2023-09-24) +- EG.4.5 (2023-09-24) +- CH.1.1.31 (2023-09-24) +- JP.1 (2023-09-24) +- CH.1.1.32 (2023-09-24) +- JD.1.1.1 (2023-09-26) +- JD.1.1.2 (2023-09-26) +- XCP (2023-09-26) +- EG.5.1.10 (2023-09-26) +- GA.4.1.1 (2023-09-26) +- FR.1.5 (2023-09-26) +- EP.1.1 (2023-09-26) +- EP.1.1.1 (2023-09-26) +- HC.3 (2023-09-26) +- FL.36 (2023-09-26) +- HC.4 (2023-09-26) +- FL.15.1 (2023-09-27) +- FL.15.1.1 (2023-09-27) +- FL.15.2 (2023-09-27) +- FL.15.3 (2023-09-27) +- JN.1 (2023-09-29) +- JD.1.1.3 (2023-10-04) +- JD.2 (2023-10-04) +- GJ.1.2.6 (2023-10-04) +- GJ.1.2.7 (2023-10-04) +- JE.1.1 (2023-10-04) +- GJ.1.2.8 (2023-10-04) +- GJ.5 (2023-10-04) +- GJ.5.1 (2023-10-04) +- BA.2.86.2 (2023-10-12) +- BA.2.86.3 (2023-10-12) +- JQ.1 (2023-10-12) +- JN.2 (2023-10-12) +- JN.3 (2023-10-12) +- GK.2.4 (2023-10-12) +- HK.12 (2023-10-12) +- EG.6.1.2 (2023-10-12) +- HV.1.1 (2023-10-13) +- HV.1.2 (2023-10-13) +- HV.1.3 (2023-10-13) +- HV.1.4 (2023-10-13) +- HK.13 (2023-10-13) +- HK.13.1 (2023-10-13) +- HK.13.2 (2023-10-13) +- HK.1.1 (2023-10-13) +- HK.1.2 (2023-10-13) +- HK.14 (2023-10-13) +- HK.15 (2023-10-13) +- EG.5.1.11 (2023-10-13) +- JR.1 (2023-10-13) +- JR.1.1 (2023-10-13) +- GA.2.1 (2023-10-13) +- GA.2.1.1 (2023-10-13) +- GA.4.2 (2023-10-13) +- GA.4.3 (2023-10-13) +- GA.4.1.2 (2023-10-13) +- HK.16 (2023-10-13) +- HK.17 (2023-10-13) +- HK.18 (2023-10-13) +- HK.19 (2023-10-13) +- XBB.2.3.15 (2023-10-13) +- JS.1 (2023-10-13) +- JS.2 (2023-10-13) +- XCQ (2023-10-13) +- XBB.2.3.16 (2023-10-13) +- XBB.2.3.17 (2023-10-13) +- JD.2.1 (2023-10-13) +- GW.5.2 (2023-10-13) +- GW.5.3 (2023-10-13) +- GW.5.3.1 (2023-10-13) +- HW.1.2 (2023-10-13) +- HW.1.3 (2023-10-13) +- XBC.1.6.5 (2023-10-13) +- JT.1 (2023-10-13) +- XBC.1.6.6 (2023-10-13) +- GL.2 (2023-10-13) +- GL.3 (2023-10-13) +- XCR (2023-10-13) +- GK.5 (2023-10-15) +- GK.5.1 (2023-10-15) +- GK.6 (2023-10-15) +- GK.7 (2023-10-15) +- GK.8 (2023-10-15) +- GK.8.1 (2023-10-15) +- GK.9 (2023-10-15) +- GK.10 (2023-10-15) +- GK.11 (2023-10-15) +- GK.1.5 (2023-10-15) +- GK.1.6 (2023-10-15) +- GK.1.6.1 (2023-10-15) +- GK.1.2.1 (2023-10-15) +- GK.1.7 (2023-10-15) +- GK.1.8 (2023-10-15) +- GK.12 (2023-10-15) +- GK.1.9 (2023-10-15) +- XBB.1.16.25 (2023-10-15) +- XCS (2023-10-15) +- GK.1.1.1 (2023-10-15) +- FU.1.1 (2023-10-15) +- FU.1.1.1 (2023-10-15) +- HG.3 (2023-10-15) +- HG.1.1 (2023-10-15) +- XBB.2.3.18 (2023-10-15) +- GS.6 (2023-10-15) +- GS.4.1.1 (2023-10-15) +- GS.7 (2023-10-15) +- GS.7.1 (2023-10-15) +- GS.8 (2023-10-15) +- GJ.6 (2023-10-15) +- GJ.7 (2023-10-15) +- JU.1 (2023-10-15) +- JV.1 (2023-10-15) +- JV.2 (2023-10-15) +- JC.2 (2023-10-15) +- JC.3 (2023-10-15) +- JC.4 (2023-10-15) +- JC.5 (2023-10-15) +- JC.6 (2023-10-15) +- XBB.1.41.3 (2023-10-15) +- JW.1 (2023-10-15) +- FL.30.1 (2023-10-15) +- FL.13.2.1 (2023-10-15) +- FL.13.4 (2023-10-15) +- FL.13.4.1 (2023-10-15) +- FL.13.5 (2023-10-15) +- JG.4 (2023-10-15) +- DV.7.1.3 (2023-10-15) +- DV.7.1.4 (2023-10-15) +- DV.7.1.5 (2023-10-15) +- XCT (2023-10-15) +- XBC.1.7.2 (2023-10-15) +- XBC.1.7.1 (2023-10-15) +- FL.23.2.1 (2023-10-15) +- FL.23.2 (2023-10-15) +- XCU (2023-10-15) +- HH.2.1 (2023-10-15) +- HH.3 (2023-10-15) +- HH.4 (2023-10-15) +- HH.5 (2023-10-15) +- HH.6 (2023-10-15) +- HH.7 (2023-10-15) +- HH.8 (2023-10-15) +- HH.8.1 (2023-10-15) +- GE.1.4 (2023-10-15) +- GE.1.5 (2023-10-15) +- GE.1.6 (2023-10-15) +- XBB.2.3.19 (2023-10-15) +- JY.1 (2023-10-15) +- JY.1.1 (2023-10-15) +- JG.3.1 (2023-10-15) +- HK.2.1 (2023-10-15) +- HK.3.4 (2023-10-15) +- HK.3.5 (2023-10-15) +- HK.3.6 (2023-10-15) +- HK.3.7 (2023-10-15) +- HK.11.1 (2023-10-15) +- FL.35.1 (2023-10-15) +- GA.7 (2023-10-15) +- GA.7.1 (2023-10-15) +- GA.7.2 (2023-10-15) +- GA.8 (2023-10-15) +- GA.8.1 (2023-10-15) +- GA.9 (2023-10-15) +- GA.10 (2023-10-15) +- XCV (2023-10-15) +- XBB.2.3.20 (2023-10-15) +- XCW (2023-10-15) +- XBB.1.5.107 (2023-10-16) +- JZ.1 (2023-10-16) +- FD.5 (2023-10-16) +- FD.5.1 (2023-10-16) +- HE.2 (2023-10-16) +- FE.1.1.5 (2023-10-16) +- KA.1 (2023-10-16) +- GN.1.2 (2023-10-16) +- GN.1.3 (2023-10-16) +- XCY (2023-10-16) +- XCZ (2023-10-16) +- FY.8 (2023-10-16) +- FY.6.2 (2023-10-16) +- FY.6.1 (2023-10-16) +- FY.9 (2023-10-16) +- FY.1.4 (2023-10-16) +- FY.1.4.1 (2023-10-16) +- FY.5.1 (2023-10-16) +- FY.5.1.1 (2023-10-16) +- HN.2 (2023-10-17) +- HN.2.1 (2023-10-17) +- HN.3 (2023-10-17) +- HN.3.1 (2023-10-17) +- HN.4 (2023-10-17) +- HN.5 (2023-10-17) +- HN.6 (2023-10-17) +- GA.4.1.3 (2023-10-17) +- XDA (2023-10-18) +- XDB (2023-10-18) +- XDC (2023-10-18) + +
+ +## 2023-10-03 + +### New RSV datasets with consortium nomenclature (tag `2023-10-02T12:00:00Z`) + +- this adds a new developed nomenclature for RSV-A and RSV-B by the international RSV nomenclature consortium +- the old `G_clade` nomenclature is kept for backwards compatibility + +## 2023-09-21 + +### New SARS-CoV-2 dataset version (tag `2023-09-21T12:00:00Z`) + +- Add extra example sequences (GL.1, FL.1.5.1, EG.5.1, HV.1, DV.7.1, GK.2, BA.2.86) +- Add new frame shifts and stop codons to be ignored by QC +- Pango lineages designated between 2023-08-09 and 2023-09-20 are now included, unfold below to see a list with designation dates: + +
+ Newly included lineages, with designation date in parentheses + +- JA.1 (2023-08-10) +- JB.1 (2023-08-10) +- JB.2 (2023-08-10) +- FW.1.1 (2023-08-22) +- JC.1 (2023-08-22) +- XBB.1.41.2 (2023-08-22) +- GA.4.1 (2023-08-22) +- GE.1.1 (2023-08-22) +- GE.1.2 (2023-08-22) +- XBB.1.5.102 (2023-08-22) +- JD.1 (2023-08-22) +- FL.1.5.2 (2023-08-23) +- JB.2.1 (2023-08-24) +- HK.6 (2023-08-24) +- GS.2 (2023-08-24) +- GS.3 (2023-08-24) +- GS.4 (2023-08-24) +- GS.4.1 (2023-08-24) +- GE.1.3 (2023-08-24) +- JE.1 (2023-08-24) +- HG.2 (2023-08-24) +- JF.1 (2023-08-24) +- JF.2 (2023-08-24) +- GK.1.4 (2023-08-24) +- GK.2.1 (2023-08-24) +- HK.3.1 (2023-08-24) +- XCH (2023-08-24) +- XCJ (2023-08-24) +- GM.3 (2023-08-24) +- GM.3.1 (2023-08-24) +- HC.2 (2023-08-25) +- EG.5.1.7 (2023-08-25) +- JD.1.1 (2023-08-25) +- JD.1.2 (2023-08-25) +- XBB.1.5.103 (2023-08-30) +- XCH.1 (2023-08-30) +- JG.1 (2023-08-30) +- HK.7 (2023-08-30) +- EG.2.2 (2023-08-30) +- EG.2.3 (2023-08-30) +- EG.2.4 (2023-08-30) +- EG.2.5 (2023-08-30) +- EG.13 (2023-08-31) +- FL.4.8 (2023-08-31) +- FL.4.9 (2023-08-31) +- FL.4.10 (2023-08-31) +- FY.3.2 (2023-08-31) +- FY.3.3 (2023-08-31) +- JH.1 (2023-08-31) +- JH.2 (2023-08-31) +- FL.2.6 (2023-08-31) +- XCK (2023-08-31) +- FL.10.2 (2023-08-31) +- XCL (2023-09-01) +- FL.30 (2023-09-01) +- GW.1.1 (2023-09-01) +- GK.2.2 (2023-09-01) +- HF.1.1 (2023-09-01) +- HF.1.2 (2023-09-01) +- XBB.1.5.104 (2023-09-01) +- XBB.1.16.23 (2023-09-01) +- XBB.1.5.105 (2023-09-01) +- HK.8 (2023-09-01) +- HK.9 (2023-09-01) +- JJ.1 (2023-09-01) +- HK.10 (2023-09-01) +- JK.1 (2023-09-01) +- HS.1.1 (2023-09-01) +- HK.11 (2023-09-04) +- JG.2 (2023-09-04) +- XBB.1.16.24 (2023-09-04) +- JL.1 (2023-09-04) +- BA.2.86.1 (2023-09-05) +- XCM (2023-09-05) +- FY.4.1.2 (2023-09-06) +- EG.6.1.1 (2023-09-07) +- GJ.1.2.2 (2023-09-10) +- GJ.1.2.3 (2023-09-10) +- GJ.1.2.4 (2023-09-10) +- GJ.1.2.5 (2023-09-10) +- FL.4.11 (2023-09-10) +- HK.3.2 (2023-09-10) +- HK.3.3 (2023-09-10) +- EG.14 (2023-09-10) +- GK.3.2 (2023-09-10) +- CK.1.1.2 (2023-09-10) +- EF.3 (2023-09-10) +- GW.5.1 (2023-09-11) +- GW.5.1.1 (2023-09-11) +- DV.7.1.1 (2023-09-11) +- DV.7.1.2 (2023-09-11) +- EG.5.1.8 (2023-09-11) +- GK.2.3 (2023-09-17) +- GK.4 (2023-09-17) +- EG.5.1.9 (2023-09-17) +- JG.3 (2023-09-17) +- XBB.1.5.106 (2023-09-17) + +
+ ## 2023-08-22 ### New influenza dataset version (tag `2023-08-10T12:00:00Z`) @@ -1093,7 +1687,7 @@ Add robots.txt to prevent data endpoints from indexing by search engines. #### New clade definitions for default influenza datasets (tag `2023-01-19T12:00:00Z`) The default influenza datasets were updated to include recent consensus on clade definitions and more recent sequences in their reference tree to better reflect current circulation. -In addition, these data sets contain a `short_clade` column which omits the long prefix and definition of glycosylation motifs for a future software release. +In addition, these data sets contain a `short_clade` column which omits the long prefix and definition of glycosylation motifs for a future software release. ## 2023-01-09 @@ -1425,7 +2019,7 @@ The existing dataset with reference sequence B/Brisbane/60/2008 (KX058884) was u #### New dataset version (tag `2022-10-19T12:00:00Z`) -- New clade `22E (Omicron)` (BQ.1*) added, see for details +- New clade `22E (Omicron)` (BQ.1\*) added, see for details - The SARS-CoV-2 trees are now purely based on Pango consensus sequences, and no longer contain any actual sequences. This makes builds more stable and helps mitigate issues with sequence artefacts. For the Omicron part of the tree, no actual sequences were ever included, so this change only affects the pre-Omicron part of the reference tree. - This release contains the first recombinant sublineages. These work in the same way as the other sublineages. - Data update: New Pango lineages, with designation date between 2022-09-25 and 2022-10-19 are now included, unfold below to see all the lineages: @@ -1594,7 +2188,7 @@ The existing dataset with reference sequence B/Brisbane/60/2008 (KX058884) was u #### All SARS-CoV-2 datasets - Data update: New Pango lineages are included, see for new designations that are included -- Identical sequences have been removed from B.1* lineages to reduce size of that part of the tree from ~1.6k to ~800. +- Identical sequences have been removed from B.1\* lineages to reduce size of that part of the tree from ~1.6k to ~800. ##### BA.2 dataset (experimental)