nextstrain/nextclade_data 2022-10-31--11-48-49--UTC

2022-10-27

on GitHub

All SARS-CoV-2 datasets

New dataset version (tag 2022-10-27T12:00:00Z)

• Phase 1 of migration of clade labels started: We will migrate clade labels from being a composite of Nextstrain clade, WHO name and legacy names (e.g. 20J (Gamma, V3)) to a set of independent clade labels.
  Phase 1 does not make braking changes. clade remains composite as in the past. However, 3 new clade columns are introduced (in the TSV/CSV only so far): clade_nextstrain (e.g. 20J) and clade_who (e.g. Gamma) and clade_legacy (e.g. 20J (Gamma, V3).
  If you don't want to change your code, you can future proof it by starting to use clade_legacy instead of clade, which is identical at the moment, but in the mid-term (earliest a month) clade may change. However, clade_legacy will remain part of the dataset for much longer.
  If you want to start using new split clades, you can start using clade_nextstrain and clade_who from now on.
  Phase 2 which will happen at the earliest in a month (2022-12-01) will involve changing clade from being composite and identical with clade_legacy to being identical with clade_nextstrain.
  Phase 3 which will happen at the earliest in 6 months (2023-04-01) may involve dropping clade_legacy and clade_nextstrain.

• New clade 22F (Omicron) (XBB) added, see nextstrain/ncov#1020 for details, e.g. on the reasons for elevation

• virus_properties.json has been updated with mutations characteristic of clades 22E (BQ.1) and 22F (XBB) to enable detection of contamination/recombination involving these clades

• qc.json has been updated with common frameshifts and stop codons that appear in hundreds of sequences and plausibly occur in viable virus

• Data update: New Pango lineages, with designation date between 2022-09-20 and 2022-10-27 are now included, unfold below to see all the lineages:

  New Pango lineages included in this release

  • XBB.4 (2022-10-20)
  • XBB.3.1 (2022-10-20)
  • XBB.5 (2022-10-20)
  • BQ.1.1.3 (2022-10-20)
  • BQ.1.1.4 (2022-10-20)
  • BQ.1.1.5 (2022-10-20)
  • BQ.1.1.6 (2022-10-20)
  • BQ.1.1.7 (2022-10-20)
  • BQ.1.1.8 (2022-10-20)
  • BQ.1.1.9 (2022-10-20)
  • BQ.1.1.10 (2022-10-20)
  • BN.1.2.1 (2022-10-20)
  • BN.1.4 (2022-10-20)
  • BN.1.5 (2022-10-20)
  • BN.1.6 (2022-10-20)
  • CK.2 (2022-10-20)
  • CK.2.1 (2022-10-20)
  • CK.2.1.1 (2022-10-20)
  • CQ.2 (2022-10-20)
  • BQ.1.1.11 (2022-10-21)
  • BQ.1.1.12 (2022-10-21)
  • BY.1.1 (2022-10-21)
  • BY.1.1.1 (2022-10-21)
  • BY.1.2 (2022-10-21)
  • BY.1.2.1 (2022-10-21)
  • CM.4 (2022-10-21)
  • CM.5 (2022-10-21)
  • CM.6 (2022-10-21)
  • XBE (2022-10-22)
  • BU.3 (2022-10-23)
  • BA.5.1.30 (2022-10-23)
  • CV.1 (2022-10-23)
  • XBB.1.3 (2022-10-23)
  • BQ.1.1.13 (2022-10-23)
  • CA.7 (2022-10-24)