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v0.6.0 - Sublineages and Immunity
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@github-actions github-actions released this 08 Nov 00:03
v0.6.0
2506e90

v0.6.0

Notes

This is a major release that includes the following changes:

Dataset

  • Issue #168: NULL collection dates and NULL country is implemented.
  • controls was updated to in include 1 strain from XBB for a total of 22 positive controls. The 28 negative controls were unchanged from v0.5.1.
  • controls-gisaid strain list was updated to include XA through to XBE for a total of 528 positive controls. This includes sublineages such as XBB.1 and XBB.1.2 which synchronizes with Nextclade Dataset 2022-10-19. The 187 negatives controls were unchanged from v0.5.1.

Nextclade

  • Issue #176: Upgrade Nextclade dataset to tag 2022-10-27 and upgrade Nextclade to v2.8.0.
  • Issue #193: Use the nextclade dataset sars-cov-2-21L to calculate immune_escape and ace2_binding.

RBD Levels

  • Issue #193: Create new rule rbd_levels to calculate the number of key receptor binding domain (RBD) mutations.

Lineage Tree

  • Issue #185: Use nextclade dataset Auspice tree for lineage hierarchy. Previously, the phylogeny of lineages was constructed from the cov-lineages website YAML. Instead, we now use the tree provided with nextclade datasets, to better synchronize the lineage model with the output.

Rather than creating the output tree in resources/lineages.nwk, the lineage tree will output to data/sars-cov-2_<DATE>/tree.nwk. This is because different builds might use different nextclade datasets, and so are dataset specific output.

sc2rf

  • Issue #179: Fix bug where sc2rf/recombinants.ansi.txt is truncated.
  • Issue #180: Fix recombinant sublineages (ex. XAY.1) missing their derived mutations in the cov-spectrum_query. Previously, the cov-spectrum_query mutations were only based on the parental alleles (before recombination). This led to sublinaeges (ex. XAY.1, XAY.2) all having the exact same query. Now, the cov-spectrum_query will include all substitutions shared between all sequences in the cluster_id.
  • Issue #187: Document bug that occurs if duplicate sequences are present, and the initial validation was skipped by not running scripts/create_profile.sh.
  • Issue #191 and Issue #192: Reduce false positives by ensuring that each mode of sc2rf has at least one additional parental population that serves as the alternative hypothesis.
  • Issue #195: Implement a filter on the ratio of intermissions to alleles. Sequences will be marked as false positives if the number of intermissions (i.e. alleles that conflict with the identified parental region) is greater than or equal to the number of alleles contributed by the minor parent. This ratio indicates that there is more evidence that conflicts with recombination than there is allele evidence that supports a recombinant origin.

Linelist

  • Issue #183: Recombinant sublineages. When nextclade calls a lineage (ex. XAY.1) which is a sublineage of a sc2rf lineage (XAY), we prioritize the nextclade assignment.
  • Issue #193: Add immune-related statistics: rbd_levels, rbd_substitutions, immune_escape, and ace2_binding.

Plot

  • Issue #57: Include substitutions within breakpoint intervals for breakpoint plots. This is a product of Issue #180 which provides access to all substitutions.
  • Issue #112: Fix bug where breakpoints plot image was out of bounds.
  • Issue #188: Remove the breakpoints distribution axis (ex. breakpoints_clade.png) in favor of putting the legend at the top. This significant reduces plotting issues (ex. Issue #112).
  • Issue #193: Create new plot rbd_level.

Validate

Designated Lineages
Proposed Lineages

Commits

  • 2506e907 docs: update changelog and add v0.6.0 testing summary package
  • 0cc421e0 docs: update all contributors
  • cd9b6cbb resources: update issues
  • 0fa2e3c1 docs: update readme
  • 375c3a76 resources: add proposed lineages for #197 #198 #199
  • dad989e7 param: remove BQ.1 from sc2rf mode VOC as its too close to BA.5.3
  • d7cb005f docs: update issue template lineage-validation
  • 1beac97e resources: add XBF to curated breakpoints for #196
  • fae7bfdb script: sc2rf implement intermission allele ratio for #195
  • 89a41265 script: additional manual curation of lineage_tree
  • ebd3ce1f resources: update validation strains for controls-gisaid
  • d8bff572 script: add RBD Level slide to report
  • c1879c1d script: catch errors in rbd_level plotting with no recombinants
  • 63545a08 script: fix bug in linelist with cluster_privates
  • c24a7179 resources: update issues
  • d32d557f docs: update development notes
  • 7f825a41 script: manual fix for CK in lineage_tree
  • fdd6f66d workflow: implement rbd levels for #193
  • 0058dd6e param: upgrade nextclade dataset to 2022-10-27 and reduce breakpoints of XA mode
  • fb062c32 env: upgrade nextclade to v2.8.0
  • See CHANGELOG.md for additional commits.
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