Lineage nomenclature

Reviewed 2026-10-01 using current Pango files, official naming/tool documentation, and the live LAPIS schemas. Labels below illustrate naming structure, never current prevalence or dominance.

Pango designation versus database assignment

The Pango designation repository is the source for SARS-CoV-2 designations. Its current lineage_notes.txt contains descriptions and withdrawn/redesignated names marked with *; pango_designation/alias_key.json resolves aliases. Do not bake the number of designations or withdrawals into an answer: it changes continuously.

Ordinary alias entries are strings. Repeated expansion follows the alias chain until it reaches A/B or a recombinant root. Recombinant entries are lists of parental lineage descriptions, not one dotted ancestral path. Expand an ordinary alias before looking for recombinant ancestry. A recombinant's descendants still have ordinary parent/child relationships within that lineage. The live files, not reasoning from the spelling, determine these relationships.

The scripts fetch current files independently and record content SHA-256. Their HTTP ETags are not Git blob/commit IDs. For archival work, retain both files from one explicit repository commit; distinguish that historical naming snapshot from a fresh check of designation status. A source failure must not turn a cached assignment into a claim of current designation.

LAPIS pangoLineage and nextcladePangoLineage share naming vocabulary but can disagree because assignment pipelines and datasets differ. A withdrawn name can remain assigned to records. Indexed membership establishes that a database can query a name, not that Pango still designates it. resolve_lineage.py uses Pango notes as the authority for Pango status, and returns failure for unverified names. Counts on indexed fields include descendants; the provenance says so.

Nextstrain, Nextclade and WHO

Do not claim all recombinants always collapse into one Nextstrain label. Inspect actual values, the current reference dataset, and the question's required resolution. Likewise a null whoClade is not evidence that WHO's tracking system is retired. Consult the current WHO tracking page for official labels/classifications; do not invent Greek labels or infer a risk classification from a name.

The instance may expose nextcladeDatasetVersion, which should accompany assignment comparisons. For separately authorized Nextclade analysis, the official CLI uses nextclade dataset list, nextclade dataset get and nextclade run --input-dataset. Record tool version, dataset name, tag/version and reference. Refresh for a current naming task; pin for reproducible reruns. Do not treat a dataset-server root as an inference endpoint or silently replace a study's dataset. These commands are documentation-reviewed here, not locally executed. Official Nextclade usage.

Influenza

HA and NA labels describe different segments; their differing values alone do not diagnose reassortment. These analyses need their own phylogenetic context. unassigned is a genuine category. Missing calls are different from it; retain both in denominator accounting.

H5N1 HA clade labels and whole-genome genotypes are different entities. A query for a clade cannot produce a genotype count, and neither geography nor host can substitute for genotype assignment. USDA GenoFLU describes a specialist genotype workflow for North American H5N1 clade 2.3.4.4b sequences. Its scope and database do not generalize to every influenza genome. Genotyping is outside these scripts and was not executed in this audit.

Other reviewed instances

Keep original case for non-Pango labels, particularly Ia/Ib or composite outbreak labels. resolve_lineage.py prints alternate candidate fields. Its automatic choice is a convenience; select the field that answers the question, and report whether descendants were included. The Pathoplexus API guide and each instance's /sample/databaseConfig provide deployment-specific field names. A naming field being indexed does not make it a validated phenotype or transmission history.