Lineage Format Audit

Validate Pango-style alias-and-numeric lineage syntax with a caller depth limit; syntax does not confirm an assigned lineage.

Description

Check a Pango-style uppercase prefix and positive numeric suffixes against a supplied depth limit without verifying lineage assignment.

Pango names organize SARS-CoV-2 lineages using hierarchical labels and aliases. A lineage name is a label for an assigned group in a maintained nomenclature, rather than a sequence description that can be proved from spelling alone.^[1]

A syntactic check can still catch lowercase prefixes, empty dot-separated components, and leading-zero numeric fields. This tool implements its own fixed Pango-style pattern and a caller-selected numeric-depth ceiling; it does not consult the maintained alias or designation records.^[2]

Lineage Format Audit returns a validity flag plus the raw prefix and number of dot-separated suffix positions. The latter two outputs remain available when the format fails.

When to screen lineage-label formatting

Use the audit during data entry or record cleanup when a limited syntax rule is useful. Preserve the original value so failed strings can be inspected instead of silently normalized.

Check an uppercase alias-like prefix and numeric components.
Apply a local depth ceiling independently of designation status.

How to enter a label and evaluate its syntax

Enter Lineage exactly as recorded. The tool does not trim whitespace or uppercase text.
Enter Maximum numeric depth as a positive integer.
Run the audit and inspect Valid format, Alias prefix, and Numeric depth.
Verify actual designation and alias meaning separately when they matter.

pattern = ^[A-Z]{1,3}(?:.[1-9]d*)*$; numericDepth = max(0, split(".").length − 1)

The flag is true only when the entire string matches the pattern and numericDepth is at most the supplied maximum. A prefix without numeric suffixes has depth zero and can pass.

json

{
  "input": {
    "lineage": "BA.2.86",
    "maximumNumericDepth": 3
  },
  "output": {
    "validFormat": true,
    "aliasPrefix": "BA",
    "numericDepth": 2
  }
}

The prefix is simply the text before the first dot, even for an invalid label. Numeric depth counts dot-separated suffix positions rather than validating that they contain numbers. A malformed label normally returns false; an invalid depth parameter or malformed tool input produces an error.

Limitations and interpretation

No alias expansion, registry lookup, sequence classification, phylogenetic analysis, or current nomenclature synchronization is performed.
Passing the pattern does not establish that a lineage is assigned, active, or biologically related to another label.
The fixed one-to-three-letter pattern and supplied depth ceiling are this tool’s rules, not a complete implementation of evolving designation policy.
Whitespace, case, empty components, and leading zeros are not repaired.

Alternative or Complementary methods

Use maintained designation records for label identity. For supplied mutations or distance data, signature matching and graph clustering offer separate summaries; neither turns this syntax check into a lineage classifier.

References

A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology — Nature Microbiology; A. Rambaut and colleagues (2020)
Pango designation: maintained lineage designations and alias records — Pango nomenclature project

Similar or alternative tools

Clade Signature Support
Compare supplied mutation identifiers with caller-defined candidate signature sets.
Genomic Distance Clusters
Group samples by connected paths in a supplied thresholded distance matrix.