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PANGO Lineage - Naming conventions for SARS-CoV-2
Some useful reference links on the naming of variants, for those curious about such things. I do find it unfortunate that this is called "pangolineage" though, adds a confusing element imho.
https://virological.org/t/pango-lineage-nomenclature-provisional-rules-for-naming-recombinant-lineages/657
General naming conventions:
• Pango lineage names comprise an alphabetical prefix and a numerical suffix. The alphabetical prefix contains latin characters only which are case insensitive.
• The letters I, O and X are not used in the prefix of the names of standard lineages.
• Each dot in the numerical suffix means “descendent of” and is applied when one ancestor can be clearly identified. So lineage B.1.1.7 is the seventh named descendent of lineage B.1.1 and C.1 is the first named descendent of lineage C.
• The suffix can contain a maximum of 3 hierarchical levels, referred to as the primary, secondary and tertiary suffixes.
• In order to avoid four or more suffix levels, a new lineage suffix is introduced, which acts as an alias. For example, C is an alias of B.1.1.1 hence the descendent of B.1.1.1 is called C.1 (rather than B.1.1.1.1). Consequently the name C, by itself, is never directly applied to a sequence.
• In some instances, it is not possible to unambiguously identify an ancestral lineage within the Pango nomenclature for a given lineage of interest. This is the case for lineages A and B, because of their position near the root of the phylogeny. For these “special case ancestors”, the alphabetical part alone can be applied directly to sequences. In all other cases the suffix is mandatory.
• Pango lineage names comprise an alphabetical prefix and a numerical suffix. The alphabetical prefix contains latin characters only which are case insensitive.
• The letters I, O and X are not used in the prefix of the names of standard lineages.
• Each dot in the numerical suffix means “descendent of” and is applied when one ancestor can be clearly identified. So lineage B.1.1.7 is the seventh named descendent of lineage B.1.1 and C.1 is the first named descendent of lineage C.
• The suffix can contain a maximum of 3 hierarchical levels, referred to as the primary, secondary and tertiary suffixes.
• In order to avoid four or more suffix levels, a new lineage suffix is introduced, which acts as an alias. For example, C is an alias of B.1.1.1 hence the descendent of B.1.1.1 is called C.1 (rather than B.1.1.1.1). Consequently the name C, by itself, is never directly applied to a sequence.
• In some instances, it is not possible to unambiguously identify an ancestral lineage within the Pango nomenclature for a given lineage of interest. This is the case for lineages A and B, because of their position near the root of the phylogeny. For these “special case ancestors”, the alphabetical part alone can be applied directly to sequences. In all other cases the suffix is mandatory.
A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology
https://www.nature.com/articles/s41564-020-0770-5
The PANGO Lineage website:
https://cov-lineages.org/index.html
