What are Pango lineages?
Pango is a rule-based system for naming SARS-CoV-2 genetic lineages. It provides a shared, common terminology for everyone who is investigating or discussing the transmission and spread of the virus.
Pango is a dynamic and flexible system that can adapt to the changing nature of the pandemic and to growth in the generation of SARS-CoV-2 genomic data. The Pango nomenclature is used by researchers and public health agencies worldwide and you may have come across Pango lineage names, such as B.1.1.7 or B.1.351, in the news. Pango lineages are designed to support epidemic surveillance and outbreak investigation, and capture the leading edge of ongoing transmission at a high resolution.
Each Pango lineage defines a group of SARS-CoV-2 genome sequences and is created according to two guiding principles. First, Pango lineages signify groups or clusters of infections with shared ancestry. If the whole pandemic can be thought of as a vast branching tree of transmission, then Pango lineages represent the individual branches within that tree. Second, Pango lineages are intended to highlight epidemiologically-relevant events, such as the appearance of the virus in a new location, a rapid increase in cases, or the evolution of viruses with new phenotypes.
The current rules and criteria used to create new Pango lineages can be found here and include minimum standards of lineage size, genome quality, genetic distinctiveness, and epidemiological importance. These criteria change through time, to adapt to changing needs and circumstances.
The Pango nomenclature is a hierarchical system and that is reflected in the way lineages are named. Each lineage is given a unique alphanumeric code that contains partial, but not complete, information about the phylogenetic history of that lineage. The lineage naming conventions are described here and represent a compromise between the requirements of human comprehension and machine-readability.
Full details of each Pango lineage are provided in the lineage description list, which can be found here.