Question 1

What is the Pango Network's primary role?

Accepted Answer

The Pango Network is a global consortium of scientists and public health experts. Its primary role is to develop and maintain the Pango nomenclature, a dynamic and hierarchical system for naming and classifying genetic lineages of SARS-CoV-2. This structured system is essential for tracking the virus's evolution, understanding its spread, and providing a common language for researchers, clinicians, and policymakers worldwide.

Question 2

How do Pango, Nextclade, and GISAID differ?

Accepted Answer

These three resources serve different but complementary functions in genomic surveillance. Pango provides the nomenclature—the naming system itself—for classifying viral lineages. Nextclade is a powerful tool used for clade assignment, mutation calling, and sequence quality control. GISAID is a global data repository, a massive database where scientists from around the world submit, store, and share SARS-CoV-2 genomic data, which then serves as the raw data for tools like Nextclade and for the designation of Pango lineages.

Question 3

How are Pango lineages named?

Accepted Answer

Pango uses a hierarchical alpha-numeric system to reflect evolutionary relationships. A name like B.1.1.7 indicates that it is the 7th named descendant of lineage B.1.1. To prevent names from becoming excessively long, the system uses aliasing after three numerical levels. For example, the first descendant of B.1.1.1 is not B.1.1.1.1 but is aliased as C.1. Recombinant lineages, which have parents from different branches of the tree, are a special case and are always given a prefix beginning with 'X' (e.g., XA, XB, XBB).

Question 4

What is the difference between lineage 'designation' and 'assignation'?

Accepted Answer

This is a critical distinction. Designation is the definitive, 'gold standard' classification of a sequence into a lineage. This process is done with careful manual analysis and curation by the Lineage Designation Committee (LDC) and is recorded in the official pango-designation repository. Assignation, on the other hand, is a provisional, automated inference of the most likely lineage for a given sequence. This is performed by software tools like Pangolin. Assignation is essential for rapid, high-throughput analysis in real-time surveillance but carries a degree of uncertainty and can change as the software and lineage definitions are updated.

Question 5

How can I propose a new lineage?

Accepted Answer

The Pango system is community-driven. Researchers can propose new lineages by filing an issue on the pango-designation GitHub repository. A strong proposal must provide evidence that the cluster of sequences meets the criteria defined in the nomenclature rules, including evidence of shared ancestry, distinguishing mutations, and epidemiological significance (e.g., rapid growth or a founder event in a new region). The proposal should include a list of sequence IDs and ideally a phylogenetic tree.

Question 6

What are the core software tools in the Pango ecosystem?

Accepted Answer

Pangolin: The primary tool for assigning lineages to query sequences.Scorpio: A tool for rapidly identifying known Variants of Concern by scanning for their defining mutation constellations.Civet: A tool for generating real-time reports for outbreak investigations.Hedgehog: A tool for lineage set assignment based on spikey SARS-CoV-2 sequences.

Question 7

What is a 'constellation' and where are they defined?

Accepted Answer

A constellation is a collection of mutations that are functionally meaningful but may arise independently in different lineages. They serve as a useful shorthand for tracking important sets of mutations, especially those found in Variants of Concern. The definitions for these constellations are maintained in the constellations GitHub repository.

Question 8

Why was my sequence not assigned a lineage by Pangolin?

Accepted Answer

This can happen for several reasons. The most common are low sequence quality, such as having too many ambiguous bases ('N's) or missing data. The sequence may also belong to a new, not-yet-designated lineage. Additionally, your version of Pangolin or its data files might be out of date; always ensure you are using the latest version of Pangolin and its associated data from the pangolin-data repository. If you believe you've found a new lineage, you can consider proposing it through the official channels.

Question 9

I'm having a technical issue with Pangolin. Where can I get help?

Accepted Answer

For technical support, bug reports, or feature requests related to the Pangolin software, the best place to go is the issues section of the Pangolin GitHub repository. You can browse existing closed issues to see if your problem has already been solved or open a new issue to get help from the developers.

Question 10

Who governs the Pango nomenclature system?

Accepted Answer

The system is run by two committees to ensure robust and transparent governance. The Pango Committee (PC) is responsible for maintaining and amending the rules of the nomenclature system. The Lineage Designation Committee (LDC) handles the day-to-day scientific work of analyzing genome data and designating new lineages according to the rules.

Question 11

How should I cite the Pango nomenclature in my research?

Accepted Answer

Proper citation is crucial for acknowledging the work that underpins this system. The primary citation for the Pango nomenclature system is the paper by Rambaut A, Holmes EC, O'Toole Á, et al. (2020) in Nature Microbiology. For specific citations for lineage reports or the Pangolin software, please refer to our comprehensive 'How to Cite' page.

Question 12

Where can I find the most up-to-date lineage assignments?

Accepted Answer

The most current, definitive lineage designations are in the pango-designation repository. For the latest automated assignments from the Pangolin tool, you can refer to the pangolin-assignment repository.

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