Pango lineages: guidelines for suggesting novel and recombinant lineages
13.04.22 | Christopher Ruis
27.08.21 | New lineages
The latest release of the pangoLEARN model (2021-08-24, trained on pango-designation v1.2.66) includes new lineages AY.13-AY.25 and an update to the previously designated AY.4-AY.12 lineages. As previously outlined for AY.4-AY.12, each of the new AY.13-AY.25 lineages shows significant geographical clustering and these lineages have been designated to help researchers track the virus on a finer scale. Their designation does not imply any functional biological difference from B.1.617.2 and, like B.1.617.2, they correspond to the WHO-defined Delta variant (https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/). The table at the bottom of this article shows the countries and mutations that are associated with each of the AY lineages.
With this release we expect that some genomes will be assigned to a different Delta lineage compared to previous releases. We’ve expanded the number of virus genomes designated to each of the lineages AY.4-AY.12 since the previous pangoLEARN release. This expansion enables pangoLEARN to better learn what each of the AY lineages looks like and therefore enables improved lineage assignment of other genomes. Specifically, we’ve designated all of the genomes to an AY lineage if they exhibit the full set of mutations expected of that lineage and are found in the respective AY clade in the UShER global phylogenetic tree. This means that a number of virus genomes that were previously designated B.1.617.2 are now designated to one of the AY lineages compared to their assignment with previous pangoLEARN versions. We believe this expansion of designated sequences will help improve stability of the assignments of AY lineages.
We expect that more AY lineages will continue to follow. As previously outlined, unless stated otherwise by the WHO or other public health bodies, these lineages should be treated as the Delta variant and their designation to a sub-lineage does not necessarily imply any functional biological difference from B.1.617.2. Lineages are by definition associated with epidemiological data, such as novel introduction and spread, geographical clustering or by a series of significant mutations. In these cases, the mutations associated with sublineages are essentially ‘genetic placeholders’ to help track the virus lineages, rather than being of any biological concern or significance.
If you think you’ve identified a new lineage of B.1.617.2 (or any other lineage) based on the rules set out here, please let us know by submitting an issue here.
Table of currently designated AY lineages, their predominant geographical location(s) and their associated mutation(s). Note that the listed mutations are those that occurred along the phylogenetic branch immediately preceding the common ancestor of the lineage. These mutations are therefore those that separate the AY lineage from closely related sequences but may not be all of the mutations that separate them from other AY lineages or more distant B.1.617.2 sequences.
13.04.22 | Christopher Ruis
01.04.22 | Christopher Ruis
09.12.21 | Rachel Colquhoun