B.1.10-A.2.2_2022-09-26.md

Designation of three B.1 sublineage and one A.2 sublineage

Continued sequencing and sharing of monkeypox genomes has further expanded the diversity of the B.1 ('outbreak') clade, leading to the designation of three further B.1 lineages: B.1.10, B.1.11, B.1.12. Additional sequencing of samples from outside the 'outbreak' clade has led to the designation of one further A.2 lineage: A.2.2.

The criteria used to designate these lineages are the same as previously, and are based on genomes available in INSDC databases and:

• International spread
• Having at least 1 mutation above the parent lineage
• Containing at least 15 sequences or plausibly represents undersampled diversity
• Clear common phylogenetic structure (no uncertainty about possibly being designated as 2 lineages instead of 1)
• Has at least one freely available high quality reference sequence

Despite only having a small number of samples at date of designation, sequences that are part of the newly designated A.2.2 lineage are not part of the B.1 ('outbreak') clade and thus are likely undersampled. Hence, designation seems to be in the public health interest.

B.1.10

At date of designation, this is a mostly Colombian lineage with additional circulation in multiple European countries. It is defined by nucleotide T at position 89906 and G at position 94798 (in NC_063383 coordinates). At date of designation, the cluster is comprised of around 40 sequences. This lineage was internally proposed in issue 19. The yaml file can be found here.

B.1.11

At date of designation, this is a mostly US lineage with one additional sequence from Colombia countries. It is defined by four SNPs: C18133T, G67611A, G130231A, G159277A. At date of designation, the cluster is comprised of around 40 sequences. This lineage was internally proposed in issue 20. The yaml file can be found here.

B.1.12

At date of designation, this is a lineage with global circulation, having been sequenced in Europe, North and South America. It is defined by C182950T. At date of designation, the cluster is comprised of around 20 sequences. This lineage was internally proposed in issue 22. The yaml file can be found here.

A.2.2

At date of designation, this lineage has been detected 2 times, once in the UK in June 2022 and once in the US state Philadelphia in July 2022. This lineage is defined by a long branch with around 20 nucleotide mutations, an arbitrary subset of which is used to define the lineage: 21991A, 103019T, 158424A. If additional samples are found, the defining mutations may change to delineate the lineage. This lineage was internally proposed in issue 21. The yaml file can be found here.