Continued sequencing and sharing of monkeypox genomes has further expanded the diversity of the B.1 ('outbreak') clade, leading to the designation of two further B.1 lineages: B.1.13, B.1.14. Additional sequencing of samples from outside the 'outbreak' clade has led to the designation of one further A.2 lineage: A.2.3 and one further A sublineage: A.3.
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.
At date of designation, this is a mostly US lineage with additional circulation in the UK and Germany. It is defined by ncleotide SNP 175093A.
At date of designation, the cluster is comprised of around 40 sequences.
This lineage was externally proposed by @mbosm in issue 24.
The yaml file can be found here.
At date of designation, this is a mostly European lineage with some circulation in the US.
It is defined by two SNPs: 36617A, 159779T. At date of designation, the cluster is comprised of around 30 sequences.
This lineage was internally proposed in issue 27.
The yaml file can be found here.
At date of designation, this lineage has been sequenced once in the US state of Texas in July 2021 and once in Portugal in August 2022.
This lineage is defined by 15 nucleotide mutations, an arbitrary subset of which is used to define the lineage: 57284T, 74226T.
If additional samples are found, the defining mutations may change to delineate the lineage.
This lineage was internally proposed in issue 25.
The yaml file can be found here.
At date of designation, this lineage has been detected 5 times, 3 times in Nigeria between 2017 and 2019, and two times in the UK in September 2022.
This lineage is defined by 6 nucleotide mutations, an arbitrary subset of which is used to define the lineage: 96841A, 100971T.
If additional samples are found, the defining mutations may change to delineate the lineage.
This lineage was discussed in a UKHSA report and then proposed in issue 26.
The yaml file can be found here.