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B.1.9-A.2.1_2022-09-13.md

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Designation of one 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 one further B.1 lineage: B.1.9. Additional sequencing of samples from outside the 'outbreak' clade has led to the designation of one further A.2 lineage: A.2.1.

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 B.1 polytomy
  • 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.2.1 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.1.9

At date of designation, this is a mostly Portugese lineage with some sequences from Brazil and one from Canada. It is defined by nucleotide A at position 181367 (in NC_063383 coordinates). At date of designation, the cluster is comprised of around 30 sequences (around 15 not available on INSDC databases; see GISAID for additional sequences). This lineage was internally proposed in issue 14. The yaml file can be found here.

A.2.1

At date of designation, this lineage has been detected 4 times, once in Florida in May 2022, once in the UK in June 2022 and twice in India, each in travellers from the United Arab Emirates in July 2022 (not all available on INSDC databases; see GISAID for additional sequences). This lineage is defined by a long branch with around 10 nucleotide mutations, an arbitrary subset of which is used to define the lineage: 25072T, 140492C, 179537T. If additional samples are found, the defining mutations may change to delineate the lineage. This lineage was internally proposed in issue 15. The yaml file can be found here.