This repository contains updates and details about mpox virus outbreak and lineage designations. Outbreak and lineage naming systems are meant to assist genomic epidemiology of mpox in humans and provide a fine-grained systematic nomenclature to refer to different circulating lineages. They do not imply any phenotypic differences. These lineages only apply to recent human cases and are distinct from broader clades of monkeypox viruses circulating in the animal reservoir Ia, Ib, IIa, and IIb, see Happi et al and the recent announcement by the WHO. Outbreak lineages are defined in line with the nomenclature proposed in the paper A systematic nomenclature for mpox viruses causing outbreaks with sustained human-to-human transmission (https://www.nature.com/articles/s41591-025-03820-6).
Lineage designations are independent between sustained outbreaks. Different outbreaks reuse the same lineage names (e.g. A.1 in outbreak sh2017 is not the same as A.1 in outbreak sh2023). The lineage names are only unique within a sustained outbreak. Unless obvious from context, the outbreak name should be included when referring to a lineage.
Each sustained outbreak definition is in its own yaml file within the corresponding clade's folder. Lineages within sustained outbreaks are defined in subfolders named after the sustained outbreak. This results in the following structure:
definitions/
IIb/
sh2017.yml
sh2017/
A.yml
A.1.yml
...
Ib/
sh2023/
A.yml
A.1.yml
...
Ia/
sh2024.yml
designation_records/
B.1.1-B.1.5_2022-08-08.md
B.1.6-B.1.8_2022-08-25.md
...Each new lineage is defined by a yaml file according the schema.
For outbreak sh2017's lineage B.1, for example, this looks like this:
# yaml-language-server: $schema=../schemas/single_lineage/lineage_schema_1-0-0.yml
name: B.1
unaliased_name: A.1.1.1
parent: A.1.1
designation_date: "2022-06-10"
defining_snps:
- pos: 77383
nucleotide: A
reference_sequences:
- source: genbank
accession: ON563414
isolate: MPXV_USA_2022_MA001Defining SNPs are given with respect to the reference sequence NC_063383 (MPXV-M5312_HM12_Rivers).
New lineages are designated as more cases are sequenced and the outbreak gets more diverse. The criteria for lineage designation will evolve as the outbreak continues. Currently, we aim to designate a new lineage if it
- has spread internationally
- has at least 1 mutation above its parent
- contains at least 15 sequences or plausibly represents undersampled diversity
- has a 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 (high quality meaning that it doesn't show unusually large numbers of frame shifts and/or stop codons)
You can find markdown documents describing the rationale of lineage designation (including which lineages and why) in the "designation_records" folder.
- 2022-08-08: B.1.1-B.1.5
- 2022-08-25: B.1.6-B.1.8
- 2022-09-13: B.1.9-A.2.1
- 2022-09-26: B.1.10-A.2.2
- 2022-10-31: B.1.13-B.1.14-A.2.3-A.3
- 2023-01-11: B.1.15-B.1.16-B.1.17
- 2023-08-01: B.1.18-B.1.19-B.1.20-C.1
- 2024-04-15: B.1.21-B.1.22-C.1.1
- 2024-11-05: B.1.23-D.1-E.1-3-F.1-6
- 2025-09-07: A.2.5-C.1.3-E.3.1-E-4-F.4.1-G.1-etc
Lineages within the clade Ib/sh2023 outbreak are designated in the same way as for clade IIb/sh2017, with broadly similar criteria.
You can find markdown documents describing the rationale of lineage designation (including which lineages and why) in the "designation_records" folder:
To propose additional lineages, open a GitHub issue in this repository.