New clade/lineage/sublineage criteria for mpox

General
1

Hi everyone,

I would like to know what criteria are used in Nextstrain to define a new clade, lineage, or sublineage for mpox. I reviewed the literature and documentation and found some information for SARS-CoV-2 (example below), but not for mpox. Thank you in advance!

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Best regards,
Pedro

2

Hi Pedro,

The lineages used by nextstrain.org/mpox are the ones curated in the mpxv-lineages/lineage-designation GitHub repository. From the README:

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)

I hope this helps!

– Victor

3

Hi Pedro,

in addition to Victor’s answer below, I want to point out that these criteria being adapted to the changing viral diversity and public health needs. While the criteria have not been formally revised, current practice deviates a bit from these initial criteria.

4

Clade I and clade II, with clade II further split into IIa and IIb, were proposed in Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus. That paper proposed the name “hMPXV1” for the clade IIb outbreak that went global in 2022 but had probably been transmitting in humans since 2016 (https://doi.org/10.1126/science.adg8116).

The lineages in GitHub - mpxv-lineages/lineage-designation: Official place for proposals and details around monkeypox virus lineage designations are specifically for hMPXV1, the clade IIb outbreak.

More recently, with the sequencing of highly diverged clade I sequences, clade I was split into Ia and Ib. Clade I mpox virus genomic diversity in the Democratic Republic of the Congo, 2018–2024: Predominance of zoonotic transmission - ScienceDirect I’m not aware of a lineage system analogous to mpxv-lineages/lineage-designation for clade Ia or Ib so far, but that paper refers to Groups I-V within Ia.