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NGA/TCN context of G→A/C→T mutations
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Genomic epidemiology of mpox clade IIb viruses
avatarBuilt with nextstrain/mpox. Maintained by Nextstrain team. Data updated 2025-07-09. Enabled by data from GenBank.
Showing 479 of 479 genomes sampled between Oct 2017 and Jun 2025.
Phylogeny
000.1110.1110.2220.2220.3330.3330.4440.4440.5550.5550.6660.6660.7770.7770.8880.88811NGA/TCN context of G→A/C→T mutations2017201820192020202120222023202420252026DateAA.2A.2.1A.2.3A.2.2A.1A.1.1B.1B.1.20B.1.3C.1C.1.1
Geography
000.1110.1110.2220.2220.3330.3330.4440.4440.5550.5550.6660.6660.7770.7770.8880.88811NGA/TCN context of G→A/C→T mutations

We gratefully acknowledge the authors, originating and submitting laboratories of the genetic sequences and metadata for sharing their work. Please note that although data generators have generously shared data in an open fashion, that does not mean there should be free license to publish on this data. Data generators should be cited where possible and collaborations should be sought in some circumstances. Please try to avoid scooping someone else's work. Reach out if uncertain.

We maintain four views of MPXV evolution:

The first is mpox/lineage-B.1, which focuses on lineage B.1 of the global outbreak that started in 2022 and includes as many sequences as possible. Here, we conduct a molecular clock analysis in which evolutionary rate is estimated from the data (with a resulting estimate of ~6 × 10-5 subs per site per year).

The second is mpox/clade-IIb, which focuses on recent viruses transmitting from human-to-human and includes viruses belonging to clade IIb. All good quality sequences that are not lineage B.1 are included, while lineage B.1 sequences is heavily subsampled to allow non-B.1 diversity to be studied.Here, we also conduct a molecular clock analysis in which evolutionary rate is estimated from the data (with a resulting estimate of ~6 × 10-5 subs per site per year).

The third is mpox/all-clades, which focuses on broader viral diversity and includes viruses from the animal reservoir and previous human outbreaks, encompassing clades I, IIa and IIb as described in Happi et al and endorsed by a WHO convened consultation.

The fourth is mpox/clade-I, which focuses on clade I sequences and includes as many sequences as possible.

Analysis

Our bioinformatic processing workflow can be found at github.com/nextstrain/mpox and includes:

  • sequence alignment by Nextclade
  • masking several regions of the genome, including the first 1350 and last 6422 base pairs and multiple repetitive regions of variable length
  • phylogenetic reconstruction using IQTREE-2
  • ancestral state reconstruction and temporal inference using TreeTime
  • clade assignment via clade definitions defined here, to label broader MPXV clades I, IIa and IIb and to label hMPXV1 lineages A, A.1, A.1.1, etc. (defined by mpxv-lineages/lineage-designation)

Underlying data

We curate sequence data and metadata from the NCBI Datasets command line tools, using an NCBI Taxonomy ID defined in ingest/defaults/config.yaml, as starting point for these analyses.

Curated sequences and metadata are available as flat files at:

Pairwise alignments with Nextclade against the reference sequence MPXV-M5312_HM12_Rivers, Nextclade analysis results, and translated ORFs are available at

Screenshots may be used under a CC-BY-4.0 license and attribution to nextstrain.org must be provided.

IIb (479)
A (44)
A.1 (19)
A.1.1 (1)
A.2 (20)
A.2.1 (16)
A.2.2 (77)
A.2.3 (50)
A.3 (10)
B.1 (62)
B.1.1 (14)
B.1.10 (5)
B.1.11 (3)
B.1.12 (3)
B.1.13 (1)
B.1.14 (1)
B.1.15 (2)
B.1.18 (1)
B.1.19 (2)
B.1.2 (3)
B.1.20 (12)
B.1.22 (7)
B.1.23 (2)
B.1.3 (16)
B.1.4 (2)
B.1.5 (2)
B.1.6 (5)
B.1.7 (7)
C.1 (35)
C.1.1 (10)
E.1 (5)
E.2 (9)
E.3 (6)
F.1 (5)
F.2 (13)
F.4 (7)
F.5 (1)
F.6 (1)
Argentina (3)
Australia (11)
Austria (7)
Belgium (10)
Benin (3)
Brazil (2)
Cambodia (7)
Canada (5)
China (10)
Colombia (6)
Czech Republic (2)
Egypt (1)
Finland (3)
France (6)
Germany (24)
Guinea (2)
Ireland (14)
Israel (2)
Italy (8)
Japan (15)
Mexico (1)
Netherlands (3)
Nigeria (136)
Peru (5)
Philippines (2)
Portugal (22)
Puerto Rico (3)
Romania (8)
Sierra Leone (52)
Singapore (2)
Slovakia (9)
Slovenia (6)
South Africa (7)
South Korea (10)
Spain (6)
Sweden (1)
Switzerland (5)
Taiwan (6)
Thailand (5)
USA (31)
United Kingdom (15)
Vietnam (2)
Africa (201)
Asia (61)
Europe (149)
North America (40)
Oceania (11)
South America (16)
1-3 months ago (74)
1-3 years ago (302)
3-12 months ago (60)
3-15 years ago (18)
3-7 days ago (2)
One month ago (18)
One week ago (5)
Homo sapiens (469)
Amaku et al. (1)
Atkinson et al. (3)
Bado et al. (1)
Beligni et al. (1)
Betancur et al. (5)
Brinkmann et al. (24)
Camp et al. (7)
Campbell et al. (24)
Carr et al. (4)
Chan et al. (2)
Chmel et al. (1)
Chung et al. (8)
Clabby et al. (1)
Claro et al. (1)
Cohen Gihon et al. (1)
Coletti et al. (1)
Colson et al. (5)
Croxen et al. (1)
Cuesta et al. (4)
Dachung et al. (1)
De Baetselier et al. (2)
Doucette et al. (1)
Duggan et al. (2)
Edenborough et al. (6)
Faye et al. (1)
Featherston et al. (5)
Fox et al. (3)
Gagne et al. (1)
Galan-Huerta et al. (1)
Garrigues et al. (2)
Gigante et al. (9)
Gnimadi et al. (2)
Gonzalez et al. (10)
Green et al. (5)
Groves et al. (9)
Heibeck et al. (1)
Hemarajata et al. (2)
Higashi-Kuwata et al. (1)
Hohan et al. (8)
Isabel et al. (2)
Isidro et al. (21)
Israeli et al. (1)
Ji et al. (4)
Kant et al. (3)
Kasuya et al. (3)
Kath et al. (3)
Kufner et al. (2)
Kwasiborski et al. (1)
Laiton-Donato et al. (1)
Laubscher et al. (3)
Lewis et al. (3)
Li et al. (1)
Lin et al. (6)
Liu et al. (2)
Martin et al. (3)
Mauldin et al. (9)
Mertes et al. (5)
Mistral De Pascali et al. (1)
Nagy et al. (1)
Namporn et al. (1)
Ndodo et al. (18)
Nguyen et al. (2)
Nnaemeka et al. (28)
Nouhin et al. (7)
Oude Munnink et al. (1)
Padilla et al. (5)
Palomino-Cabrera et al. (1)
Parker et al. (76)
Pettke et al. (1)
Ponce-Alonso et al. (1)
Probert et al. (1)
Putcharoen et al. (4)
Rhie et al. (2)
Roshdy et al. (1)
Roychoudhury et al. (1)
Rueca et al. (1)
Sandi et al. (26)
Sereewit et al. (3)
Shi et al. (5)
Sladecek et al. (4)
Sobral et al. (1)
Taouk et al. (5)
Tutu van Furth AM et al. (1)
Vanmechelen et al. (1)
Viscardi et al. (5)
Wang et al. (1)
Wawina-Bokalanga et al. (2)
Welkers et al. (1)
Yinka-Ogunleye et al. (7)
Ylaya et al. (1)
Yong et al. (1)
Zakotnik et al. (6)
Data updated 2025-07-09•••Auspice v2.63.1
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