Fig. 1: The spatial distribution and phylogenetic placement of MPXV lineages based on global submissions.

A) B.1 and sublineages assignment of the 2022 MPXV genome sequences from NYC, North America (Excluding NYC) and Europe. Sequences from the Africa, Asia and South America were excluded from this figure due to small sample size (Africa: n = 2; Asia: n = 4; South America: n = 75). Lineage and sequence count per source were represented with x-axis and y-axis, respectively. Apart from the parent lineage B.1, the most frequently observed B.1 sublineages in Europe were B.1.1, B.1.2, B.1.7, B.1.3 and B.1.5 ( > 50 sequences per sublineage). In North America (excluding NYC), the most frequently observed B.1 sublineages were B.1.2, B.1.11, B.1.4, B.1.3, and B.1.1 ( > 50 sequences per sublineage). The most frequently observed NYC B.1 sublineages ( > 50 sequences per sublineages) were B.1.2, B.1.12, B.1.3 and B.1.7. B) Global phylogeny of MPXV genome sequences (including NYC sequences). The tree visualized with 4078 sequences where 63 and 4,015 sequences were from lineage A and B, respectively. The collection dates ranged from 10/09/2017 to 01/09/2023. In the phylogeny, the branches were colored by Nextclade lineage assignment. The outer ring was colored by geographical region. Sublineages associated with specific geographical regions were shown using colored asterisks. All the B.1 sublineages were placed as distinct clades and had a 98.9% agreement with the Nextclade lineage assignment. Most sequences (93.6%) from sublineage B.1.12 were from NYC (red asterisk). Most sequences from sublineages B.1.11, B.1.13, B.1.2 and, B.1.4 were primarily from North America (excluding NYC) (orange asterisks); and sublineages B.1.1, B.1.7 and B.1.9 were primarily from Europe (blue asterisks). B.1.6 sublineage was predominantly from South America (purple asterisk). The source data files for Fig. 1 are available in the following GitHub repository: https://github.com/sakther-NYCDOHMH/nyc_mpox_genomic_epidemiology/.