Figure. Phylogenetic tree of monkeypox virus (MPXV) sequences used in study of intrahost viral genome variation in patient with early monkeypox virus infection, Finland, 2022. The tree was inferred by the maximum-likelihood method implemented in IQtree2 software (www.iqtree.org), using 1,000 bootstrap replicates and the Hasegawa-Kishino-Yano plus empirical base frequencies plus invariate sites substitution model (Appendix). The curated dataset of MPXV reference genomes was downloaded from Nextstrain and aligned by using Nextalign (5). The reference dataset was downsampled to include only genomes with <5,000 ambiguous genome sites. For the sake of visualization, nodes with bootstrap values <70, as well as clusters with no lineage designation and no representatives from Finland, were deleted; only a subset of nearly identical genomes in the B.1 lineage is shown. Blue indicates the consensus sequences from the 4 patients from Finland; red indicates the hypothetical minority variant sequence (differing from the consensus sequence at sites G55133, C64426, and G190660) from patient 1. Lineage nomenclature (MPXV-1 clade 3, lineage B.1) is as suggested (C. Happi, unpub. data, https://virological.org/t/urgent-need-for-a-non-discriminatory-and-non-stigmatizing-nomenclature-for-monkeypox-virus/8537). The tapering bars indicate clusters of B.1.1 (pink), B.1.2 (green), and B.1.3 (blue), collapsed for clarity. Sequences are identified by GenBank accession number, date, and country of origin.