Fig. 5: Intra-host MPXV genomic variation between sequences sampled from different lesions in the same individual.

A The frequency distribution of the maximum total SNP distance with (red) and without (blue) APOBEC3 signatures between sequences from the same individual. Out of 172 individuals, sequences from 119 (69%) individuals were closely related with 1-2 total SNPs between sequences, and 53 Individuals had sequences that were divergent with >=3 SNPs. Majority of these mutational differences were due to APOBEC3. B The proportion of intra-host SNP variation due to APOBEC. For 66% (114/172) of individuals, the observed mutational difference between sequences was completely due to APOBEC3. For 22% (38/172) of individuals, APOBEC3 contributed to 50% or more (but not 100%) of the mutational differences. Only 9% (16/172) of individuals had observed mutational differences that could not be attributed to APOBEC3. C Intra-host phylogeny. Sequences from 17 individuals that had the greatest phylogenetic distance between them were annotated with colored tips and plotted on the NYC-only phylogeny. Two individuals’ sequences (J2665014/light blue and NG930408/light green) resulted in non-monophyletic placements of sequences. The source data files for Fig. 5 are available in the following GitHub repository: https://github.com/sakther-NYCDOHMH/nyc_mpox_genomic_epidemiology/.