Fig. 3: APOBEC3 signatures in MPXV genome sequences.

In the box plots, data points represent the total number of mutations identified with (red) and without (blue) APOBEC-3 signatures in individual MPXV genome sequences. The values are shown on y-axis for: (i) Sequences retrieved from NCBI for MPXV genomes prior to the 2022 outbreak (n = 81); (ii) 2022 outbreak global sequences excluding NYC (n = 2877); and (iii) 2022 NYC outbreak MPXV genomes sequenced by NYC PHL (n = 1138). The center line of each box denotes the median number of mutations per MPXV genome sequences. The whiskers extend to the minimum and maximum number of mutations per sequence within 1.5 times the interquartile range from the first and third quartiles. Mutation counts outside this range are shown as individual outlier points, representing genomes with unusually high or low numbers of mutations. The number of mutations with APOBEC3 signatures was significantly higher in the 2022 outbreak sequences (both global and NYC MPXV sequences) compared to the pre-outbreak sequences, as determined by a two sample t-test (Pre-Outbreak Global vs Outbreak Global: p.adj = 9.18e⁻²⁴; Pre-Outbreak Global vs Outbreak NYC: p.adj = 1.99e⁻²⁴; Outbreak Global vs Outbreak NYC: p.adj = 1.61e⁻¹¹⁴). In the figure, “****“ indicates a p-value < 0.0001. The source data file for Fig. 3 is available in the following GitHub repository: https://github.com/sakther-NYCDOHMH/nyc_mpox_genomic_epidemiology/.