Fig. 2

A Diagram showing workflow for preparation and sequencing of mpox sample. B Amplicon Map of Mpox Genome. Pool 1 amplicons are shown in blue, while Pool 2 amplicons are shown in orange. Amplicons 1 and 73 are inverted matches of each other, as are amplicons 2 and 72. C–E Coverage of individual amplicons in the Mpox genome during sequencing. Derived from FASTQ reads using RAMPART software [7]. The tiled amplicons are shown as the X-axis. The Y-axis indicates how many reads match that location in the genome. C First sequencing attempt of genome USA-2003, using USA-2003 as a reference genome. (D) Refined sequencing attempt of USA-2003. E An example sequencing attempt of a modern 2022 outbreak genome, using a lineage B.1 sequence as the reference genome