FIG 4.

HHV-6A strain DA shows genomic evidence of interspecies recombination between HHV-6A and HHV-6B strains. (A) Tandem repeat of the origin for strain DA showing a Z29-like length of 983 bp. Gene annotations are depicted in green below the genome. (B) RDP4 scan recombination analysis demonstrating two recombination breakpoints at nucleotides 67194 and 72681 of the HHV-6A DA genome. (C) Mapping of a selection of reads to the HHV-6B Z29 reference genome at the U41 locus, with reads depicted in gray and disagreements with the HHV-6B Z29 reference genome highlighted in black. (D) Nucleotide sequence of the 61-bp region of the tandem repeat that most closely matches the HHV-6A reference genome (NC_001664), with base agreements depicted in gray and disagreements with the HHV-6A and HHV-6B reference genomes highlighted in black. (E) Phylogenetic tree analysis of the recombination region supports the HHV-6B-like nature of the U41 locus.