FIG 4.

Phylogenetic tree showing the IR1 diversity between strains. The phylogenetic tree of the templated sequence shows branch lengths representative of degrees of difference. Nonindependent strains and strains without a complete IR1 region were excluded. The scale bar represents the tree distance corresponding to 1 nucleotide substitution/kb. The geographic origins of samples are shown by the colors of the strain names. To the right of the tree, for each strain, its EBNA-LP variant is shown by an alphanumeric designation (Table 2; Fig. 3C). BWRF1 subtypes are shown by colored boxes. The left side of each BWRF1 box is color coded for the 3 major groups (1, 2, and 3) (see Table ST2 in the supplemental material), with the presence of the indels characteristic of type 2 indicated by a dark border. The right part of the BWRF1 box is a different color in cases where subgroups are distinct from the major ones (red to indicate the disrupted BWRF1 ORF in 1X and 2X types). Strains with a type 2 EBNA2 are labeled with empty black boxes. Orange boxes indicate strains with common SNPs in the flanks, with the letter showing which SNP is present (Table ST3). A solid orange box represents a strain in which the flank SNP has propagated throughout IR1.