Table 1.
CMV isolates collected in the United States and included in the phylogenetic analysis.
Figure 1.
Black bars indicate the genomic regions analyzed in this study.
Table 2.
Population genetic parameters estimated for coding regions of the U.S. CMV isolates using the DnaSP and MEGA programs.
Figure 2.
Bayesian phylogenetic trees of CMV isolates based on six genomic regions including field collected and reference isolates.
(a) 1a, partial sequence; (b) 2a, partial sequence; (c) 2b, complete sequence; (d) MP, complete sequence; (e) CP, complete sequence; and (f) RNA3 3’NTR complete sequence. Numbers above branches indicate Bayesian inference posterior probability (PP). CMV subgroups are differentiated by colors: IA = green, IB = orange, II = purple. Reassortants have illustrated in bold.
Figure 3.
Phylogenetic relationship of CMV isolates on the basis of concatenation of nucleotide sequences of MP, CP and 3′NTR using Simplot.
Four US CMV isolates, (a) BORU93, (b) HORU94, (c) V154NYT85, and (d) AORU93 were used as query sequences and six CMV isolates as reference sequences. Y-axis varies in identity percentage within a sliding window of 200 bp and a step size of 20 bp. Black vertical dashed line shows the proposed recombination break point. Sequences compared with the query sequence are indicated in the legend.
Figure 4.
Bootscan analysis with recombinant CMV isolates as the query sequences.
Query sequences included (a) BORU93, (b) HORU94, (c) V154NYT85, and (d) AORU93 which are illustrated on the upper portion of the figures. Sequences compared with the query sequences are indicated in the legend. Analysis was performed with a sliding window of 200 bp and a step size of 20 bp. The Y-axis illustrates the percentage of permuted trees in which each selected isolate clustered with the query sequence. The 70% cutoff level, representing possible recombination, is indicated by the dashed line.
Table 3.
Codon positions of the coding regions in the U.S. CMV isolates affected by positive selection.