Figure 1.
Genome organization of HAdV-D58.
Genome is represented by a central black horizontal line marked at 5-kbp intervals. Protein encoding regions are shown as arrows indicating transcriptional orientation. Forward arrows (above the horizontal black line) denote coding regions in the 5′ to 3′ direction and arrows pointing to the left (below the horizontal black line denote coding regions in the 3′ to 5′ direction). Spliced genes are indicated by V-shaped lines.
Figure 2.
SimPlot analysis of HAdV-D genomes to HAdV-D58.
HAdV-D58 was compared to all fully sequenced HAdV genomes in species HAdV-D with SimPlot software. The arrows on the black line demarcate the approximate positions of the DNA polymerase, penton base, hexon, E3 coding region, and fiber coding sequences in the HAdV-D58 genome. Arrows pointing towards the right are encoded in the 5′ to 3′ direction and arrows pointing towards the left are encoded in the 3′ to 5′ direction. The E3 box represents eight open reading frames.
Figure 3.
SimPlot analysis of the HAdV-D58 hexon coding sequence.
L1 and L2 correspond to Loops 1 and 2 of the hexon gene, which contain the epsilon (ε) fragment, an important determinant of neutralization.
Figure 4.
Computational analysis of the E3 region.
SimPlot analysis of the E3 region of HAdV-D58 compared to fully sequenced E3 regions from species HAdV-D. The arrows over the Bootscan demarcate the approximate positions of the E3 coding sequences.
Figure 5.
Computational analysis of the Fiber regions.
(A) Bootscan and (B) SimPlot analysis of the fiber region of HAdV-D58 compared to fully sequenced E3 and fiber regions from species HAdV-D.
Figure 6.
Phylogenetic analysis of whole genome, penton base, and E3 CR1-β in HAdV-D58.
Phylogenetic nalysis is based on the nucleic acid sequence of (A) whole genomes, (B) penton base, and (C) CR1-β. Phylogenetic trees were constructed from aligned sequences using MEGA, via the neighbor-joining methods and a bootstrap test of phylogeny. Bootstrap values shown at the branching points indicate the percentages of 1000 replications produced the clade.
Figure 7.
Phylogenetic analysis of HAdV-D58 hexon loops 1 and 2.
Analysis of HAdV-D58 hexon L1 and L2 is based on the nucleic acid sequence of (A) hexon and (B) hexon L2. Phylogenetic trees were constructed from aligned sequences using MEGA, via the neighbor-joining methods and a bootstrap test of phylogeny. Bootstrap values shown at the branching points indicate the percentages of 1000 replications produced the clade.
Figure 8.
Phylogenetic analysis of the fiber coding sequence in HAdV-D58.
Analysis of HAdV-D58 is based on the nucleic acid sequence of the fiber knob. Phylogenetic trees were constructed from aligned sequences using MEGA, via the neighbor-joining methods and a bootstrap test of phylogeny. Bootstrap values shown at the branching points indicate the percentages of 1000 replications produced the clade.
Table 1.
Serum neutralization of HAdV-D58 with hyper immune serum.
Figure 9.
Bootscan analysis of selected fiber genes in species HAdV-D.
(A) HAdV-D47, (B) -D26, (C) -D20, and (D) -D30. This figure is a corrected repeat of Figure 2 in Darr et al [20].
Table 2.
Comparison of the nucleotide sequences used by Darr et al to show recombination events in the fiber/knob junction.