Computational analysis of two species C human adenoviruses provides evidence of a novel virus

Abstract

Human adenovirus C (HAdV-C) species are a common cause of respiratory infections and can occasionally produce severe clinical manifestations. A deeper understanding of the variation and evolution in species HAdV-C is especially important since these viruses, including HAdV-C6, are used as gene delivery vectors for human gene therapy and in other biotechnological applications. Here, the full-genome analysis of the prototype HAdV-C6 and a recently identified virus provisionally termed HAdV-C57 are reported. Although the genomes of all species HAdV-C members are very similar to each other, the E3 region, hexon and fiber (ten proteins total) present a wide range of identity values at the amino acid level. Studies of these viruses in comparison to the other three HAdV-C prototypes (1, 2, and 5) comprise a comprehensive analysis of the diversity and conservation within HAdV-C species. HAdV-C6 contains a recombination event within the constant region of the hexon gene. HAdV-C57 is a recombinant virus with a fiber gene nearly identical to HAdV-C6 and a unique hexon distinguished by its loop 2 motif.

Fig. 1.

Pairwise whole-genome comparative analysis. zPicture software was used to compare the genome sequences of HAdV-C6 (A) and HAdV-C57 (B) to other members of species C, with a default search window of 100. The y axis (scale, 50 to 100%) provides the percent identities between regions of HAdV genomes, with the x axis representing the genome. The colors are arbitrary and are used to provide contrast: blue regions highlight select genes or genome regions, also noted above the alignments, with the pink regions denoting the intron present in the DNA polymerase gene. The red regions include both coding and noncoding sequences.

Fig. 2.

Dot plot of the percent identity values (x axis) of the predicted proteins of HAdV-C6 versus their homologs in the other members of HAdV-C species. Amino acid comparisons were performed, with gaps considered to be mismatches. Alignments were based on a Needleman-Wunsch algorithm with the percent identification equal to the number of matches between the sequences divided by the length of the alignment. The plot was created using the R statistical computing environment (http://www.R-project.org/). The proteins appear in the order of their location within the genome (y axis), with the top of the axis representing the 5′ end. Data for HAdV-C1 (diamond), HAdV-C2 (cross), HAdV-C5 (square), and HAdV-C57 (dot) are indicated.

Fig. 3.

Genome recombination analysis of HAdV-C6 and -C57. Whole-genome (A) and hexon (C) Bootscan analyses of HAdV-C6 and whole-genome (B) and hexon (D) Bootscan analyses of HAdV-C57 are presented. For the hexon Simplot/Bootscan graphs, the default settings were used: window size, 200; a step size 20; 100 replicates used; gap stripping, on; Kimura distance model; and neighbor-joining tree model. The window size and step size were to increased 1,000 and 200, respectively, for the whole-genome scans. Genome nucleotide positions are noted along the x axis, and the percentages of permutated trees that supported grouping are marked along the y axis. For reference, gene-specific and selected genome landmarks are noted above each graph. The hexon genes of HAdV-C6 and C-57 are highly similar. To avoid signal competition and resultant artifacts, in the analysis, HAdV-C57 was masked in the final HAdV-C6 hexon Bootscan plot. Colors: red, HAdV-C1; green, HAdV-C2; black, HAdV-C5; blue, HAdV-C6; orange, HAdV-C57.

Fig. 4.

Phylogenomic analysis of HAdV-C57. Phylogenetic trees of the whole-genome, penton base, and fiber knob regions are presented in the top row with the hexon and its parts, “loop 1” and “conserved,” presented in the bottom row. All were generated after sequence alignments. Sequences for fiber knob and the hexon loop 1 and conserved region (C3) were the same those as reported by Madisch et al. (24). All alignments were completed using MAFFT software (http://www.ebi.ac.uk/tools/mafft) and default parameters. Bootstrapped, neighbor-joining trees with 1,000 replicates were constructed using MEGA4 software with a maximum-composite-likelihood model. Bootstrap numbers shown at the branching points indicate the percentages of 1,000 replications producing the clade.