Molecular evolution of human species D adenoviruses

Abstract

Adenoviruses are medium-sized double stranded DNA viruses that infect vertebrates. Human adenoviruses cause an array of diseases. Currently there are 56 human adenovirus types recognized and characterized within seven species (A-G). Of those types, a majority belongs to species D. In this review, the genomic conservation and diversity are examined among human adenoviruses within species D, particularly in contrast to other human adenovirus species. Specifically, homologous recombination is presented as a driving force for the molecular evolution of human adenoviruses and the emergence of new adenovirus pathogens.

Figure 1

Genomic analysis of human adenoviruses. (A) Whole genome bootstrap neighbor joining phylogenetic tree designed with MEGA 4.0. Species of adenoviruses are denoted. Adapted from (Robinson et al., 2011). (B) Transcriptional map of human adenovirus species D. The two central lines define the length of the HAdV-D genome with every vertical line representing 5000 bps. Black Arrows represent predicted protein coding regions. Early transcription units (E) are highlighted. Late transcription units (L) are shown by parentheses.

Figure 2

mVISTA global pairwise sequence alignment analysis of human adenoviruses. (A) HAdV-D37 compared to representative members of HAdV species D (B) HAdV-D37 compared to a representative type from each of the 6 other HAdV species. Adapted from (Robinson et al., 2008). (C) HAdV-A12 compared to other members of HAdV species A. (D) HAdV-B3 compared to representative members of HAdV species B (E) HAdV-C1 compared to members of HAdV-C. (F) HAdV-E4 compared to two SAdV types classified in HAdV-E. (G) HAdV-F40 compared to HAdV-F41. (H) HAdV-G52 compared to members of SAdV classified in HAdV-G.

Figure 3

HAdV E3 genomic analysis. (A) Annotation of E3 transcription units from a representative HAdV type for each of the seven species. (B) Annotation of the E3 transcription units from each species, arranged by length of the coding sequence. (C) Phylogenetic analysis of whole genome sequence from a representative HAdV type representing each of the seven species. Red, Blue, Orange, Green, Purple, and Teal represent conserved annotated genes in multiple HAdV species. Black represents species-specific annotated genes.

Figure 4

Recombination analysis of HAdVs. (A) Bootscan analysis of the HAdV-D22 penton base gene. Adapted from (Robinson et al., 2009a). (B) Bootscan analysis of the HAdV-D56 hexon gene. Adapted from (Robinson et al., 2011). (C) Bootscan analysis of the HAdV-D20 fiber gene. (D) Bootscan analysis of the HAdV-D48 fiber gene.

Figure 5

Recombination and diversity in HAdV-D. Transcriptional map of HAdV-D genomes. Black arrows and blue arrows represent conserved and non-conserved genes across all HAdV species, respectively. Genes identified as recombinant are denoted in green. Recombination hot spots are denoted in red. Pink represents area of major diversity in HAdV genomes.