Whole genomic analysis of two potential recombinant strains within Human mastadenovirus species C previously found in Beijing, China

Figure 1. Neighbor joining phylogenetic trees on 20 HAdV-C WGS. The genomic region used to generate the trees is indicated for each tree. Sequences of BJ04 and BJ09 viruses are in bold font. BJ04 sequences are indicated with a black square whereas BJ09 sequences are indicated with a black triangle. The Chinese sequences KR699642 (CBJ113) and KF951595 (DD28) are underlined. Each prototype sequences are indicated by a black dot. Only bootstrap values greater than 70% are indicated. Types designation for the hexon and fiber genes are indicated by brackets. Sequences are indicated by their GB ID followed by the collection year and the country of collection. The type is also indicated for the 5 prototype sequences. Finally, the name of Chinese strain CBJ113 and DD28 is also indicated.

Figure 2. Schematic representation of recombination events within BJ04 and BJ09 genomes. (A) Genomic map of HAdV-C. The l-strand of the genome is represented by a straight line. Rightward (top) and leftward (bottom) ORFs are represented by grey arrows based on NC_001405 annotation. (B) Recombination events predicted in BJ04. BJ04 genome is shown as a thick black line. The likely backbone and the other genetic components were identified based on Table 1. The likely backbone is shown as a black block. Genetic components predicted by RDP4 to be involved in a recombination event are shown as dark grey blocks whereas genetic components identified only in the bootscan analysis are shown as light grey blocks. Likely breakpoint positions are shown below the genome. The lowest (best) p-values for the prediction of recombination as well as breakpoint are indicated. The number of algorithms of the RDP4 package that were predicting the recombination event is also shown. PHF designations based on our study are identified by an asterisk. (C) Recombination events predicted in BJ09. Representation layout similar to (B).