Figure 4

Genome recombination analysis.

The genomes of HAdV-B7d strain DG_2011 (Guangdong Province, China; 2011), CQ1198_2010 (Southwestern China; 2010, unpublished) and 0901HZ/ShX/2009 (Northwestern China; 2009) were analyzed for sequence recombination events along with HAdV species B genomes using the software Simplot (http://sray.med.som.jhmi.edu/SCRoftware/simplot/). For the recombination analysis, MAFFT software was used first to align the sequences using default parameters (http://mafft.cbrc.jp/alignment/server/). Default parameter settings for the Simplot software were used for analyzing the whole genomes, with the following input: window size (2000 nucleotides [nt]), step size (200 nt), replicates used (n 100), gap stripping (on), distance model (Kimura) and tree model (neighbor-joining). Genome nucleotide positions are noted along the x-axis and the sequence similarities are indicated along the y-axis. For reference, select genome landmarks of the three major capsid protein genes are noted above each graph. Simplot analysis of the genome of strain DG_2011 (A) shows a lateral transfer of a small portion of the genome upstream of the penton base gene from HAdV-B16. This is also present in the genomes of HAdV-7d strains CQ1198_2010 and 0901HZ/ShX/2009 (B). Surprisingly, this recombination is not found in the genome from the prototype virus from which these strains descend, Gomen HAdV-B7 (Fort Ord, U.S.A.; 1955) (C). Colors: green, HAdV-B7p (AY594255); blue, HAdV-B3 (AY599834.1); magenta, HAdV-B16 (AY601636.1); light blue, HAdV-B21 (AY601633.1); dark blue, HAdV-B50 (AY737798.1); grey, HAdV-B11 (AY163756.1); brown, HAdV-B34 (AY737797.1); light grey, HAdV-B35 (AY271307.1); dark green HAdV-B14 (AY803294.1); and dark violet HAdV-B55 (FJ643676.1).