Figure 7

Identification of recombinant viral genomes among compared viruses by SGA. The 5’ half genome (4396 bp) was amplified by SGA from 47 viruses from a passage 5 culture. The Highlighter plot denotes the location of nucleotide substitutions compared to the T/F sequences, with their positions in the gag and pol genes indicated at the bottom. The three parental viruses (T/F, T242N and NIA) are indicated by thicker lines at the top. Nucleotide substitutions are color coded. The TW10 CTL epitope region (indicated by a red box) was enlarged to better show the nucleotide identities at three sites (T242N, V247I and G248A) in the viral population (right panel). Two recombinant genomes are indicated by arrows.