Recombination breakpoint analysis of 94CY032.3 in thevif/vpr region. Gao F et al. J. Virol. 1998;72:10234-10241 Recombination breakpoint analysis of 94CY032.3 in thevif/vpr region. (A) Diversity plots comparing 94CY032.3 to reference sequences from the database (U455, MN, and ELI) as well as to a recently identified (partial) nonrecombinant subtype G sequence (95ML045) (2). Sequences are color coded. Distance values were calculated for a window of 300 bp moved in steps of 10 nucleotides. The x axis indicates the nucleotide positions along the alignment (gaps were stripped and removed from the alignment). The positions of the start codons of the vif,vpr, and tat genes are shown. The yaxis denotes the distance between the viruses compared (0.05 = 5% difference). (B) Neighbor-joining trees depicting the position of 94CY032.3 in regions flanking the breakpoints identified in panel A. Trees were constructed from the genomic regions indicated. Subtypes are identified by brackets. Four sequences from Mali represent subtype G; these are the only available subtype G reference sequences in this region, since all other characterized subtype G viruses contain A fragments (2, 9, 16, 17). Numbers at nodes indicate the percentage of bootstrap values with which the adjacent cluster is supported; only values above 80% are shown. Branch lengths are drawn to scale.