MOESM3 of Tracing HIV-1 transmission: envelope traits of HIV-1 transmitter and recipient pairs

Additional file 3: Figure S3. Phylogenetic trees of gp120 sequences from transmission pairs. Neighbor joining trees of gp120 sequences from transmitters (red) and recipients (blue). Sequences derived from single genome amplification are displayed with filled circles and those inferred from cloning with open circles. Next generation sequencing haplotypes (frequency above 1 %) of plasma and primary virus isolates are indicated by filled and empty squares, respectively. X indicates the majority haplotype and the asterisks the consensus sequence. Not for all patients next generation sequencing data is present due to limitations in sample availability, failure of amplification or haplotype reconstruction. Triangles depict sequences that were used as Env-pseudoviruses for follow-up experiments. Branch lengths are drawn to scale and HIV-1 HXB2 was used as a subtype B reference.