Additional file 1:

Figure S1 – Phylogenetic tree obtained from anti-CD36 and anti-CD26 immunocapture of an artificial mixture of R5 and X4 laboratory strains. Two HIV-1 strains, genetically distinct and with different coreceptor usage (i.e. the reference R5 strain HIV-1 BaL and a clinical X4 isolate, whose V3 loop sequences are CTRPNNNTRKSIHIGPGRAFYTTGEIIGDIRQAHC, PSSM score: -12.35, and CTRPNNNTRRRMTAGPGRVYYTTGQIVGDIRKAHC, PSSM score: +3.68, respectively) were grown the first on monocytes derived macrophages (MDM) and the second on PHA activated CD4+ T lymphocytes. The R5 and the X4 viral preparations were mixed at a ratio of 1:9 and applied to 2 sets of immunocapture wells, coated with anti-CD36 and anti-CD26 antibodies, respectively; then the immunocaptured virions were analyzed by ultra-deep pyrosequencing. For comparison, the sequences obtained by ultra-deep sequencing of the R5 and X4 strains (before mixing) were included in the tree. The results indicated that >99% of the sequences captured by anti-CD36 and anti-CD26 clustered with the R5 and X4 sequences, respectively. On the contrary, only one sequence variant, representing 0.51% of virions captured by anti-CD36, segregated with the X4 sequences, and only one sequence, representing 0.12% of virions captured by anti-CD26, clustered with the R5 sequences, suggesting very low level of cross contamination. Symbols: red circle = virions captured by anti-CD36; green circle = virions captured by anti-CD26; yellow circle = R5 BaL strain; blue circle = X4 clinical isolate

Format: TIFF Size: 83KB Download file

Additional file 2:

Figure S2 – Reference plasmid flowgram. Graphical representation of the region sequenced by the Sanger method and by pyro-sequencing. The 5' and 3' termini discarded by the correction procedure described in the Materials and Methods section are shaded in grey. Coverage of the single nucleotides is shown with a cyan line. Homopolymeric regions are shaded with pink boxes and sequencing errors are indicated by histogram bars with the following colour code: T-red, G-black, C-blue, A-green, Del-grey. The sequence obtained by the Sanger sequencing is shown at the bottom.

Format: TIFF Size: 1.4MB Download file

Additional file 3:

Table S1. Total starting nucleotide reads, filtered amino acid sequences, obtained after the application of the correction algorithm described in Materials and Methods section, and number of total unique variants for each sample type.

Format: DOC Size: 49KB Download file

This file can be viewed with: Microsoft Word Viewer