File S1 - HIV-1 Quasispecies Delineation by Tag Linkage Deep Sequencing

Figures S1 and S2 and Tables S1–S4. Figure S1. Concept of complexity control. In this graphical demonstration, we employ a simple example with five amplicons and 30 reads sequenced. A total of nine viral sequences are present in the viral quasispecies with the genotype being A or B. The colored boxes represent the tag for distinguishing an individual viral sequence within the viral quasispecies. Different colors represent different nucleotide sequences in individual tags. The white boxes represent individual viral sequences. During the Amplicon generation and sequencing step, each column of amplicons represents one genomic region of the viral quasispecies. (A) Complexity is too high (complexity = 9) where each viral sequence is not sufficiently covered. (B) Complexity is too low (complexity = 1) where each viral sequence is excessively covered and therefore, there is a waste of sequencing capacity. (C) Complexity is well-controlled (complexity = 3) such that individual viral sequences are sufficiently covered for sequencing error correction and for sequence assembly. Figure S2. Key step in the experimental design. (A) A detailed representation that shows the cassette sequence in Figure 1B. (B) A detailed representation that shows the cassette sequence after ligation. (PDF)