Figure 1: Illustration of Single Nucleotide Variant (SNV) and Quasispecies-level Analysis. The upper-case letter in red color is denoted as a mutation. The small-case letter in black is denoted as a wildtype (WT) nucleotide.
A. HIV population has two sub populations (quasispecies). The SNV-level report lists two individual mutations in the HIV population at position 108 of PR and position 536 of RT separately. In contrast, the quasispecies-level report lists two tag-sequences (representing the corresponding HIV quasispecies) of “..A..t...” and “..g..C..” by linking the two nucleotide calls at the position of interest.
B. HIV population has different quasispecies composition with a distinct sub population of WT HIV. The SNV-level report gives a result identical to that of A, even though the two HIV populations have different compositions. The SNV-level report does not distinguish the different situations due to lack of haplotype information. In contrast, the quasispecies-level report reflects the difference in precision.