A. The hypothesis of two scenarios how the HDRM could be distributed in the HIV quasispecies. The marks in red are denoted as HDRM, and ones in black are wildtype.
B. MiSeq and TruGene’s SNV-level analyses show 10 out of 18 HDRMs are co-exist with wildtype sequences on the RT region. The individual SNV-level analysis without linkage information of the HDRM could not provide further detailed understanding how the HDRM distributed across quasispecies as scenario 1 or 2.
C. PacBio’s quasispecies analysis gives much clearer HDRM profiles at quasispecies level. The results support scenario 1 as demonstrated in A.
