Subject Age subtype ETI CD4 cells/mm3 VLLog copies/mL Mutation by PS mutations by HTS Change in predicted phenotype Ya42 27 B D17 330 7.78 NRTIs: T215S NRTIs: T215S100% -             NNRTIs: Y188L NNRTIs: Y188L100% -             PIs: L90M PIs: L90M99% - Ya15 30 B D30 196 5.7 NRTIs: none NRTIs: T215S1% AZT,D4T: iii             NNRTIs: none NNRTIs: none -             PIs: M46M/L PIs: M46L3% - Ya222 19 CRF01-AE D30 807 3.51 NRTIs: none NRTIs:D67G1%, T215S1% AZT,D4T: iv; ABC,DDI,TDF: iii             NNRTIs: none NNRTIs: none -             PIs: M46L PIs: M46L2%, I50L3%, L90M5% ATV/r: v; SQV/r, NFV: iv; FPV/r, IDV/r: iii Ya22 25 B D50 612 5.51 NRTIs: none NRTIs: none -             NNRTIs: none NNRTIs: none -             PIs:I50I /L PIs:I50L4% - Ya25 45 CRF01-AE D17 518 6.07 NRTIs: none NRTIs: T215S8% AZT,D4T: iii             NNRTIs: none NNRTIs: none -             PIs: M46L PIs:M46L97%, L90M6% NFV: v; SQV/r: iv; ATV/r,FPV/r,IDV/r: iii Ya55 27 CRF01-AE D87 349 4.79 NRTIs: none NRTIs: M184V1%,T215S2%,K219R1% 3TC,FTC: v; ABC: iv; AZT,D4T,DDI: iii             NNRTIs: none NNRTIs: none -             PIs:none PIs:none - Ya64 33 B D60 481 4.37 NRTIs: none NRTIs: none -             NNRTIs: none NNRTIs: none -             PIs:none PIs:none - Ya147 28 B D38 514 4.73 NRTIs: none NRTIs: none -             NNRTIs: none NNRTIs: none -             PIs:none PIs:I47V1%,N83D1% TPV/r, FPV/r: iv; IDV/r,LPV/r,NFV: iii Ya199 30 CRF01-AE D14 213 5.39 NRTIs: none NRTIs: T215S 2% AZT,D4T: iii             NNRTIs: none NNRTIs:K101E 2% NVP,RPV: iv; EFV: iii             PIs:none PIs:V82A1%,L90M 3% NFV: v; ATV/r,FPV/r,IDV,LPV/r,SQV/r: iv; Ya203 25 CRF01-AE D31 304 5.68 NRTIs: none NRTIs:M41L1%,D67G1%,L210W1%, T215S 1% AZT,D4T: v; ABC,DDI,TDF: iv;             NNRTIs: none NNRTIs: none -             PIs:none PIs:none -

Table 2: Minority mutations missed by Population-based sequencing and the discrepancies in viral susceptibility prediction.

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