Fig. 3

HIV-1 genotypic resistance interpretation based on Sanger sequencing or DEEPGEN™ at three thresholds (≥ 1%, ≥ 5%, and ≥ 20%) A list of all the amino acid substitutions (mutations) determined for all 109 viruses with each assay and condition were used with the HIVdb Program Genotypic Resistance Interpretation Algorithm from the Stanford University HIV Drug Resistance Database (http://hivdb.stanford.edu) to infer the levels of susceptibility to PIs, NRTIs, NNRTI,s and INSTIs. High-level and intermediate resistance profiles are indicated in red and yellow, respectively; while a susceptible genotype is depicted in green. Resistance profiles not obtained (Sanger sequencing not performed) are indicated in grey. All 109 HIV-infected individuals from both cohorts of patients are indicated. NRTI (abacavir, ABC; didanosine, ddI; emtricitabine, FTC; lamivudine, 3TC; stavudine, d4T; tenofovir, TDF; zidovudine, AZT), NNRTI (efavirenz, EFV; etravirine, ETR; nevirapine, NVP; rilpivirine, RPV), PI (atazanavir, ATV; darunavir, DRV; amprenavir, APV; indinavir, IDV; lopinavir, LPV; nelfinavir, NFV; saquinavir, SQV; tipranavir, TPV), and INSTI (dolutegravir, DTG; elvitegravir, EVG; raltegravir, RAL)