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Fig. 2 | AIDS Research and Therapy

Fig. 2

From: Characterization of minority HIV-1 drug resistant variants in the United Kingdom following the verification of a deep sequencing-based HIV-1 genotyping and tropism assay

Fig. 2

Comparing the determination of HIV-1 drug resistance using standard population (Sanger) and deep (DEEPGEN™) sequencing in two clinical laboratories in the U.K. Plasma samples from 59 (St. George’s) and 50 (NHS Lothian) treatment-experienced or -naive HIV-infected individuals were analyzed with Sanger sequencing and DEEPGEN™ as described in “Methods”. a Top plot compares the number of drug resistance mutations (DRM) detected by Sanger sequencing and DEEPGEN™ in each cohort of patients. Each dot corresponds to the number of mutations associated with resistance to protease (PI), reverse transcriptase (RTI) and integrase strand-transfer (INSTI) inhibitors in each patient. The mean difference in the numbers of drug resistance mutations detected by Sanger (S) and DEEPGEN™ (DG) associated with PIs, RTIs, and INSTIs in each cohort of patients is indicated in the bottom graph. b Comparing HIV-1 genotypic resistance interpretation using DEEPGEN™ with two different thresholds for mutation frequency: the standard ≥ 1% (19) and ≥ 20%, equivalent to the limit of detection for Sanger sequencing. A list of all the amino acid substitutions (mutations) identified for all 109 viruses with DEEPGEN™ at both thresholds was 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 protease, reverse transcriptase, and integrase inhibitors (i.e., HIVdb scores). c Comparing the mean differences in the HIVdb scores determined using Sanger sequencing (S) or DEEPGEN™ (DG) at two thresholds (≥ 1% and ≥ 20%) by drug class: with PI, nucleoside/tide reverse transcriptase (NRTI), non-nucleoside reverse transcriptase (NNRTI), and INSTI inhibitors. Means ± standard deviations and statistically significant differences (unpaired t test) are marked by ****(p < 0.0001), ***(p < 0.001), **(p < 0.01), *(p < 0.05), and n.s. (p > 0.05). n.d., not determined

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