Fig 3.

Prevalence of majority and minority E138 species in drug-naive patients prior to 2008. (A) Prevalence of E138 species identified by bulk sequencing. Closed bars represent drug-experienced patients, and open bars represent drug-naive patients. Results for patients with unknown treatment status are not shown. (B) Prevalence of minority E138 species in 22 patients measured by AS-PCR, as confirmed in two or three independent experiments. The dotted line represents the AS-PCR limit of detection for a specified substitution, taking into account a minimum limit of detection for patients based on viral load. (C) Prevalence of minority E138 species in the same patients as in panel B above, except that one patient, due to plasma availability, was also monitored by 454 UDS. Open circles indicate values below the sensitivity of the assay. Closed circles represent values above the sensitivity of the assay; for UDS, this meant a level significantly higher than that of background PCR mutations (P < 0.05, Fisher exact test). The solid line indicates the mean proportion of minority species detected at levels above the sensitivity of the assay.