Phylogenetic tree of samples with or without minority variants of M46I/L or L90M drug resistance.

<p>A neighbor-joining phylogenetic tree of all protease sequences using the Kimura 2-parameter model was generated in MEGA5. Numbers shown are IDs of patients with detectable minority drug resistance. Open circles (black color) are virus with M46I detected by bulk sequencing. A. Solid squares (red color) indicate sequences of M46I-specific amplicons and solid triangle (red color) indicate sequences of M46L amplicons; open circles (red color) indicate bulk sequences for persons with minority M46I/L mutations; X and Y are pairs of closely related transmitted M46I sequences. B. Solid squares indicate L90M-specific amplicon sequences; open squares indicate bulk sequences for persons with minority L90M mutations. Open circles (black color) are virus with M46I detected by bulk sequencing. Abbreviations of subtype B references: B-1; B.NL.00.671 00T36.AY423387, B-2; B.US.98.1058 11.AY331295, B-3; B.FR.83.HXB2 LAI IIIB BRU.K03455, B-4; B.TH.90.BK132.AY173951, B-5; B.US.98.15384 1.DQ853463.