Table 2

Nucleotide sequences of eight isolates from resting CD4+ T cells of patients on HAART. Sequences at codons associated with resistance to RTV or SQV for patients who received RTV or SQV (or both) are shown. Dashes indicate identity with the consensus sequence shown in the top row. Positive culture supernatants were amplified by RT-PCR and sequenced with the Affymetrix (Santa Clara, California) high-density oligonucleotide array (GeneChip) as described (14, 21) (GenBank accession numbers AF027391 to AF027402).

Patient (isolate)Protease inhibitor10 ctc/L20 aag/K33 tta/L36 atg/M46 atg/M48 ggg/G54 atc/I71 gct/A82 gtc/V84 ata/I90 ttg/L
1RTV, SQV–––––––––––––––––––––––––––––––––
9* (5M1)RTV, SQV––––––––––––––––––g––/V ––––c–/A ––––––
9* (5M2)RTV, SQV–––––––––––––––––––––––––––––––––
11RTV, SQV––––––––––––––––––c––/L ––––––––––––
13RTV–––––––––––––––––––––––––––––––––
 16 RTV–––––––––––a/I –––––––––a––/T–––––––––
19RTV–––––––––––––––––––––––––––––––––
20RTV–––––––––––––––––––––––––––––––––
Known resistance mutations for  → RTV R F I I L, V V A, T, F, S V M
→ SQVIVVVM
  • * Patient 9 was on RTV monotherapy for 15 months before starting HAART (AZT, 3TC, RTV, and SQV) 9.5 months before analysis.

  • Resistance mutations.

  • Patient 16 was on monotherapy for 7 months before beginning a combination regime.