Comparison of oligonucleotide ligation assay and consensus sequencing for detection of drug-resistant mutants of human immunodeficiency virus type 1 in peripheral blood mononuclear cells and plasma.
Drug-resistant mutants of human immunodeficiency virus type 1 (HIV-1) recede below the limit of detection of most assays applied to plasma when selective pressure is altered due to changes in antiretroviral treatment (ART). Viral variants with different mutations are selected by the new ART when replication is not suppressed or wild-type variants with greater replication fitness outgrow mutants following the cessation of ART. Mutants selected by past ART appear to persist in reservoirs even when not detected in the plasma, and when conferring cross-resistance they can compromise the efficacy of novel ART. Oligonucleotide ligation assay (OLA) of virus in plasma and peripheral blood mononuclear cells (PBMC) was compared to consensus sequence dideoxynucleotide chain terminator sequencing for detection of 91 drug resistance mutations that had receded below the limit of detection by sequencing of plasma. OLA of plasma virus detected 27.5% (95% confidence interval [CI], 19 to 39%) of mutant genotypes; consensus sequencing of the PBMC amplicon from the same specimen detected 23.1% (95% CI, 14 to 34%); and OLA of PBMC detected 53.8% (95% CI, 44 to 64%). These data suggest that concentrations of drug-resistant mutants were greater in PBMC than in plasma after changes in ART and indicate that the OLA was more sensitive than consensus sequencing in detecting low levels of select drug-resistant mutants.
Department of Pediatrics, University of Washington, Seattle, USA.
Giovanina M
GM
Ellis
Madhumita
M
Mahalanabis
Ingrid A
IA
Beck
Gregory
G
Pepper
Amy
A
Wright
Shannon
S
Hamilton
Sarah
S
Holte
Willscott E
WE
Naugler
Diane M
DM
Pawluk
Chung-Chen
CC
Li
Lisa M
LM
Frenkel
D000163:Acquired Immunodeficiency Syndrome / Q000175:diagnosis; D001483:Base Sequence; D017931:DNA Primers; D004279:DNA, Viral / Q000097:blood; D024882:Drug Resistance, Viral; D015684:Gene Products, pol / Q000235:genetics; D015658:HIV Infections / Q000097:blood / Q000175:diagnosis / Q000276:immunology; D015497:HIV-1 / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D009154:Mutation; D012367:RNA, Viral / Q000097:blood; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012680:Sensitivity and Specificity
D017931:DNA Primers; D004279:DNA, Viral; D015684:Gene Products, pol; D012367:RNA, Viral