The US Food and Drug Administration-cleared ViroSeq HIV-1 Genotyping System (ViroSeq) and other population sequencing-based human immunodeficiency virus type 1 (HIV-1) genotyping methods detect antiretroviral drug resistance mutations present in the major viral population of a test sample. These assays also detect some mutations in viral variants that are present as mixtures. We compared detection of the K103N nevirapine resistance mutation using ViroSeq and a sensitive, quantitative point mutation assay, LigAmp. The LigAmp assay measured the percentage of K103N-containing variants in the viral population (percentage of K103N). We analyzed 305 samples with HIV-1 subtypes A, C, and D collected from African women after nevirapine administration. ViroSeq detected K103N in 100% of samples with >20% K103N, 77.8% of samples with 10 to 20% K103N, 71.4% of samples with 5 to 10% K103N, and 16.9% of samples with 1 to 5% K103N. The sensitivity of ViroSeq for detection of K103N was similar for subtypes A, C, and D. These data indicate that the Viroseq system reliably detects the K103N mutation at levels above 20% and frequently detects the mutation at lower levels. Further studies are needed to compare the sensitivity of different assays for detection of HIV-1 drug resistance mutations and to determine the clinical relevance of HIV-1 minority variants.
Bibliographical noteFunding Information:
Supported by the HIV Network for Prevention Trials (sponsored by the US National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), and the Department of Health and Human Services (DHHS) , through contract N01-AI-35173 with Family Health International , and contract N01-AI-45200 with Fred Hutchinson Cancer Research Center, and subcontracts with Makerere University , contract NOI-AI-35173–417 ); the HIV Prevention Trials Network (HPTN) sponsored by the NIAID, National Institutes of Child Health and Human Development (NICH/HD), National Institute on Drug Abuse, National Institute of Mental Health, and Office of AIDS Research, of the NIH, DHHS (contracts U01-AI-46745 and U01-AI-48054 ); the Adult AIDS Clinical Trials Groups ( NIH, Division of AIDS, NIAID (grants U01-AI-38858 ); R01-HD042965–01 ); AIDS Fogarty International Research Collaborative Award (award 5R03TW01199 ) and supplement from the Fogarty International Center, NIH; The Doris Duke Charitable Foundation, New York; and the National Science Foundation (grant EIA 02–05116 ).