Design and evaluation of a human immunodeficiency virus type 1 RNA assay using nucleic acid sequence-based amplification technology able to quantify both group M and O viruses by using the long terminal repeat as target

Currently available human immunodeficiency virus type 1 (HIV-1) RNA quantif ication assays can detect most viruses of the group M subtypes, but a subst antial number are missed or not quantified reliably. Viruses of HIV-1 group O cannot be detected by any commercially available assay. We developed and evaluated a quantitative assay based on nucleic acid sequence-based amplif ication (NASBA) technology, with primers and probes located in the conserve d long terminal repeat (LTR) region of the HIV-1 genome. In 68 of 72 serum samples from individuals infected with HIV-1 subtypes A to H of group M, vi ruses could be detected and quantified. In serum samples from two patients infected with HIV-1 group O viruses, these viruses as well could be detecte d and quantified. In contrast, the currently used gag-based assay underesti mated the presence of subtype A viruses and could not detect subtype G and group O viruses. The discrepancy between the results of the two assays may be explained by the number of mismatches found within and among the probe a nd primer regions of the subtype isolates. These data indicate that LTR-bas ed assays, including the NASBA format chosen here, are better suited to mon itoring HIV-1 therapy than are gag-based assays in an era in which multiple HIV-1 subtypes and groups are spreading worldwide.