Impact of HIV type 1 subtype variation on viral RNA quantitation

We evaluated the performance of three HIV-1 RNA quantitation methods (Ampli cor HIV-1 MONITOR-1.0, NASBA, and Quantiplex HIV RNA 2.0 [branched DNA (bDN A)]) using plasma specimens (N = 60) from individuals from Asia and Africa infected with one of three HIV-1 subtypes (A, Thai B [B'] or E; N = 20 each ). Our results demonstrate that of the 20 subtype A specimens, 19 were quan tifiable by the bDNA assay compared with 15 by the MONITOR-1.0 and 13 by NA SBA, Of those quantifiable, the mean log(10) difference was 0.93 between bD NA and MONITOR-1.0 and 0.46 between bDNA and NASBA. For subtype B' specimen s, the correlation among methods was better with only 2 specimens missed by NASBA and 3 by the bDNA assay. However the missed specimens had viral burd en near the lower limit (1000 copies/ml) for these assays. For the 20 subty pe E specimens, MONITOR-1.0 and NASBA quantified RNA in 17 and 14 specimens , respectively, as compared with 19 specimens quantified by the bDNA assay. The correlation among different assays, especially between bDNA/NASBA and MONITOR-1.0/NASBA, was poor, although the mean log(10) difference for subty pe E specimens was 0.4 between bDNA and MONITOR-1.0 and only 0.08 between b DNA and NASBA. The addition of a new primer set, designed for non-B HIV-1 s ubtypes, to the existing MONITOR assay (MONITOR-1.0+) resulted in RNA detec tion in all 60 specimens and significantly improved the efficiency of quant itation for subtypes A and E. Our data indicate that HIV-1 subtype variatio n can have a major influence on viral load quantitation by different method s. Periodic. evaluation and modification of these quantitative methods may be necessary to ensure reliable quantification of divergent viruses.