Impact of HIV type 1 subtype variation on viral RNA quantitation.
We evaluated the performance of three HIV-1 RNA quantitation methods (Amplicor HIV-1 MONITOR-1.0, NASBA, and Quantiplex HIV RNA 2.0 [branched DNA (bDNA)]) 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 quantifiable by the bDNA assay compared with 15 by the MONITOR-1.0 and 13 by NASBA. Of those quantifiable, the mean log10 difference was 0.93 between bDNA and MONITOR-1.0 and 0.46 between bDNA and NASBA. For subtype B' specimens, 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 burden near the lower limit (1000 copies/ml) for these assays. For the 20 subtype 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 log10 difference for subtype E specimens was 0.4 between bDNA and MONITOR-1.0 and only 0.08 between bDNA and NASBA. The addition of a new primer set, designed for non-B HIV-1 subtypes, to the existing MONITOR assay (MONITOR-1.0+) resulted in RNA detection in all 60 specimens and significantly improved the efficiency of quantitation for subtypes A and E. Our data indicate that HIV-1 subtype variation can have a major influence on viral load quantitation by different methods. Periodic evaluation and modification of these quantitative methods may be necessary to ensure reliable quantification of divergent viruses.
Parekh
B
B
Division of HIV, STD, TB Laboratory Research, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA. bsp1@cdc.gov
Phillips
S
S
Granade
T C
TC
Baggs
J
J
Hu
D J
DJ
Respess
R
R
D007560:Cote d'Ivoire; D014644:Genetic Variation; D015497:HIV-1 / Q000145:classification* / Q000235:genetics; D006801:Humans; D012367:RNA, Viral / Q000097:blood*; D011933:Reagent Kits, Diagnostic / Q000821:virology*; D013785:Thailand; D019562:Viral Load / Q000379:methods*
D012367:RNA, Viral; D011933:Reagent Kits, Diagnostic