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.
Division of HIV, STD, TB Laboratory Research, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA. bsp1@cdc.gov
B
B
Parekh
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Phillips
T C
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Granade
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Baggs
D J
DJ
Hu
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Respess
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