Comparison of three commercial assays for the quantification of HIV-1 RNA in plasma from individuals infected with different HIV-1 subtypes

Background: Commercial human immunodeficiency virus 1 (HIV-1) ribonucleic a cid (RNA) quantification assays vary in their ability to quantify different subtypes of HIV-1, a problem in regions where multiple HIV-1 subtypes may be circulating. Objectives: To assess commercial HIV-1 RNA quantification a ssays on two plasma panels. Panel 1 consisted of HIV-1 seronegative plasma 'spiked' with a known amount of cultured virus of different subtypes, and P anel 2 comprised plasma collected from individuals infected with different HIV-1 subtypes. Study design: The comparison involved the Amplicor HIV-1 re verse transcriptase-polymerase chain reaction (RT-PCR), Quantiplex branched DNA, and NucliSens HIV-1 QT assays. Panel 1 consisted of 11 plasma 'spiked ' with cultured viruses of HIV-1 subtypes A-F, and Panel 2 included 33 plas ma samples from 16 patients infected with subtypes A, B, C, E and G. Result s: In Panel 1, the Quantiplex branched deoxyribonucleic acid (bDNA) assay q uantified subtypes A-F efficiently, comparable to published results from tw o other laboratories. The Amplicor RT-PCR assay quantified subtypes B, C, a nd D but was relatively less efficient with subtypes E, F, and did not or p oorly quantified subtype A. Testing of Panel 2 showed some inter-assay diff erences. In contrast to Panel 1, the Amplicor RT-PCR assay performed variab ly with subtype A when compared with the Quantiplex bDNA and NucliSens QT a ssays, and higher viral load levels were generated with subtype E using the Amplicor RT-PCR assay. Subtypes B and C showed some inter-patient differen ces but the Quantiplex bDNA generally gave a lower quantification than the Amplicor RT-PCR and NucliSens QT assays. Conclusions: These studies confirm that commercial HIV-1 load assays vary in their ability to quantify differ ent HIV-1 subtypes. This may be:more apparent with individual patient sampl es than with 'spiked' panels. This variability emphasizes that it is prefer able for patient samples to be tested with the same assay, and care should be taken where infection with unusual subtypes is suspected. (C) 1999 Elsev ier Science B.V. All rights reserved.