title: Comparison of three commercial assays for the quantification of HIV-1 RNA in plasma from individuals infected with different HIV-1 subtypes.
abstract: BACKGROUND
  Commercial human immunodeficiency virus 1 (HIV-1) ribonucleic acid (RNA) quantification assays vary in their ability to quantify different subtypes of HIV-1, a problem in regions where multipte HIV-1 subtypes may be circulating.
  
  
  OBJECTIVE
  To assess commercial HIV-1 RNA quantification assays on two plasma panels. Panel 1 consisted of HIV-1 seronegative plasma 'spiked' with a known amount of cultured virus of different subtypes, and Panel 2 comprised plasma collected from individuals infected with different HIV-1 subtypes.
  
  
  METHODS
  The comparison involved the Amplicor HIV-1 reverse 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 plasma samples from 16 patients infected with subtypes A, B, C, E and G.
  
  
  RESULTS
  In Panel 1, the Quantiplex branched deoxyribonucleic acid (bDNA) assay quantified subtypes A-F efficiently, comparable to published results from two other laboratories. The Amplicor RT-PCR assay quantified subtypes B, C, and D but was relatively less efficient with subtypes E, F, and did not or poorly quantified subtype A. Testing of Panel 2 showed some inter-assay differences. In contrast to Panel 1, the Amplicor RT-PCR assay performed variably with subtype A when compared with the Quantiplex bDNA and NucliSens QT assays, and higher viral load levels were generated with subtype E using the Amplicor RT-PCR assay. Subtypes B and C showed some inter-patient differences 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 different HIV-1 subtypes. This may be more apparent with individual patient samples than with 'spiked' panels. This variability emphasizes that it is preferable for patient samples to be tested with the same assay, and care should be taken where infection with unusual subtypes is suspected.
authors.affiliation: Department of Virology, CIDMLS, ICPMR, and Centre for Virus Research, Westmead Millenium Institute, Westmead Hospital, NSW, Australia.
authors.forename: C B
authors.initials: CB
authors.lastname: Chew
authors.forename: B L
authors.initials: BL
authors.lastname: Herring
authors.forename: F
authors.initials: F
authors.lastname: Zheng
authors.forename: C
authors.initials: C
authors.lastname: Browne
authors.forename: N K
authors.initials: NK
authors.lastname: Saksena
authors.forename: A L
authors.initials: AL
authors.lastname: Cunningham
authors.forename: D E
authors.initials: DE
authors.lastname: Dwyer
mesh_terms: D004279:DNA, Viral / Q000097:blood*; D015658:HIV Infections / Q000097:blood / Q000175:diagnosis* / Q000821:virology*; D015497:HIV-1 / Q000145:classification / Q000302:isolation & purification*; D006801:Humans; D012367:RNA, Viral / Q000032:analysis*; D011933:Reagent Kits, Diagnostic; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods; D019562:Viral Load
chemical_list: D004279:DNA, Viral; D012367:RNA, Viral; D011933:Reagent Kits, Diagnostic