title: Subtype-specific problems with qualitative Amplicor HIV-1 DNA PCR test.
abstract: BACKGROUND
  commercial HIV-1 qualitative DNA PCR tests have the potential to detect virus in patients in whom antibody tests may be ineffective, such as patients with primary HIV infection and infants born to HIV seropositive mothers. However, the genetic diversity of HIV-1 raises concern about the ability of the PCR tests to detect all current subtypes.
  
  
  OBJECTIVE
  to asses the sensitivity of the Amplicor HIV-1 test on 126 whole-blood samples representing seven different subtypes and to investigate the sensitivity when the standard assay was modified by including the primer pair SK145 and SKCC1B.
  
  
  RESULTS
  of the 126 HIV-1 infected persons, 113 were tested positive and 13 were DNA PCR negative. On the basis of these results, the standard Amplicor HIV-1 test had a sensitivity of 90% in our cohort. In addition, 9% of the positive samples showed a low reactivity but above the cut-off of the assay. The standard assay yielded sensitivities of 100% for subtype B (n=16), D (n=9) and G (n=1), but only 83% for subtype A (n=41), 98% for subtype C (n=43), 79% for subtype E (n=14) and 0% for subtype F (n=2). All samples with low reactivity were non-B subtype. Eight of the DNA PCR negative samples, four subtype A, one C and three E were amplified with the modified Amplicor HIV-1 test with addition of SK145/SKCC1B primers. Using this modified protocol, six samples out of eight became positive. However, two samples (one A and one C) remained DNA PCR negative.
  
  
  CONCLUSIONS
  this study confirms that the Amplicor HIV-1 test does not detect all subtypes with equivalent sensitivity and 10% of the samples, tested negative. Thus, it is preferable to add the SK145/SKCC1B primers to the standard test, where infection with non-B subtype is suspected.
authors.affiliation: Retrovirus laboratory, Department of Virology, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark. mrb@ssi.dk
authors.forename: M
authors.initials: M
authors.lastname: Bøgh
authors.forename: R
authors.initials: R
authors.lastname: Machuca
authors.forename: J
authors.initials: J
authors.lastname: Gerstoft
authors.forename: C
authors.initials: C
authors.lastname: Pedersen
authors.forename: N
authors.initials: N
authors.lastname: Obel
authors.forename: B
authors.initials: B
authors.lastname: Kvinesdal
authors.forename: H
authors.initials: H
authors.lastname: Nielsen
authors.forename: C
authors.initials: C
authors.lastname: Nielsen
mesh_terms: D004279:DNA, Viral / Q000097:blood*; D005260:Female; D014644:Genetic Variation; D015699:HIV Envelope Protein gp120 / Q000235:genetics; D015658:HIV Infections / Q000175:diagnosis / Q000821:virology*; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D006801:Humans; D008297:Male; D016133:Polymerase Chain Reaction / Q000379:methods*; D011933:Reagent Kits, Diagnostic; D012680:Sensitivity and Specificity
chemical_list: D004279:DNA, Viral; D015699:HIV Envelope Protein gp120; D011933:Reagent Kits, Diagnostic