Subtype-specific problems with qualitative Amplicor HIV-1 DNA PCR test

Background: commercial HIV-1 qualitative DNA PCR tests have the potential t o 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. Objectives: to ass es the sensitivity of the Amplicor HIV-1 test on 126 whole-blood samples re presenting seven different subtypes and to investigate the sensitivity when the standard assay was modified by including the primer pair SK145 and SKC C1B. Results: of the 126 HIV-1 infected persons, 113 were tested positive a nd 13 were DNA PCR negative. On the basis of these results, the standard Am plicor HIV-1 test had a sensitivity of 90% in our cohort. In addition, 9% o f 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% fo r 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 PC R negative samples, four subtype A, one C and three E were amplified with t he modified Amplicor HIV-1 test with addition of SK145/SKCC1B primers. Usin g this modified protocol, six samples out of eight became positive. However , two samples (one A and one C) remained DNA PCR negative. Conclusion: this study confirms that the Amplicor HIV-1 test does not detect all subtypes w ith equivalent sensitivity and 10% of the samples, tested negative. Thus, i t is preferable to add the SK145/SKCC1B primers to the standard test, where infection with non-B subtype is suspected. (C) 2001 Elsevier Science B.V. All rights reserved.