Detection of HIV-1 DNA by PCR: evaluation of primer pair concordance and sensitivity of a single primer pair

Concordance between two primer pairs and the clinical sensitivity of a single primer pair-probe system were evaluated for a human immunodeficiency virus type 1 (HIV-1) polymerase chain reaction (PCR) assay. Six-hundred sixty-three clinically defined HIV-1 specimens were analyzed in a blind fashion for HIV-1 DNA using an optimized, well-characterized PCR assay. All samples were amplified in duplicate with each of two primer pairs targeting distinct, highly conserved regions within the HIV-1 gag genome. Amplified product was detected by oligomer hybridization using 32P-labeled probes. Correlation between PCR, culture, and serology data was achieved in 661 of 663 (99.7%) specimens. After initial analysis, discordant PCR results due to discrepancies between primer pairs were observed in 9 of 663 (1.4%) specimens. All nine specimens were resolved as negative on reevaluation. After retesting of discordant PCR results, concordance between the two primer pairs was achieved in 100% of samples. These data indicate that the two primer pair systems performed comparably and that good clinical sensitivity (100%) would be achieved using a single primer-probe system. Factors and procedures that influence the reproducibility and accuracy of this HIV-1 PCR assay are discussed.