Genetic polymorphism near HIV-1 reverse transcriptase resistance-associated codons is a major obstacle for the line probe assay as an alternative method to sequence analysis

The performance of the line probe assay (LIPA) for the detection of mutatio ns conferring resistance to nucleoside inhibitors of HIV-1 reverse transcri ptase was evaluated in comparison with sequence analysis. The tests were un dertaken on plasma samples from 63 patients (61 receiving combination thera py and 2 without treatment at the time of inclusion). In 27 cases (43%) whi ch included codons 41, 69, 70, 74, 184 and 215, the sequence of the RT gene was distinct from the hybridization probes used in LIPA. Correspondingly, LIPA gave uninterpretable results in 15, 30 and 41% of cases for codons 184 , 215 and 41, respectively. Overall, the concordance between LIPA and seque nce analysis varied from 52% (codons 41 and 215) to 85% (codon 70). These d ata show that the polymorphism of the nucleotide sequence near resistance-a ssociated codons is a major shortcoming of LIPA. (C) 1999 Elsevier Science B.V. All rights reserved.