Effects of sequence alterations on results from genotypic tropism testing

Results of the first international HIV-1 coreceptor proficiency panel test

BACKGROUND

Quality Assurance (QA) programs are essential to evaluate performance in diagnostics laboratories.

OBJECTIVES

We present the results from the first QA for HIV-1 genotypic tropism testing, organized and coordinated by the Institute of Virology at the University of Cologne.

STUDY DESIGN

12 cell culture-derived viral strains of different HIV-1 clades from the NIH AIDS Reagent Program were sent to the participants to be processed with their standard diagnostic methods Fasta files containing the V3 region sequence were centrally analyzed at the Institute of Virology, Cologne. All samples were sent in parallel for phenotypic testing.

RESULTS

36 laboratories from 16 countries reported genotypic results. The sequence-generation efficacy was 95.1%, while the phenotypic assays ESTA^® and PhenXR only achieved results for 58.3% of the samples. All four X4 samples were identified by 31/36 laboratories, two laboratories amplified 3/4×4 samples, and three detected 2/4×4 samples. There was high concordance among the genotypic and phenotypic results, although differences in FPR values were detected. Most deficiencies in sequence editing did not result in wrong classification of X4 viruses as R5, with the exception of sample NRZ05 by laboratory 38, but in an overestimation of CXCR4 use.

CONCLUSIONS

This demonstrates that genotypic tropism prediction is a safe procedure for clinical purposes. As we used homogeneous cell culture samples and all sequence fasta files were centrally analyzed, variations in FPR values can only be attributed to sample preparation, RT-PCR or sequence editing protocols.