Coreceptor Usage of Syncytium-Inducing-HIV-1 Isolates Depends on the Target Cell and Evolves during Pediatric Infection

Comparisons between different phenotypic and sequence-based bioniformatic methods for coreceptor usage prediction were performed to establish the role and variation of syncytium-inducing (SI) HIV-1 phenotype on CCR5 and CXCR4 coreceptor usage along the course of vertical infection. Thirty-one SI HIV-1 isolates were studied (12 from the acute and 19 from the chronic stage). Infection capacity dependent on CXCR4 only (X4) or on both CXCR4 and CCR5 (R5X4) was determined by re-infection on two cell systems: PHA-activated PBMCs and GHOST coreceptorransfected cells using CXCR4 blockers when necessary. Coreceptor usage strikingly differed between those two cell systems. On GHOST cells 95% of SI-isolates were dual tropic (R5X4). On PBMCs, strains obtained at acute infection were predominantly R5X4 (75%), while 70% of SI HIV-1 from chronic stages was X4. In addition, four V3loop-sequence-based algorithms were applied to the previously mentioned isolates in order to classify them as R5 or X4/R5X4 variants (the net charge, 11/25 rule, PSSM and geno2pheno). Only 66% of SI isolates were classified as X4 using the bioinformatic algorithms. Our study demonstrated that computational algorithms were notoriously inaccurate in predicting tropism of SI-isolates, particularly for those obtained at primary infection since half of them were misclassified as R5 variants by three of the V3-sequence-based phenotype-predictor algorithms. In conclusion, SI variants coreceptor usage may vary according to the method used. Tropism determination of SI strains on PBMCs may more closely indicate the viral behavior in vivo since we use the natural virus target. Differences along the course of infection, such as predominance of dual-R5X4 tropic in the acute stage and prevalence of X4 variants in chronic infection, probably reflect the evolution of coreceptor usage of SI variants during pediatric infection. We also provide strong evidence suggesting that coreceptor usage of HIV-1 should be carefully determined before CCR5 blockers were implemented, particularly in pediatric infection.