The genotypic false positive rate determined by V3 population sequencing can predict the burden of HIV-1 CXCR4-using species detected by pyrosequencing.
OBJECTIVE
The false-positive rate (FPR) is a percentage-score provided by Geno2Pheno-algorithm indicating the likelihood that a V3-sequence is falsely predicted as CXCR4-using. We evaluated the correlation between FPR obtained by V3 population-sequencing and the burden of CXCR4-using variants detected by V3 ultra-deep sequencing (UDPS) and Enhanced-Sensitivity Trofile assay (ESTA).


METHODS
54 HIV-1 B-subtype infected-patients (all maraviroc-naïve), with viremia >10,000copies/ml, were analyzed. HIV-tropism was assessed by V3 population-sequencing, UDPS (considering variants with >0.5% prevalence), and ESTA.


RESULTS
By UDPS, CCR5-using variants were detected in 53/54 patients, irrespective of FPR values, and their intra-patient prevalence progressively increased by increasing the FPR obtained by V3 population-sequencing (rho = 0.75, p = 5.0e-8). Conversely, the intra-patient prevalence of CXCR4-using variants in the 54 patients analyzed progressively decreased by increasing the FPR (rho = -0.61; p = 9.3e-6). Indeed, no CXCR4-using variants were detected in 13/13 patients with FPR>60. They were present in 7/18 (38.8%) patients with FPR 20-60 (intra-patient prevalence range: 2.1%-18.4%), in 5/7 (71.4%) with FPR 10-20, in 4/6 (66.7%) with FPR 5-10, and in 10/10(100%) with FPR<5 (intra-patient prevalence range: 12.1%-98.1%).


CONCLUSIONS
FPR by V3 population-sequencing can predict the burden of CXCR4-using variants. This information can be used to optimize the management of tropism determination in clinical practice. Due to its low cost and short turnaround time, V3 population-sequencing may represent the most feasible test for HIV-1 tropism determination. More sensitive methodologies (as UDPS) might be useful when V3 population-sequencing provides a FPR >20 (particularly in the range 20-60), allowing a more careful identification of patients harboring CXCR4-using variants.
Department of Experimental Medicine and Surgery, University of Tor Vergata Rome, Italy.
Valentina
V
Svicher
Valeria
V
Cento
Gabriella
G
Rozera
Isabella
I
Abbate
Maria Mercedes
MM
Santoro
Daniele
D
Armenia
Lavinia
L
Fabeni
Alessandro
A
Bruselles
Alessandra
A
Latini
Guido
G
Palamara
Valeria
V
Micheli
Giuliano
G
Rizzardini
Caterina
C
Gori
Federica
F
Forbici
Giuseppe
G
Ippolito
Massimo
M
Andreoni
Andrea
A
Antinori
Francesca
F
Ceccherini-Silberstein
Maria Rosaria
MR
Capobianchi
Carlo Federico
CF
Perno
D000328:Adult; D001483:Base Sequence; D005189:False Positive Reactions; D005260:Female; D014644:Genetic Variation; D005838:Genotype; D060005:Genotyping Techniques; D015699:HIV Envelope Protein gp120 / Q000737:chemistry* / Q000235:genetics*; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008297:Male; D017434:Protein Structure, Tertiary; D019718:Receptors, CXCR4 / Q000378:metabolism*; D017422:Sequence Analysis, DNA / Q000379:methods*; D013696:Temperature; D019562:Viral Load / Q000235:genetics*
D015699:HIV Envelope Protein gp120; D019718:Receptors, CXCR4