Genotypic Tropism Prediction from Paired Cell and Plasma Using Single and Replicate Sequences

Author(s)

Ozorio Coelho, Luana Portes ^[1] ; de Paula Ferreira, Joao Leandro ^[2] ; Cabral, Gabriela Bastos ^[3] ; de Souza Guimaraes, Paula Morena ^[4] ; de Macedo Brigido, Luis Fernando ^[5]

Affiliation

^[1] Adolfo Lutz Inst. Virol Ctr

^[2] Adolfo Lutz Inst. Virol Ctr

^[3] Adolfo Lutz Inst. Virol Ctr

^[4] Adolfo Lutz Inst. Virol Ctr

^[5] Adolfo Lutz Inst. Virol Ctr

• Document type: Journal article
• Source: AIDS Research and Human Retroviruses; v. 30, n. 7, p. 711-716, JUL 2014.
• Web of Science Citations: 0

Abstract

HIV-1 tropism determination is necessary prior to CCR5 antagonist use as antiretroviral therapy. Genotypic prediction of coreceptor use is a practical alternative to phenotypic tests. Cell DNA and plasma RNA-based prediction has shown discordance in many studies. We evaluate paired cell and plasma either as single or replicate V3 sequences to assess prediction comparability. The HIV-1 partial env region was sequenced and tropism was predicted using geno2pheno and position-specific scoring matrices (PSSM). Nucleotide ambiguities at V3 were quantified and genetic distance (Protdist) was determined using BioEdit. Wilcoxon signed-rank test, t tests, and Spearman correlation were performed with Prism GraphPad5.0. Results are expressed as medians, with a level of significance of p < 0.05, two tailed. Single (n = 28) or replicate (n = 26) paired cell/plasma sequences were obtained from 54 patients. Although the (clonal)false-positive rate (FPR) value from both compartments strongly correlated (r = 0.86 p < 0.0001), discordance in tropism prediction was observed in both singles and replicates using geno2pheno or PSSM. Applying clonalFPR10% 46% (25/54) were X4 tropic, with a plasma/cell discordance of 11% in singles and 23% in replicates. Genetic distance (p < 0.0001) and clonalFPR value dispersion (p = 0.003) were significantly higher among replicate sequences from cells. Discordance of viral tropism prediction is not uncommon and the use of replicates does not decrease its occurrence, but improves X4 sensitivity. Sequences from provirus had greater genetic distance and dispersion of clonalFPR values. This may suggest that DNA replicate assays may better represent the diversity of HIV-1 variants, but the clinical significance of these findings needs further evaluation. (AU)

• FAPESP's process: 09/08215-0 - Biological and molecular characterization of HIV-1: identification of epitopes relevant to viral tropism and infection control
• Grantee: Luís Fernando de Macedo Brígido
• Support Opportunities: Regular Research Grants
• FAPESP's process: 11/21958-2 - Genetic resistance to HIV-1 in the salvage therapy with new antiretroviral drug classes
• Grantee: Luís Fernando de Macedo Brígido
• Support Opportunities: Regular Research Grants