Analysis of co-receptor usage of circulating viral and proviral HIV genome quasispecies by ultra-deep pyrosequencing in patients who are candidates for CCR5 antagonist treatment

I. Abbate, G. Rozera, C. Tommasi, A. Bruselles, B. Bartolini, G. Chillemi, E. Nicastri, P. Narciso, G. Ippolito, M. R. Capobianchi

Research output: Contribution to journalArticlepeer-review

Abstract

UDPS combined with genotypic algorithms for prediction of HIV-1 co-receptor usage may provide quantitative data about the tropism of each variant present in the viral quasispecies. The aim of the present study was to assess co-receptor usage by ultra-deep pyrosequencing (UDPS), in comparison with the reference phenotypic test (Trofile), in patients who are candidates for CCR5 antagonist treatment, in both circulating and proviral HIV-1. Seventeen patients who were tested by Trofile were enrolled. UDPS of the V3 loop region was carried out on both plasma RNA and proviral DNA. Genotypic prediction of co-receptor usage was established by position-specific score matrices (PSSM) and confirmed, in discordant cases, with geno2pheno. Genetic heterogeneity of the RNA and DNA quasispecies was assessed as well. A total of 196729V3 sequences were considered (mean coverage per site, 6346). Concordance between phenotypic test and UDPS with PSSM was 0.82. Geno2pheno results were in line with those obtained with PSSM. Proviral quasispecies were more heterogeneous than those found in circulating HIV. In most patients eligible for CCR5 antagonist treatment, X4 variants were detected in proviral DNA, ranging from 1.0% to 52.7%. UDPS combined with genotypic algorithms for co-receptor usage prediction highlighted the presence of minority variants, with a discordant tropism with respect to the predominant population, in both circulating viral and proviral HIV. In most patients treated with Maraviroc the virological response was independent of the presence of X4 in proviral DNA. The clinical impact of minority X4 variants present in patients who are candidates for anti-CCR5 antagonists remains a crucial point to be addressed.

Original languageEnglish
Pages (from-to)725-731
Number of pages7
JournalClinical Microbiology and Infection
Volume17
Issue number5
DOIs
Publication statusPublished - May 2011

Keywords

  • CCR5
  • Co-receptor
  • CXCR4
  • HIV
  • Maraviroc
  • NGS
  • Pyrosequencing
  • Tropism
  • UDPS

ASJC Scopus subject areas

  • Microbiology (medical)
  • Infectious Diseases

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