HIV-1 biological phenotype and predicted coreceptor usage based on V3 loop sequence in paired PBMC and plasma samples

A. Saracino, L. Monno, G. Punzi, D. C. Cibelli, A. Tartaglia, L. Scudeller, G. Brindicci, A. Lagioia, G. Scotto, G. Angarano

Research output: Contribution to journalArticle

Abstract

Paired PBMCs and plasma samples from 34 HIV-infected patients were studied to verify the relationship between coreceptor use based on genotyping of V3 region of HIV-1 envelope gp120 and biological phenotype with virus isolation and subsequent correlation to clinical characteristics. The "11/25" rule, geno2pheno and PSSM were compared. All SI patients were HIV-1 subtype B (p = 0.04) and had a lower CD4 count than NSI patients (p = 0.01), while no differences were observed in mean HIV-RNA log (p = 0.6). SI phenotype was not associated with AIDS-defining events (p = 0.1) or with concurrent antiretroviral therapy (p = 0.4). With geno2pheno, which shows the highest sensibility (83%), an X4 or X4/R5 genotype in PBMC DNA was also associated to B-subtype and lower CD4 count (p = 0.01) compared to R5 isolates. Based on plasma RNA sequences, the predicted coreceptor usage agreed with PBMC DNA in 79% of cases with the "11/25" rule, 82% with geno2pheno, and 82% with PSSM. A X4 virus in plasma (but not in PBMCs) was significantly associated with HAART in all three methods (p = 0.01 for "11/25" rule, p = 0.01 for geno2pheno and p = 0.03 for PSSM). Due to viral mixtures and/or difficulties in genotype interpretation, current V3 sequence-based methods cannot accurately predict HIV-1 coreceptor use.

Original languageEnglish
Pages (from-to)34-42
Number of pages9
JournalVirus Research
Volume130
Issue number1-2
DOIs
Publication statusPublished - Dec 2007

Keywords

  • Biological phenotype
  • Coreceptor usage
  • env V3 loop
  • HIV-1

ASJC Scopus subject areas

  • Cancer Research
  • Molecular Biology
  • Virology

Fingerprint Dive into the research topics of 'HIV-1 biological phenotype and predicted coreceptor usage based on V3 loop sequence in paired PBMC and plasma samples'. Together they form a unique fingerprint.

  • Cite this

    Saracino, A., Monno, L., Punzi, G., Cibelli, D. C., Tartaglia, A., Scudeller, L., Brindicci, G., Lagioia, A., Scotto, G., & Angarano, G. (2007). HIV-1 biological phenotype and predicted coreceptor usage based on V3 loop sequence in paired PBMC and plasma samples. Virus Research, 130(1-2), 34-42. https://doi.org/10.1016/j.virusres.2007.05.011