title: HIV-1 biological phenotype and predicted coreceptor usage based on V3 loop sequence in paired PBMC and plasma samples.
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.
authors.affiliation: Clinic of Infectious Diseases, University of Foggia, Italy.
authors.forename: A
authors.initials: A
authors.lastname: Saracino
authors.forename: L
authors.initials: L
authors.lastname: Monno
authors.forename: G
authors.initials: G
authors.lastname: Punzi
authors.forename: D C
authors.initials: DC
authors.lastname: Cibelli
authors.forename: A
authors.initials: A
authors.lastname: Tartaglia
authors.forename: L
authors.initials: L
authors.lastname: Scudeller
authors.forename: G
authors.initials: G
authors.lastname: Brindicci
authors.forename: A
authors.initials: A
authors.lastname: Lagioia
authors.forename: G
authors.initials: G
authors.lastname: Scotto
authors.forename: G
authors.initials: G
authors.lastname: Angarano
mesh_terms: D018791:CD4 Lymphocyte Count; D015726:Giant Cells / Q000821:virology*; D015699:HIV Envelope Protein gp120 / Q000737:chemistry / Q000235:genetics / Q000502:physiology*; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000235:genetics / Q000302:isolation & purification / Q000502:physiology*; D006801:Humans; D007963:Leukocytes, Mononuclear / Q000821:virology*; D008969:Molecular Sequence Data; D012367:RNA, Viral / Q000097:blood; D017422:Sequence Analysis, DNA; D053585:Virus Attachment
chemical_list: D015699:HIV Envelope Protein gp120; D012367:RNA, Viral; C514793:gp120 protein, Human immunodeficiency virus 1