TY - JOUR
T1 - HIV-1 biological phenotype and predicted coreceptor usage based on V3 loop sequence in paired PBMC and plasma samples
AU - Saracino, A.
AU - Monno, L.
AU - Punzi, G.
AU - Cibelli, D. C.
AU - Tartaglia, A.
AU - Scudeller, L.
AU - Brindicci, G.
AU - Lagioia, A.
AU - Scotto, G.
AU - Angarano, G.
PY - 2007/12
Y1 - 2007/12
N2 - 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.
AB - 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.
KW - Biological phenotype
KW - Coreceptor usage
KW - env V3 loop
KW - HIV-1
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U2 - 10.1016/j.virusres.2007.05.011
DO - 10.1016/j.virusres.2007.05.011
M3 - Article
C2 - 17582634
AN - SCOPUS:35748940958
SN - 0168-1702
VL - 130
SP - 34
EP - 42
JO - Virus Research
JF - Virus Research
IS - 1-2
ER -