| Literature DB >> 20008905 |
L L Ross1, E Rouse, P Gerondelis, E DeJesus, C Cohen, J Horton, B Ha, E R Lanier, R Elion.
Abstract
BACKGROUND: HIV clonal genotypic analysis (CG) was used to investigate whether a more sensitive analysis method would detect additional low-abundance mutations compared with population genotyping (PG) in antiretroviral-naive patients who experienced virological failure (VF) during treatment with abacavir/lamivudine/zidovudine and tenofovir.Entities:
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Year: 2009 PMID: 20008905 PMCID: PMC2809245 DOI: 10.1093/jac/dkp419
Source DB: PubMed Journal: J Antimicrob Chemother ISSN: 0305-7453 Impact factor: 5.790
Comparison of HIV resistance-associated mutations detected when analysed by conventional sequencing techniques (population genotype) and when using the more sensitive method of clonal analysis to analyse HIV-1 isolated at the baseline (pre-therapy) visit and virological failure (VF) for the 14 subjects who met VF criteria in COL40263
| Pre-therapy baseline sample | VF sample | ||||||
|---|---|---|---|---|---|---|---|
| Subject | HIV RNA log10 copies/mL | population genotype | clonal genotypea | timepoint | HIV RNA log10 copies/mL | population genotype | clonal genotypea |
| 1 | 5.25 | WT | WT (17/17) | week 32 | 2.77 | ||
| 3.52 | Additional (post-VF) clonal analysis ∼at week 36 WT (6/23) | ||||||
| 2 | 5.3 | WT | WT (58/105) | week 48 | 2.87 | ||
| V118I (45/105) | |||||||
| 3 | 5.85 | WT | WT (33/33) | week 32 | 3.36 | WT (7/46) | |
| V118I (8/46) | |||||||
| 4 | 6.11 | WT | WT (77/77) | week 32 | 4.55 | WT (7/74) | |
| 5 | 5.34 | K103K/N + Y188F/H/L/Y | WT (8/30) | week 32 | 4.23 | WT (11/50) | |
| Y188L (7/30) | |||||||
| K103N (13/30) | |||||||
| K103N + | Y188L (3/50) | ||||||
| 6 | 5.18 | WT | WT (127/128) | week 24 | 4.15 | WT | WT (31/31) |
| 7 | 5.72 | WT | WT (53/53) | week 32 | 3.59 | ||
| 8 | 4.4 | WT | WT (44/46) | week 32 | 2.68 | WT | WT (35/36) |
| 9 | 5.84 | T215T/A | WT (47/56) | week 28 | 5.08 | ||
| 10 | 5.30 | WT | WT (68/73) | week 24 | 3.54 | ||
| M41I (1/73) | |||||||
| K103R (1/73) | |||||||
| Y181H (1/73) | |||||||
| M41V + | |||||||
| G190E (1/73) | M41V + | ||||||
| A62T + | |||||||
| 11 | 5.11 | WT | WT (13/13) | week 40 | 2.8 | WT (10/16) | |
| 12 | 4.72 | WT | WT (49/58) | week 24 | 4.2 | WT | WT (56/57) |
| Y188L (9/58) | Y188L (1/57) | ||||||
| 13 | 5.54 | WT | WT (66/67) | week 40 | 4.6 | WT | WT (30/31) |
| 14 | 5.56 | WT | WT (56/60) | week 24 | 5.66 | ||
NRTI resistance mutations are shown in bold and WT indicates wild-type HIV. For Subject 1, clonal analysis results are also presented for an additional post-VF timepoint.
aClonal variant abundance is expressed as the number of clones with that genotype/total number of clones analysed from that sample.
Figure 1Phylogenetic analysis of plasma HIV variants isolated from a representative subject (Subject 5) whose baseline HIV-1 RNA was 5.34 log10 copies/mL and whose baseline (pre-therapy) population genotype resistance mutations included K103K/N + Y188F/H/L/Y and who at failure had an HIV-1 RNA of 4.23 log10 copies/mL and a population genotype of M41L + D67N + K70R + M184V + T215F + K219E. Clonal analysis detected distinct viral species, and some of these clonal variants contained different mutational patterns at baseline and at VF from those observed by population sequencing. Phylogenetic trees were constructed by using the neighbour-joining method and out-grouped with HXB2RT (HXB2 reverse transcriptase reference sequence). The scale indicates the relative phylogenetic distance. WT, wild-type.
Figure 2Phylogenetic analysis of plasma HIV variants isolated from a representative subject (Subject 2) whose baseline HIV-1 RNA was 5.30 log10 copies/mL and whose baseline (pre-therapy) population genotype was wild-type and who at failure had an HIV-1 RNA of 2.87 log10 copies/mL and a population genotype of K65R + S68N/S + Y115F/Y + V118I. Clonal analysis detected distinct viral species, and some of these clonal variants contained different mutational patterns at baseline and at VF from those observed by population sequencing. Phylogenetic trees were constructed by using the neighbour-joining method and out-grouped with HXB2RT (HXB2 reverse transcriptase reference sequence). The scale indicates the relative phylogenetic distance. WT, wild-type.