Preferred Sample Type
Suitable Specimen Types
- EDTA Whole Blood
- EDTA Plasma
- Special Collection Procedures Apply
Turnaround Time
14 daysSample Stability
Any remaining plasma is stored for 2 years after testing at -20C.HIV CCR5 Tropism
General Information
The assay is an in-house genotypic assay for the determination of HIV-1 Co-receptor usage for use in HIV-1 patients contemplating the use of CCR5 antagonists. The sequence of the V3 loop of gp120 can be used to predict the co-receptor usage of HIV-1. The genotypic assay can distinguish CXCR4 usage accurately but only has a sensitivity of 20% for minority populations. Dual and mixed tropism usage is contra-indicated for use with CCR5 antagonists.
Patient Preparation
For patients with a low (<500 copies/ml) or undetectable viral load, HIV proviral DNA is extracted so we need PBMC samples which ideally have to be extracted within 24 hours of being taken. For samples with viral loads over 500 copies/ml plasma samples are extracted in a batch once a week. For both plasma and PBMC samples 1.2ml of either plasma or whole blood is required.
For taking blood samples we recommend that users follow either their local protocols or “The Royal Marsden Manual of Clinical Nursing Procedures”.
Lavender top blood (EDTA) sample
- Sufficient blood for the test should be drawn into lavender topped (EDTA) vacuum tubes
- Invert tube 8–10 times.
Notes
3 PCRs are performed on each sample and 3 products sequenced. The 3 consensus sequences are submitted to the Geno2pheno website (see URL above). Geno-2-Pheno is a prediction of the co-receptor usage, based on algorithms derived from both the genotype sequence and clinical parameters. Therefore, the amount of clinical data used with the input sequence will affect the algorithms used by the programme. The clonal result uses the V3 sequence alone, while the clinical result uses the V3 sequence and clinical parameters. In addition, different levels of stringency can be applied to the algorithm. We use the FPR (false positive rate) % set at 5% in the significance box.
The HIV Tropism testing request form is available from the following link HIV CCR5 TROPISM REQUEST FORM
Specifications
- EQA Scheme?: Yes
- EQA Status: HIV genotypic resistance EQA scheme