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Epidemiology and Molecular Monitoring of HIV drug resistance in Tanzania
| Third-party funded project |
| Project title |
Epidemiology and Molecular Monitoring of HIV drug resistance in Tanzania |
| Principal Investigator(s) |
Felger, Ingrid
Tanner, Marcel
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| Project Members |
Felger, Ingrid
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| Organisation / Research unit |
Swiss Tropical and Public Health Institute (Swiss TPH) / Molecular Diagnostics (Felger) |
| Project start |
01.01.2010 |
| Probable end |
01.10.2013 |
| Status |
Completed |
| Abstract |
Chip-based genotyping of HIV resistance – an alternative test system for HIV resistance in resource-poor settings? A large number of countries, struck by the HIV epidemic, possess only very limited resources for combination treatment. Due to international initiatives, also in resource poor settings combination therapy as 1st and 2nd line treatment is finally becoming available for HIV/AIDS. However, this improved therapy situation necessitates the availability of key technologies for monitoring therapeutic failure. Besides determination of CD4-count and viral load also methods for identifying treatment failure will be needed in order to save in a combination regimen those drugs with remaining activity. We designed a prototypic low density chip for monitoring HIV drug resistance by genotyping single nucleotide polymorphisms. The development was guided by our previous experience from a successful malaria drug resistance chip project (Crameri et al. 2007). We are targeting the common resistance mutations to the NRTI and NNRTI that are in therapeutic use in African countries. DNA oligonucleotides were designed for optimal Tm, hybridization features and for a broadest possible coverage across all common HIV subtypes. Differential labeling of wild-type and mutant sequence allows to correlate a specific signal at the unique position of each SNP on a glass slide directly with treatment response or predicted failure and to identify mixed virus populations. In a first pilot using clinical samples from a non-B cohort as well as using specimens with known and verified (ViroSeq, Abbott) drug resistances we have identified for a number of common mutations highly selective conditions that do discriminate between wild type and mutant. The results are validated 1:1 against population sequencing (ViroSeq, capillary sequencing). Currently the system is in its optimization phase to eliminate suboptimal, ambiguous calls, to address deletion mutations and to assess less common HIV subtypes in the validation. Technically chip production and spotting process as well as suitability of the process for local production are under evaluation. With the design of a reliable, easy-to-handle low density glass chip that can be operated with simple laboratory technology we aim at addressing all key mutations in the RT gene of HIV that are relevant for combination therapy in African countries. We hope to be able to establish a starting point for a new platform for HIV resistance determination suitable for resource-poor settings. |
| Keywords |
HIV drug resistance, monitoring, genotyping, single nucleotide polymorphism, microarray, non-B subtypes |
| Financed by |
Swiss National Science Foundation (SNSF)
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12/05/2024
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