Author: Justen Manasa, Tulio de Oliveira - 2012-06-01Tweet
The demand for dug resistance testing in resource limited settings has been exponentially increasing with the increasing numbers of patients accessing antiretroviral therapy. This needs to be backed up by increasing the number of specialist scientist required for drug resistance surveillance and monitoring. In an effort to capacitated laboratories in from resource limited settings to perform high quality genotyping service for HIV-1 drug resistance, the Africa Centre for Integrated Laboratory training (ACiLT) hosted the 1st practical course on quality assurance of HIV-1 drug resistance interpretation in sequence editing and data management between the 7th and 11th of May 2012.
The course was facilitated by a pair of experts from the CDC (Mr. Joshua DeVos and Dr. Yang Chunfu) with support from local experts at the NICD (Dr. Gillian Hunt). The countries represented amongst the participants included South Africa, Zimbabwe, Botswana, Uganda, Ghana and Jamaica. The five day workshop main focus was on HIV-1 drug resistance surveillance and started with a review of the WHO strategy for HIV DR surveillance in RLS, including the use of dried blood spot for sample collection. This was followed by a review of the currently available commercial HIV-1 drug resistance genotyping methods as well as in-house methods.
After the 1st day of reviews, the rest of the course focused on the theoretical and practical bioinformatics component drug resistance testing using methods that use Sanger sequencing protocols. The theoretical components involved reviews of some of the major bioinformatics tools. The use ABI Sequence Scanner for sequence data quality determination was reviewed and participants also had some time to do their own analysis and interpretation of the quality reports generated. Once the data was deemed to be of appropriate quality ChromasPro (Technelysium Pvt Lyd), and Recall (University of British Columbia?s Centre for Excellence in HIV/AIDS Research) for sequence assembly and sequence editing. The use of ClustalX, BioEdit, Mega and Geneious (Biomatters) for sequence manipulation, alignment and phylogenetics analysis to test for any possibility of contaminations was also discussed and participants also spent some considerable amount of time getting their hand dirty with some analysis. The course participants accessed the SATuRN mirror of the Stanford University HIVDB programme and Calibrated Population Resistance (CPR) were used for drug resistance interpretation and analyses. The HIVAlg programme also accessed through the HIVDB website was also used to compare the interpretation of drug resistance by the three major HIVDR interpretation algorithms (REGA, ANRS and HIVDB).
At the end of the workshop most of the participants had a better understating of the quality assurance and quality control systems that needed to be in place to ensure the provision of high quality genotyping services. Participants were also able to identify quality related problems at the different stages of the genotyping process.
Interested in training and capacity building? Please visit our annual SATuRN workshop webpage:
KRISP has been created by the coordinated effort of the University of KwaZulu-Natal (UKZN), the Technology Innovation Agency (TIA) and the South African Medical Research Countil (SAMRC).