HIV-1 Genotypic Drug Resistance Testing

Quick links

• Scope of the tests
• Test details
• Reporting results
• Turnaround time
• Assay failure rate
• Complaints

Further information

• User instructions
• HIV request form
  

Scope of the tests

Decreased susceptibility of HIV-1 to antiretroviral drugs (phenotypic drug resistance) is usually associated with sequence changes in the viral genome (genotypic drug resistance). Detection of these mutations in the viral genome can be used to predict accurately the susceptibility of the virus to all currently licensed antiretroviral drugs and thus can be used to optimise the use of antiretroviral treatment on an individual patient basis. Currently, the Molecular Diagnostics Unit (MDU) routinely offers sequencing of the protease and reverse transcriptase genes of HIV-1 of plasma viral RNA. Samples with any viral load greater than 50 HIV RNA copies/ml plasma can be analysed, with increasing success rates as the virus load increases (see below). Additionally, by special request,MDUoffers sequencing of the gp41 gene to predict resistance to enfuvirtide (T20), the integrase gene to predict resistance to integrase inhibitors and sequencing of the V3 region of the envelope gene for tropism prediction. TheMDUwill accept requests for sequencing of virus or provirus in samples other than plasma, such as lymphocytes, cerebrospinal fluid (CSF) and semen.

Test details

The routine test for resistance to protease and reverse-transcriptase inhibitors generates a sequence covering the whole of the protease gene (99 codons) and the first 260 codons of reverse-transcriptase. The method is a fully validated in-house method. A summary of the validation is available from the Unit Manager. Sequencing of gP41 covers the first 150 codons, integrase sequencing covers the complete gene and tropism testing covers the V3 region and flanking C2/C3 regions.

Reporting results (back to top)

The resistance assay produces an edited nucleotide sequence which is used to generate a usable protease/RT or integrase resistance report by submission to an on-line algorithm hosted by Stanford University (http://hivdb.stanford.edu/). The Stanford interpretation is included in the final MDU report. If the user requires the sequence file (“FASTA” file) or the sequencing chromatogram these can be supplied by arrangement with the Unit Manager. Tropism reports are produced by submission to the geno2pheno algorithms (http://www.geno2pheno.org) hosted by the Max Planck Institute. T20 resistance reports are produced from manual interpretations of available data. Reports are routinely sent out as hard copy but can be supplied as email attachments, if required. MDU does not provide additional clinical interpretation beyond that provided by the Stanford algorithm.

Turnaround time (back to top)

We aim to issue reports within two weeks of receiving a sample. However, as we offer a bespoke service and make rigorous efforts to produce a result from any sample, turnaround times may be extended if repeat testing is required.

Assay failure rate (back to top)

Samples to be sequenced are first amplified using the polymerase chain reaction (PCR) and it is inherent in the nature of PCR that occasional amplification failures will occur due to the virus having an unusual sequence variation (rarely) or due to a low virus load. The success rates for amplification of low load samples (based on 2008 data) are:

Complaints (back to top)

If you are unhappy with the service provided by MDU or if you wish to make suggestions on how our service can be improved, please contact the Unit Manager.