HIV-1 genotypic drug resistance testing

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 the susceptibility of the virus to currently licensed antiretroviral drugs and, thus, can optimise antiretroviral treatment on an individual patient basis. Currently, the Molecular Diagnostics Unit (MDU) offers sequencing of the protease, reverse transcriptase and integrase genes of HIV-1 plasma viral RNA. Samples with a viral load greater than 50 HIV RNA copies/ml plasma can be accepted for analysis, with the success rate increasing as the virus load increases (see below). The MDU will accept requests for sequencing of virus or provirus in samples other than plasma, such as lymphocytes, and cerebrospinal fluid (CSF).

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 process is a fully validated ‘in-house’ NGS method. A summary of the validation is available from the Quality Manager. Sequencing of integrase covers the complete gene.

Reporting results

The resistance assay produces an edited nucleotide sequence from which a protease/RT or integrase resistance report is generated by submission to an online algorithm hosted by Stanford University. 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. Reports are normally sent out as email attachments, preferably to an nhs.net account. The MDU does not provide additional clinical interpretation beyond that provided by the Stanford algorithm.

Turnaround time

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.

Complaints

If you are unhappy with the service provided by the MDU, or if you would like to suggest how our service can be improved, please contact the Deputy Head of Unit, Anjna Badhan anjna.badhan@imperial.ac.uk.

User instructions

For routine testing, the required sample is either two 1ml vials of EDTA plasma, prepared by your local virology or microbiology department or two 6ml EDTA Vacutainers of whole blood. If plasma is prepared locally, please contact the laboratory for its sample collection requirements. For example, the anticoagulant must be EDTA and the plasma should be stored at -70 ᵒC or lower prior to shipping to the MDU. Each sample should be accompanied by a request form obtained through the linked request form and should contain the following details: patient clinic number (not the patient’s name), date of birth, sample date, most recent virus load and test required (standard protease-reverse transcriptase, integrase). Other details, such as the reason for the request, current and previous antiretroviral therapy are useful, but not essential. If requesting a tropism assay, the additional clinical details requested on the form will allow an improved interpretation of the sequence.
Whole blood samples should be sent by courier to the MDU on the same day that the sample has been taken, if possible. However, the MDU closes at 5-00pm, hence if a sample is not guaranteed to arrive before that time (e.g. from a late afternoon or evening clinic), it may be kept in a refrigerator (not freezer) and shipped the next day or it can be shipped on the following Monday if taken late on a Friday. Plasma samples can be shipped at ambient temperature if they are guaranteed to arrive the next day.

Each request accepted by the laboratory for examination(s) shall be considered an agreement.