HIV Genotyping Survey

Genotypic resistance testing plays an important role in the clinical management of HIV-1 infection with the results informing therapeutic decision making. Antiviral resistance is one of the primary reasons for antiretroviral therapy (ART) failure over time, with the emergence of HIV-1 drug resistant variants within treated patients being attributed to viral replication errors.  HIV-1 genetic variability is a result of the inability of HIV-1 reverse transcription to proof read nucleotide sequences during replication 1.  This is also prompted by the high rate of HIV-1 replication in vivo and the accumulation of proviral variants during the course of infection. Genetic recombination, which occurs when viruses with different sequences infect the same cell, also contributes to genetic diversity and as a result, countless genetically distinct variants (quasispecies) evolve in individuals in the months following primary infection 1. Although HIV-1 drug resistance is usually acquired during anti-HIV drug therapy, drug resistance can also be transmitted between individuals.

To investigate whether a HIV-positive individual has become /will become resistant to an anti-retroviral therapy (ART) requires complex investigations. HIV genotyping allows detection of mutations that signal the emergence of resistant virus.  Genotyping is carried out by sequencing specific regions of the circulating viral genome that are drug targets.  HIV genotyping assays for drug resistance determine the mutations sequence of HIV-1 reverse transcriptase, protease, integrase and envelope (for tropism) allowing the detection of resistance associated with mutations in the genome that may confer drug resistance.


  1. Shafer, RW. Dupnik, K. Winters, M. Eshleman, S. (2001) HIV-1 reverse transcription and protease sequencing for drug resistance studies. HIV Sequence Compendium 2001: 1-51

UK NEQAS for Microbiology is planning to introduce a HIV genotyping scheme in the near future. We would therefore welcome information and feedback from participants who would be interested in this scheme so the design is most suitable for your laboratory requirements.

Please complete the following survey no later than Monday, 16th October 2017.

Thank you for taking the time to complete the survey.

Laboratory Identification No.*
1. Does your laboratory perform HIV genotyping?*
2. Does your laboratory refer these samples?*
3. Is your laboratory planning to introduce HIV genotyping in the future? *
4. Which method do you use for your HIV genotyping?
5. Which platform do you use?
6. What type of kit is used?
Please specify make or reference:
7. Which regions do you genotype?
8. How do you derive your consensus sequence?
9. How do you analyse your mutations to determine resistance?
10. Would your laboratory be interested in participating in a free of charge HIV genotyping pilot distribution set?
11. Would you be interested in participating in a UKNEQAS HIV Genotyping scheme?
12. Any additional information you may want to share that may be useful in setting up the EQA?
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