Resistance mutations in patients with persistent viraemia show need to improve clinical assays

Graham McKerrow, HIV i-Base

Richard Nettles and colleagues at Johns Hopkins University and the Howard Hughes Medical centre, Maryland, USA, conclude from a study of 21 patients who had persistent, detectable, low level viraemia while on highly active antiretroviral therapy, that there is a need to improve the sensitivity of clinical assays for the detection of drug resistance.

The researchers were concerned that technical limitations in the sensitivity of commercial genotyping methods might prevent clinicians from determining whether drug-resistant HIV-1 was present in patients with low-level viraemia. They performed ultra sensitive HIV-1 genotyping for 21 patients with persistent plasma virus loads of 50–400 copies/mL to better define the prevalence of drug resistance and the most common resistance mutations during persistently detectable low-level viraemia. They studied the 21 patients for a median of 11 months and found that nine (43%) had HIV-1 isolates with significant resistance mutations. The most common mutations were M184V, K65R, and M41L/T215Y.

They report that for isolates in some patients, the resistance was both diverse (ie there was resistance to all classes of antiretroviral drugs) and significant (ie there was resistance to a median of 3 of 5 antiretroviral drugs received by the patients during the study). In certain cases, the resistance mutations appeared to have been selected for by the study regimen and may have arisen during the period of low-level viraemia. The researchers write: “In such cases, we cannot exclude transmission or superinfection with resistant virus.”

All the patients in whom resistance mutations were detected had mutations that could compromise the efficacy of the regimen they were on. The availability of genotypic information at this level of viraemia has the clear potential to guide the choice of an alternative regimen before overt failure occurs.

They also write that for the 43% of patients with isolates that were resistant to at least 1 antiretroviral agent in the HAART regimen they were on during the study, persistent, low-level viraemia was “particularly concerning because sequential accumulation of additional mutations conferring resistance to the remaining antiretroviral drugs in the regimen may lead to virologic failure and may limit future treatment options”. It may be necessary to intensify or modify the HAART regimes for these patients.

The authors conclude: “Because persistent, detectable, low-level viraemia has been associated with the development of resistance and the failure of HAART regimens, and because of the technological limitations of commercial genotyping laboratories, clinicians currently have to make educated guesses as to the presence of resistance in HIV-1 isolates from patients with low-level viraemia. This study used novel ultra sensitive genotype assays at the clonal level to confirm that detectable, low-level viraemia is frequently, but not always, associated with resistance. We have found that previous nonsuppressive HAART, exposure to antiretroviral drugs before the current HAART regimen, and longer duration of protease inhibitor exposure were associated with the presence of resistance. The findings of this study point to the importance of improving genotype technology and demonstrate multiple clinical applications for such ultra sensitive genotypes when available.”


Importance of assuming resistance at low levels from treatment history. This has previously most clearly been shown with NNRTI exposure (Mellors et al).


Nettles R et al. Genotypic resistance in HIV-1–infected patients with persistently detectable low-level viraemia while receiving highly active antiretroviral therapy. Clinical Infectious Diseases 39(7): 1030-1037. 1 October 2004.

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