Research Article: Should We Include Connection Domain Mutations of HIV-1 Reverse Transcriptase in HIV Resistance Testing?

Date Published: December 1, 2007

Publisher: Public Library of Science

Author(s): Matthias Götte

Abstract: The author discusses a new study that found a common mutation in the connection domain of reverse transcriptase, a mutation that confers resistance to two antiretroviral drug classes.

Partial Text: Despite the remarkable achievements in discovery and development of antiretroviral agents for the treatment of infection with human immunodeficiency virus type 1 (HIV-1), drug resistance remains a major reason for viral rebound and treatment failure. Therefore, resistance testing has become an important tool in clinical decision making. HIV genotype testing, to look for mutations that confer drug resistance, is now widely established as the standard of care to guide treatment in the context of both primary infection and virological failure [1].

Several clinical trials showed a beneficial effect of resistance testing [2–6]. However, there are also intrinsic limitations and caveats associated with the practical use of genotyping.

The C-terminal region of RT includes the “connection” domain (289–423) and the ribonuclease H (RNase H) domain (424–560). RNase H activity is required to cleave the RNA moiety of RNA/DNA replication intermediates. G333D/E polymorphisms have been associated with dual resistance to AZT and 3TC [13,14], and Y318F has been linked to decreased susceptibility to NNRTIs [15]. More recently, Nikolenko and colleagues have shown that mutations in the C-terminal domains of HIV-1 RT can markedly increase the level of resistance to AZT, provided that these amino acid substitutions are combined with classic TAMs [16].

In this issue of PLoS Medicine, Soo-Huey Yap et al. report on a detailed clinical and biochemical characterization of the connection mutation N348I [24], which turned out to be a highly interesting mutation in many ways. Clinical samples were collected at the British Columbia Centre for Excellence in HIV/AIDS, in Vancouver, Canada. The authors compared sequences from individuals with known treatment history (n = 1,009) with patient samples from treatment-naïve individuals (n = 368) and found that N348I is highly prevalent among treatment-experienced patients. With a 12% prevalence, it ranked as the 9th most prevalent RT-associated mutation in this group of individuals.

Yap et al. have also addressed the potential biochemical mechanism for how N348I confers drug resistance—they provide evidence to show that this mutation can augment levels of excision of AZT. Increased rates of excision are selectively seen on RNA/DNA substrates when TAM-containing mutant RT was compared with TAMs/N348I. Such differences are not evident on DNA/DNA substrates, which pointed to an involvement of the RT-associated RNase H activity in AZT resistance. Indeed, mutant enzymes containing N348I show significant reductions in RNase H cleavage. Thus, the biochemical data are consistent with the notion that diminished RNase H cleavage facilitates excision by delaying degradation of the template.

The multidisciplinary approach is a major strength of Yap and colleagues’ study. Their retrospective clinical studies are in good agreement with in vitro susceptibility measurements and biochemical mechanistic analyses. The combined data provide strong evidence to show that N348I can contribute to AZT resistance. N348I may not be considered as a “secondary mutation” that solely improves the replication capacity of resistant viruses, because this mutation appears to emerge early after initiation of therapy and the diminished RNase H activity combined with elevated levels of excision provide a plausible molecular mechanism. At the same time, the decrease in AZT susceptibility is relatively small in the absence of TAMs. In this context, the authors argue that the individual effect of each of the known TAMs is likewise subtle. It is therefore tempting to categorize N348I as yet another TAM. However, there are noticeable differences between classic TAMs and N348I. The classic TAMs at positions 219, 215, 210, 41, 67, and 70 are clustered around the putative binding site of the pyrophosphate donor ATP that promotes excision of AZT. In contrast, N348I is distant from the active site and the NNRTI binding site. As the authors point out, the structural mechanism by which N348I confers resistance to AZT remains to be delineated. Moreover, the mechanism and structural basis for NNRTI resistance in association with N348I have yet to be addressed as well.



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