Mutational patterns in the HIV genome and cross-resistance following nucleoside and nucleotide analogue drug exposure

A variety of key mutations in HIV reverse transcriptase (RT) have been asso ciated with nucleoside reverse transcriptase inhibitor (NRTI) exposure, whi ch give rise to a diverse range of effects in terms of altered drug suscept ibilities, viral replicative capacity and RT biochemistry. There are three basic mechanisms of resistance conferred by specific mutations in the codin g region of RT. The first is drug discrimination, whereby a particular drug or drugs are either selectively excluded from uptake or from the RT-primer -template catalytic complex. Drug discrimination is, for the most part, rel atively specific for individual drugs. Repositioning of the template-primer to prevent a catalytically competent complex in the presence of a bound dr ug molecule has also been observed in some instances, and forms a second me chanism. The third, and potentially most significant for long-term efficacy of the NRTIs, is pyrophosphorolysis, the primary mode of resistance to zid ovudine. Mutations selected by this drug or stavudine serve to elevate the natural rate of the reverse reaction for RT. Pyrophosphorolysis uncouples t he last nucleoside monophosphate added to the proviral transcript, and atta ches it to either a free pyrophosphate (regenerating a deoxynucleoside trip hosphate) or to a nucleoside di- or triphosphate (usually ATP). Uncoupling a chain-terminating NRTI residue therefore rescues reverse transcription an d reduces drug susceptibility across the class, since the process is not sp ecific for the selecting drug. Of all the nucleoside-associated mutations, the best known and most studied are the six associated with thymidine analo gue exposure. These six mutations (M41L, D67N, K70R, L210W, T215Y/F, K219Q) enhance RT pyrophosphorolysis to confer high-level viral resistance to zid ovudine, and clinically significant loss of response to stavudine and didan osine. They have also been found to confer reduced susceptibility to lamivu dine and abacavir, particularly when present alongside other NRTI-induced c hanges. Other key mutations generally confer more limited resistance to spe cific agents, although the primary lamivudine- and abacavir-associated M184 V substitution generates a broad spectrum of drug-dependent phenotypes, and uncommon mutational complexes conferring resistance across the entire clas s are well known. In addition to 'classical' multi-nucleoside-resistant gen otypes, database-driven 'virtual phenotyping' for accumulations of NRTI-ass ociated mutations around a core of thymidine analogue-induced changes predi cts drug susceptibilities below wild-type across the entire NRTI class, eve n in the absence of key mutations associated with individual agents. When t he natural range of drug susceptibilities for treatment-naive isolates is u sed as the basis for defining resistance, retrospective analysis of clinica l isolates in the Virco database shows a significantly increased incidence of reduced susceptibility for the dideoxy NRTIs (didanosine, stavudine and zalcitabine) that was undetected in previous assays. These data imply a cum ulative degradation of response to NRTI drugs incident on the failure of th ymidine analogue-based combinations, consistent with observations of treatm ent-experienced versus treatment-naive individuals. Among the investigation al agents, response to tenofovir disproxil fumarate (TDF) appears to be ess entially independent of baseline genotype in NRTI-experienced individuals, and its sole selected resistance mutation, K65R, has been observed to emerg e only rarely (2%) and without loss of clinical response. In vitro results also show very little effect on TDF susceptibility for the most common of t he multi-nucleoside resistance patterns. This drug has also been shown to display a substantially reduced sensitivit y to pyrophosphorolytic uncoupling in vitro, which may, in part, explain th e surprisingly sustained response observed over 48 weeks for TDF intensific ation of an existing regimen.