Pathogen micro-evolution in the host organism creates many similar variants of the same pathogen, a quasispecies. Human immunodeficiency virus is one such pathogen which undergoes rapid genome diversification after the infection is established. The prevalence of any one variant in an intra-patient quasispecies is thought to be governed by principles of classical Darwinian fitness, determined by factors intrinsic to the virus as well as environmental pressures such as host immunity and drug pressure.
Antiretroviral drugs select for drug-resistant variants if they exist in the quasispecies. Most drug resistant variants have low fitness in the context of wild-type variants, so they exist at low levels in the untreated individual. During antiretroviral drug treatment, wild-type variants are prevented from replicating while drug resistant variants are less affected. Continued replication of drug-resistant variants under sustained drug pressure produce still more variants which replicate better than previous variants. In this way, prior low-level drug resistance may be amplified to precipitate clinical drug failure.
In this text, we describe our efforts to detect minor drug resistant variants before clinical drug failure using ligase discrimination. A template-dependent DNA ligase is used to join two oligonucleotide probes at a mutation. The ligated probes are detected using either a radiolabel or enrichment of a reporter fluorophore on oligonucleotide-conjugated beads. This technique is amenable to minor variant detection because it can detect mutant sequences in the presence of a vast majority of wild-type sequences.