Complex genetic encoding of the hepatitis B virus on-drug persistence

Tenofovir disoproxil fumarate (TDF) is one of the nucleotide analogs capable of inhibiting the reverse transcriptase (RT) activity of HIV and hepatitis B virus (HBV). There is no known HBV resistance to TDF. However, detectable variation in duration of HBV persistence in patients on TDF therapy suggests the existence of genetic mechanisms of on-drug persistence that reduce TDF efficacy for some HBV strains without affording actual resistance. Here, the whole genome of intra-host HBV variants (N = 1,288) was sequenced from patients with rapid (RR, N = 5) and slow response (SR, N = 5) to TDF. Association of HBV genomic and protein polymorphic sites to RR and SR was assessed using phylogenetic analysis and Bayesian network methods. We show that, in difference to resistance to nucleotide analogs, which is mainly associated with few specific mutations in RT, the HBV on-TDF persistence is defined by genetic variations across the entire HBV genome. Analysis of the inferred 3D-structures indicates no difference in affinity of TDF binding by RT encoded by intra-host HBV variants that rapidly decline or persist in presence of TDF. This finding suggests that effectiveness of TDF recognition and binding does not contribute significantly to on-drug persistence. Differences in patterns of genetic associations to TDF response between HBV genotypes B and C and lack of a single pattern of mutations among intra-host variants sensitive to TDF indicate a complex genetic encoding of the trait. We hypothesize that there are many genetic mechanisms of on-drug persistence, which are differentially available to HBV strains. These pervasive mechanisms are insufficient to prevent viral inhibition completely but may contribute significantly to robustness of actual resistance. On-drug persistence may reduce the overall effectiveness of therapy and should be considered for development of more potent drugs.

HIV-1 reverse transcriptase inhibitor resistance mutations and fitness: a view from the clinic and ex vivo

Genetic diversity plays a key role in human immunodeficiency virus (HIV) adaptation, providing a mechanism to escape host immune responses and develop resistance to antiretroviral drugs. This process is driven by the high-mutation rate during DNA synthesis by reverse transcriptase (RT), by the large viral populations, by rapid viral turnover, and by the high-recombination rate. Drugs targeting HIV RT are included in all regimens of highly active antiretroviral therapy (HAART), which helps to reduce the morbidity and mortality of HIV-infected patients. However, the emergence of resistant viruses is a significant obstacle to effective long-term management of HIV infection and AIDS. The increasing complexity of antiretroviral regimens has favored selection of HIV variants harboring multiple drug resistance mutations. Evolution of drug resistance is characterized by severe fitness losses when the drug is not present, which can be partially overcome by compensatory mutations or other adaptive changes that restore replication capacity. Here, we review the impact of mutations conferring resistance to nucleoside and nonnucleoside RT inhibitors on in vitro and in vivo fitness, their involvement in pathogenesis, persistence upon withdrawal of treatment, and transmission. We describe the techniques used to estimate viral fitness, the molecular mechanisms that help to improve the viral fitness of drug-resistant variants, and the clinical implications of viral fitness data, by exploring the potential relationship between plasma viral load, drug resistance, and disease progression.