Transmission Of Drug-resistant Human Immunodeficiency Virus Research Articles

Deep Sequencing of HIV: Clinical and Research Applications

Human immunodeficiency virus (HIV) exhibits remarkable diversity in its genomic makeup and exists in any given individual as a complex distribution of closely related but nonidentical genomes called a viral quasispecies, which is subject to genetic variation, competition, and selection. This viral diversity clinically manifests as a selection of mutant variants based on viral fitness in treatment-naive individuals and based on drug-selective pressure in those on antiretroviral therapy (ART). The current standard-of-care ART consists of a combination of antiretroviral agents, which ensures maximal viral suppression while preventing the emergence of drug-resistant HIV variants. Unfortunately, transmission of drug-resistant HIV does occur, affecting 5% to >20% of newly infected individuals. To optimize therapy, clinicians rely on viral genotypic information obtained from conventional population sequencing-based assays, which cannot reliably detect viral variants that constitute <20% of the circulating viral quasispecies. These low-frequency variants can be detected by highly sensitive genotyping methods collectively grouped under the moniker of deep sequencing. Low-frequency variants have been correlated to treatment failures and HIV transmission, and detection of these variants is helping to inform strategies for vaccine development. Here, we discuss the molecular virology of HIV, viral heterogeneity, drug-resistance mutations, and the application of deep sequencing technologies in research and the clinical care of HIV-infected individuals.

Sexual networks and the transmission of drug-resistant HIV

We investigate the role that sexual networks may play in the dynamics of transmitted drug resistance (TDR) in human immunodeficiency virus (HIV) infection. Studies examining individual correlates of TDR have generally failed to find strong predictors of TDR, with most only examining basic demographics and risk groups. Ecological studies that compare potential transmitters of drug resistance and the frequency of TDR in drug naïve individuals have demonstrated that declines in TDR in some populations are mirrored by increasing efficacy of antiretroviral therapy and that the frequency of TDR is low given the number of potential transmitters; sexual networks may play a role in these phenomena. Phylogenetic approaches are becoming increasingly used to examine transmission networks of HIV but have yet to convincingly demonstrate clustering of sequences by drug resistance. There are relatively few studies that suggest a role of sexual networks in the transmission of drug-resistant HIV. We believe that this is due to the difficulty in collecting sexual network data. Studies that integrate genotypic and behavioral data collection on recently HIV-infected individuals, potential transmitters, and their partners are needed in order to establish causal links between the structure of the sexual network and transmission of drug-resistant HIV.

Reduced antiretroviral drug susceptibility among patients with primary HIV infection.

The transmission of drug-resistant human immunodeficiency virus (HIV) has been documented, but the prevalence of such transmission is unknown. To assess the spectrum and frequency of antiretroviral susceptibility among subjects with primary HIV infection. Retrospective analysis of 141 subjects identified from clinical research centers in 5 major metropolitan areas, enrolled from 1989 to 1998, with HIV seroconversion within the preceding 12 months and no more than 7 days' prior antiretroviral (ARV) therapy. Phenotypic and genotypic ARV susceptibility of HIV from plasma samples. The transmission of drug-resistant HIV as assessed by a greater than 10-fold reduction in ARV susceptibility to 1 or more drugs was observed in 3 (2%) of 141 subjects, including to a nonnucleoside reverse transcriptase inhibitor in 1 patient and to a nucleoside reverse transcriptase inhibitor and a protease inhibitor in 2 patients. Population-based sequence analysis of these 3 samples identified multidrug-resistance mutations in reverse transcriptase (M184V, T215Y, K219K/R) and protease (L101/V, K20R, M361, M46I, G48V, L63P, A71T, V771, V82T, 184V, L90M) in the 2 latter patient samples, along with numerous polymorphisms. A reduction in susceptibility of greater than 2.5- to 10-fold to 1 or more drugs was observed in viral isolates from 36 patients (26%). Sequence analysis of these 36 samples identified well-characterized drug resistance mutation in reverse transcriptase and protease in only 1 of these patients. Reductions in drug susceptibility of more than 10-fold were rare among this cohort of recently HIV-infected subjects and were distributed among each of the 3 major classes of ARV drugs tested. Reductions in susceptibility of more than 2.5- to 10-fold to certain ARV drugs of unknown clinical significance were highly prevalent among newly infected patients. Resistance testing may be warranted to monitor the frequency of drug resistance over time and to assess the potential for geographic variability.