Observational studyPLoS pathogens2018
Quantifying the fitness cost of HIV-1 drug resistance mutations through phylodynamics.
Observational study in PLoS pathogens, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed, 80 citations in OpenAlex.
- Pretreatment Resistance to Integrase Inhibitors in the Swiss HIV Cohort Study From 1995 to 2025.Open forum infectious diseases · 2026Article
- HIV-1 virologic failure in the RESINA cohort: lessons from two decades of real-world data.Infection · 2026Article
- Phylogenetics and molecular evolution to understand and curb the HIV pandemic.Nature reviews. Microbiology · 2026Review
- Population structure reverses selection of variants with proportionally scaled birth and death rates.Nature communications · 2025Article
- HIV drug resistance during antiretroviral therapy scale-up in Uganda, 2012-19: a population-based, longitudinal study.The Lancet. Microbe · 2025Article
- Exploring evolutionary trajectories of drug resistance.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Utilizing HIV Proviral DNA to Assess for the Presence of HIV Drug Resistance.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2025Review
- Assessing fitness costs in malaria parasites: a comprehensive review and implications for drug resistance management.Malaria journal · 2025Review
- HIV drug resistance and its associated factors among patients during interruption of antiretroviral therapy in China.Frontiers in microbiology · 2025Article
- Population dynamics of HIV drug resistance during treatment scale-up in Uganda: a population-based longitudinal study.medRxiv : the preprint server for health sciences · 2024Article
- QuickFit: A High-Throughput RT-qPCR-Based Assay to Quantify Viral Growth and Fitness In Vitro.Viruses · 2024Article
- Prioritization of ethical concerns regarding HIV molecular epidemiology by public health practitioners and researchers.BMC public health · 2024Article
- The Phenomenon of Antiretroviral Drug Resistance in the Context of Human Immunodeficiency Virus Treatment: Dynamic and Ever Evolving Subject Matter.Biomedicines · 2024Review
- Frequency-dependent ecological interactions increase the prevalence, and shape the distribution, of pre-existing drug resistance.bioRxiv : the preprint server for biology · 2024Article
- Phylogenetic signatures reveal multilevel selection and fitness costs in SARS-CoV-2.Wellcome open research · 2024Article
- Changing selection on amino acid substitutions in Gag protein between major HIV-1 subtypes.Virus evolution · 2024Article
- Estimating the fitness cost and benefit of antimicrobial resistance from pathogen genomic data.Journal of the Royal Society, Interface · 2023Article
- Article
- The mechanism shaping the logistic growth of mutation proportion in epidemics at population scale.Infectious Disease Modelling · 2023Article
- Machine learning aided multiscale modelling of the HIV-1 infection in the presence of NRTI therapy.PeerJ · 2023Article
Corrections and comments
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Authors and funding
13 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Drug resistant HIV is a major threat to the long-term efficacy of antiretroviral treatment. Around 10% of ART-naïve patients in Europe are infected with drug-resistant HIV type 1. Hence it is important to understand the dynamics of transmitted drug resistance evolution. Thanks to routinely performed drug resistance tests, HIV sequence data is increasingly available and can be used to reconstruct the phylogenetic relationship among viral lineages. In this study we employ a phylodynamic approach to quantify the fitness costs of major resistance mutations in the Swiss HIV cohort. The viral phylogeny reflects the transmission tree, which we model using stochastic birth-death-sampling processes with two types: hosts infected by a sensitive or resistant strain. This allows quantification of fitness cost as the ratio between transmission rates of hosts infected by drug resistant strains and transmission rates of hosts infected by drug sensitive strains. The resistance mutations 41L, 67N, 70R, 184V, 210W, 215D, 215S and 219Q (nRTI-related) and 103N, 108I, 138A, 181C, 190A (NNRTI-related) in the reverse trancriptase and the 90M mutation in the protease gene are included in this study. Among the considered resistance mutations, only the 90M mutation in the protease gene was found to have significantly higher fitness than the drug sensitive strains. The following mutations associated with resistance to reverse transcriptase inhibitors were found to be less fit than the sensitive strains: 67N, 70R, 184V, 219Q. The highest posterior density intervals of the transmission ratios for the remaining resistance mutations included in this study all included 1, suggesting that these mutations do not have a significant effect on viral transmissibility within the Swiss HIV cohort. These patterns are consistent with alternative measures of the fitness cost of resistance mutations. Overall, we have developed and validated a novel phylodynamic approach to estimate the transmission fitness cost of drug resistance mutations.
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