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1. Changes in hepatitis C burden and treatment trends in Europe during the era of direct-acting antivirals: a modelling study

   https://doi.org/10.1136/bmjopen-2018-026726  

   Chen, Qiushi; Ayer, Turgay; Bethea, Emily; Kanwal, Fasiha; Wang, Xiaojie; Roberts, Mark; Zhuo, Yueran; Fagiuoli, Stefano; Petersen, Jorg; Chhatwal, Jagpreet (June 2019, BMJ Open)

   Objectives Oral direct-acting antivirals (DAAs) for hepatitis C virus (HCV) have dramatically changed the treatment paradigm. Our aim was to project temporal trends in HCV diagnosis, treatment and disease burden in France, Germany, Italy, Spain and the UK. Design A mathematical simulation model of natural history of HCV infection. Participants HCV-infected patients defined based on country-specific age, fibrosis and genotype distributions. Interventions HCV screening practice and availability of different waves of DAA treatment in each country. Outcome measures Temporal trends in the number of patients who achieve sustained virological response (SVR), fail treatment (by drug regimen) and develop advanced sequelae from 2014 to 2030 in each country. Results We projected that 1 324 000 individuals would receive treatment from 2014 to 2030 in the five European countries and 12 000–37 000 of them would fail to achieve SVR. By 2021, the number of individuals cured of HCV would supersede the number of actively infected individuals in France, Germany, Spain and the UK. Under status quo, the diagnosis rate would reach between 65% and 75% and treatment coverage between 65% and 74% by 2030 in these countries. The number of patients who fail treatment would decrease over time, with the majority of those who fail treatment having been exposed to non-structural protein 5A inhibitors. Conclusions In the era of DAAs, the number of people with HCV who achieved a cure will exceed the number of viraemic patients, but many patients will remain undiagnosed, untreated, fail multiple treatments and develop advanced sequelae. Scaling-up screening and treatment capacity, and timely and effective retreatment are needed to avail the full benefits of DAAs and to meet HCV elimination targets set by WHO. 

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2. Probability of Antibiotic Resistance During Treatment in Stochastic PK/PD-Based Bacterial Model with Distinct Drug and Mutation Modes

   https://doi.org/10.64898/2026.06.17.732999  

   Izuazu, Chimezie; Browne, Cameron (June 2026, bioRxiv (accepted for publication in Bulletin of Mathematical Biology on Aug. 1, 2026))

   Abstract Mathematical models, e.g. differential equations and stochastic processes, have gained considerable attention for understanding evolution of antibiotic resistance. However, most existing models assume standing genetic variation and do not consider the possibility of random or drug-induced mutation of reference bacterial strains. Therefore, we propose a pharmacokinetics/pharmacodynamics (PK/PD)-based continuous-time Markov chain considering the competition and mutation between sensitive and resistant bacterial within an infected host during treatment. The proposed model is approximated as a generalized birth–death process with immigration, allowing for explicit derivation of the probability resistant population establishes during treatment. Besides capturing the stochasticity ofde novoemergence of a resistant bacterial strain, we explore the effects of different antibiotic modes of action, horizontal gene transfer, nutrient availability and drug pharmacokinetics on antibiotic resistance. We find that replication-targeting (biostatic) drugs suppress resistance more than death-targeting (biocidal) drugs. Like prior works, we obtain maximized resistance at intermediate drug concentrations, however the consideration ofde novomutation magnifies the superiority of higher doses in preventing resistance emergence. 

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3. The Landscape of Phenotypic and Transcriptional Responses to Ciprofloxacin in Acinetobacter baumannii: Acquired Resistance Alleles Modulate Drug-Induced SOS Response and Prophage Replication

   https://doi.org/10.1128/mBio.01127-19  

   Geisinger, Edward; Vargas-Cuebas, Germán; Mortman, Nadav J.; Syal, Sapna; Dai, Yunfei; Wainwright, Elizabeth L.; Lazinski, David; Wood, Stephen; Zhu, Zeyu; Anthony, Jon; et al (June 2019, mBio)

   Miller, Samuel I. (Ed.)

   ABSTRACT The emergence of fluoroquinolone resistance in nosocomial pathogens has restricted the clinical efficacy of this antibiotic class. In Acinetobacter baumannii , the majority of clinical isolates now show high-level resistance due to mutations in gyrA (DNA gyrase) and parC (topoisomerase IV [topo IV]). To investigate the molecular basis for fluoroquinolone resistance, an exhaustive mutation analysis was performed in both drug-sensitive and -resistant strains to identify loci that alter ciprofloxacin sensitivity. To this end, parallel fitness tests of over 60,000 unique insertion mutations were performed in strains with various alleles in genes encoding the drug targets. The spectra of mutations that altered drug sensitivity were found to be similar in the drug-sensitive and gyrA parC double-mutant backgrounds, having resistance alleles in both genes. In contrast, the introduction of a single gyrA resistance allele, resulting in preferential poisoning of topo IV by ciprofloxacin, led to extreme alterations in the insertion mutation fitness landscape. The distinguishing feature of preferential topo IV poisoning was enhanced induction of DNA synthesis in the region of two endogenous prophages, with DNA synthesis associated with excision and circularization of the phages. Induction of the selective DNA synthesis in the gyrA background was also linked to heightened prophage gene transcription and enhanced activation of the mutagenic SOS response relative to that observed in either the wild-type (WT) or gyrA parC double mutant. Therefore, the accumulation of mutations that result in the stepwise evolution of high ciprofloxacin resistance is tightly connected to modulation of the SOS response and endogenous prophage DNA synthesis. IMPORTANCE Fluoroquinolones have been extremely successful antibiotics due to their ability to target multiple bacterial enzymes critical to DNA replication, the topoisomerases DNA gyrase and topo IV. Unfortunately, mutations lowering drug affinity for both enzymes are now widespread, rendering these drugs ineffective for many pathogens. To undermine this form of resistance, we examined how bacteria with target alterations differentially cope with fluoroquinolone exposures. We studied this problem in the nosocomial pathogen A. baumannii , which causes drug-resistant life-threatening infections. Employing genome-wide approaches, we uncovered numerous pathways that could be exploited to raise fluoroquinolone sensitivity independently of target alteration. Remarkably, fluoroquinolone targeting of topo IV in specific mutants caused dramatic hyperinduction of prophage replication and enhanced the mutagenic DNA damage response, but these responses were muted in strains with DNA gyrase as the primary target. This work demonstrates that resistance evolution via target modification can profoundly modulate the antibiotic stress response, revealing potential resistance-associated liabilities. 

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4. Mathematical Modeling of RNA Virus Sensing Pathways Reveals Paracrine Signaling as the Primary Factor Regulating Excessive Cytokine Production

   https://doi.org/10.3390/pr8060719  

   Weaver, Jordan J.; Shoemaker, Jason E. (June 2020, Processes)

   null (Ed.)

   RNA viruses, such as influenza and Severe Acute Respiratory Syndrome (SARS), invoke excessive immune responses; however, the kinetics that regulate inflammatory responses within infected cells remain unresolved. Here, we develop a mathematical model of the RNA virus sensing pathways, to determine the intracellular events that primarily regulate interferon, an important protein for the activation and management of inflammation. Within the ordinary differential equation (ODE) model, we incorporate viral replication, cell death, interferon stimulated genes’ antagonistic effects on viral replication, and virus sensor protein (TLR and RIG-I) kinetics. The model is parameterized to influenza infection data using Markov chain Monte Carlo and then validated against infection data from an NS1 knockout strain of influenza, demonstrating that RIG-I antagonism significantly alters cytokine signaling trajectory. Global sensitivity analysis suggests that paracrine signaling is responsible for the majority of cytokine production, suggesting that rapid cytokine production may be best managed by influencing extracellular cytokine levels. As most of the model kinetics are host cell specific and not virus specific, the model presented provides an important step to modeling the intracellular immune dynamics of many RNA viruses, including the viruses responsible for SARS, Middle East Respiratory Syndrome (MERS), and Coronavirus Disease (COVID-19). 

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5. Intracellular interactions shape antiviral resistance outcomes in poliovirus via eco-evolutionary feedback

   https://doi.org/10.1038/s41559-025-02926-x  

   Robertson, Alexander J; Kerr, Benjamin; Feder, Alison F (December 2025, Nature Ecology & Evolution)

   Resistance evolution can undermine antiviral treatment. However, targeting antivirals to shared viral proteins could inhibit resistance evolution if susceptible viruses sensitize resistant ones during cellular coinfection. Pocapavir, a poliovirus capsid inhibitor, uses this sociovirological interference strategy. While susceptible viruses substantially suppress pocapavir resistance in cell culture, a pocapavir clinical trial found widespread resistance and limited clearance time improvements in treated participants. Here, to reconcile these findings, we present an intrahost eco-evolutionary model of pocapavir-treated poliovirus, which reproduces both in vitro interference and clinical resistance evolution. In the short term, high densities of susceptible viruses sensitize resistant ones, mirroring cell culture results. However, over multiple replication cycles, pocapavir’s high potency collapses viral density, reducing coinfection and enabling resistance evolution, as observed clinically. Because resistance suppression relies on coinfection, enhancing susceptible virus survival could offer therapeutic advantages. Counterintuitively, we demonstrate that lessening antiviral potency can increase coinfection, limiting resistance while also maintaining low viral load. These findings suggest that antivirals relying on viral intracellular interactions must balance immediate neutralization with preserving future coinfection for sustained inhibition. Explicitly considering the eco-evolutionary feedback encompassing viral density, shared phenotypes and absolute fitness provides new insights for effective therapy design and illuminates viral evolutionary dynamics more broadly. 

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