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Mathematical modeling of HIV rebound dynamics following treatment interruption in infant macaques

Mathematical modeling of HIV rebound dynamics following treatment interruption in infant macaques

In 2017, WHO statistics indicated that 1.8M children under 15 years of age are currently living with HIV worldwide. A total of 180,000 cases of new pediatric infections. Most children were infected by their HIV-positive mothers during pregnancy, childbirth, and/or breastfeeding. The standard of care is lifelong Anti-RRetroviral Therapy (ART), but this has the following problems: Children more at risk of metabolic complications; development of multi-ART resistance strains; ART toxicities; and in resource-limited settings, early ART is not always feasible with breast milk transmission

Our overall goal is to develop an Non-Human Primate (NHP) mathematical model of pediatric HIV-1 infection/ART treatment. This model can then be used to define the origin, kinetics, and predictors of viral rebound in postnatally-infected infants, and assess the impact of immune-based interventions to induce virus remission in infants. The intern will perform steady state analyses of different dynamic models of viral proliferation after treatment interruption, estimate model parameters by fitting to experimental viral outgrowth assay data, and run computer simulations using the Gillespie algorithm to evaluate different immune control scenarios.


  • Familiarity with nonlinear ordinary differential equation models
  • Able to code numerical simulations in Python, R or Matlab
  • Wil interact frequently with laboratory researchers


  • Weeks 1–2: Review and summarize literature on mathematical models for viral rebound
  • Weeks 3–4: Perform steady state and bifurcation analysis of competing mathematical models
  • Weeks 5–6: Estimate model parameters from literature and experimental assay data sets
  • Weeks 7–10: Develop software to easily run stochastic simulations of viral rebound dynamics for the best model

Special Features

  • Opportunity to perform supervised benchwork in Sallie's lab if desired