scholarly journals Parameter Estimation in Mathematical Models of Viral Infections Using R

Author(s):  
Van Kinh Nguyen ◽  
Esteban A. Hernandez-Vargas
2017 ◽  
Author(s):  
Van Kinh Nguyen ◽  
Esteban A. Hernandez-Vargas

AbstractIn recent years, mathematical modeling approaches have played a central role to understand and to quantify mechanisms in different viral infectious diseases. In this approach, biological-based hypotheses are expressed via mathematical relations and then tested based on empirical data. The simulation results can be used to either identify underlying mechanisms, provide predictions on infection outcomes, or evaluate the efficacy of a treatment.Conducting parameter estimation for mathematical models is not an easy task. Here we detail an approach to conduct parameter estimation and to evaluate the results using the free software R. The method is applicable to influenza virus dynamics at different complexity levels, widening experimentalists capabilities in understanding their data. The parameter estimation approach presented here can be also applied to other viral infections or biological applications.


2019 ◽  
Vol 467 ◽  
pp. 87-99 ◽  
Author(s):  
Karen Larson ◽  
Loukas Zagkos ◽  
Mark Mc Auley ◽  
Jason Roberts ◽  
Nikos I. Kavallaris ◽  
...  

2018 ◽  
Author(s):  
Laura Matrajt ◽  
M. Elizabeth Halloran ◽  
Rustom Antia

Live-attenuated vaccines are usually highly effective against many acute viral infections. However, the effective- ness of the live attenuated influenza vaccine (LAIV) can vary widely, ranging from 0% effectiveness in some studies done in the United States to 50% in studies done in Europe. The reasons for these discrepancies remain largely unclear. In this paper we use mathematical models to explore how the efficacy of LAIV is affected by the degree of mismatch with the currently circulating influenza strain and interference with pre-existing immunity. The model incorporates two key antigenic distances - the distance between pre-existing immunity and the currently circulating strain as well as the LAIV strain. Our models show that a LAIV that is matched with the currently circulating strain is likely to have only modest efficacy. Our results suggest that the efficacy of the vaccine would be increased (optimized) if, rather than being matched to the circulating strain, it is antigenically slightly further from pre-existing immunity compared with the circulating strain. The models also suggest two regimes in which LAIV that is matched to circulating strains may provide effective protection. The first is in children before they have built immunity from circulating strains. The second is in response to novel strains (such as antigenic shifts) which are at substantial antigenic distance from previously circulating strains. Our models provide an explanation for the variation in vaccine effectiveness, both between children and adults as well as between studies of vaccine effectiveness observed during the 2014-15 influenza season in different countries.


2016 ◽  
Vol 3 (2) ◽  
pp. 150661 ◽  
Author(s):  
Shaun R. Stipp ◽  
Abdon Iniguez ◽  
Frederic Wan ◽  
Dominik Wodarz

CD8 T cell or cytotoxic T lymphocyte (CTL) responses are an important branch of the immune system in the fight against viral infections. The dynamics of anti-viral CTL responses have been characterized in some detail, both experimentally and with mathematical models. An interesting experimental observation concerns the timing of CTL responses. A recent study reported that in pneumonia virus of mice the effector CTL tended to arrive in the lung only after maximal virus loads had been achieved, an observation that seems at first counterintuitive because prevention of pathology would require earlier CTL-mediated activity. A delay in CTL-mediated effector activity has also been quoted as a possible explanation for the difficulties associated with CTL-based vaccines. This paper uses mathematical models to show that in specific parameter regimes, delayed CTL effector activity can be advantageous for the host in the sense that it can increase the chances of virus clearance. The increased ability of the CTL to clear the infection, however, is predicted to come at the cost of acute pathology, giving rise to a trade-off, which is discussed in the light of evolutionary processes. This work provides a theoretical basis for understanding the described experimental observations.


1987 ◽  
Vol 30 (5) ◽  
pp. 1353-1357
Author(s):  
T. C. Bridges ◽  
E. M. Smith ◽  
L. W. Turner

Sign in / Sign up

Export Citation Format

Share Document