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A runtime alterable epidemic model with genetic drift, waning immunity and vaccinations

We present methods for building a Java Runtime-Alterable-Model Platform (RAMP) of complex dynamical systems. We illustrate our methods by building a multivariant SEIR (epidemic) RAMP. Underlying our RAMP is an individual-based model that includes adaptive contact rates, pathogen genetic drift, wanin...

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Autores principales: Getz, Wayne M., Salter, Richard, Luisa Vissat, Ludovica, Koopman, James S., Simon, Carl P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Royal Society 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8611333/
https://www.ncbi.nlm.nih.gov/pubmed/34814729
http://dx.doi.org/10.1098/rsif.2021.0648
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author Getz, Wayne M.
Salter, Richard
Luisa Vissat, Ludovica
Koopman, James S.
Simon, Carl P.
author_facet Getz, Wayne M.
Salter, Richard
Luisa Vissat, Ludovica
Koopman, James S.
Simon, Carl P.
author_sort Getz, Wayne M.
collection PubMed
description We present methods for building a Java Runtime-Alterable-Model Platform (RAMP) of complex dynamical systems. We illustrate our methods by building a multivariant SEIR (epidemic) RAMP. Underlying our RAMP is an individual-based model that includes adaptive contact rates, pathogen genetic drift, waning and cross-immunity. Besides allowing parameter values, process descriptions and scriptable runtime drivers to be easily modified during simulations, our RAMP can used within R-Studio and other computational platforms. Process descriptions that can be runtime altered within our SEIR RAMP include pathogen variant-dependent host shedding, environmental persistence, host transmission and within-host pathogen mutation and replication. They also include adaptive social distancing and adaptive application of vaccination rates and variant-valency of vaccines. We present simulation results using parameter values and process descriptions relevant to the current COVID-19 pandemic. Our results suggest that if waning immunity outpaces vaccination rates, then vaccination rollouts may fail to contain the most transmissible variants, particularly if vaccine valencies are not adapted to deal with escape mutations. Our SEIR RAMP is designed for easy use by others. More generally, our RAMP concept facilitates construction of highly flexible complex systems models of all types, which can then be easily shared as stand-alone application programs.
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spelling pubmed-86113332021-11-29 A runtime alterable epidemic model with genetic drift, waning immunity and vaccinations Getz, Wayne M. Salter, Richard Luisa Vissat, Ludovica Koopman, James S. Simon, Carl P. J R Soc Interface Life Sciences–Mathematics interface We present methods for building a Java Runtime-Alterable-Model Platform (RAMP) of complex dynamical systems. We illustrate our methods by building a multivariant SEIR (epidemic) RAMP. Underlying our RAMP is an individual-based model that includes adaptive contact rates, pathogen genetic drift, waning and cross-immunity. Besides allowing parameter values, process descriptions and scriptable runtime drivers to be easily modified during simulations, our RAMP can used within R-Studio and other computational platforms. Process descriptions that can be runtime altered within our SEIR RAMP include pathogen variant-dependent host shedding, environmental persistence, host transmission and within-host pathogen mutation and replication. They also include adaptive social distancing and adaptive application of vaccination rates and variant-valency of vaccines. We present simulation results using parameter values and process descriptions relevant to the current COVID-19 pandemic. Our results suggest that if waning immunity outpaces vaccination rates, then vaccination rollouts may fail to contain the most transmissible variants, particularly if vaccine valencies are not adapted to deal with escape mutations. Our SEIR RAMP is designed for easy use by others. More generally, our RAMP concept facilitates construction of highly flexible complex systems models of all types, which can then be easily shared as stand-alone application programs. The Royal Society 2021-11-24 /pmc/articles/PMC8611333/ /pubmed/34814729 http://dx.doi.org/10.1098/rsif.2021.0648 Text en © 2021 The Authors. https://creativecommons.org/licenses/by/4.0/Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, provided the original author and source are credited.
spellingShingle Life Sciences–Mathematics interface
Getz, Wayne M.
Salter, Richard
Luisa Vissat, Ludovica
Koopman, James S.
Simon, Carl P.
A runtime alterable epidemic model with genetic drift, waning immunity and vaccinations
title A runtime alterable epidemic model with genetic drift, waning immunity and vaccinations
title_full A runtime alterable epidemic model with genetic drift, waning immunity and vaccinations
title_fullStr A runtime alterable epidemic model with genetic drift, waning immunity and vaccinations
title_full_unstemmed A runtime alterable epidemic model with genetic drift, waning immunity and vaccinations
title_short A runtime alterable epidemic model with genetic drift, waning immunity and vaccinations
title_sort runtime alterable epidemic model with genetic drift, waning immunity and vaccinations
topic Life Sciences–Mathematics interface
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8611333/
https://www.ncbi.nlm.nih.gov/pubmed/34814729
http://dx.doi.org/10.1098/rsif.2021.0648
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