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Analysis of the risk and pre-emptive control of viral outbreaks accounting for within-host dynamics: SARS-CoV-2 as a case study

In the era of living with COVID-19, the risk of localised SARS-CoV-2 outbreaks remains. Here, we develop a multiscale modelling framework for estimating the local outbreak risk for a viral disease (the probability that a major outbreak results from a single case introduced into the population), acco...

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Autores principales: Hart, William S., Park, Hyeongki, Jeong, Yong Dam, Kim, Kwang Su, Yoshimura, Raiki, Thompson, Robin N., Iwami, Shingo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: National Academy of Sciences 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10576149/
https://www.ncbi.nlm.nih.gov/pubmed/37788317
http://dx.doi.org/10.1073/pnas.2305451120
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author Hart, William S.
Park, Hyeongki
Jeong, Yong Dam
Kim, Kwang Su
Yoshimura, Raiki
Thompson, Robin N.
Iwami, Shingo
author_facet Hart, William S.
Park, Hyeongki
Jeong, Yong Dam
Kim, Kwang Su
Yoshimura, Raiki
Thompson, Robin N.
Iwami, Shingo
author_sort Hart, William S.
collection PubMed
description In the era of living with COVID-19, the risk of localised SARS-CoV-2 outbreaks remains. Here, we develop a multiscale modelling framework for estimating the local outbreak risk for a viral disease (the probability that a major outbreak results from a single case introduced into the population), accounting for within-host viral dynamics. Compared to population-level models previously used to estimate outbreak risks, our approach enables more detailed analysis of how the risk can be mitigated through pre-emptive interventions such as antigen testing. Considering SARS-CoV-2 as a case study, we quantify the within-host dynamics using data from individuals with omicron variant infections. We demonstrate that regular antigen testing reduces, but may not eliminate, the outbreak risk, depending on characteristics of local transmission. In our baseline analysis, daily antigen testing reduces the outbreak risk by 45% compared to a scenario without antigen testing. Additionally, we show that accounting for heterogeneity in within-host dynamics between individuals affects outbreak risk estimates and assessments of the impact of antigen testing. Our results therefore highlight important factors to consider when using multiscale models to design pre-emptive interventions against SARS-CoV-2 and other viruses.
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spelling pubmed-105761492023-10-15 Analysis of the risk and pre-emptive control of viral outbreaks accounting for within-host dynamics: SARS-CoV-2 as a case study Hart, William S. Park, Hyeongki Jeong, Yong Dam Kim, Kwang Su Yoshimura, Raiki Thompson, Robin N. Iwami, Shingo Proc Natl Acad Sci U S A Biological Sciences In the era of living with COVID-19, the risk of localised SARS-CoV-2 outbreaks remains. Here, we develop a multiscale modelling framework for estimating the local outbreak risk for a viral disease (the probability that a major outbreak results from a single case introduced into the population), accounting for within-host viral dynamics. Compared to population-level models previously used to estimate outbreak risks, our approach enables more detailed analysis of how the risk can be mitigated through pre-emptive interventions such as antigen testing. Considering SARS-CoV-2 as a case study, we quantify the within-host dynamics using data from individuals with omicron variant infections. We demonstrate that regular antigen testing reduces, but may not eliminate, the outbreak risk, depending on characteristics of local transmission. In our baseline analysis, daily antigen testing reduces the outbreak risk by 45% compared to a scenario without antigen testing. Additionally, we show that accounting for heterogeneity in within-host dynamics between individuals affects outbreak risk estimates and assessments of the impact of antigen testing. Our results therefore highlight important factors to consider when using multiscale models to design pre-emptive interventions against SARS-CoV-2 and other viruses. National Academy of Sciences 2023-10-03 2023-10-10 /pmc/articles/PMC10576149/ /pubmed/37788317 http://dx.doi.org/10.1073/pnas.2305451120 Text en Copyright © 2023 the Author(s). Published by PNAS. https://creativecommons.org/licenses/by/4.0/This open access article is distributed under Creative Commons Attribution License 4.0 (CC BY) (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Biological Sciences
Hart, William S.
Park, Hyeongki
Jeong, Yong Dam
Kim, Kwang Su
Yoshimura, Raiki
Thompson, Robin N.
Iwami, Shingo
Analysis of the risk and pre-emptive control of viral outbreaks accounting for within-host dynamics: SARS-CoV-2 as a case study
title Analysis of the risk and pre-emptive control of viral outbreaks accounting for within-host dynamics: SARS-CoV-2 as a case study
title_full Analysis of the risk and pre-emptive control of viral outbreaks accounting for within-host dynamics: SARS-CoV-2 as a case study
title_fullStr Analysis of the risk and pre-emptive control of viral outbreaks accounting for within-host dynamics: SARS-CoV-2 as a case study
title_full_unstemmed Analysis of the risk and pre-emptive control of viral outbreaks accounting for within-host dynamics: SARS-CoV-2 as a case study
title_short Analysis of the risk and pre-emptive control of viral outbreaks accounting for within-host dynamics: SARS-CoV-2 as a case study
title_sort analysis of the risk and pre-emptive control of viral outbreaks accounting for within-host dynamics: sars-cov-2 as a case study
topic Biological Sciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10576149/
https://www.ncbi.nlm.nih.gov/pubmed/37788317
http://dx.doi.org/10.1073/pnas.2305451120
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