ArticleProceedings of the National Academy of Sciences of the United States of America2023
Analysis of the risk and pre-emptive control of viral outbreaks accounting for within-host dynamics: SARS-CoV-2 as a case study.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Disentangling the drivers of heterogeneity in SARS-CoV-2 transmission from data on viral load and daily contact rates.PLoS computational biology · 2026Article
- Integrating viral kinetics and population spread in a one health framework to explain variant-specific epidemic dynamics.One health (Amsterdam, Netherlands) · 2026Article
- Identifying the optimal rapid antigen test for screening and determining the end of isolation: A modeling study.PLoS computational biology · 2026Article
- VIBES: A multiscale modeling approach integrating within-host and between-hosts dynamics in epidemics.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Modeling the effectiveness of RT-PCR, RT-LAMP, and antigen testing strategies for COVID-19 control.BMC infectious diseases · 2025Article
- Effects of individual variation and seasonal vaccination on disease risks.Nature communications · 2025Article
- Viral Dynamic Models During COVID-19: Are We Ready for the Next Pandemic?CPT: pharmacometrics & systems pharmacology · 2025Review
- A modeling study to define guidelines for antigen screening in schools and workplaces to mitigate COVID-19 outbreaks.Communications medicine · 2025Article
- Predicting pathogen evolution and immune evasion in the age of artificial intelligence.Computational and structural biotechnology journal · 2025Review
- Development of a SARS-CoV-2 viral dynamic model for patients with COVID-19 based on the amount of viral RNA and viral titer.CPT: pharmacometrics & systems pharmacology · 2024Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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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