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Selection for infectivity profiles in slow and fast epidemics, and the rise of SARS-CoV-2 variants
Evaluating the characteristics of emerging SARS-CoV-2 variants of concern is essential to inform pandemic risk assessment. A variant may grow faster if it produces a larger number of secondary infections (“R advantage”) or if the timing of secondary infections (generation time) is better. So far, as...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
eLife Sciences Publications, Ltd
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9205634/ https://www.ncbi.nlm.nih.gov/pubmed/35587653 http://dx.doi.org/10.7554/eLife.75791 |
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author | Blanquart, François Hozé, Nathanaël Cowling, Benjamin John Débarre, Florence Cauchemez, Simon |
author_facet | Blanquart, François Hozé, Nathanaël Cowling, Benjamin John Débarre, Florence Cauchemez, Simon |
author_sort | Blanquart, François |
collection | PubMed |
description | Evaluating the characteristics of emerging SARS-CoV-2 variants of concern is essential to inform pandemic risk assessment. A variant may grow faster if it produces a larger number of secondary infections (“R advantage”) or if the timing of secondary infections (generation time) is better. So far, assessments have largely focused on deriving the R advantage assuming the generation time was unchanged. Yet, knowledge of both is needed to anticipate the impact. Here, we develop an analytical framework to investigate the contribution of both the R advantage and generation time to the growth advantage of a variant. It is known that selection on a variant with larger R increases with levels of transmission in the community. We additionally show that variants conferring earlier transmission are more strongly favored when the historical strains have fast epidemic growth, while variants conferring later transmission are more strongly favored when historical strains have slow or negative growth. We develop these conceptual insights into a new statistical framework to infer both the R advantage and generation time of a variant. On simulated data, our framework correctly estimates both parameters when it covers time periods characterized by different epidemiological contexts. Applied to data for the Alpha and Delta variants in England and in Europe, we find that Alpha confers a+54% [95% CI, 45–63%] R advantage compared to previous strains, and Delta +140% [98–182%] compared to Alpha, and mean generation times are similar to historical strains for both variants. This work helps interpret variant frequency dynamics and will strengthen risk assessment for future variants of concern. |
format | Online Article Text |
id | pubmed-9205634 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | eLife Sciences Publications, Ltd |
record_format | MEDLINE/PubMed |
spelling | pubmed-92056342022-06-18 Selection for infectivity profiles in slow and fast epidemics, and the rise of SARS-CoV-2 variants Blanquart, François Hozé, Nathanaël Cowling, Benjamin John Débarre, Florence Cauchemez, Simon eLife Epidemiology and Global Health Evaluating the characteristics of emerging SARS-CoV-2 variants of concern is essential to inform pandemic risk assessment. A variant may grow faster if it produces a larger number of secondary infections (“R advantage”) or if the timing of secondary infections (generation time) is better. So far, assessments have largely focused on deriving the R advantage assuming the generation time was unchanged. Yet, knowledge of both is needed to anticipate the impact. Here, we develop an analytical framework to investigate the contribution of both the R advantage and generation time to the growth advantage of a variant. It is known that selection on a variant with larger R increases with levels of transmission in the community. We additionally show that variants conferring earlier transmission are more strongly favored when the historical strains have fast epidemic growth, while variants conferring later transmission are more strongly favored when historical strains have slow or negative growth. We develop these conceptual insights into a new statistical framework to infer both the R advantage and generation time of a variant. On simulated data, our framework correctly estimates both parameters when it covers time periods characterized by different epidemiological contexts. Applied to data for the Alpha and Delta variants in England and in Europe, we find that Alpha confers a+54% [95% CI, 45–63%] R advantage compared to previous strains, and Delta +140% [98–182%] compared to Alpha, and mean generation times are similar to historical strains for both variants. This work helps interpret variant frequency dynamics and will strengthen risk assessment for future variants of concern. eLife Sciences Publications, Ltd 2022-05-19 /pmc/articles/PMC9205634/ /pubmed/35587653 http://dx.doi.org/10.7554/eLife.75791 Text en © 2022, Blanquart et al https://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited. |
spellingShingle | Epidemiology and Global Health Blanquart, François Hozé, Nathanaël Cowling, Benjamin John Débarre, Florence Cauchemez, Simon Selection for infectivity profiles in slow and fast epidemics, and the rise of SARS-CoV-2 variants |
title | Selection for infectivity profiles in slow and fast epidemics, and the rise of SARS-CoV-2 variants |
title_full | Selection for infectivity profiles in slow and fast epidemics, and the rise of SARS-CoV-2 variants |
title_fullStr | Selection for infectivity profiles in slow and fast epidemics, and the rise of SARS-CoV-2 variants |
title_full_unstemmed | Selection for infectivity profiles in slow and fast epidemics, and the rise of SARS-CoV-2 variants |
title_short | Selection for infectivity profiles in slow and fast epidemics, and the rise of SARS-CoV-2 variants |
title_sort | selection for infectivity profiles in slow and fast epidemics, and the rise of sars-cov-2 variants |
topic | Epidemiology and Global Health |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9205634/ https://www.ncbi.nlm.nih.gov/pubmed/35587653 http://dx.doi.org/10.7554/eLife.75791 |
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