Mathematical modeling of SARS-CoV-2 variant substitutions in European countries: transmission dynamics and epidemiological insights

Background: Countries across Europe have faced similar evolutions of SARS-CoV-2 variants of concern, including the Alpha, Delta, and Omicron variants. Materials and methods: We used data from GISAID and applied a robust, automated mathematical substitution model to study the dynamics of COVID-19 var...

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Autores: López de Rioja, Víctor, Perramon Malavez, Aida, Alonso, Sergio, Andrés, Cristina, Antón, Andrés, Bordoy, Antoni E., Càmara Mas, Jordi, Cardona, Pere-Joan, Català, Martí, López, Daniel, Martí Martí, Sara, Martró, Elisa, Saludes, Verónica, Prats, Clara, Alvarez Lacalle, Enrique
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2024
País:España
Institución:Universidad de Barcelona
Repositorio:Dipòsit Digital de la UB
OAI Identifier:oai:diposit.ub.edu:2445/214825
Acceso en línea:https://hdl.handle.net/2445/214825
Access Level:acceso abierto
Palabra clave:SARS-CoV-2
Models matemàtics
Mathematical models
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spelling Mathematical modeling of SARS-CoV-2 variant substitutions in European countries: transmission dynamics and epidemiological insightsLópez de Rioja, Víctor Perramon Malavez, AidaAlonso, SergioAndrés, CristinaAntón, AndrésBordoy, Antoni E.Càmara Mas, Jordi Cardona, Pere-JoanCatalà, MartíLópez, DanielMartí Martí, SaraMartró, ElisaSaludes, VerónicaPrats, ClaraAlvarez Lacalle, EnriqueSARS-CoV-2Models matemàticsSARS-CoV-2Mathematical modelsBackground: Countries across Europe have faced similar evolutions of SARS-CoV-2 variants of concern, including the Alpha, Delta, and Omicron variants. Materials and methods: We used data from GISAID and applied a robust, automated mathematical substitution model to study the dynamics of COVID-19 variants in Europe over a period of more than 2 years, from late 2020 to early 2023. This model identifies variant substitution patterns and distinguishes between residual and dominant behavior. We used weekly sequencing data from 19 European countries to estimate the increase in transmissibility ( Delta beta ) between consecutive SARS-CoV-2 variants. In addition, we focused on large countries with separate regional outbreaks and complex scenarios of multiple competing variants. Results: Our model accurately reproduced the observed substitution patterns between the Alpha, Delta, and Omicron major variants. We estimated the daily variant prevalence and calculated Delta beta between variants, revealing that: ( i ) Delta beta increased progressively from the Alpha to the Omicron variant; ( i i ) Delta beta showed a high degree of variability within Omicron variants; ( i i i ) a higher Delta beta was associated with a later emergence of the variant within a country; ( i v ) a higher degree of immunization of the population against previous variants was associated with a higher Delta beta for the Delta variant; ( v ) larger countries exhibited smaller Delta beta , suggesting regionally diverse outbreaks within the same country; and finally ( v i ) the model reliably captures the dynamics of competing variants, even in complex scenarios. Conclusion: The use of mathematical models allows for precise and reliable estimation of daily cases of each variant. By quantifying Delta beta , we have tracked the spread of the different variants across Europe, highlighting a robust increase in transmissibility trend from Alpha to Omicron. Additionally, we have shown that the geographical characteristics of a country, as well as the timing of new variant entrances, can explain some of the observed differences in variant substitution dynamics across countries.Frontiers Media SA2024info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfhttps://hdl.handle.net/2445/214825Articles publicats en revistes (Institut d'lnvestigació Biomèdica de Bellvitge (IDIBELL))reponame:Dipòsit Digital de la UBinstname:Universidad de BarcelonaInglésReproducció del document publicat a: https://doi.org/10.3389/fpubh.2024.1339267Frontiers in Public Health, 2024, vol. 12https://doi.org/10.3389/fpubh.2024.1339267cc by (c) López de Rioja, Víctor et al., 2024http://creativecommons.org/licenses/by/3.0/es/info:eu-repo/semantics/openAccessoai:diposit.ub.edu:2445/2148252026-05-27T06:46:51Z
dc.title.none.fl_str_mv Mathematical modeling of SARS-CoV-2 variant substitutions in European countries: transmission dynamics and epidemiological insights
title Mathematical modeling of SARS-CoV-2 variant substitutions in European countries: transmission dynamics and epidemiological insights
spellingShingle Mathematical modeling of SARS-CoV-2 variant substitutions in European countries: transmission dynamics and epidemiological insights
López de Rioja, Víctor
SARS-CoV-2
Models matemàtics
SARS-CoV-2
Mathematical models
title_short Mathematical modeling of SARS-CoV-2 variant substitutions in European countries: transmission dynamics and epidemiological insights
title_full Mathematical modeling of SARS-CoV-2 variant substitutions in European countries: transmission dynamics and epidemiological insights
title_fullStr Mathematical modeling of SARS-CoV-2 variant substitutions in European countries: transmission dynamics and epidemiological insights
title_full_unstemmed Mathematical modeling of SARS-CoV-2 variant substitutions in European countries: transmission dynamics and epidemiological insights
title_sort Mathematical modeling of SARS-CoV-2 variant substitutions in European countries: transmission dynamics and epidemiological insights
dc.creator.none.fl_str_mv López de Rioja, Víctor
Perramon Malavez, Aida
Alonso, Sergio
Andrés, Cristina
Antón, Andrés
Bordoy, Antoni E.
Càmara Mas, Jordi
Cardona, Pere-Joan
Català, Martí
López, Daniel
Martí Martí, Sara
Martró, Elisa
Saludes, Verónica
Prats, Clara
Alvarez Lacalle, Enrique
author López de Rioja, Víctor
author_facet López de Rioja, Víctor
Perramon Malavez, Aida
Alonso, Sergio
Andrés, Cristina
Antón, Andrés
Bordoy, Antoni E.
Càmara Mas, Jordi
Cardona, Pere-Joan
Català, Martí
López, Daniel
Martí Martí, Sara
Martró, Elisa
Saludes, Verónica
Prats, Clara
Alvarez Lacalle, Enrique
author_role author
author2 Perramon Malavez, Aida
Alonso, Sergio
Andrés, Cristina
Antón, Andrés
Bordoy, Antoni E.
Càmara Mas, Jordi
Cardona, Pere-Joan
Català, Martí
López, Daniel
Martí Martí, Sara
Martró, Elisa
Saludes, Verónica
Prats, Clara
Alvarez Lacalle, Enrique
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv SARS-CoV-2
Models matemàtics
SARS-CoV-2
Mathematical models
topic SARS-CoV-2
Models matemàtics
SARS-CoV-2
Mathematical models
description Background: Countries across Europe have faced similar evolutions of SARS-CoV-2 variants of concern, including the Alpha, Delta, and Omicron variants. Materials and methods: We used data from GISAID and applied a robust, automated mathematical substitution model to study the dynamics of COVID-19 variants in Europe over a period of more than 2 years, from late 2020 to early 2023. This model identifies variant substitution patterns and distinguishes between residual and dominant behavior. We used weekly sequencing data from 19 European countries to estimate the increase in transmissibility ( Delta beta ) between consecutive SARS-CoV-2 variants. In addition, we focused on large countries with separate regional outbreaks and complex scenarios of multiple competing variants. Results: Our model accurately reproduced the observed substitution patterns between the Alpha, Delta, and Omicron major variants. We estimated the daily variant prevalence and calculated Delta beta between variants, revealing that: ( i ) Delta beta increased progressively from the Alpha to the Omicron variant; ( i i ) Delta beta showed a high degree of variability within Omicron variants; ( i i i ) a higher Delta beta was associated with a later emergence of the variant within a country; ( i v ) a higher degree of immunization of the population against previous variants was associated with a higher Delta beta for the Delta variant; ( v ) larger countries exhibited smaller Delta beta , suggesting regionally diverse outbreaks within the same country; and finally ( v i ) the model reliably captures the dynamics of competing variants, even in complex scenarios. Conclusion: The use of mathematical models allows for precise and reliable estimation of daily cases of each variant. By quantifying Delta beta , we have tracked the spread of the different variants across Europe, highlighting a robust increase in transmissibility trend from Alpha to Omicron. Additionally, we have shown that the geographical characteristics of a country, as well as the timing of new variant entrances, can explain some of the observed differences in variant substitution dynamics across countries.
publishDate 2024
dc.date.none.fl_str_mv 2024
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://hdl.handle.net/2445/214825
url https://hdl.handle.net/2445/214825
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Reproducció del document publicat a: https://doi.org/10.3389/fpubh.2024.1339267
Frontiers in Public Health, 2024, vol. 12
https://doi.org/10.3389/fpubh.2024.1339267
dc.rights.none.fl_str_mv cc by (c) López de Rioja, Víctor et al., 2024
http://creativecommons.org/licenses/by/3.0/es/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv cc by (c) López de Rioja, Víctor et al., 2024
http://creativecommons.org/licenses/by/3.0/es/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Frontiers Media SA
publisher.none.fl_str_mv Frontiers Media SA
dc.source.none.fl_str_mv Articles publicats en revistes (Institut d'lnvestigació Biomèdica de Bellvitge (IDIBELL))
reponame:Dipòsit Digital de la UB
instname:Universidad de Barcelona
instname_str Universidad de Barcelona
reponame_str Dipòsit Digital de la UB
collection Dipòsit Digital de la UB
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,812429

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