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 ()Db 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 Db between variants, revealing that: (i) Db increased progressively from the Alpha to the Omicron variant; (ii) Db showed a high degree of variability within Omicron variants; (iii) a higher Db was associated with a later emergence of the variant within a country; (iv) a higher degree of immunization of the population against previous variants was associated with a higher Db for the Delta variant; (v) larger countries exhibited smaller Db, suggesting regionally diverse outbreaks within the same country; and finally (vi) 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 Db, we have tracked the OPEN ACCESSEDITED BYTamer Oraby, The University of Texas Rio Grande Valley, United StatesREVIEWED BYFulvia Pimpinelli, San Gallicano Dermatological Institute IRCCS, ItalyMd Rafiul Islam, University of the Incarnate Word, United States*CORRESPONDENCEClara Prats clara.prats@upc.eduRECEIVED 15 November 2023ACCEPTED 08 April 2024PUBLISHED 15 May 2024CITATIONde Rioja VL, Perramon-Malavez A, Alonso S, Andrés C, Antón A, Bordoy AE, Càmara J, Cardona P-J, Català M, López D, Martí S, Martró E, Saludes V, Prats C and Alvarez-Lacalle E (2024) Mathematical modeling of SARS-CoV-2 variant substitutions in European countries: transmission dynamics and epidemiological insights.Front. Public Health 12:1339267.doi: 10.3389/fpubh.2024.1339267COPYRIGHT© 2024 de Rioja, Perramon-Malavez, Alonso, Andrés, Antón, Bordoy, Càmara, Cardona, Català, López, Martí, Martró, Saludes, Prats and Alvarez-Lacalle. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.TYPE Original ResearchPUBLISHED 15 May 2024DOI 10.3389/fpubh.2024.1339267 de Rioja et al. 10.3389/fpubh.2024.1339267Frontiers in Public Health02frontiersin.orgspread 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.
