{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T19:04:41Z","timestamp":1789499081960,"version":"build-2803163510"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1014707","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T00:00:00Z","timestamp":1789430400000}}],"reference-count":31,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["Chaire industrielle VIRESP, ANR-23-CHIN-0002-01"],"award-info":[{"award-number":["Chaire industrielle VIRESP, ANR-23-CHIN-0002-01"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004339","name":"Sanofi","doi-asserted-by":"publisher","award":["ANR-23-CHIN-0002-01"],"award-info":[{"award-number":["ANR-23-CHIN-0002-01"]}],"id":[{"id":"10.13039\/100004339","id-type":"DOI","asserted-by":"publisher"}]},{"name":"NextGenerationEU-MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases","award":["PE00000007"],"award-info":[{"award-number":["PE00000007"]}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>The COVID-19 pandemic highlighted the critical need for robust methods to monitor viral evolution and detect emerging variants of concern (VOCs). This study expanded an unsupervised clustering algorithm, based on Levenshtein distance, to track and predict variant predominance across six European countries from 2020 to January 2024. We also investigated the influence of genetic distances and containment strategies on hospitalization rates. Spike protein sequences were transformed into temporal chains. A deep neural network (DNN) was trained to classify emerging chains as likely dominant, while a CatBoost model assessed important variables, and simulations explored modifying vaccine genetic distance, containment measures, and vaccination coverage. Approximately 5,000 sequences per week enabled early chain detection within four weeks. The DNN achieved high classification performance for identifying future predominant chains within 3\u20134 weeks of detection. Genetic distance metrics between consecutive chains and between circulating and vaccine strains were among the most informative variables associated with hospitalization patterns. Model-based simulations suggested that scenarios involving improved vaccine matching or stronger containment measures were associated with lower predicted hospitalization burdens. Doubling vaccination coverage alone had minimal effect but showed additional reductions when combined with strict containment. Our findings from this integrated framework highlight the potential relevance of genetic distance metrics and public health interventions when assessing hospitalization risk associated with emerging variants.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1014707","type":"journal-article","created":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T17:48:08Z","timestamp":1788284888000},"page":"e1014707","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["From sequences to strategies: Early detection of new SARS-CoV-2 variants via genetic distance to reduce hospitalizations"],"prefix":"10.1371","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-3624-3887","authenticated-orcid":true,"given":"Marika","family":"D\u2019Avanzo","sequence":"first","affiliation":[{"name":"Experimental and Forensic Medicine, University of Pavia","place":["Pavia, Italy"],"department":["PhD National Programme in One Health approaches to infectious diseases and life science research, Department of Public Health"]},{"name":"Complesso Universitario di Monte S. Angelo Edificio 6","place":["Naples, Italy"],"department":["INFN Sezione di Napoli"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5603-8724","authenticated-orcid":true,"given":"Aung Pone","family":"Myint","sequence":"additional","affiliation":[{"name":"Center of Excellence in Respiratory Pathogens (CERP), Hospices Civils de Lyon (HCL) and Centre International de Recherche en Infectiologie (CIRI), \u00c9quipe Sant\u00e9 Publique, \u00c9pid\u00e9miologie et \u00c9cologie \u00c9volutive des Maladies Infectieuses (PHE3ID), Inserm U1111, CNRS UMR5308, ENS de Lyon, Universit\u00e9 Claude Bernard Lyon 1","place":["Lyon, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giacomo","family":"Cacciapaglia","sequence":"additional","affiliation":[{"name":"Laboratoire de Physique Th\u00e9orique et Hautes Energies (LPTHE), UMR, Sorbonne Universit\u00e9 & CNRS","place":["France"]},{"name":"Quantum Theory Center (\u210fQTC) at IMADA & D-IAS, Southern Denmark Univ","place":["Odense M, Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Hohenegger","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Claude Bernard Lyon 1, CNRS\/IN2P3, IP2I UMR 5822","place":["Villeurbanne, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francesco","family":"Conventi","sequence":"additional","affiliation":[{"name":"Complesso Universitario di Monte S. Angelo Edificio 6","place":["Naples, Italy"],"department":["INFN Sezione di Napoli"]},{"name":"Universit\u00e0 degli studi di Napoli Parthenope, Centro Direzionale di Napoli","place":["Naples, Italy"],"department":["Dipartimento di Ingegneria"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3788-878X","authenticated-orcid":true,"given":"Marta","family":"Nunes","sequence":"additional","affiliation":[{"name":"Center of Excellence in Respiratory Pathogens (CERP), Hospices Civils de Lyon (HCL) and Centre International de Recherche en Infectiologie (CIRI), \u00c9quipe Sant\u00e9 Publique, \u00c9pid\u00e9miologie et \u00c9cologie \u00c9volutive des Maladies Infectieuses (PHE3ID), Inserm U1111, CNRS UMR5308, ENS de Lyon, Universit\u00e9 Claude Bernard Lyon 1","place":["Lyon, France"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,9,1]]},"reference":[{"issue":"1","key":"pcbi.1014707.ref001","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1038\/s41580-021-00418-x","article-title":"Mechanisms of SARS-CoV-2 entry into cells","volume":"23","author":"CB Jackson","year":"2022","journal-title":"Nat Rev Mol Cell Biol"},{"issue":"6","key":"pcbi.1014707.ref002","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1038\/s41579-023-00878-2","article-title":"The evolution of SARS-CoV-2","volume":"21","author":"PV Markov","year":"2023","journal-title":"Nat Rev Microbiol"},{"key":"pcbi.1014707.ref003","unstructured":"WHO. Updated working definitions and primary actions for SARSCoV2 variants. https:\/\/www.who.int\/publications\/m\/item\/updated-working-definitions-and-primary-actions-for--sars-cov-2-variants. 2023. Accessed 2025 July 23."},{"key":"pcbi.1014707.ref004","unstructured":"WHO. Statement on the fifteenth meeting of the IHR (2005) Emergency Committee on the COVID-19 pandemic. https:\/\/www.who.int\/news\/item\/05-05-2023-statement-on-the-fifteenth-meeting-of-the-international-health-regulations-(2005)-emergency-committee-regarding-the-coronavirus-disease-(covid-19)-pandemic. 2023. 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