{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T15:40:45Z","timestamp":1785426045778,"version":"3.56.0"},"reference-count":74,"publisher":"American Society for Microbiology","issue":"2","license":[{"start":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T00:00:00Z","timestamp":1770768000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T00:00:00Z","timestamp":1770768000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100018332","name":"Harvard Global Health Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100018332","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001732","name":"Danish National Research Foundation","doi-asserted-by":"publisher","award":["DNRF 170"],"award-info":[{"award-number":["DNRF 170"]}],"id":[{"id":"10.13039\/501100001732","id-type":"DOI","asserted-by":"publisher"}]},{"name":"JPB Foundation"},{"name":"Conacyt","award":["F002-314296"],"award-info":[{"award-number":["F002-314296"]}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mBio"],"published-print":{"date-parts":[[2026,2,11]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines reduced severe coronavirus disease 2019, but variants like Delta and Omicron caused widespread breakthrough infections (BIs). Mexico, offering diverse vaccines, and its Yucat\u00e1n region, a major travel hub, provide a unique setting to study BIs. We characterized SARS-CoV-2 BIs in Yucat\u00e1n during the Delta-to-Omicron transition (September 2021\u2013January 2022), assessing disease severity, symptoms, and viral transmission dynamics using epidemiological and genomic data. A case-control study using health system data (\n                      <jats:italic toggle=\"yes\">n<\/jats:italic>\n                      = 13,325) compared outcomes in BIs (\n                      <jats:italic toggle=\"yes\">n<\/jats:italic>\n                      = 5,183) versus unvaccinated infections (UIs;\n                      <jats:italic toggle=\"yes\">n<\/jats:italic>\n                      = 8,142) via logistic regression, also comparing Delta versus Omicron waves. Phylodynamic modeling of 205 BI sequences, contextualized globally (\n                      <jats:italic toggle=\"yes\">n<\/jats:italic>\n                      = 1,152 total), reconstructed the evolutionary history and transmission routes. Vaccination significantly reduced hospitalization (odds ratio [OR] = 0.38) and death (OR = 0.45) in BIs compared to UIs. Omicron infections were less severe than Delta (hospitalization OR = 0.60; death OR = 0.33) and presented with less loss of smell\/taste but more upper respiratory symptoms. Phylodynamics revealed numerous introductions (17 Delta, 36 Omicron). Delta BIs in Yucat\u00e1n originated mainly from within Mexico, Guatemala, Europe, and the United States. Omicron BIs in Yucat\u00e1n had more diverse origins including from North and South America and Africa, coinciding with eased travel restrictions. Vaccines maintained protection against severe outcomes during the Delta and Omicron waves in Yucat\u00e1n. Omicron, though less severe, showed enhanced transmissibility with increased introductions linked to relaxed public health measures. Findings highlight the critical role of continued vaccination, genomic surveillance, adaptive policies, and cross-border collaboration for pandemic preparedness and health security.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>Our understanding of severe acute respiratory syndrome coronavirus 2 breakthrough infections in Latin America is limited, specifically in regions with unique epidemiological dynamics. In this study, we fill a knowledge gap by characterizing these infections in Yucat\u00e1n, Mexico, a major international travel hub with one of the world's most diverse vaccine rollouts, during the critical transition from the Delta variant to the Omicron variant. The translational importance of our investigation is twofold. First, through case-control data analysis, we provide robust, real-world evidence that vaccination significantly reduced the risk of hospitalization and death, offering crucial data to support ongoing vaccination campaigns against emerging variants. Second, by combining epidemiological data with phylodynamic analysis, we demonstrate a direct link between the easing of public health restrictions and the increased number and diversity of viral introductions that sparked the Omicron wave. This highlights the critical importance of coordinating genomic tracking with public health policy to mitigate the spread of future pandemic threats and strengthen global health security.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/mbio.02432-25","type":"journal-article","created":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T14:00:20Z","timestamp":1767880820000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":1,"title":["Case-control and genomic epidemiology characterization of SARS-CoV-2 breakthrough infections during the Delta-to-Omicron transition"],"prefix":"10.1128","volume":"17","author":[{"given":"Erin","family":"Yuan","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03vek6s52","id-type":"ROR","asserted-by":"publisher"}],"name":"Harvard University","place":["Cambridge, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chelsea 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