Case-control and genomic epidemiology characterization of SARS-CoV-2 breakthrough infections during the delta-to-Omicron transition
Document Type
Artefact
Department
Paediatrics and Child Health
Abstract
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 Yucatán region, a major travel hub, provide a unique setting to study BIs. We characterized SARS-CoV-2 BIs in Yucatán during the Delta-to-Omicron transition (September 2021-January 2022), assessing disease severity, symptoms, and viral transmission dynamics using epidemiological and genomic data. A case-control study using health system data (n = 13,325) compared outcomes in BIs (n = 5,183) versus unvaccinated infections (UIs; n = 8,142) via logistic regression, also comparing Delta versus Omicron waves. Phylodynamic modeling of 205 BI sequences, contextualized globally (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 Yucatán originated mainly from within Mexico, Guatemala, Europe, and the United States. Omicron BIs in Yucatán 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 Yucatán. 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.
AKU Student
no
Publication (Name of Journal)
mBio
DOI
10.1128/mbio.02432-25
Recommended Citation
Yuan, E.,
Hansen, C. L.,
Tamim, S.,
Kanwar, S.,
Spiro, D. J.,
Losa, R. G.,
Pérez, P. G.,
Badillo, G. B.,
Fennessey, S.,
Zody, M. C.
(2026). Case-control and genomic epidemiology characterization of SARS-CoV-2 breakthrough infections during the delta-to-Omicron transition. mBio, 17(2).
Available at:
https://ecommons.aku.edu/pakistan_fhs_mc_women_childhealth_paediatr/1634
Comments
Pagination is not provided by author/publisher.