biostudies-literatureZhang XBeijing Municipal Natural Science FoundationGuangdong-PHOENIX Center Joint Lab on Chinese MedicineState Key Laboratory of ProteomicsScience and Technology Planning Project of Guangdong ProvinceNational Key R&D Program of ChinaCapital Health Development Research ProjectNational Key Research and Development Program of ChinaBeijing Municipal International Cooperation and Exchange ProjectInnovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicinee2402639https://www.ebi.ac.uk/biostudies/studies/S-EPMC11516136biostudies-literatureUnknown11(40)Host immunity is central to the virus's spread dynamics, which is significantly influenced by vaccination and prior infection experiences. In this work, we analyzed the co-evolution of SARS-CoV-2 mutation, angiotensin-converting enzyme 2 (ACE2) receptor binding, and neutralizing antibody (NAb) responses across various variants in 822 human and mice vaccinated with different non-Omicron and Omicron vaccines is analyzed. The link between vaccine efficacy and vaccine type, dosing, and post-vaccination duration is revealed. The classification of immune protection against non-Omicron and Omicron variants is co-evolved with genetic mutations and vaccination. Additionally, a model, the Prevalence Score (P-Score) is introduced, which surpasses previous algorithm-based models in predicting the poteAdvanced science (Weinheim, Baden-Wurttemberg, Germany)SARS-CoV-2 Evolution: Immune Dynamics, Omicron Specificity, and Predictive Modeling in Vaccinated Populations.PMC11516136ZYYCXTD-C-2022042024-1-40932022YFE02104002023YFC08724002020B1111100006Z231100002723004L234034SKLP-O202007SKLP-O2022052021YFA1301604YN2021DB062024-1-1201M23010YN2021DB03Li HZhu YWang BZhang NTeng FGuo SLi MLi YZhang XJia YXu XWang YYu XQin CfalseSARS-CoV-2 Evolution: Immune Dynamics, Omicron Specificity, and Predictive Modeling in Vaccinated Populations.Host immunity is central to the virus's spread dynamics, which is significantly influenced by vaccination and prior infection experiences. In this work, we analyzed the co-evolution of SARS-CoV-2 mutation, angiotensin-converting enzyme 2 (ACE2) receptor binding, and neutralizing antibody (NAb) responses across various variants in 822 human and mice vaccinated with different non-Omicron and Omicron vaccines is analyzed. The link between vaccine efficacy and vaccine type, dosing, and post-vaccination duration is revealed. The classification of immune protection against non-Omicron and Omicron variants is co-evolved with genetic mutations and vaccination. Additionally, a model, the Prevalence Score (P-Score) is introduced, which surpasses previous algorithm-based models in predicting the pote2024-01-01T00:00:00Z2024 Oct2026-04-30T00:11:37.464Z2025-04-04T00:30:02.57ZS-EPMC115161363920681310.1002/advs.202402639