{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,17]],"date-time":"2026-01-17T16:22:15Z","timestamp":1768666935555,"version":"3.49.0"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1013582","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T00:00:00Z","timestamp":1768521600000}}],"reference-count":70,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2026,1,12]],"date-time":"2026-01-12T00:00:00Z","timestamp":1768176000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Key Research and Development Program of China","award":["2022YFC2303803"],"award-info":[{"award-number":["2022YFC2303803"]}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["2233300001"],"award-info":[{"award-number":["2233300001"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82204160, 62272020"],"award-info":[{"award-number":["82204160, 62272020"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100018537","name":"National Science and Technology Major Project","doi-asserted-by":"publisher","award":["2021ZD0111201"],"award-info":[{"award-number":["2021ZD0111201"]}],"id":[{"id":"10.13039\/501100018537","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Beijing Natural Science Foundation","award":["L232014"],"award-info":[{"award-number":["L232014"]}]},{"name":"Research on Key Technologies of Plague Prevention and Control in Inner Mongolia Autonomous Region","award":["2021ZD0006"],"award-info":[{"award-number":["2021ZD0006"]}]},{"name":"Beijing Research Center for Respiratory Infectious Diseases Project","award":["BJRID2025-001"],"award-info":[{"award-number":["BJRID2025-001"]}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>Understanding the heterogeneity of population-level viral fitness dynamics, which reflect the interplay between intrinsic viral properties and population immunity, is critical for pandemic preparedness. However, how these dynamics vary across diverse immune backgrounds and mutational landscapes remain poorly characterized. We present Geno-GNN, a graph representation learning approach for retrospectively characterizing the viral fitness dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Geno-GNN accurately predicts angiotensin-converting enzyme 2 (ACE2) binding affinity and immune escape potential across multiple external datasets. Using Geno-GNN, we identified temporal patterns in SARS-CoV-2 fitness and detected varying rates of fitness change associated with distinct immune backgrounds. Virtual mutation scanning revealed two fitness trajectories: broad immune evasion at the cost of ACE2 affinity and ACE2 affinity maintenance at or above the Wuhan-Hu-1 level along with moderate immune escape. Notably, real-world SARS-CoV-2 variants predominantly followed the latter trajectory, sustaining ACE2 affinity via fixed mutations. These findings underscore the heterogeneous, immune-contextualized nature of viral fitness dynamics and the complex evolutionary pathways of SARS-CoV-2.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1013582","type":"journal-article","created":{"date-parts":[[2026,1,12]],"date-time":"2026-01-12T18:40:47Z","timestamp":1768243247000},"page":"e1013582","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Characterization of the heterogeneity in SARS-CoV-2 fitness dynamics via graph representation learning"],"prefix":"10.1371","volume":"22","author":[{"given":"Zengmiao","family":"Wang","sequence":"first","affiliation":[]},{"given":"Ziqin","family":"Zhou","sequence":"additional","affiliation":[]},{"given":"Junfu","family":"Wang","sequence":"additional","affiliation":[]},{"given":"Lingyue","family":"Yang","sequence":"additional","affiliation":[]},{"given":"Zhirui","family":"Zhang","sequence":"additional","affiliation":[]},{"given":"Weina","family":"Xu","sequence":"additional","affiliation":[]},{"given":"Zeming","family":"Liu","sequence":"additional","affiliation":[]},{"given":"Yuxi","family":"Ge","sequence":"additional","affiliation":[]},{"given":"Liang","family":"Yang","sequence":"additional","affiliation":[]},{"given":"Xiaoli","family":"Wang","sequence":"additional","affiliation":[]},{"given":"Peng","family":"Yang","sequence":"additional","affiliation":[]},{"given":"Quanyi","family":"Wang","sequence":"additional","affiliation":[]},{"given":"Yunlong","family":"Cao","sequence":"additional","affiliation":[]},{"given":"Yuanfang","family":"Guo","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4466-0858","authenticated-orcid":true,"given":"Huaiyu","family":"Tian","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2026,1,12]]},"reference":[{"issue":"6","key":"pcbi.1013582.ref001","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"},{"issue":"3","key":"pcbi.1013582.ref002","first-page":"162","article-title":"SARS-CoV-2 variant biology: immune escape, transmission and fitness","volume":"21","author":"COVID-19 Genomics UK Consortium","year":"2023","journal-title":"Nat Rev Microbiol"},{"key":"pcbi.1013582.ref003","unstructured":"Clade and lineage nomenclature aids in genomic epidemiology studies of active hCoV-19 viruses. 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