{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T18:19:00Z","timestamp":1790014740980,"version":"4.0.1"},"reference-count":30,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2025,9,18]],"date-time":"2025-09-18T00:00:00Z","timestamp":1758153600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Hangzhou Medical and Health Science and Technology Project","award":["A20200487"],"award-info":[{"award-number":["A20200487"]}]},{"name":"Hangzhou Medical and Health Science and Technology Project","award":["2024ZY01026"],"award-info":[{"award-number":["2024ZY01026"]}]},{"name":"Hangzhou Medical and Health Science and Technology Project","award":["2025HZGF13"],"award-info":[{"award-number":["2025HZGF13"]}]},{"name":"Zhejiang Provincial Key Laboratory Construction Project","award":["A20200487"],"award-info":[{"award-number":["A20200487"]}]},{"name":"Zhejiang Provincial Key Laboratory Construction Project","award":["2024ZY01026"],"award-info":[{"award-number":["2024ZY01026"]}]},{"name":"Zhejiang Provincial Key Laboratory Construction Project","award":["2025HZGF13"],"award-info":[{"award-number":["2025HZGF13"]}]},{"name":"Construction Fund of Key Medical Disciplines of Hangzhou","award":["A20200487"],"award-info":[{"award-number":["A20200487"]}]},{"name":"Construction Fund of Key Medical Disciplines of Hangzhou","award":["2024ZY01026"],"award-info":[{"award-number":["2024ZY01026"]}]},{"name":"Construction Fund of Key Medical Disciplines of Hangzhou","award":["2025HZGF13"],"award-info":[{"award-number":["2025HZGF13"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Knowledge gaps exist on whether SARS-CoV-2 co-infection alters recombination frequency or induces phylogenetic incongruities in endemic \u03b2-coronaviruses (HCoV-OC43, HCoV-HKU1), limiting our understanding of cross-species evolution. Among 7213 COVID-19 and 1590 non-COVID-19 acute respiratory cases (2021\u20132022) screened via multiplex PCR, \u03b2-coronavirus co-infections (SARS-CoV-2 + HCoV-OC43\/HKU1) and single HCoV-OC43\/HKU1 infections were identified. Whole-genome sequencing (Illumina NovaSeq) was performed. Phylogenies were reconstructed using Bayesian inference (MrBayes). Recombination was assessed via Bootscan analysis (SimPlot). Co-infection prevalence was low (0.51%, mainly HCoV-HKU1: 0.28%, HCoV-OC43: 0.11%). HCoV-OC43 diverged into lineage 1 (genotype K) and a novel recombinant lineage 2 (genotypes F\/J\/G\/I segments), exhibiting accelerated evolution. HCoV-HKU1 remained genetically stable (genotype B). Co-infection status did not influence evolutionary outcomes. While SARS-CoV-2 co-infection may favor transmission of endemic HCoVs, their evolution appears driven by population-level selection, not co-infection. HCoV-OC43 underwent recombination-driven diversification, contrasting sharply with HCoV-HKU1\u2019s stasis, highlighting distinct evolutionary strategies. Integrated genomic and clinical surveillance is critical for tracking coronavirus adaptation.<\/jats:p>","DOI":"10.3390\/v17091263","type":"journal-article","created":{"date-parts":[[2025,9,18]],"date-time":"2025-09-18T14:45:46Z","timestamp":1758206746000},"page":"1263","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Neutral Impact of SARS-CoV-2 Coinfection on the Recombination-Driven Evolution of Endemic HCoV-OC43"],"prefix":"10.3390","volume":"17","author":[{"given":"Xueling","family":"Zheng","sequence":"first","affiliation":[{"name":"Hangzhou Center for Disease Control and Prevention (Hangzhou Health Supervision Institution), Hangzhou 310002, China"},{"name":"Zhejiang Key Laboratory of Multi-Omics in Infection and Immunity, Hangzhou 310002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yinyan","family":"Zhou","sequence":"additional","affiliation":[{"name":"Hangzhou Center for Disease Control and Prevention (Hangzhou Health Supervision Institution), Hangzhou 310002, China"},{"name":"Zhejiang Key Laboratory of Multi-Omics in Infection and Immunity, Hangzhou 310002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-6614-6086","authenticated-orcid":false,"given":"Yue","family":"Yu","sequence":"additional","affiliation":[{"name":"Hangzhou Center for Disease Control and Prevention (Hangzhou Health Supervision Institution), Hangzhou 310002, China"},{"name":"Zhejiang Key Laboratory of Multi-Omics in Infection and Immunity, Hangzhou 310002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shi","family":"Cheng","sequence":"additional","affiliation":[{"name":"Hangzhou Center for Disease Control and Prevention (Hangzhou Health Supervision Institution), Hangzhou 310002, China"},{"name":"Zhejiang Key Laboratory of Multi-Omics in Infection and Immunity, Hangzhou 310002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feifei","family":"Cao","sequence":"additional","affiliation":[{"name":"Hangzhou Center for Disease Control and Prevention (Hangzhou Health Supervision Institution), Hangzhou 310002, China"},{"name":"Zhejiang Key Laboratory of Multi-Omics in Infection and Immunity, Hangzhou 310002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhou","family":"Sun","sequence":"additional","affiliation":[{"name":"Zhejiang Key Laboratory of Multi-Omics in Infection and Immunity, Hangzhou 310002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Li","sequence":"additional","affiliation":[{"name":"Hangzhou Center for Disease Control and Prevention (Hangzhou Health Supervision Institution), Hangzhou 310002, China"},{"name":"Zhejiang Key Laboratory of Multi-Omics in Infection and Immunity, Hangzhou 310002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinfen","family":"Yu","sequence":"additional","affiliation":[{"name":"Hangzhou Center for Disease Control and Prevention (Hangzhou Health Supervision Institution), Hangzhou 310002, China"},{"name":"Zhejiang Key Laboratory of Multi-Omics in Infection and Immunity, Hangzhou 310002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,9,18]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"105246","DOI":"10.1016\/j.jcv.2022.105246","article-title":"Human coronaviruses: Origin, host and receptor","volume":"155","author":"Tang","year":"2022","journal-title":"J. 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