{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T00:41:53Z","timestamp":1791333713655,"version":"4.3.1"},"reference-count":39,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2022,11,2]],"date-time":"2022-11-02T00:00:00Z","timestamp":1667347200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100006190","name":"Research and Development","doi-asserted-by":"publisher","award":["2021YFC2302003"],"award-info":[{"award-number":["2021YFC2302003"]}],"id":[{"id":"10.13039\/100006190","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>Human coronaviruses (HCoVs) HCoV-NL63, HCoV-229E, HCoV-HKU1 and HCoV-OC43 have been circulated in the human population worldwide, and they are associated with a broad range of respiratory diseases with varying severity. However, there are neither effective therapeutic drugs nor licensed vaccines available for the treatment and prevention of infections by the four HCoVs. In this study, we collected nasopharyngeal aspirates of children hospitalized for respiratory tract infection in China during 2014\u20132018 and conducted next-generation sequencing. Sequences of four HCoVs were then selected for an in-depth analysis. Genome sequences of 2 HCoV-NL63, 8 HCoV-229E, 2 HCoV-HKU1, and 6 HCoV-OC43 were obtained. Based on the full-length <jats:italic>S<\/jats:italic> gene, a strong temporal signal was found in HCoV-229E and the molecular evolutionary rate was 6\u2009\u00d7\u200910<jats:sup>\u22124<\/jats:sup> substitutions\/site\/year. Based on the maximum-likelihood (ML) phylogenetic tree of complete <jats:italic>S<\/jats:italic> gene, we designated H78 as a new sub-genotype C2 of HCoV-HKU1, and the obtained P43 sequence was grouped into the reported novel genotype K of HCoV-OC43 circulating in Guangzhou, China. Based on the complete genome, potential recombination events were found to occur as two phenomena, namely intraspecies and interspecies. Moreover, we observed two amino acid substitutions in the S1 subunit of obtained HCoV-NL63 (G534V) and HCoV-HKU1 (H512R), while residues 534 and 512 are important for the binding of angiotensin-converting enzyme 2 and neutralizing antibodies, respectively. Our findings might provide a clue for the molecular evolution of the four HCoVs and help in the early diagnosis, treatment and prevention of broad-spectrum HCoV infection.<\/jats:p>","DOI":"10.3389\/fmicb.2022.1023847","type":"journal-article","created":{"date-parts":[[2022,11,2]],"date-time":"2022-11-02T05:47:20Z","timestamp":1667368040000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":34,"title":["Molecular evolution of human coronavirus-NL63, -229E, -HKU1 and -OC43 in hospitalized children in China"],"prefix":"10.3389","volume":"13","author":[{"given":"Nan","family":"Shao","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chi","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jie","family":"Dong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lilian","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiangpeng","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhengde","family":"Xie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Baoping","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuhua","family":"An","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ting","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fan","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2022,11,2]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"1058","DOI":"10.4269\/ajtmh.15-0810","article-title":"Diversity and evolutionary histories of human coronaviruses NL63 and 229E associated with acute upper respiratory tract symptoms in Kuala Lumpur, Malaysia","volume":"94","author":"Al-Khannaq","year":"2016","journal-title":"Am J Trop Med Hyg"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"2157","DOI":"10.1093\/molbev\/mss084","article-title":"Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty","volume":"29","author":"Baele","year":"2012","journal-title":"Mol. 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