{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T08:54:11Z","timestamp":1778057651829,"version":"3.51.4"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2022,1,19]],"date-time":"2022-01-19T00:00:00Z","timestamp":1642550400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"National Key Research and Development Project of China","award":["2020YFC084-7000"],"award-info":[{"award-number":["2020YFC084-7000"]}]},{"DOI":"10.13039\/501100002367","name":"Chinese Academy of Sciences","doi-asserted-by":"publisher","award":["XDB38030100"],"award-info":[{"award-number":["XDB38030100"]}],"id":[{"id":"10.13039\/501100002367","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shanghai Municipal Science and Technology Major Project","award":["2017SHZDZX01"],"award-info":[{"award-number":["2017SHZDZX01"]}]},{"name":"Shanghai Institute of Nutrition and Health","award":["JBGSRWBD-SINH-2021-10"],"award-info":[{"award-number":["JBGSRWBD-SINH-2021-10"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,3,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Genomic epidemiology is important to study the COVID-19 pandemic, and more than two million severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic sequences were deposited into public databases. However, the exponential increase of sequences invokes unprecedented bioinformatic challenges. Here, we present the Coronavirus GenBrowser (CGB) based on a highly efficient analysis framework and a node-picking rendering strategy. In total, 1,002,739 high-quality genomic sequences with the transmission-related metadata were analyzed and visualized. The size of the core data file is only 12.20 MB, highly efficient for clean data sharing. Quick visualization modules and rich interactive operations are provided to explore the annotated SARS-CoV-2 evolutionary tree. CGB binary nomenclature is proposed to name each internal lineage. The pre-analyzed data can be filtered out according to the user-defined criteria to explore the transmission of SARS-CoV-2. Different evolutionary analyses can also be easily performed, such as the detection of accelerated evolution and ongoing positive selection. Moreover, the 75 genomic spots conserved in SARS-CoV-2 but non-conserved in other coronaviruses were identified, which may indicate the functional elements specifically important for SARS-CoV-2. The CGB was written in Java and JavaScript. It not only enables users who have no programming skills to analyze millions of genomic sequences, but also offers a panoramic vision of the transmission and evolution of SARS-CoV-2.<\/jats:p>","DOI":"10.1093\/bib\/bbab583","type":"journal-article","created":{"date-parts":[[2021,12,21]],"date-time":"2021-12-21T07:09:05Z","timestamp":1640070545000},"source":"Crossref","is-referenced-by-count":23,"title":["Coronavirus GenBrowser for monitoring the transmission and evolution of SARS-CoV-2"],"prefix":"10.1093","volume":"23","author":[{"given":"Dalang","family":"Yu","sequence":"first","affiliation":[{"name":"National Genomics Data Center, Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China"},{"name":"University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China"}]},{"given":"Xiao","family":"Yang","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China"},{"name":"Shanghai Shenyou Biotechnology Co. LTD, Shanghai 201315, China"}]},{"given":"Bixia","family":"Tang","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics (China National Center for Bioinformation), Chinese Academy of Sciences, Beijing 100101, China"}]},{"given":"Yi-Hsuan","family":"Pan","sequence":"additional","affiliation":[{"name":"Key Laboratory of Brain Functional Genomics of Ministry of Education, School of Life Science, East China Normal University, Shanghai 200062, China"}]},{"given":"Jianing","family":"Yang","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China"},{"name":"University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China"}]},{"given":"Guangya","family":"Duan","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics (China National Center for Bioinformation), Chinese Academy of Sciences, Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China"}]},{"given":"Junwei","family":"Zhu","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics (China National Center for Bioinformation), Chinese Academy of Sciences, Beijing 100101, China"}]},{"given":"Zi-Qian","family":"Hao","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China"},{"name":"University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China"}]},{"given":"Hailong","family":"Mu","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China"}]},{"given":"Long","family":"Dai","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China"},{"name":"Shanghai Shenyou Biotechnology Co. LTD, Shanghai 201315, China"}]},{"given":"Wangjie","family":"Hu","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China"},{"name":"University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China"}]},{"given":"Mochen","family":"Zhang","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics (China National Center for Bioinformation), Chinese Academy of Sciences, Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China"}]},{"given":"Ying","family":"Cui","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics (China National Center for Bioinformation), Chinese Academy of Sciences, Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China"}]},{"given":"Tong","family":"Jin","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics (China National Center for Bioinformation), Chinese Academy of Sciences, Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China"}]},{"given":"Cui-Ping","family":"Li","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics (China National Center for Bioinformation), Chinese Academy of Sciences, Beijing 100101, China"}]},{"given":"Lina","family":"Ma","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics (China National Center for Bioinformation), Chinese Academy of Sciences, Beijing 100101, China"}]},{"name":"Language translation team","sequence":"additional","affiliation":[]},{"given":"Xiao","family":"Su","sequence":"additional","affiliation":[{"name":"Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China"}]},{"given":"Guoqing","family":"Zhang","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China"},{"name":"University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China"}]},{"given":"Wenming","family":"Zhao","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics (China National Center for Bioinformation), Chinese Academy of Sciences, Beijing 100101, China"},{"name":"University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7856-4488","authenticated-orcid":false,"given":"Haipeng","family":"Li","sequence":"additional","affiliation":[{"name":"National Genomics Data Center, Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China"},{"name":"University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China"}]}],"member":"286","published-online":{"date-parts":[[2022,1,19]]},"reference":[{"key":"2022031506295918700_ref1","doi-asserted-by":"crossref","first-page":"987","DOI":"10.1126\/science.1176297","article-title":"Epidemic science in real time","volume":"324","author":"Fineberg","year":"2009","journal-title":"Science"},{"key":"2022031506295918700_ref2","doi-asserted-by":"crossref","first-page":"247","DOI":"10.24272\/j.issn.2095-8137.2020.022","article-title":"Decoding the evolution and transmissions of the novel pneumonia 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