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Briefings in bioinformatics
03 10, 2022;23 (2):

Coronavirus GenBrowser for monitoring the transmission and evolution of SARS-CoV-2.

Dalang Yu, Xiao Yang, Bixia Tang, Yi-Hsuan Pan, Jianing Yang, Guangya Duan, Junwei Zhu, Zi-Qian Hao, Hailong Mu, Long Dai, Wangjie Hu, Mochen Zhang, Ying Cui, Tong Jin, Cui-Ping Li, Lina Ma, Language translation team, Xiao Su, Guoqing Zhang, Wenming Zhao, Haipeng Li
Author Information
  1. Dalang Yu: 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.
  2. Xiao Yang: 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.
  3. Bixia Tang: National Genomics Data Center, Beijing Institute of Genomics (China National Center for Bioinformation), Chinese Academy of Sciences, Beijing 100101, China.
  4. Yi-Hsuan Pan: Key Laboratory of Brain Functional Genomics of Ministry of Education, School of Life Science, East China Normal University, Shanghai 200062, China.
  5. Jianing Yang: 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.
  6. Guangya Duan: National Genomics Data Center, Beijing Institute of Genomics (China National Center for Bioinformation), Chinese Academy of Sciences, Beijing 100101, China.
  7. Junwei Zhu: National Genomics Data Center, Beijing Institute of Genomics (China National Center for Bioinformation), Chinese Academy of Sciences, Beijing 100101, China.
  8. Zi-Qian Hao: 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.
  9. Hailong Mu: 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.
  10. Long Dai: 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.
  11. Wangjie Hu: 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.
  12. Mochen Zhang: National Genomics Data Center, Beijing Institute of Genomics (China National Center for Bioinformation), Chinese Academy of Sciences, Beijing 100101, China.
  13. Ying Cui: National Genomics Data Center, Beijing Institute of Genomics (China National Center for Bioinformation), Chinese Academy of Sciences, Beijing 100101, China.
  14. Tong Jin: National Genomics Data Center, Beijing Institute of Genomics (China National Center for Bioinformation), Chinese Academy of Sciences, Beijing 100101, China.
  15. Cui-Ping Li: National Genomics Data Center, Beijing Institute of Genomics (China National Center for Bioinformation), Chinese Academy of Sciences, Beijing 100101, China.
  16. Lina Ma: National Genomics Data Center, Beijing Institute of Genomics (China National Center for Bioinformation), Chinese Academy of Sciences, Beijing 100101, China.
  17. Xiao Su: Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China.
  18. Guoqing Zhang: 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.
  19. Wenming Zhao: National Genomics Data Center, Beijing Institute of Genomics (China National Center for Bioinformation), Chinese Academy of Sciences, Beijing 100101, China.
  20. Haipeng Li: 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. ORCID
PMID: 35043153 DOI: 10.1093/bib/bbab583

Abstract

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.

Keywords

SARS-CoV-2 coronavirus GenBrowser evolution genomic epidemiology transmission

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Grants

  1. 2020YFC084-7000/National Key Research and Development Project of China
  2. XDB38030100/Chinese Academy of Sciences
  3. 2017SHZDZX01/Shanghai Municipal Science and Technology Major Project
  4. JBGSRWBD-SINH-2021-10/Shanghai Institute of Nutrition and Health

MeSH Term

COVID-19
Computational Biology
DNA Mutational Analysis
Databases, Genetic
Genome, Viral
Genomics
Humans
Molecular Epidemiology
Molecular Sequence Annotation
Mutation
Public Health Surveillance
SARS-CoV-2
Software
Web Browser
Journal Article Research Support, Non-U.S. Gov't

Links to CNCB-NGDC Resources

Database Commons: DBC007545 (CGB)

Word Cloud

Created with Highcharts 10.0.0SARS-CoV-2genomicsequencestransmissionevolutionGenBrowserCGBdataepidemiologyimportantcoronavirusCoronavirushighlyefficientexploreevolutionarycanalsoGenomicstudyCOVID-19pandemictwomillionsevereacuterespiratorysyndrome2depositedpublicdatabasesHoweverexponentialincreaseinvokesunprecedentedbioinformaticchallengespresentbasedanalysisframeworknode-pickingrenderingstrategytotal1002739high-qualitytransmission-relatedmetadataanalyzedvisualizedsizecorefile1220MBcleansharingQuickvisualizationmodulesrichinteractiveoperationsprovidedannotatedtreebinarynomenclatureproposednameinternallineagepre-analyzedfilteredaccordinguser-definedcriteriaDifferentanalyseseasilyperformeddetectionacceleratedongoingpositiveselectionMoreover75spotsconservednon-conservedcoronavirusesidentifiedmayindicatefunctionalelementsspecificallywrittenJavaJavaScriptenablesusersprogrammingskillsanalyzemillionsofferspanoramicvisionmonitoring

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