RCoV19: A One-stop Hub for SARS-CoV-2 Genome Data Integration, Variant Monitoring, and Risk Pre-warning.

Cuiping Li, Lina Ma, Dong Zou, Rongqin Zhang, Xue Bai, Lun Li, Gangao Wu, Tianhao Huang, Wei Zhao, Enhui Jin, Yiming Bao, Shuhui Song
Author Information
  1. Cuiping Li: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  2. Lina Ma: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
  3. Dong Zou: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  4. Rongqin Zhang: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China.
  5. Xue Bai: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  6. Lun Li: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China.
  7. Gangao Wu: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
  8. Tianhao Huang: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
  9. Wei Zhao: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
  10. Enhui Jin: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
  11. Yiming Bao: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: baoym@big.ac.cn.
  12. Shuhui Song: National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: songshh@big.ac.cn.

Abstract

The Resource for Coronavirus 2019 (RCoV19) is an open-access information resource dedicated to providing valuable data on the genomes, mutations, and variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this updated implementation of RCoV19, we have made significant improvements and advancements over the previous version. Firstly, we have implemented a highly refined genome data curation model. This model now features an automated integration pipeline and optimized curation rules, enabling efficient daily updates of data in RCoV19. Secondly, we have developed a global and regional lineage evolution monitoring platform, alongside an outbreak risk pre-warning system. These additions provide a comprehensive understanding of SARS-CoV-2 evolution and transmission patterns, enabling better preparedness and response strategies. Thirdly, we have developed a powerful interactive mutation spectrum comparison module. This module allows users to compare and analyze mutation patterns, assisting in the detection of potential new lineages. Furthermore, we have incorporated a comprehensive knowledgebase on mutation effects. This knowledgebase serves as a valuable resource for retrieving information on the functional implications of specific mutations. In summary, RCoV19 serves as a vital scientific resource, providing access to valuable data, relevant information, and technical support in the global fight against COVID-19. The complete contents of RCoV19 are available to the public at https://ngdc.cncb.ac.cn/ncov/.

Keywords

References

  1. Lancet Infect Dis. 2021 May;21(5):602 [PMID: 33571446]
  2. Yi Chuan. 2020 Feb 20;42(2):212-221 [PMID: 32102777]
  3. Nat Immunol. 2021 Jan;22(1):74-85 [PMID: 32999467]
  4. Cell Host Microbe. 2021 Dec 8;29(12):1788-1801.e6 [PMID: 34822776]
  5. Virus Evol. 2021 Jul 30;7(2):veab064 [PMID: 34527285]
  6. Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42 [PMID: 23193287]
  7. Virus Evol. 2022 Mar 18;8(1):veac023 [PMID: 35502202]
  8. Bioinformatics. 2023 Sep 2;39(9): [PMID: 37651464]
  9. Nat Immunol. 2020 Nov;21(11):1336-1345 [PMID: 32887977]
  10. Nucleic Acids Res. 2004 Mar 19;32(5):1792-7 [PMID: 15034147]
  11. Nat Microbiol. 2020 Nov;5(11):1403-1407 [PMID: 32669681]
  12. Brief Bioinform. 2023 Jan 19;24(1): [PMID: 36567622]
  13. Yi Chuan. 2020 Aug 20;42(8):799-809 [PMID: 32952115]
  14. Nucleic Acids Res. 2021 Jan 8;49(D1):D817-D824 [PMID: 33045721]
  15. J Clin Virol. 2022 Dec;157:105323 [PMID: 36334368]
  16. Genomics Proteomics Bioinformatics. 2020 Dec;18(6):640-647 [PMID: 32663617]
  17. China CDC Wkly. 2021 Dec 3;3(49):1049-1051 [PMID: 34934514]
  18. Nat Methods. 2023 Apr;20(4):512-522 [PMID: 36823332]
  19. Nucleic Acids Res. 2019 Jan 8;47(D1):D637-D648 [PMID: 30365027]
  20. Bioinformatics. 2022 Mar 4;38(6):1735-1737 [PMID: 34954792]
  21. J Med Virol. 2022 Mar;94(3):847-857 [PMID: 34609003]
  22. BMC Genom Data. 2022 May 4;23(1):34 [PMID: 35508965]
  23. iScience. 2021 Nov 19;24(11):103353 [PMID: 34729465]
  24. Bioinformatics. 2023 Jan 1;39(1): [PMID: 36342236]
  25. Bioinformatics. 2022 Mar 28;38(7):1988-1994 [PMID: 35040923]
  26. Bioinformatics. 2018 Dec 1;34(23):4121-4123 [PMID: 29790939]
  27. Brief Bioinform. 2023 May 19;24(3): [PMID: 37170752]
  28. Genomics Proteomics Bioinformatics. 2020 Dec;18(6):749-759 [PMID: 33704069]
  29. Mol Biol Evol. 2018 Jan 1;35(1):247-251 [PMID: 29029186]
  30. Nature. 2022 Sep;609(7929):994-997 [PMID: 35952714]
  31. Cell Mol Immunol. 2022 Nov;19(11):1302-1310 [PMID: 36224497]
  32. Virus Evol. 2020 Apr 12;7(1):veaa087 [PMID: 33936774]
  33. Gigascience. 2022 Dec 28;12: [PMID: 37222749]
  34. J Clin Med. 2021 Jun 15;10(12): [PMID: 34203844]
  35. Elife. 2021 Feb 23;10: [PMID: 33620031]
  36. PLoS One. 2022 Mar 9;17(3):e0261045 [PMID: 35263335]
  37. Nucleic Acids Res. 2015 Jan;43(Database issue):D571-7 [PMID: 25428358]
  38. Science. 2022 Jun 17;376(6599):1327-1332 [PMID: 35608456]
  39. Wellcome Open Res. 2021 May 19;6:121 [PMID: 34095513]
  40. Front Public Health. 2022 Jul 04;10:915363 [PMID: 35859775]
  41. Front Med (Lausanne). 2022 Feb 22;9:815389 [PMID: 35273977]
  42. Nucleic Acids Res. 2022 Jan 7;50(D1):D888-D897 [PMID: 34634813]

MeSH Term

Humans
SARS-CoV-2
COVID-19
Knowledge Bases
Mutation

Word Cloud