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Ren H, Ling Y, Cao R, Wang Z, Li Y, Huang T. Early warning of emerging infectious diseases based on multimodal data. BIOSAFETY AND HEALTH 2023; 5:S2590-0536(23)00074-5. [PMID: 37362865 PMCID: PMC10245235 DOI: 10.1016/j.bsheal.2023.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/18/2023] [Accepted: 05/31/2023] [Indexed: 06/28/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has dramatically increased the awareness of emerging infectious diseases. The advancement of multiomics analysis technology has resulted in the development of several databases containing virus information. Several scientists have integrated existing data on viruses to construct phylogenetic trees and predict virus mutation and transmission in different ways, providing prospective technical support for epidemic prevention and control. This review summarized the databases of known emerging infectious viruses and techniques focusing on virus variant forecasting and early warning. It focuses on the multi-dimensional information integration and database construction of emerging infectious viruses, virus mutation spectrum construction and variant forecast model, analysis of the affinity between mutation antigen and the receptor, propagation model of virus dynamic evolution, and monitoring and early warning for variants. As people have suffered from COVID-19 and repeated flu outbreaks, we focused on the research results of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza viruses. This review comprehensively viewed the latest virus research and provided a reference for future virus prevention and control research.
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Affiliation(s)
- Haotian Ren
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yunchao Ling
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ruifang Cao
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhen Wang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yixue Li
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- Guangzhou Laboratory, Guangzhou 510005, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 200433, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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CNCB-NGDC Members and Partners, Xue Y, Bao Y, Zhang Z, Zhao W, Xiao J, He S, Zhang G, Li Y, Zhao G, Chen R, Ma Y, Chen M, Li C, Jiang S, Zou D, Gong Z, Zhao X, Wang Y, Zhu J, Zhang Z, Zhao W, Xue Y, Bao Y, Song S, Zhang G, Ling Y, Wang Y, Yang J, Zhuang X, Duan G, Wu G, Chen X, Tian D, Li Z, Sun Y, Du Z, Hao L, Song S, Gao Y, Xiao J, Zhang Z, Bao Y, Tang B, Zhao W, Zhang Y, Zhang H, Zhang Z, Qian Q, Zhang Z, Xiao J, Kang H, Huang T, Chen X, Xia Z, Zhou X, Chao J, Tang B, Wang Z, Zhu J, Du Z, Zhang S, Xiao J, Tian W, Wang W, Zhao W, Wu S, Huang Y, Zhang M, Gong Z, Wang G, Zheng X, Zong W, Zhao W, Xing P, Li R, Liu Z, Bao Y, Lu M, Zhang Y, Yang F, Mai J, Gao Q, Xu X, Kang H, Hou L, Shang Y, Qain Q, Liu J, Jiang M, Zhang H, Bu C, Wang J, Zhang Z, Zhang Z, Zeng J, Li J, Xiao J, Pan S, Kang H, et alCNCB-NGDC Members and Partners, Xue Y, Bao Y, Zhang Z, Zhao W, Xiao J, He S, Zhang G, Li Y, Zhao G, Chen R, Ma Y, Chen M, Li C, Jiang S, Zou D, Gong Z, Zhao X, Wang Y, Zhu J, Zhang Z, Zhao W, Xue Y, Bao Y, Song S, Zhang G, Ling Y, Wang Y, Yang J, Zhuang X, Duan G, Wu G, Chen X, Tian D, Li Z, Sun Y, Du Z, Hao L, Song S, Gao Y, Xiao J, Zhang Z, Bao Y, Tang B, Zhao W, Zhang Y, Zhang H, Zhang Z, Qian Q, Zhang Z, Xiao J, Kang H, Huang T, Chen X, Xia Z, Zhou X, Chao J, Tang B, Wang Z, Zhu J, Du Z, Zhang S, Xiao J, Tian W, Wang W, Zhao W, Wu S, Huang Y, Zhang M, Gong Z, Wang G, Zheng X, Zong W, Zhao W, Xing P, Li R, Liu Z, Bao Y, Lu M, Zhang Y, Yang F, Mai J, Gao Q, Xu X, Kang H, Hou L, Shang Y, Qain Q, Liu J, Jiang M, Zhang H, Bu C, Wang J, Zhang Z, Zhang Z, Zeng J, Li J, Xiao J, Pan S, Kang H, Liu X, Lin S, Yuan N, Zhang Z, Bao Y, Jia P, Zheng X, Zong W, Li Z, Sun Y, Ma Y, Xiong Z, Wu S, Yang F, Zhao W, Bu C, Du Z, Xiao J, Bao Y, Chen X, Chen T, Zhang S, Sun Y, Yu C, Tang B, Zhu J, Dong L, Zhai S, Sun Y, Chen Q, Yang X, Zhang X, Sang Z, Wang Y, Zhao Y, Chen H, Lan L, Wang Y, Zhao W, Wang A, Yu C, Wang Y, Zhang S, Ma Y, Jia Y, Zhao X, Chen M, Li C, Tian D, Tang B, Pan Y, Dong L, Liu X, Song S, Liu X, Tian D, Li C, Tang B, Wang Z, Zhang R, Pan Y, Wang Y, Zou D, Song S, Li C, Zou D, Ma L, Gong Z, Zhu J, Teng X, Li L, Li N, Cui Y, Duan G, Zhang M, Jin T, Kang H, Wang Z, Wu G, Huang T, Zhao W, Jin E, Zhang T, Zhang Z, Zhao W, Xue Y, Bao Y, Song S, Xu T, Zou D, Chen M, Niu G, Pan R, Zhu T, Chu Y, Hao L, Sang J, Pan R, Zou D, Zhang Y, Wang Z, Chen M, Zhang Y, Xu T, Yao Q, Zhu T, Niu G, Hao L, Xiong Z, Yang F, Wang G, Li R, Zong W, Zhang M, Zou D, Zhao W, Wang G, Yang F, Wu S, Zhang X, Guo X, Ma Y, Xiong Z, Li R, Li Z, Liu L, Feng C, Qin Y, Xiao J, Ma L, Jing W, Luo S, Li Z, Ma L, Jiang S, Qian Q, Zhu T, Zong W, Shang Y, Jin T, Zhang Y, Chen M, Wu Z, Chu Y, Zhang R, Luo S, Jing W, Zou D, Bao Y, Xiao J, Zhang Z, Zou D, Liu L, Qin Y, Luo S, Jing W, Li Q, Liu P, Sun Y, Ma L, Jiang S, Fan Z, Zhao W, Xiao J, Bao Y, Zhang Z, Shen WK, Guo AY, Zuo Z, Ren J, Zhang X, Xiao Y, Li X, Zhang X, Xiao Y, Li X, Liu D, Zhang C, Xue Y, Zhao Z, Jiang T, Wu W, Zhao F, Meng X, Chen M, Gou Y, Chen M, Xue Y, Peng D, Xue Y, Luo H, Gao F, Ning W, Xue Y, Liu W, Ling Y, Cao R, Zhang G, Wei Y, Xue Y, Liu CJ, Guo AY, Xie GY, Guo AY, Yuan H, Su T, Zhang YE, Zhou C, Wang P, Zhang G, Zhou Y, Chen M, Guo G, Zhang Q, Guo AY, Fu S, Tan X, Xue Y, Tang D, Xue Y, Zhang W, Xue Y, Luo M, Guo AY, Xie Y, Ren J, Miao YR, Guo AY, Zhou Y, Chen M, Guo G, Huang X, Feng Z, Xue Y, Liu CJ, Guo AY, Liao X, Gao X, Wang J, Xie G, Guo AY, Yuan C, Chen M, Yang D, Tian F, Gao G, Wu W, Chen M, Han C, Xue Y, Cui Q, Xiao C, Li CY, Luo X, Ren J, Zhang X, Xiao Y, Li X, Tang Q, Guo AY, Luo H, Gao F, Xue Y, Bao Y, Zhang Z, Zhao W, Xiao J, He S, Zhang G, Li Y, Zhao G, Chen R. Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2023. Nucleic Acids Res 2023; 51:D18-D28. [PMID: 36420893 PMCID: PMC9825504 DOI: 10.1093/nar/gkac1073] [Show More Authors] [Citation(s) in RCA: 97] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/14/2022] [Accepted: 10/27/2022] [Indexed: 11/27/2022] Open
Abstract
The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a family of database resources to support global academic and industrial communities. With the explosive accumulation of multi-omics data generated at an unprecedented rate, CNCB-NGDC constantly expands and updates core database resources by big data archive, integrative analysis and value-added curation. In the past year, efforts have been devoted to integrating multiple omics data, synthesizing the growing knowledge, developing new resources and upgrading a set of major resources. Particularly, several database resources are newly developed for infectious diseases and microbiology (MPoxVR, KGCoV, ProPan), cancer-trait association (ASCancer Atlas, TWAS Atlas, Brain Catalog, CCAS) as well as tropical plants (TCOD). Importantly, given the global health threat caused by monkeypox virus and SARS-CoV-2, CNCB-NGDC has newly constructed the monkeypox virus resource, along with frequent updates of SARS-CoV-2 genome sequences, variants as well as haplotypes. All the resources and services are publicly accessible at https://ngdc.cncb.ac.cn.
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