The 2019 novel coronavirus resource

Wenming Zhao, Shuhui Song, Meili Chen, Dong Zou, Lina Ma, Yingke Ma, Rujiao Li, Lili Hao, Cuiping Li, Dongmei Tian, Bixia Tang, Yanqing Wang, Junwei Zhu, Huanxin Chen, Zhang Zhang, Yongbiao Xue, Yiming Bao

doi:10.16288/j.yczz.20-030

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Hereditas(Beijing) >

2020 , Vol. 42 >Issue 2: 212 - 221

DOI: https://doi.org/10.16288/j.yczz.20-030

Resource and Platform

The 2019 novel coronavirus resource

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^1. China National Center for Bioinformation & National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China;
^2. CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
^3. University of Chinese Academy of Sciences, Beijing 100049, China

Received date: 2020-01-31

Revised date: 2020-02-07

Online published: 2020-02-08

Supported by

the National Key Research & Development Program of China(2016YFE0206600);the National Key Research & Development Program of China(2017YFC1201202);13th Five-year Informatization Plan of CAS(XXH13505-05);Strategic Priority Research Program of the Chines Academy of Sciences (CAS)(XDA19050302);Capacity building project of genome science data center of Chinese Academy of Sciences(0202);Key Technology Talent Program of the CAS, The Youth Innovation Promotion Association of Chinese Academy of Sciences

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Abstract

An ongoing outbreak of a novel coronavirus infection in Wuhan, China since December 2019 has led to 31,516 infected persons and 638 deaths across 25 countries (till 16:00 on February 7, 2020). The virus causing this pneumonia was then named as the 2019 novel coronavirus (2019-nCoV) by the World Health Organization. To promote the data sharing and make all relevant information of 2019-nCoV publicly available, we construct the 2019 Novel Coronavirus Resource (2019nCoVR, https://bigd.big.ac.cn/ncov). 2019nCoVR features comprehensive integration of genomic and proteomic sequences as well as their metadata information from the Global Initiative on Sharing All Influenza Data, National Center for Biotechnology Information, China National GeneBank, National Microbiology Data Center and China National Center for Bioinformation (CNCB)/National Genomics Data Center (NGDC). It also incorporates a wide range of relevant information including scientific literatures, news, and popular articles for science dissemination, and provides visualization functionalities for genome variation analysis results based on all collected 2019-nCoV strains. Moreover, by linking seamlessly with related databases in CNCB/NGDC, 2019nCoVR offers virus data submission and sharing services for raw sequence reads and assembled sequences. In this report, we provide comprehensive descriptions on data deposition, management, release and utility in 2019nCoVR, laying important foundations in aid of studies on virus classification and origin, genome variation and evolution, fast detection, drug development and pneumonia precision prevention and therapy.

Key words： 2019nCoVR; 2019 novel coronavirus; China National Center for Bioinformation (CNCB); National Genomics Data Center (NGDC); genomic data sharing

Cite this article

Wenming Zhao, Shuhui Song, Meili Chen, Dong Zou, Lina Ma, Yingke Ma, Rujiao Li, Lili Hao, Cuiping Li, Dongmei Tian, Bixia Tang, Yanqing Wang, Junwei Zhu, Huanxin Chen, Zhang Zhang, Yongbiao Xue, Yiming Bao . The 2019 novel coronavirus resource[J]. Hereditas(Beijing), 2020 , 42(2) : 212 -221 . DOI: 10.16288/j.yczz.20-030

References

[1]	WHO. Novel Coronavirus (2019-nCoV). https://www.who.int/emergencies/diseases/novel-coronavirus-2019, 2020.
[2]	Xu XT, Chen P, Wang JF, Feng JN, Zhou H, Li X, Zhong W, Hao P . Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission. Sci China Life Sci, 2020, doi: 10.1007/s11427-020-1637-5.
[3]	Zhou P, Yang XL, Wang XG, Hu B, Zhang L, Zhang W, Si HR, Zhu Y, Li B, Huang CL, Chen HD, Chen J, Luo Y, Guo H, Jiang RD, Liu MQ, Chen Y, Shen XR, Wang X, Zheng XS, Zhao K, Chen QJ, Deng F, Liu LL, Yan B, Zhan FX, Wang YY, Xiao GF, Shi ZL . Discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin. bioRxiv, 2020, doi: 10.1101/2020.01.22.914952.
[4]	Ji W, Wang W, Zhao XF, Zai JJ, Li XG . Homologous recombination within the spike glycoprotein of the newly identified coronavirus may boost cross-species transmission from snake to human. J Med Virol, 2020, doi: 10.1002/jmv.25682.
[5]	Dong N, Yang XM, Ye LW, Chen KC, Chan EWC, Yang MS, Chen S . Genomic and protein structure modelling analysis depicts the origin and infectivity of 2019-nCoV, a new coronavirus which caused a pneumonia outbreak in Wuhan, China. bioRxiv, 2020, doi: 10.1101/2020.01.20. 913368.
[6]	Benvenuto D, Giovanetti M, Ciccozzi A, Spoto S, Angeletti S, Ciccozzi M . The 2019-new Coronavirus epidemic: evidence for virus evolution. J Med Virol, 2020, doi: 10.1101/2020.01.24.915157.
[7]	Chen JY, Shi JS, Qiu DA, Liu C, Li X, Zhao Q, Ruan JS, Gao S . Bioinformatics analysis of the Wuhan 2019 human coronavirus genome. Chin J Bio, 2020, doi: 10.12113/ 202001007.
[7]	陈嘉源, 施劲松, 丘栋安, 刘畅, 李鑫, 赵强, 阮吉寿, 高山 . 武汉2019冠状病毒基因组的生物信息学分析. 生物信息学, 2020, doi: 10.12113/202001007.
[8]	Heymann DL . Data sharing and outbreaks: best practice exemplified. Lancet, 2020, doi: 10.1016/S0140-6736(20)30184-7.
[9]	Munster VJ , Koopmans M, van Doremalen N, van Riel D, de Wit E. A novel coronavirus emerging in China - key questions for impact assessment. N Engl J Med, 2020, doi: 10.1056/NEJMp2000929.
[10]	Sayers EW, Beck J, Brister JR, Bolton EE, Canese K, Comeau DC, Funk K, Ketter A, Kim S, Kimchi A, Kitts PA, Kuznetsov A, Lathrop S, Lu Z , McGarvey K, Madden TL, Murphy TD, O'Leary N, Phan L, Schneider VA, Thibaud-Nissen F, Trawick BW, Pruitt KD, Ostell J. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res, 2020,48:D9-D16.
[11]	Shu YL , McCauley J. GISAID: Global initiative on sharing all influenza data-from vision to reality. Euro Surveill, 2017,22(13):30494.
[12]	Wang B, Liu F, Zhang EC, Wo CL, Chen J, Qian PY, Lu HR, Zeng WJ, Chen T, Wei JP, Wan Q, Wang R, Xu X . The China National GeneBank—owned by all, completed by all and shared by all. Hereditas(Beijing), 2019,41(8):761-772.
[12]	王博, 刘芳, 张二春, 沃晨亮, 陈振家, 钱璞毅, 卢浩荣, 曾文君, 陈泰, 危金普, 万仟, 王韧, 徐讯 . 国家基因库: 共有、共为、共享. 遗传, 2019,41(8):761-72.
[13]	Wu LH, Sun QL, Desmeth P, Sugawara H, Xu ZH , McCluskey K, Smith D, Alexander V, Lima N, Ohkuma M, Robert V, Zhou YG, Li JH, Fan GM, Ingsriswang S, Ozerskaya S, Ma JC. World data centre for microorganisms: an information infrastructure to explore and utilize preserved microbial strains worldwide. Nucleic Acids Res, 2017,45(D1):D611-D618.
[14]	Zhang Z, Bao Y, Zhao W, Xiao J, Chen R, Zhang G, Li Y, Zhao G, Pervaiz N, Li R, Gao F, Zhi X, Lu Y, Liu L, He S, Li Q, Yuan C, Ma L, Xiao Y, Wang J, Hao Y, Wang Q, Shang Y, Zhang Y, Yuan N, Song S, Tian F, Sun L, Teng Y, Sun X, Chen H, Xue Y, Zhang Q, Teng X, Huang Z, Wang H, Zhu T, Zhang C, Ma Y, Zhang X, Lin S, Gao Y, Zhou J, Guo J, Liu X, Kang H, Tian D, Gao G, Ling Y, Xu S, Wang P, Zhou H, Niu Y, Ruan C, Lv D, Dong L, Zhu Q, Abbasi AA, Tang Q, Li H, Yao L, Chen M, Gao Q, Cao R, Guo Y, Zhai S, Shi S, Guo AY, Shireen H, Miao YR, Jin JP, Qian Q, Wang Y, Cao J, Duan G, Ning Z, Yu L, Li Z, Du Q, Wu W, Zhou Q, Hu H, Wang G, Wu S, Li CY, Zhao F, Xiong Z, Wang C, Gong Z, Zeng J, Yuan L, Xia X, Sun M, Batool F, Xue H, Sang J, Du Z, Wang X, Lan L, Fang S, Cui Q, Wang Z, Hao L, Liu W, Jiang Z, Zhang H, Raza RZ, Wu Y, Luo H, Zhang YE, Zhu J, Jiang M, Li M, Ying C, Li X, Li C, Zhao Y, Kang Q, Klenk HP, Zheng Y, Yang F, Tang B, Zhang P, Chen X, Zhang L, Zhao L, Tu Y, Chen T, Zou D, Zhang S, Ning W, Niu G, Guo H, Yan J, Shi Y, Sun Y, Pan M, Lu M, Ji P, Peng D, Yuan H . Database resources of the National Genomics Data Center in 2020. Nucleic Acids Res, 2020,48(D1):D24-D33.
[15]	Wang YQ, Song FH, Zhu JW, Zhang SS, Yang YD, Chen TT, Tang BX, Dong LL, Ding N, Zhang Q, Bai ZX, Dong XN, Chen HX, Sun MY, Zhai S, Sun YB, Yu L, Lan L, Xiao JF, Fang XD, Lei HX, Zhang Z, Zhao WM . GSA: genome sequence archive. Genomics Proteomics Bioinformatics, 2017,15(1):14-18.
[16]	Zhang SS, Chen TT, Zhu JW, Zhou Q, Chen X, Wang YQ, Zhao WM . GSA: genome sequence archive. Hereditas (Beijing), 2018,40(11):1044-1047.
[16]	张思思, 陈婷婷, 朱军伟, 周晴, 陈旭, 王彦青, 赵文明 . GSA: 组学原始数据归档库. 遗传, 2018,40(11):1044-1047.
[17]	Zhang YS, Xia L, Sang J, Li M, Liu L, Li MW, Niu GY, Cao JB, Teng XF, Zhou Q, Zhang Z . The BIG Data Center’s database resources. Hereditas(Beijing), 2018,40(11):1039-1043.
[17]	张源笙, 夏琳, 桑健, 李漫, 刘琳, 李萌伟, 牛广艺, 曹佳宝, 滕徐菲, 周晴, 章张 . 生命与健康大数据中心资源. 遗传, 2018,40(11):1039-1043.
[18]	Ma YK, Bao YM . Prospects for national biological big data centers. Hereditas(Beijing), 2018,40(11):938-943.
[18]	马英克, 鲍一明 . 国家级生物大数据中心展望. 遗传, 2018,40(11):938-943.
[19]	Edgar RC . MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res, 2004,32(5):1792-1797.
[20]	Bodenhofer U, Bonatesta E, Horej?-Kainrath C , Hochreiter S. msa: an R package for multiple sequence alignment. Bioinformatics, 2015,31(24):3997-3999.
[21]	Donlin MJ . Using the generic genome browser(GBrowse) . Curr Protoc Bioinformatics, 2009, 28(1): 9.9.1-9.9.25.
[22]	McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GRS, Thormann A, Flicek P, Cunningham F . The ensembl variant effect predictor. Genome Biol, 2016,17:122.

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