The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR

Shuhui Song(Chinese Academy of Sciences), Lina Ma(Chinese Academy of Sciences), Dong Zou(Chinese Academy of Sciences), Dongmei Tian(Beijing Institute of Genomics), Cuiping Li(Beijing Institute of Genomics), Junwei Zhu(Beijing Institute of Genomics), Meili Chen(Chinese Academy of Sciences), Anke Wang(Beijing Institute of Genomics), Yingke Ma(Beijing Institute of Genomics), Mengwei Li(Chinese Academy of Sciences), Xufei Teng(Chinese Academy of Sciences), Ying Cui(Chinese Academy of Sciences), Guangya Duan(Chinese Academy of Sciences), Mochen Zhang(Chinese Academy of Sciences), Tong Jin(Chinese Academy of Sciences), Cheng‐Min Shi(Chinese Academy of Sciences), Zhenglin Du(Chinese Academy of Sciences), Yadong Zhang(Chinese Academy of Sciences), Chuandong Liu(Chinese Academy of Sciences), Rujiao Li(Chinese Academy of Sciences), Jingyao Zeng(Chinese Academy of Sciences), Lili Hao(Chinese Academy of Sciences), Shuai Jiang(Beijing Institute of Genomics), Hua Chen(Chinese Academy of Sciences), Dali Han(Chinese Academy of Sciences), Jingfa Xiao(Chinese Academy of Sciences), Zhang Zhang(Chinese Academy of Sciences), Wenming Zhao(Chinese Academy of Sciences), Yongbiao Xue(Beijing Institute of Genomics), Yīmíng Bào(Chinese Academy of Sciences)
Genomics Proteomics & Bioinformatics
December 1, 2020
10.1016/j.gpb.2020.09.001
Cited by 117Open Access
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Abstract

On January 22, 2020, China National Center for Bioinformation (CNCB) released the 2019 Novel Coronavirus Resource (2019nCoVR), an open-access information resource for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). 2019nCoVR features a comprehensive integration of sequence and clinical information for all publicly available SARS-CoV-2 isolates, which are manually curated with value-added annotations and quality evaluated by an automated in-house pipeline. Of particular note, 2019nCoVR offers systematic analyses to generate a dynamic landscape of SARS-CoV-2 genomic variations at a global scale. It provides all identified variants and their detailed statistics for each virus isolate, and congregates the quality score, functional annotation, and population frequency for each variant. Spatiotemporal change for each variant can be visualized and historical viral haplotype network maps for the course of the outbreak are also generated based on all complete and high-quality genomes available. Moreover, 2019nCoVR provides a full collection of SARS-CoV-2 relevant literature on the coronavirus disease 2019 (COVID-19), including published papers from PubMed as well as preprints from services such as bioRxiv and medRxiv through Europe PMC. Furthermore, by linking with relevant databases in CNCB, 2019nCoVR offers data submission services for raw sequence reads and assembled genomes, and data sharing with NCBI. Collectively, SARS-CoV-2 is updated daily to collect the latest information on genome sequences, variants, haplotypes, and literature for a timely reflection, making 2019nCoVR a valuable resource for the global research community. 2019nCoVR is accessible at https://bigd.big.ac.cn/ncov/.

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