An online coronavirus analysis platform from the National Genomics Data Center

Gong, Zheng; Jun, Zhu; Li, Cui Ping; Jiang, Shuai; Ma, Lijiao; Tang, Bi Xia; Zou, Dong; Chen, Mei Li; Sun, Yu; Song, Shu Hui; Zhang, Zhang; Xiao, Jing; Xue, Yong; Bao, Yi; Du, Zheng; Zhao, Wen

doi:10.24272/j.issn.2095-8137.2020.065

Cited by 67 publications

(76 citation statements)

References 14 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, as a human intestinal cell line, culture in Caco-2 cells resulted in a 27-nt deletion in the NTD of the spike glycoprotein, whereas a mutant with this deletion was not found in human clinical specimens. These results suggest that the spike glycoprotein of SARS-CoV-2 is more likely to mutate during in vitro passage, which is consistent with the reported outcomes of person-to-person transmission (Gong et al 2020 ). It remains largely unknown whether mutations acquired during in vitro passages additionally affect viral intrinsic characteristics.…”

supporting

confidence: 90%

Genetic Mutation of SARS-CoV-2 during Consecutive Passages in Permissive Cells

et al. 2021

View full text Add to dashboard Cite

supporting

confidence: 90%

Genetic Mutation of SARS-CoV-2 during Consecutive Passages in Permissive Cells

et al. 2021

View full text Add to dashboard Cite

“…All identified variants and their functional annotations are publicly available in the database. In addition, an online pipeline for variant identification and functional annotation is also provided for free access at https://bigd.big.ac.cn/ncov/analysis [13] .…”

Section: Database Content and Featuresmentioning

confidence: 99%

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

Song¹,

Ma²,

Zou³

et al. 2020

Genomics, Proteomics &Amp; Bioinformatics

Self Cite

View full text Add to dashboard Cite

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/.

show abstract

“…We compared the SNPs in our datasets with SNPs from assembled genomes deposited in the GISAID online datasets [53][54][55] as of April 11, 2020 and found differences in the mutation spectrum (Figure 3a). 5ʹ-UTR is the functional region most significantly enriched with SNPs at an average of 449.06 SNPs per KB compared to an average of 104.43 SNPs per KB across the genome of SARS-CoV-2 based on GISAID SNP dataset (Odd Ratio, OR = 4.30, p-value = 1.89034E-10, (Figure 3b).…”

Section: Genomic Distribution Of Snps Reveals That Orf8 Can Bear Alternate Alleles With High Frequencymentioning

confidence: 99%

Quasispecies of SARS-CoV-2 revealed by single nucleotide polymorphisms (SNPs) analysis

Gao

Liu

et al. 2021

Virulence

View full text Add to dashboard Cite

New SARS-CoV-2 mutants have been continuously indentified with enhanced transmission ever since its outbreak in early 2020. As an RNA virus, SARS-CoV-2 has a high mutation rate due to the low fidelity of RNA polymerase. To study the single nucleotide polymorphisms (SNPs) dynamics of SARS-CoV-2, 158 SNPs with high confidence were identified by deep meta-transcriptomic sequencing, and the most common SNP type was C > T. Analyses of intra-host population diversity revealed that intra-host quasispecies' composition varies with time during the early onset of symptoms, which implicates viral evolution during infection. Network analysis of co-occurring SNPs revealed the most abundant non-synonymous SNP 22,638 in the S glycoprotein RBD region and 28,144 in the ORF8 region. Furthermore, SARS-CoV-2 variations differ in an individual's respiratory tissue (nose, throat, BALF, or sputum), suggesting independent compartmentalization of SARS-CoV-2 populations in patients. The positive selection analysis of the SARS-CoV-2 genome uncovered the positive selected amino acid G251V on ORF3a. Alternative allele frequency spectrum (AAFS) of all variants revealed that ORF8 could bear alternate alleles with high frequency. Overall, the results show the quasispecies' profile of SARS-CoV-2 in the respiratory tract in the first two months after the outbreak.

show abstract

An online coronavirus analysis platform from the National Genomics Data Center

Cited by 67 publications

References 14 publications

Genetic Mutation of SARS-CoV-2 during Consecutive Passages in Permissive Cells

Genetic Mutation of SARS-CoV-2 during Consecutive Passages in Permissive Cells

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

Quasispecies of SARS-CoV-2 revealed by single nucleotide polymorphisms (SNPs) analysis

Contact Info

Product

Resources

About