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

Dong, Ning; Yang, Xuemei; Ye, Lianwei; Chen, Kaichao; Chan, Edward Wai-Chi; Yang, Moon-Sik; Chen, Sheng

doi:10.1101/2020.01.20.913368

Cited by 114 publications

(128 citation statements)

References 5 publications

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“…Till now most of the deaths have occurred in the elderly population due to novel coronavirus infection whereas, children and Table 2. Key interacting residues between RBD of spike protein of different corona viruses and host receptor ACE2 of human, bat, mouse civet and different avian species (modified from Dong et al 2020). 41 42 45 79 82 83 90 325 329 353 Amino Acid (aa) position relative to human ACE2…”

Section: Resultsmentioning

confidence: 99%

Emergence of Novel Coronavirus and COVID-19: whether to stay or die out?

Biswas

Bhattacharjee

Chakrabarti

et al. 2020

Critical Reviews in Microbiology

127

103

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The last century has witnessed several assaults from RNA viruses, resulting in millions of death throughout the world. The 21st century appears no longer an exception, with the trend continued with escalated fear of SARS coronavirus in 2002 and further concern of influenza H5N1 in 2003. A novel influenza virus created the first pandemic of the 21st century, the pandemic flu in 2009 preceded with the emergence of another deadly virus, MERS-CoV in 2012. A novel coronavirus "SARS-CoV-2" (and the disease COVID-19) emerged suddenly, causing a rapid outbreak with a moderate case fatality rate. This virus is continuing to cause health care providers grave concern due to the lack of any existing immunity in the human population, indicating their novelty and lack of previous exposure. The big question is whether this novel virus will be establishing itself in an endemic form or will it eventually die out? Endemic viruses during circulation may acquire mutations to infect naïve, as well as individual with pre-existing immunity. Continuous monitoring is strongly advisable, not only to the newly infected individuals, but also to those recovered individuals who were infected by SARS-CoV-2 as re-infection may lead to the selection of escape mutants and subsequent dissemination to the population. ARTICLE HISTORY

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Section: Resultsmentioning

confidence: 99%

Emergence of Novel Coronavirus and COVID-19: whether to stay or die out?

Biswas

Bhattacharjee

Chakrabarti

et al. 2020

Critical Reviews in Microbiology

127

103

View full text Add to dashboard Cite

show abstract

“…From previous reports, the interaction with ACE2 was responsible for SARS-CoV entering human cells [31 , 32] . Dong et al compared the structural similarity of the S protein in various viruses and speculated that SARS-CoV-2 could most likely use the same receptor as SARS-CoV [33] . Zhou et al conducted virus infectivity studies using HeLa cells with or without ACE2 proteins obtained from humans or animals and found that SARS-CoV-2 could invade all ACE2 proteinexpressing cells except for mouse cells [34] .…”

Section: Pathogenic Mechanismsmentioning

confidence: 99%

Recent progress in understanding 2019 novel coronavirus (SARS-CoV-2) associated with human respiratory disease: detection, mechanisms and treatment

Kang

Peng

Zhu

et al. 2020

International Journal of Antimicrobial Agents

165

139

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“…Analyzing of the genome of 2019-nCoV showed that this new virus shared around 80~90% sequence identity to SARS-CoV (2). Both bioinformatics modeling and in vitro experiments indicated that 2019-nCoV was more likely to use the angiotensin-converting enzyme 2 (ACE2) as the entry receptor (3,4). ACE2 is previously known as the receptor for SARS-CoV and HCoV-NL63 (5,6).…”

Section: Introductionmentioning

confidence: 99%

Integrative Bioinformatics Analysis Provides Insight into the Molecular Mechanisms of 2019-nCoV

Zhang

Qin

et al. 2020

Preprint

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The 2019-nCoV is reported to share the same entry (ACE2) as SARS-CoV according to the updated findings. Analyzing the distribution and expression level of the route of coronavirus may help reveal underlying mechanisms of viral susceptibility and post-infection modulation. In this study, we found that the expression of ACE2 in healthy populations and patients with underlying diseases was not significantly different, suggesting relatively similar susceptibility. Besides, based on the expression of ACE2 in smoking individuals, we inferred that long-term smoking might be a risk factor for 2019-nCoV. Analyzing the ACE2 in SARS-CoV infected cells suggested that ACE2 was more than just a receptor but also participated in post-infection regulation, including immune response, cytokine secretion, and viral genome replication. Moreover, we also constructed Protein-protein interaction (PPI) networks and identified hub genes in viral activity and cytokine secretion. Our findings may explain the clinical symptoms so far and help clinicians and researchers understand the pathogenesis and design therapeutic strategies for 2019-nCoV. : medRxiv preprint GO biological process annotation gmt file was downloaded from MSigDB (https://www.gsea-msigdb.org/gsea/msigdb/). GSEA was performed to analyze the possible biological processes related to ACE2 in healthy people using clusterProfiler (12). The parameters were nPerm = 1000, minGSSize = 10, maxGSSize = 500, the biological processes with p-value < 0.05 were considered significant. GSVA was performed using GSVA R package. The immune infiltrating was quantified using the ssGSEA method in GSVA R package. The gene list for immune cells was derived from Bindea G et al.(13). PPIAll viral-related biological process and cytokine secretion-biological process proteins were extracted from the gmt file, Cytoscape v3.7.2 was used to construct the PPI network using BisoGenet application, the PPI sources include DIP, BIOGRID, HPRD, INTACT, MINT and BIND. And the nodes with topological importance in the interaction network were screened by calculating Degree Centrality (DC) with the Cytoscape plugin CytoNCA. Hub proteins were identified using Cytoscape plugin CytoHubba.

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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

Abstract: 3Detailed genomic and structure-based analysis of a new coronavirus, namely 2019-nCoV, 2 4 1 9 2 1 9 3 author/funder. All rights reserved. No reuse allowed without permission.

Cited by 114 publications

References 5 publications

Emergence of Novel Coronavirus and COVID-19: whether to stay or die out?

Emergence of Novel Coronavirus and COVID-19: whether to stay or die out?

Recent progress in understanding 2019 novel coronavirus (SARS-CoV-2) associated with human respiratory disease: detection, mechanisms and treatment

Integrative Bioinformatics Analysis Provides Insight into the Molecular Mechanisms of 2019-nCoV

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