Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (654)

ProteinN (149)

NSP5 (75)

ComplexRdRp (46)

ProteinE (43)


SARS-CoV-2 Proteins
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    The digestive system is a potential route of 2019-nCov infection MESHD: a bioinformatics analysis based on single-cell transcriptomes

    Authors: Hao Zhang; Zijian Kang; Haiyi Gong; Da Xu; Jing Wang; Zifu Li; Xingang Cui; Jianru Xiao; Tong Meng; Wang Zhou; Jianmin Liu; Huji Xu

    doi:10.1101/2020.01.30.927806 Date: 2020-01-31 Source: bioRxiv

    Since December 2019, a newly identified coronavirus (2019 novel coronavirus, 2019-nCov) is causing outbreak of pneumonia MESHD in one of largest cities, Wuhan, in Hubei province of China and has draw significant public health attention. The same as severe acute respiratory syndrome coronavirus (SARS-CoV) MESHD, 2019-nCov enters into host cells via cell receptor angiotensin converting enzyme II (ACE2). In order to dissect the ACE2-expressing cell composition and proportion and explore a potential route of the 2019-nCov infection MESHD in digestive system infection MESHD, 4 datasets with single-cell transcriptomes of lung, esophagus, gastric, ileum and colon MESHD were analyzed. The data showed that ACE2 was not only highly expressed in the lung AT2 cells, esophagus upper and stratified epithelial cells but also in absorptive enterocytes from ileum and colon MESHD. These results indicated along with respiratory systems, digestive system is a potential routes for 2019-nCov infection MESHD. In conclusion, this study has provided the bioinformatics evidence of the potential route for infection of 2019-nCov in digestive system along with respiratory tract and may have significant impact for our healthy policy setting regards to prevention of 2019-nCoV infection MESHD.

    Therapeutic Drugs Targeting 2019-nCoV Main Protease PROTEIN by High-Throughput Screening

    Authors: Yan Li; Jinyong Zhang; Ning Wang; Haibo Li; Yun Shi; Gang Guo; Kaiyun Liu; Hao Zeng; Quanming Zou

    doi:10.1101/2020.01.28.922922 Date: 2020-01-29 Source: bioRxiv

    2019 Novel Coronavirus (2019-nCoV) is a virus identified as the cause of the outbreak of pneumonia MESHD first detected in Wuhan, China. Investigations on the transmissibility, severity, and other features associated with this virus are ongoing. Currently, there is no vaccine or therapeutic antibody to prevent the infection, and more time is required to develop an effective immune strategy against the pathogen. In contrast, specific inhibitors targeting the key protease involved in replication and proliferation of the virus are the most effective means to alleviate the epidemic. The main protease PROTEIN of SARS-CoV MESHD is essential for the life cycle of the virus, which showed 96.1% of similarity with the main proteaseof 2019-nCoV, is considered to be an attractive target for drug development. In this study, we have identified 4 small molecular drugs with high binding capacity with SARS-CoV MESHD main protease PROTEIN by high-throughput screening based on the 8,000 clinical drug libraries, all these drugs have been widely used in clinical applications with guaranteed safety, which may serve as promising candidates to treat the infection of 2019-nCoV.

    Potent binding of 2019 novel coronavirus spike protein PROTEIN by a SARS coronavirus-specific human monoclonal antibody

    Authors: Xiaolong Tian; Cheng Li; Ailing Huang; Shuai Xia; Sicong Lu; Zhengli Shi; Lu Lu; Shibo Jiang; Zhenlin Yang; Yanling Wu; Tianlei Ying

    doi:10.1101/2020.01.28.923011 Date: 2020-01-28 Source: bioRxiv

    The newly identified 2019 novel coronavirus (2019-nCoV) has caused more than 800 laboratory-confirmed human infections, including 25 deaths MESHD, posing a serious threat to human health. Currently, however, there is no specific antiviral treatment or vaccine. Considering the relatively high identity of receptor binding domain (RBD) in 2019-nCoV and SARS-CoV MESHD, it is urgent to assess the cross-reactivity of anti-SARS-CoV antibodies with 2019-nCoV spike protein PROTEIN, which could have important implications for rapid development of vaccines and therapeutic antibodies against 2019-nCoV. Here, we report for the first time that a SARS-CoV-specific human monoclonal antibody, CR3022, could bind potently with 2019-nCoV RBD (KD of 6.3 nM). The epitope of CR3022 does not overlap with the ACE2 HGNC binding site within 2019-nCoV RBD. Therefore, CR3022 has the potential to be developed as candidate therapeutics, alone or in combination with other neutralizing antibodies, for the prevention and treatment of 2019-nCoV infection MESHDs. Interestingly, some of the most potent SARS-CoV-specific neutralizing antibodies (e.g., m396, CR3014) that target the ACE2 HGNC binding site of SARS-CoV MESHD failed to bind 2019-nCoV spike protein PROTEIN, indicating that the difference in the RBD of SARS-CoV MESHD and 2019-nCoV has a critical impact for the cross-reactivity of neutralizing antibodies, and that it is still necessary to develop novel monoclonal antibodies that could bind specifically to 2019-nCoV RBD.

    Protective Population Behavior Change in Outbreaks of Emerging Infectious Disease

    Authors: Evans K Lodge; Annakate M Schatz; John M Drake

    doi:10.1101/2020.01.27.921536 Date: 2020-01-28 Source: bioRxiv

    During outbreaks of emerging infections MESHD, the lack of effective drugs and vaccines increases reliance on non-pharmacologic public health interventions and behavior change to limit human-to-human transmission. Interventions that increase the speed with which infected individuals remove themselves from the susceptible population are paramount, particularly isolation and hospitalization. Ebola virus disease MESHD ( EVD MESHD), Severe Acute Respiratory Syndrome MESHD (SARS), and Middle East Respiratory Syndrome MESHD ( MERS MESHD) are zoonotic viruses that have caused significant recent outbreaks with sustained human-to-human transmission. This investigation quantified changing mean removal rates (MRR) and days from symptom onset to hospitalization (DSOH) of infected individuals from the population in seven different outbreaks of EVD MESHD, SARS, and MERS MESHD, to test for statistically significant differences in these metrics between outbreaks. We found that epidemic week and viral serial interval were correlated with the speed with which populations developed and maintained health behaviors in each outbreak.

    Single-cell RNA expression profiling of ACE2 HGNC, the putative receptor of Wuhan 2019-nCov

    Authors: Yu Zhao; Zixian Zhao; Yujia Wang; Yueqing Zhou; Yu Ma; Wei Zuo

    doi:10.1101/2020.01.26.919985 Date: 2020-01-26 Source: bioRxiv

    A novel coronavirus SARS-CoV-2 MESHD was identified in Wuhan, Hubei Province, China in December of 2019. According to WHO report, this new coronavirus has resulted in 76,392 confirmed infections and 2,348 deaths in China by 22 February, 2020, with additional patients being identified in a rapidly growing number internationally. SARS-CoV-2 was reported to share the same receptor, Angiotensin-converting enzyme 2 HGNC ( ACE2 HGNC), with SARS-CoV MESHD. Here based on the public database and the state-of-the-art single-cell RNA-Seq technique, we analyzed the ACE2 HGNC RNA expression profile in the normal human lungs. The result indicates that the ACE2 HGNC virus receptor expression is concentrated in a small population of type II alveolar MESHD cells ( AT2 HGNC). Surprisingly, we found that this population of ACE2 HGNC-expressing AT2 HGNC also highly expressed many other genes that positively regulating viral entry, reproduction and transmission. This study provides a biological background for the epidemic investigation of the COVID-19 MESHD, and could be informative for future anti- ACE2 HGNC therapeutic strategy development.

    Pattern of early human-to-human transmission of Wuhan 2019-nCoV

    Authors: Julien Riou; Christian L Althaus

    doi:10.1101/2020.01.23.917351 Date: 2020-01-24 Source: bioRxiv

    On December 31, 2019, the World Health Organization was notified about a cluster of pneumonia MESHD of unknown aetiology in the city of Wuhan, China. Chinese authorities later identified a new coronavirus (2019-nCoV) as the causative agent of the outbreak. As of January 23, 2020, 655 cases have been confirmed in China and several other countries. Understanding the transmission characteristics and the potential for sustained human-to-human transmission of 2019-nCoV is critically important for coordinating current screening and containment strategies, and determining whether the outbreak constitutes a public health emergency of international concern (PHEIC). We performed stochastic simulations of early outbreak trajectories that are consistent with the epidemiological findings to date. We found the basic reproduction number, R0, to be around 2.2 (90% high density interval 1.4--3.8), indicating the potential for sustained human-to-human transmission. Transmission characteristics appear to be of a similar magnitude to severe acute respiratory syndrome MESHD-related coronavirus ( SARS-CoV MESHD) and the 1918 pandemic influenza. These findings underline the importance of heightened screening, surveillance and control efforts, particularly at airports and other travel hubs, in order to prevent further international spread of 2019-nCoV.

    Host and infectivity prediction of Wuhan 2019 novel coronavirus using deep learning algorithm

    Authors: Qian Guo; Mo Li; Chunhui Wang; Zhengcheng Fang; Peihong Wang; Jie Tan; Shufang Wu; Yonghong Xiao; Huaiqiu Zhu

    doi:10.1101/2020.01.21.914044 Date: 2020-01-24 Source: bioRxiv

    The recent outbreak of pneumonia MESHD in Wuhan, China caused by the 2019 Novel Coronavirus (2019-nCoV) emphasizes the importance of detecting novel viruses and predicting their risks of infecting people. In this report, we introduced the VHP (Virus Host Prediction) to predict the potential hosts of viruses using deep learning algorithm. Our prediction suggests that 2019-nCoV has close infectivity with other human coronaviruses, especially the severe acute respiratory syndrome coronavirus (SARS-CoV) MESHD, Bat SARS-like Coronaviruses and the Middle East respiratory syndrome coronavirus (MERS-CoV) MESHD. Based on our prediction, compared to the Coronaviruses infecting other vertebrates, bat coronaviruses are assigned with more similar infectivity patterns with 2019-nCoVs. Furthermore, by comparing the infectivity patterns of all viruses hosted on vertebrates, we found mink viruses show a closer infectivity pattern to 2019-nCov. These consequences of infectivity pattern analysis illustrate that bat and mink may be two candidate reservoirs of 2019-nCov.These results warn us to beware of 2019-nCoV and guide us to further explore the properties and reservoir of it. One Sentence SummaryIt is of great value to identify whether a newly discovered virus has the risk of infecting human. Guo et al. proposed a virus host prediction method based on deep learning to detect what kind of host a virus can infect with DNA sequence as input. Applied to the Wuhan 2019 Novel Coronavirus, our prediction demonstrated that several vertebrate-infectious coronaviruses have strong potential to infect human. This method will be helpful in future viral analysis and early prevention and control of viral pathogens.

    Discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin

    Authors: Peng Zhou; Xing-Lou Yang; Xian-Guang Wang; Ben Hu; Lei Zhang; Wei Zhang; Hao-Rui Si; Yan Zhu; Bei Li; Chao-Lin Huang; Hui-Dong Chen; Jing Chen; Yun Luo; Hua Guo; Ren-Di Jiang; Mei-Qin Liu; Ying Chen; Xu-Rui Shen; Xi Wang; Xiao-Shuang Zheng; Kai Zhao; Quan-Jiao Chen; Fei Deng; Lin-Lin Liu; Bing Yan; Fa-Xian Zhan; Yan-Yi Wang; Gengfu Xiao; Zheng-Li Shi

    doi:10.1101/2020.01.22.914952 Date: 2020-01-23 Source: bioRxiv

    Since the SARS outbreak 18 years ago, a large number of severe acute respiratory syndrome MESHD related coronaviruses ( SARSr-CoV MESHD) have been discovered in their natural reservoir host, bats1-4. Previous studies indicated that some of those bat SARSr-CoVs have the potential to infect humans5-7. Here we report the identification and characterization of a novel coronavirus (nCoV-2019) which caused an epidemic of acute respiratory syndrome MESHD in humans, in Wuhan, China. The epidemic, started from December 12th, 2019, has caused 198 laboratory confirmed infections with three fatal cases by January 20th, 2020. Full-length genome sequences were obtained from five patients at the early stage of the outbreak. They are almost identical to each other and share 79.5% sequence identify to SARS-CoV MESHD. Furthermore, it was found that nCoV-2019 is 96% identical at the whole genome level to a bat coronavirus. The pairwise protein sequence analysis of seven conserved non-structural proteins show that this virus belongs to the species of SARSr-CoV MESHD. The nCoV-2019 virus was then isolated from the bronchoalveolar lavage fluid of a critically ill patient, which can be neutralized by sera from several patients. Importantly, we have confirmed that this novel CoV uses the same cell entry receptor, ACE2 HGNC, as SARS-CoV MESHD.

    Functional assessment of cell entry and receptor usage for lineage B β-coronaviruses, including 2019-nCoV

    Authors: Michael C Letko; Vincent Munster

    doi:10.1101/2020.01.22.915660 Date: 2020-01-22 Source: bioRxiv

    Over the past 20 years, several coronaviruses have crossed the species barrier into humans, causing outbreaks of severe, and often fatal, respiratory illness MESHD. Since SARS- CoV MESHD was first identified in animal markets, global viromics projects have discovered thousands of coronavirus sequences in diverse animals and geographic regions. Unfortunately, there are few tools available to functionally test these novel viruses for their ability to infect humans, which has severely hampered efforts to predict the next zoonotic viral outbreak. Here we developed an approach to rapidly screen lineage B betacoronaviruses, such as SARS-CoV MESHD and the recent 2019-nCoV, for receptor usage and their ability to infect cell types from different species. We show that host protease processing during viral entry is a significant barrier for several lineage B viruses and that bypassing this barrier allows several lineage B viruses to enter human cells through an unknown receptor. We also demonstrate how different lineage B viruses can recombine to gain entry into human cells and confirm that human ACE2 HGNC is the receptor for the recently emerging 2019-nCoV.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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