Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (722)

NSP5 (34)

ProteinN (30)

ProteinS1 (28)

ComplexRdRp (23)


SARS-CoV-2 Proteins
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    A Hint on the COVID-19 MESHD Risk: Population Disparities in Gene Expression of Three Receptors of SARS-CoV

    Authors: Guoshuai Cai; Xiang Cui; Xia Zhu; Jun Zhou

    id:10.20944/preprints202002.0408.v1 Date: 2020-02-27 Source:

    The current spreading novel coronavirus SARS-CoV-2 is highly infectious and pathogenic and has attracted global attention. Recent studies have found that SARS-CoV-2 and SARS-CoV share around 80% of homology and use the same cell entry receptor, ACE2 HGNC. These inspired us to study other receptors of SARS-CoV, which may be used for SARS-CoV-2 binding as well. In this study, we screened the gene expression of three receptors ( ACE2 HGNC, DC-SIGN and L-SIGN HGNC) in four datasets of normal lung tissue from lung adenocarcinoma patients and two single-cell RNA sequencing datasets from normal lung and bronchial epithelial cells separately. No significant difference in gene expression of these three receptors were found between gender groups (male vs female). We found higher gene expression of DC-SIGN in elder with age>60 and higher gene expression of L-SIGN HGNC in Caucasian than Asian. Similar to ACE2 HGNC, we observed significantly higher DC-SIGN gene expression in the lungs of smokers, especially former smokers. However, smokers upregulate ACE2 HGNC and DC-SIGN gene expression in different cell types. In the whole lung, ACE2 HGNC is actively expressed in remodeled Alveolar Type II MESHD cells of former smokers, while DC-SIGN is largely expressed in monocytes of former smokers and dendritic cells of current smokers. In bronchial epithelium, no obvious gene expression of DC-SIGN and L-SIGN HGNC was observed while ACE2 HGNC was found to be actively expressed in goblet cells of current smokers and club cells of non-smokers. In conclusion, our findings may indicate that smokers, especially former smokers, and people over 60 have higher risk and are more susceptible to SARS-CoV-2 infection MESHD. Also, this study provides hints on possible SARS-CoV-2 pathogenicity mechanisms in lung infection MESHD.

    The ACE2 HGNC expression of maternal-fetal interface and fetal organs indicates potential risk of vertical transmission of SARS-COV-2

    Authors: Mengmeng Li; Liang Chen; Chenglong Xiong; Xiangjie Li

    doi:10.1101/2020.02.27.967760 Date: 2020-02-27 Source: bioRxiv

    Recent studies have demonstrated that SARS-CoV-2 cell entry depends on both ACE2 HGNC and TMPRSS2 HGNC genes (DOI: 10.1016/j.cell.2020.02.052), but our current work only focus on ACE2 HGNC, which is insufficient to support the conclusion of this paper. So the authors have withdrawn their manuscript whilst they perform additional experiments and analysis to test some of their conclusions further. Therefore, the authors do not wish this work to be cited as reference for the project.

    Spike protein PROTEIN binding prediction with neutralizing antibodies of SARS-CoV-2

    Authors: Tamina Park; Sang-Yeop Lee; Seil Kim; Mi Jeong Kim; Hong Gi Kim; Sangmi Jun; Seung Il Kim; Bum Tae Kim; Edmond Changkyun Park; Daeui Park

    doi:10.1101/2020.02.22.951178 Date: 2020-02-27 Source: bioRxiv

    Coronavirus disease 2019 MESHD ( COVID-19 MESHD) is a new emerging human infectious disease MESHD caused by Severe Acute Respiratory Syndrome Coronavirus 2 MESHD (SARS-CoV-2, also previously known as 2019-nCoV), originated in Wuhan seafood and animal market, China. Since December 2019, more than 69,000 cases of COVID-19 MESHD have been confirmed in China and quickly spreads to other counties. Currently, researchers put their best efforts to identify effective drugs for COVID-19 MESHD. The neutralizing antibody, which binds to viral capsid in a manner that inhibits cellular entry of virus and uncoating of the genome, is the specific defense against viral invaders. In this study, we investigate to identify neutralizing antibodies that can bind to SARS-CoV-2 Sipke MESHD ( S) protein PROTEIN and interfere with the interaction between viral S protein PROTEIN and a host receptor by bioinformatic methods. The sequence analysis of S protein PROTEIN showed two major differences in the RBD region of the SARS-CoV-2 S protein PROTEIN compared to SARS-CoV and SARS-CoV MESHD related bat viruses (btSARS-CoV). The insertion regions were close to interacting residues with the human ACE2 HGNC receptor. Epitope analysis of neutralizing antibodies revealed that SARS-CoV neutralizing antibodies used conformational epitopes, whereas MERS-CoV neutralizing antibodies used a common linear epitope region, which contributes to form the {beta}-sheet structure in MERS-CoV S protein MESHD S protein PROTEIN and deleted in SARS-CoV-2 S protein PROTEIN. To identify effective neutralizing antibodies for SARS-CoV-2, the binding affinities of neutralizing antibodies with SARS-CoV-2 S MESHD S protein PROTEIN were predicted and compared by antibody-antigen docking simulation. The result showed that CR3022 neutralizing antibody from human may have higher binding affinity with SARS-CoV-2 S protein PROTEIN than SARS-CoV S protein MESHD S protein PROTEIN. We also found that F26G19 and D12 mouse antibodies could bind to SARS-CoV S MESHD S protein PROTEIN with high affinity. Our findings provide crucial clues towards the development of antigen diagnosis, therapeutic antibody, and the vaccine against SARS-CoV-2.

    Clinical features and sexual transmission potential of SARS-CoV-2 infected female patients: a descriptive study in Wuhan, China

    Authors: Pengfei Cui; Zhe Chen; Tian Wang; Jun Dai; Jinjin Zhang; Ting Ding; Jingjing Jiang; Jia Liu; Cong Zhang; Wanying Shan; Sheng Wang; Yueguang Rong; Jiang Chang; Xiaoping Miao; Xiangyi Ma; Shixuan Wang

    doi:10.1101/2020.02.26.20028225 Date: 2020-02-27 Source: medRxiv

    Background: As of March 2, 2020, SARS-CoV-2 has infected more than 80174 people and caused 2915 deaths in China. This virus rapidly spreads to 56 countries worldwide. Thus, in order to effectively block its transmission, it is urgent to uncover all the possible transmission routes of SARS-CoV-2. Methods: From January 28 to February 18, 2020, 35 female patients diagnosed with COVID-19 MESHD in Tongji Hospital were included in this descriptive study. The gynecologic history, clinical characteristics, laboratory findings and chest computed tomography (CT) of all patients were recorded in detail. To examine whether there is sexual transmission through vaginal from female to her partner, we employed real-time polymerase chain reaction testing (RT-PCR) to detect SARS-CoV-2 in vaginal environment (including vaginal discharge, cervical or vaginal residual exfoliated cells) and anal swab samples, and inquired recent sexual behaviors from the patients. Findings: The age range of the 35 patients with COVID-19 MESHD was 37-88 years. Over 50% patients infected with SARS-CoV-2 had chronic diseases. We tested the vaginal environment and anal swabs from the 35 female patients with COVID-19 MESHD and found that only an anal swab sample from one patient was positive for SARS-CoV-2. All the samples from vaginal environment were negative for SARS-CoV-2. The infection rate of the patients' sexual partner was 42.9%. Additionally, two female patients admitted having sex with their partners during a possible infection incubation period, while one patient's partner was uninfected and the other patient's partner was diagnosed with COVID-19 MESHD (after the diagnosis of the female patient). Conclusion: No positive RT-PCR result was found in the vaginal environment perhaps due to the lack of ACE2 HGNC expression, which is the receptor of SARS-CoV-2, in the vagina MESHD and cervix tissues (human protein atlas). The results from this study show no evidence of transmission of SARS-CoV-2 through vaginal sex from female to her partner. However, the risk of infection of non vaginal sex and other intimate contacts during vaginal sex should not be ignored.

    An Investigation of the Expression of 2019 Novel Coronavirus Cell Receptor Gene ACE2 HGNC in a Wide Variety of Human Tissues

    Authors: Mengyuan Li; Lin Li; Yue Zhang; Xiaosheng Wang

    doi:10.21203/rs.2.24751/v2 Date: 2020-02-26 Source: ResearchSquare

    Background: The 2019 novel coronavirus (2019-nCoV) has affected more than 72,000 people worldwide and caused more than 1,800 deaths so far. 2019-nCoV uses the angiotensinconverting enzyme 2 ( ACE2 HGNC) as the cell receptor to invade the human host and primarily causes pneumonia MESHD. Thus, ACE2 HGNC is the key to understanding the mechanism of 2019-nCoV infection MESHD. Methods: We compared ACE2 HGNC expression levels across 31 human normal tissues, between males and females, and between younger (ages <= 49 years) and older (ages > 49 years) persons in these tissues. We also investigated the correlations between ACE2 HGNC expression and immune signatures in various tissues. Results: ACE2 HGNC expression levels were the highest in small intestine, testis MESHD, kidney, heart, thyroid, and adipose tissue, and were the lowest in blood, spleen, bone marrow MESHD, brain, blood vessel, and muscle. In lungs, colon MESHD, liver, bladder, and adrenal gland, ACE2 HGNC showed the medium expression levels. ACE2 HGNC was not differentially expressed between males and females and between younger and older persons in any tissue. In skin, digestive system, brain, and blood vessel, ACE2 HGNC expression levels were positively associated with immune signatures in both males and females. In thyroid and lungs, ACE2 HGNC expression levels were positively and negatively associated with immune signatures in males and females, respectively.Conclusions: Our data provide potential cues for the 2019-nCoV epidemic may infect other tissues outside lungs, affect males and females and young and old persons equally, and old age and male are associated with higher mortality risk for 2019-nCoV infection MESHD.  

    Lung Adenocarcinoma Patients Own Higher Risk of SARS-CoV-2 Infection MESHD

    Authors: Long Chen; Li Zhong

    id:202002.0386/v1 Date: 2020-02-26 Source:

    Both lung adenocarcinoma and SARS-CoV-2 infection MESHD could cause pulmonary inflammation MESHD. Angiotensin-converting enzyme 2 HGNC, not only as the functional receptor of SARS-CoV-2 but also play key role in lung adenocarcinoma. To study the risk of SARS-CoV-2 infection MESHD in lung adenocarcinoma patients, mRNA and miRNA profiles were obtained from TCGA and GEO databases followed by bioinformatics analysis. A regulatory network which regards angiotensin-converting enzyme 2 HGNC as the center would be structured. In addition, via immunological analysis about key factors in lung adenocarcinoma patients, to explore the essential reasons for the susceptibility of SARS-CoV-2. Compared with normal tissue, angiotensin-converting enzyme 2 HGNC was increased in lung adenocarcinoma patients. Furthermore, a total of 7 differently expressed correlated mRNAs ( ACE2 HGNC, CXCL9 HGNC, MMP12 HGNC, IL6 HGNC, AZU1 HGNC, FCN3 HGNC, HYAL1 HGNC and IRAK3 HGNC) and 5 differently expressed correlated miRNAs (miR-125b-5p, miR-9-5p HGNC, miR-130b-5p, miR-381-3p and miR-421 HGNC) were screened followed by enrichment analysis. Interestingly, toll-like receptor signaling pathway with the most frequent occurrence was enriched by mRNA ( IL6 HGNC) and miRNA (miR-125b-5p) sets simultaneously. Finally through comprehensive analysis, it was assumed that miR-125b-5p- ACE2 HGNC- IL6 HGNC axis in the structured regulatory network could alter risk of SARS-CoV-2 infection MESHD in lung adenocarcinoma patients.

    TWIRLS, an automated topic-wise inference method based on massive literature, suggests a possible mechanism via ACE2 HGNC for the pathological changes in the human host after coronavirus infection

    Authors: Xiaoyang Ji; Chunming Zhang; Yubo Zhai; Zhonghai Zhang; Yiqing Xue; Chunli Zhang; Guangming Tan; Gang Niu

    doi:10.1101/2020.02.24.20025437 Date: 2020-02-26 Source: medRxiv

    Faced with the current large-scale public health emergency, collecting, sorting, and analyzing biomedical information related to the "coronavirus" should be done as quickly as possible to gain a global perspective, which is a basic requirement for strengthening epidemic control capacity. However, for human researchers studying the viruses and the hosts, the vast amount of information available cannot be processed effectively and in a timely manner, particularly when the scientific understanding may be limited, which can further lower the information processing efficiency. We present TWIRLS, a method that can automatically acquire, organize, and classify information. Additionally, independent functional data sources can be added to build an inference system using a machine-based approach, which can provide relevant knowledge to help human researchers quickly establish subject cognition and to make more effective decisions. TWIRLS can automatically analyze more than three million words in more than 14,000 literature articles in only 4 hours. Combining with generalized gene interaction databases creates a data interface that can help researchers to further analyze the information. Using the TWIRLS system, we found that an important regulatory factor angiotensin-converting enzyme 2 HGNC ( ACE2 HGNC) may be involved in the host pathological changes on binding to the coronavirus after infection. After triggering functional changes in ACE2 HGNC/AT2R, an imbalance in the steady-state cytokine regulatory axis involving the Renin-Angiotensin System and IP-10 HGNC leads to a cytokine storm.

    Discovery of potential drugs for COVID-19 MESHD based on the connectivity map

    Authors: Zhonglin Li; Tao Bai; Ling Yang; Xiaohua Hou

    doi:10.21203/rs.2.24684/v1 Date: 2020-02-25 Source: ResearchSquare

    Background: Corona virus infective disease MESHD 19 ( COVID-19 MESHD) is the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and spreads very rapidly, which become a worldwide public healthy crisis. Until now, there is no effective antivirus drugs or vaccines specifically used for its treatment. So it is urgent to discover efficient therapeutic methods. The same as SARS-CoV, SARS-CoV-2 MESHD also invades organism by combining with Angiotensin-converting enzyme 2 HGNC ( ACE2 HGNC). Recently, there are reports about SARS-CoV-2 infected MESHD host not only through the respiratory tract, but also gastrointestinal tract. However, it is proved that ACE2 HGNC plays a key role in protecting subjects from lung injury MESHD and resisting the inflammation MESHD caused by intestinal epithelial damage. Interestingly, the expression of ACE2 HGNC protein is reduced after SARS-CoV infection MESHD. Methods: According to the dataset of genes co-expressed with ACE2 HGNC in the colonic epithelial cells, we established a protein-protein interaction (PPI) Network and selected hub genes from them. The cluster analysis was performed to find out the dense region of the PPI Network. Then, gene ontology (GO) and pathway enrichment analysis were performed to explore the main function of genes co-expressed with ACE2 HGNC. Finally, we predicted the potential drugs for the treatment of COVID-19 MESHD based on the connectivity map ( Cmap HGNC) . Results: We constructed a PPI network containing 125 hub genes of genes co-expressed with ACE2 HGNC in the colonic epithelial cells and obtained two modules through cluster analysis. The GO analysis and the KEGG pathway revealed these genes were aggregated in ribosome, exosomes, extracellular cellular components; structure constituent of ribosome, G-protein coupled receptor activity, MHC class I and II receptor activity biological processes; immune response, protein metabolism, signal transduction biological processes; and ribosome, graft-versus-host disease MESHD, viral myocarditis MESHD pathways. The result from Cmap HGNC indicated ikarugamycin, molsidomine had highly correlated scores with the query files. Conclusion: We found out that ikarugamycin and molsidomine were the potential drugs for the treatment of COVID-19 MESHD.

    Asians Do Not Exhibit Elevated Expression or Unique Genetic Polymorphisms for ACE2 HGNC, the Cell-Entry Receptor of SARS-CoV-2

    Authors: Ying Chen; Kejia Shan; Wenfeng Qian

    id:10.20944/preprints202002.0258.v2 Date: 2020-02-25 Source:

    The recurrent coronavirus outbreaks in China ( SARS-CoV MESHD and its relative, SARS-CoV-2) have raised speculations that perhaps Asians are somehow more susceptible to these coronaviruses. Here, we test this possibility based on an analysis of the lung-specific expression of ACE2 HGNC, which encodes the known cell-entry receptor of both SARS-CoV and SARS-CoV-2 MESHD. We show that ACE2 HGNC expression is not affected during tumorigenesis, supporting that the abundant transcriptomes in cancer MESHD genomic studies can be informatively used to study ACE2 HGNC expression among diverse individuals without cancer MESHD. We find that ACE2 HGNC expression in the lung increases with age, but is not associated with sex. Further, Asians do not differ from other populations for ACE2 HGNC expression and do not harbor unique genetic polymorphisms in the ACE2 HGNC locus. Thus, beyond illustrating an innovative method for assessing the potential impacts of demographic factors for non-cancer diseases MESHD from large-scale cancer sample datasets, our statistically robust findings emphasize that individuals of all races require the same level of personal protection against SARS-CoV-2.

    Structural basis for receptor recognition by the novel coronavirus from Wuhan

    Authors: Jian Shang; Gang Ye; Ke Shi; Yushun Wan; Chuming Luo; Hideki Aihara; Qibin Geng; Ashley Auerbach; Fang Li

    doi:10.21203/rs.2.24749/v1 Date: 2020-02-25 Source: ResearchSquare

    A novel SARS-like coronavirus (2019-nCoV) recently emerged from Wuhan, China and is quickly spreading in humans. A key to tackling this epidemic is to understand the virus’s receptor recognition mechanism, which regulates its infection, pathogenesis, and host range. 2019-nCoV and SARS-CoV MESHD recognize the same host receptor ACE2 HGNC. Here we determined the crystal structure of 2019-nCoV receptor-binding domain (RBD) (engineered to facilitate crystallization) in complex of human ACE2 HGNC.Compared with SARS-CoV MESHD, an ACE2 HGNC-binding ridge in 2019-nCoV RBD takes more compact conformations, causing structural changes at the RBD/ ACE2 HGNC interface. Adaptive to these structural changes, several mutations in 2019-nCoV RBD enhance ACE2 HGNC- binding affinity, contributing to the high infectivity of 2019-CoV. These mutations also reveal the molecular mechanisms of the animal-to-human transmission of 2019-nCoV. Alarmingly, a single N439R mutation in 2019-nCoV RBD further enhances its ACE2 HGNC- binding affinity, indicating possible future evolution of 2019-nCoV in humans. This study sheds light on the epidemiology and evolution of 2019-nCoV, and provides guidance for intervention strategies targeting receptor recognition by 2019-nCoV.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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