Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (1768)

ProteinN (482)

NSP5 (390)

ComplexRdRp (224)

ProteinE (128)


SARS-CoV-2 Proteins
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    The epidemic characteristics, guidelines and policies: A compared analysis of literature between COVID-19 MESHD and SARS

    Authors: Jing Li; Jiayi Yang; Kaili Wen; Rong Lu; Xiaoliang Du

    doi:10.21203/ Date: 2020-02-26 Source: ResearchSquare

    Background: COVID-19 MESHD broke out in Wuhan, and rapidly spread to other province of China and other countries. To understand epidemic characteristics, guidelines and policiesof COVID-19 MESHD compared to SARS, and further explore the gap of health system facing with major outbreaks for improvement in China. Methods: A systematic review was performed using China academic literature (CNKI), Wan Fang, PubMed, medRxiv, bioRxiv,offical website of World Health Organization, National Health Commission of the People’s Republic of China, the Hubei Province Health Commission, and Wuhan City Health Commission for literature of epidemiological and clinical characteristics, guidelines an policies of COVID-19 MESHD and SARS from 2003 to 2020. Two dataset were obtained from the National Health Commission's open data information, and daily SARS epidemic section authorized by the State Council`s Information Office.Results: The 113 related studies finally entered final analysis, among which 63 were Chinese articles. Severe acute respiratory syndrome MESHD-associated coronavirus ( SARS-CoV MESHD) and 2019 novel coronavirus (SARS-CoV-2) caused outbreak in 2002 and 2019 in China called SARS and 2019 coronavirus disease MESHD ( COVID-19 MESHD). Both belong to Beta Coronavirus (β-CoV). Their original cluster confirmed cases had contact history to wild animals, and clinical symptoms are similar. However, COVID-19 MESHD has a high human-to-human transmission capability, and more rapidly spread from Hubei province (97.9% cases) across China and over the world. R0 was estimated around 2.2 (1.4-3.8), and incubation period of COVID-19 MESHD is 1-14 days. Transmission routes predominantly have respiratory droplets, close contact and even air transmission by aerosols. A fatality rate was 2.70% (2004/74185) with the highest of 14.8% at over 80 years old, and cases mainly were males in the middle and elder ages. For prevention and control, strategies and policies consecutively were issued. Compared to those of SARS, responsiveness for COVID-19 MESHD is more prompt.  Policy priorities tend to multi-sectors of cooperation, strong action to cut off source of infection (sealed Wuhan city),strengthening community prevention and mental health. Conclusions: The major gap facing with epidemic outbreak exists in the weak health system especially public health system, although we already made a great progress and improvement in our preventive awareness. Therefore, we forcefully appeal to a strong public health system by government for continuous investment and improvement. An advanced public health system stands by us in times of peace, and while fights for us during epidemic outbreak period. 

    Genomic variations of COVID-19 MESHD suggest multiple outbreak sources of transmission

    Authors: Liangsheng Zhang; Jian-Rong Yang; Zhenguo Zhang; Zhenguo Lin

    doi:10.1101/2020.02.25.20027953 Date: 2020-02-26 Source: medRxiv

    We examined 169 genomes of SARS-CoV-2 and found that they can be classified into two major genotypes, Type I and Type II. Type I can be further divided into Type IA and IB. Our phylogenetic analysis showed that the Type IA resembles the ancestral SARS-CoV-2 most. Type II was likely evolved from Type I and predominant in the infections. Our results suggest that Type II SARS-CoV-2 MESHD was the source of the outbreak in the Wuhan Huanan market and it was likely originated from a super-spreader. The outbreak caused by the Type I virus should have occurred somewhere else, because the patients had no direct link to the market. Furthermore, by analyzing three genomic sites that distinguish Type I and Type II strains, we found that synonymous changes at two of the three sites confer higher protein translational efficiencies in Type II strains than in Type I strains, which might explain why Type II strains are predominant, implying that Type II is more contagious (transmissible) than Type I. These findings could be valuable for the current epidemic prevention and control.

    Case fatality rate of novel coronavirus disease 2019 MESHD in China

    Authors: Rui Qi; Chao Ye; Xiang-rong Qin; Xue-Jie Yu

    doi:10.1101/2020.02.26.20028076 Date: 2020-02-26 Source: medRxiv

    Abstract Background: A pandemic of coronavirus disease 2019 MESHD ( COVID-19 MESHD) which have caused more than 80 thousand persons infected globally is still ongoing. This study aims to calculate its case fatality rate (CFR). Methods: The method, termed as converged CFR calculation, was based on the formula of dividing the number of known deaths MESHD by the number of confirmed cases T days before, where T was an average time period from case confirmation to death. It was found that supposing a T, if it was smaller (bigger) than the true T, calculated CFRs would gradually increase (decrease) to infinitely near the true T with time went on. According to the law, the true T value could be determined by trends of daily CFRs calculated with different assumed T values (left of true T is decreasing, right is increasing). Then the CFR could be calculated. Results: CFR of COVID-19 MESHD in China except Hubei Province was 0.8% to 0.9%. So far, the CFR had accurately predicted the death MESHD numbers more than 3 weeks. CFR in Hubei of China was 5.4% by which the calculated death number corresponded with the reported number for 2 weeks. Conclusion: The method could be used for CFR calculating while pandemics are still ongoing. Dynamic monitoring of the daily CFRs trends could help outbreak-controller to have a clear vision in the timeliness of the case confirmation.

    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.

    Evolution of CT Manifestations of 105 novel coronavirus pneumonia patients in Wuhan, China

    Authors: Hanxiong Guan; Shuchang Zhou; Tingting Zhu; Liming Xia; Yujin Wang; Yueying Pan

    doi:10.21203/ Date: 2020-02-26 Source: ResearchSquare

    Objectives: The purpose of this study was to observe the chest HRCT manifestation evolution of the 105 patients with pneumonia MESHD caused by SARS-CoV-2.Methods: 105 confirmed patients were enrolled from January 11, 2020 to February 9, 2020. Chest HRCT were performed. The number of affected lung lobes MESHD, lesion shape, density, range, and dynamic changes of various lesions in each CT examination of each patient were recorded to comprehensively evaluate whether it is improved. Results: CT images of 105 confirmed patients were collected. The patients underwent 2-7 chest CT examinations. M/F ratio: 49/56. The age range was 23-72 y, and the mean age was 48.6±13.1 y. The patients' chest CT examinations were divided into 5 groups according to the re-examination interval, group A (25 cases): ≤3 days, group B (70 cases): 4-7 days, group C (75 cases): 8-14 days, group D (29 cases): 15-21 days, group E (4 cases):> 21 days. There was significant difference in the improvement and progress rates between group B and C. Furthermore, the changes of ground glass nodules (GGO), consolidation and cord lesions MESHD in each group were recorded.Conclusions: The chest CT manifestations of the patients changed rapidly, and the re-examination of 7-14 days was of great significance in evaluating the prognosis of patients while minimizing the radiation dose.

    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.

    CT Manifestations and Clinical Features of the 2019 Novel Coronavirus Pneumonia Infected by Cluster Transmission Within a Family: Case Report

    Authors: Jin-ming Cao; Yu-ping Wu; Tian-wu Chen; Li-qin Yang; Xiao-ming Zhang; Qi-wen Mu; Hong-jun Li

    doi:10.21203/rs.2.24752/v1 Date: 2020-02-26 Source: ResearchSquare

    Background: In December 2019, a cluster of patients associated with a seafood wholesale market was confirmed having infected the 2019 novel coronavirus (2019-nCoV) in Wuhan, China. As of Feb 11 HGNC, 2020, 43144 cases of the 2019-nCoV infection MESHD have been confirmed in the world, and person-to-person transmission has been recognized. To our knowledge, there are no reports regarding the 2019-nCoV pneumonia infected MESHD by cluster transmission within a family. The amount of close contact suspect was increasing. We reported cases of family cluster transmission of the 2019-nCoV infection MESHD, showing the differences in computed tomography (CT) manifestations and symptoms between patients with and without history of exposure to the epidemic area (Wuhan).Case Presentation: A 48-year-old man was presented to the hospital in Jan 30, 2020 with a 2-day history of low fever MESHD and chill. He had traveled to Wuhan City of Hubei Province of China 12 days before, and was confirmed having the 2019-nCoV infection MESHD based on his positive CT manifestations, clinical signs, and real-time fluorescence polymerase chain reaction results. The other three members of his family without history of exposure to the epidemic area (Wuhan) were subsequently identified having the 2019-nCoV transmissive infection based on the positive findings of real-time fluorescence polymerase chain reaction, but they did not have abnormal CT manifestations and clinical signs.Conclusion: For patients who have history of exposure to the epidemic area (Wuhan), the 2019-nCoV infected pneumonia MESHD can be identified by real-time fluorescence polymerase chain reaction testing and chest CT together with the symptoms. But for patients without exposure to the epidemic area, the 2019-nCoV infection MESHD can be confirmed by real-time fluorescence polymerase chain reaction testing and history of close contact with confirmed patients who have history of exposure to the epidemic area.

    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.  

    Trends in Transmissibility of 2019 Novel Coronavirus-infected Pneumonia in Wuhan and 29 Provinces in China

    Authors: Huazhen Lin; Wei Liu; Hong Gao; Jinyu Nie; Qiao Fan

    doi:10.1101/2020.02.21.20026468 Date: 2020-02-25 Source: medRxiv

    Background The 2019 coronavirus disease MESHD ( COVID-19 MESHD) represents a sig- nificant p ublic h ealth t hreat g lobally. H ere w e d escribe e fforts to compare epidemic growth, size and peaking time for countries in Asia, Europe, North America, South America and Australia in the early epidemic phase. Methods Using the time series of cases reported from January 20, 2020 to February 13, 2020 and transportation data from December 1, 2019 to January 23, 2020 we have built a novel time-varying growth model to predict the epidemic trend in China. We extended our method, using cases reported from January 26, 2020 - or the date of the earliest case reported, to April 9, 2020 to predict future epidemic trend and size in 41 countries. We estimated the impact of control measures on the epidemic trend. Results Our time-varying growth model yielded high concordance in the predicted epidemic size and trend with the observed figures in C hina. Among the other 41 countries, the peak time has been observed in 28 countries before or around April 9, 2020; the peak date and epidemic size were highly consistent with our estimates. We predicted the remaining countries would peak in April or May 2020, except India in July and Pakistan in August. The epidemic trajectory would reach the plateau in May or June for the majority of countries in the current wave. Countries that could emerge to be new epidemic centers are India, Pakistan, Brazil, Mexico, and Russia with a prediction of 105 cases for these countries. The effective reproduction number Rt displayed a downward trend with time across countries, revealing the impact of the intervention remeasures i.e. social distancing. Rt remained the highest in the UK (median 2.62) and the US (median 2.19) in the fourth week after the epidemic onset. Conclusions New epidemic centers are expected to continue to emerge across the whole world. Greater challenges such as those in the healthcare system would be faced by developing countries in hotspots. A domestic approach to curb the pandemic must align with joint international efforts to effectively control the spread of COVID-19 MESHD. Our model promotes a reliable transmissibility characterization and epidemic forecasting using the incidence of cases in the early epidemic phase.

    Conjunctival polymerase chain reaction-tests of 2019 novel coronavirus in patients in Shenyang,China

    Authors: li Xu; Xinyue Zhang; Wei Song; Baijun Sun; Jinping Mu; Xue Dong; Bing Wang

    doi:10.1101/2020.02.23.20024935 Date: 2020-02-25 Source: medRxiv

    Purpose: The 2019 novel coronavirus( COVID-19 MESHD) mainly transmitted by person-to-person through inhalation of respiratory droplets. We report the laboratory results of conjunctival PCR-tests and some clinical features of these patients in shenyang China. Design: This is a cross-sectional non-randomized study. Subjects: The study include 14 confirmly diagnosed cases, 16 suspected cases and some medical observed patients. Methods: All patients with diagnosed and suspected COVID-19 MESHD were admitted to a designated hospital in Shenyang,China. We collected conjunctival samples of these patients to do the laboratory tests by real time RT-PCR.Medical observed patients were enrolled if they had clinical symptoms. Then we analysed the PCR results and clinical data from eletronic medical records in order to find some relationships. Main Outcome Measures: Clinical condition and PCR results of conjunctival swabs compared with other specimens. Results: One of the identified case coverted from suspected case without typical clinical symptoms. Twenty-two medical observed cases were removed because none of them converted to identified cases.One of the suspected converted to identified case recently.The included cases in our study are imported cases with less underlying diseases and the severity of their infection was relatively moderate. All the conjunctival results of PCR-test were negative. Two cases had typical clinical symptoms but were finally confirmed by repeated pharynx swab tests. Conclusion: Conjunctiva may be a transmission way of COVID-19 MESHD. And ocular conjunctival swabs in combination with PCR test could be a non-invasive,convenient and feasible diagnostic method for identifying the infection of COVID-19 MESHD. Emphasis on the false-negative results is vital.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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