Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (2227)

ProteinN (575)

NSP5 (418)

ComplexRdRp (253)

ProteinE (148)


SARS-CoV-2 Proteins
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    Inhibition of the Main Protease PROTEIN 3CL-pro of the Coronavirus Disease 19 via Structure-Based Ligand Design and Molecular Modeling

    Authors: Marina Macchiagodena; Marco Pagliai; Piero Procacci

    id:2002.09937v2 Date: 2020-02-23 Source: arXiv

    We have applied a computational strategy, based on the synergy of virtual screening, docking and molecular dynamics techniques, aimed at identifying possible lead compounds for the non-covalent inhibition of the main protease PROTEIN 3CL-pro of the SARS-Cov2 Coronavirus. Based on the recently resolved 6LU7 PDB structure, ligands were generated using a multimodal structure-based design and then optimally docked to the 6LU7 monomer. Docking calculations show that ligand-binding is strikingly similar in SARS-CoV MESHD and SARS-CoV2 main proteases PROTEIN, irrespectively of the protonation state of the catalytic CYS-HIS dyad. The most potent docked ligands are found to share a common binding pattern with aromatic moieties connected by rotatable bonds in a pseudo-linear arrangement. Molecular dynamics calculations fully confirm the stability in the 3CL-pro binding pocket of the most potent binder identified by docking, namely a chlorophenyl-pyridyl-carboxamide derivative.

    CoVID-19 MESHD in Japan: What could happen in the future?

    Authors: Nian Shao; Hanshuang Pan; Xingjie Li; Weijia Li; Shufen Wang; Yan Xuan; Yue Yan; Yu Jiang; Keji Liu; Yu Chen; Boxi Xu; Xinyue Luo; Christopher Y. Shen; Min Zhong; Xiang Xu; Xu Chen; Shuai Lu; Guanghong Ding; Jin Cheng; Wenbin Chen

    doi:10.1101/2020.02.21.20026070 Date: 2020-02-23 Source: medRxiv

    COVID-19 MESHD has been impacting on the whole world critically and constantly Since December 2019. We have independently developed a novel statistical time delay dynamic model on the basis of the distribution models from CCDC. Based only on the numbers of confirmed cases in different regions in China, the model can clearly reveal that the containment of the epidemic highly depends on early and effective isolation. We apply the model on the epidemic in Japan and conclude that there could be a rapid outbreak in Japan if no effective quarantine measures are carried out immediately.

    ACP risk grade: a simple mortality index for patients with confirmed or suspected severe acute respiratory syndrome coronavirus 2 disease ( COVID-19 MESHD) during the early stage of outbreak in Wuhan, China

    Authors: Jiatao Lu; Shufang Hu; Rong Fan; Zhihong Liu; Xueru Yin; Qiongya Wang; Qingquan Lv; Zhifang Cai; Haijun Li; Yuhai Hu; Ying Han; Hongping Hu; Wenyong Gao; Shibo Feng; Qiongfang Liu; Hui Li; Jian Sun; Jie Peng; Xuefeng Yi; Zixiao Zhou; Yabing Guo; Jinlin Hou

    doi:10.1101/2020.02.20.20025510 Date: 2020-02-23 Source: medRxiv

    Background: Since the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease MESHD ( COVID-19 MESHD) outbreaks in Wuhan, China, healthcare systems capacities in highly endemic areas have been overwhelmed. Approaches to efficient management are urgently needed and key to a quicker control of the outbreaks and casualties. We aimed to characterize the clinical features of hospitalized patients with confirmed or suspected COVID-19 MESHD, and develop a mortality risk index for COVID-19 MESHD patients. Methods: In this retrospective one-centre cohort study, we included all the confirmed or suspected COVID-19 MESHD patients hospitalized in a COVID-19 MESHD-designated hospital from January 21 to February 5, 2020. Demographic, clinical, laboratory, radiological and clinical outcome data were collected from the hospital information system, nursing records and laboratory reports. Results: Of 577 patients with at least one post-admission evaluation, the median age was 55 years (interquartile range [IQR], 39 - 66); 254 (44.0%) were men; 22.8% (100/438) were severe pneumonia MESHD on admission, and 37.7% (75/199) patients were SARS-CoV-2 positive. The clinical, laboratory and radiological data were comparable between positive and negative SARS-CoV-2 patients. During a median follow-up of 8.4 days (IQR, 5.8 - 12.0), 39 patients died with a 12-day cumulative mortality of 8.7% (95% CI, 5.9% to 11.5%). A simple mortality risk index (called ACP index), composed of Age and C-reactive Protein HGNC, was developed. By applying the ACP index, patients were categorized into three grades. The 12-day cumulative mortality in grade three (age [≥] 60 years and CRP [≥] 34 mg/L) was 33.2% (95% CI, 19.8% to 44.3%), which was significantly higher than those of grade two (age [≥] 60 years and CRP < 34 mg/L; age < 60 years and CRP [≥] 34 mg/L; 5.6% [95% CI, 0 to 11.3%]) and grade one (age < 60 years and CRP < 34 mg/L, 0%) (P <0.001), respectively. Conclusion: The ACP index can predict COVID-19 MESHD related short-term mortality, which may be a useful and convenient tool for quickly establishing a COVID-19 MESHD hierarchical management system that can greatly reduce the medical burden and therefore mortality in highly endemic areas.

    Estimating the Asymptomatic Ratio of 2019 Novel Coronavirus onboard the Princess Cruises Ship HGNC, 2020

    Authors: Kenji Mizumoto; Katsushi Kagaya; Alexander Zarebski; Gerardo Chowell

    doi:10.1101/2020.02.20.20025866 Date: 2020-02-23 Source: medRxiv

    The potential infectiousness of asymptomatic COVID-19 MESHD cases together with a substantial fraction of asymptomatic infections among all infections, have been highlighted in clinical studies. We conducted statistical modeling analysis to derive the delay-adjusted asymptomatic proportion of the positive COVID-19 MESHD infections onboard the Princess Cruises ship MESHD ship HGNC along with the timeline of infections. We estimated the asymptomatic proportion at 17.9% (95% CrI: 15.5%-20.2%), with most of the infections occurring before the start of the 2-week quarantine.

    Public Exposure to Live Animals, Behavioural Change, and Support in Containment Measures in response to COVID-19 MESHD Outbreak: a population-based cross sectional survey in China

    Authors: Zhiyuan Hou; Leesa Lin; Liang Lu; Fanxing Du; Mengcen Qian; Yuxia Liang; Juanjuan Zhang; Hongjie Yu

    doi:10.1101/2020.02.21.20026146 Date: 2020-02-23 Source: medRxiv

    Background In response to the COVID-19 MESHD outbreak, we aimed to investigate behavioural change on exposure to live animals before and during the outbreak, and public support and confidence for governmental containment measures. Methods A population-based cross-sectional telephone survey via random dialing was conducted in Wuhan (the epicentre) and Shanghai (an affected city with imported cases) between 1 and 10 February, 2020. 510 residents in Wuhan and 501 residents in Shanghai were randomly sampled. Differences of outcome measures were compared before and during the outbreak, and between two cities. Findings Proportion of respondents visiting wet markets at usual was 23.3% (119/510) in Wuhan and 20.4% (102/501) in Shanghai. During the outbreak, it decreased to 3.1% (16) in Wuhan (p<0.001), and 4.4% (22) in Shanghai (p<0.001). Proportion of those consuming wild animal products declined from 10.2% (52) to 0.6% (3) in Wuhan (p<0.001), and from 5.2% (26) to 0.8% (4) in Shanghai (p<0.001). 79.0% (403) of respondents in Wuhan and 66.9% (335) of respondents in Shanghai supported permanent closure of wet markets (P<0.001). 95% and 92% of respondents supported banning wild animal trade and quarantining Wuhan, and 75% were confident towards containment measures. Females and the more educated were more supportive for the above containment measures. Interpretation The public responded quickly to the outbreak, and reduced exposure to live animals, especially in Wuhan. With high public support in containment measures, better regulation of wet markets and healthy diets should be promoted.

    Clinical characteristics of 51 patients discharged from hospital with COVID-19 MESHD in Chongqing,China

    Authors: liu lei; Gao Jian-ya

    doi:10.1101/2020.02.20.20025536 Date: 2020-02-23 Source: medRxiv

    Abstract BackgroundSince December 2019, Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)-infected disease MESHD ( Coronavirus Disease 2019 MESHD COVID-19 MESHD) emerged in Wuhan , Chinaand rapidly spread throughout Chinaeven throughout the world. We try to describe the epidemiological and clinical characteristics of COVID-19 MESHD in non-Wuhan areaand explore its effective treatment. MethodsRetrospective, single-center case series of the 51 hospitalized patients with confirmed COVID-19 MESHD at Chongqing University Three Gorges Hospital in Chongqing, China, from January 20 to February 3, 2020The discharge time was from January 29 to February 11, 2020. The main results and indicators of epidemiology, demography, clinical manifestation, laboratory examination, imaging data and treatment data of 51 patients with covid-19 MESHD were collected and analyzed. The changes of blood routine and biochemical indexes at discharge and admission were compared. Compare the clinical characteristics of severe patients (including severe and critical patients) and non- severe patients (general patients). Results Of 51 hospitalized patients with COVID-19 MESHD, the median age was 45 years (interquartile range, 34-51; range, 16-68 years) and 32 (62.7%) were men.43(84.3%)patients had been to Wuhan or Other Hubei areas outside Wuhanand 4(7.7%) patients had a clear contact history of COVID-19 MESHD patients before the onset of the disease, and 4(7.7%) patients had no clear epidemiological history of COVID-19 MESHD.Common symptoms included fever MESHD (43 [84.3%]), cough (38 [74.5%]) and fatigue MESHD (22 [43.1%]). Lymphopenia MESHD was observed in 26 patients (51.0%), and elevated C-reactive protein HGNC level in 32 patients (62.7%). Ground-glass opacity was the typical radiological finding on chest computed tomography (41 [80.4%])Local consolidation of pneumonia MESHD in some patients(17 [33.3%]).Most of the patients were treated with traditional Chinese medicine decoction (28 [54.9%])all of them received aerosol inhalation of recombinant human interferon a-1b for injection and oral antiviral therapy with Lopinavir and Ritonavir tablets (51 [100%]); Most of the patients were given Bacillus licheniformis capsules regulated intestinal flora treatment (44 [86.3%]). 10 patients (19.6%) received short-term (3-5 days) glucocorticoid treatment. Compared with non-severe patients (n = 44), severe patients (n = 7) were older (median age, 52 years vs 44 years), had a higher proportion of diabetes mellitus (4 [57.1%] vs 0 [0.0%]), most of them needed antibiotic treatment (7 [100%] vs 4 [9.1%], most of them needed nutritional diet (6 [85.7%) vs 0 [0.0%], and were more likely to have dyspnea (6 [85.7%] vs 5 [11.4%])most of them needed noninvasive mechanical ventilation (6 [85.7%] vs 0 [0.0%]). Except one patient died, the remaining 50 patients were discharged according to the discharge standard, the common clinical symptoms disappeared basically, the lymphocyte increased significantly (P=0.008), CRP HGNC decreased significantly (P <0.001). The median length of stay was 12 days (IQR, 9-13). ConclusionIn 51 single center cases confirmed as COVID-19 MESHD and discharged from the hospital, 13.7% of the patients were severe. The main clinical symptoms of patients with COVID-19 MESHD were fever, cough and astheniaSome patients had obvious dyspnea. They had clinical laboratory and radiologic characteristics. There is no specific drug treatment for the disease. For the treatment of COVID-19 MESHD, in addition to oxygen inhalation and antiviral treatment, attention should be paid to the dialectical treatment of traditional Chinese medicine, regulation of intestinal flora, nutritional support treatment and other comprehensive treatment.

    Trends and prediction in daily incidence of novel coronavirus infection in China, Hubei Province and Wuhan City: an application of Farr law

    Authors: Jie Xu; Yajiao Cheng; Xiaoling Yuan; Wei V. Li; Lanjing Zhang

    doi:10.1101/2020.02.19.20025148 Date: 2020-02-23 Source: medRxiv

    Background: The recent outbreak of novel coronavirus (2019-nCoV) has infected tens of thousands of patients in China. Studies have forecasted future trends of the incidence of 2019-nCoV infection MESHD, but appeared unsuccessful. Farr law is a classic epidemiology theory/practice for predicting epidemics. Therefore, we used and validated a model based on Farr law to predict the daily-incidence of 2019-nCoV infection MESHD in China and 2 regions of high-incidence. Methods: We extracted the 2019-nCoV incidence data of China, Hubei Province and Wuhan City from websites of the Chinese and Hubei health commissions. A model based on Farr law was developed using the data available on Feb. 8, 2020, and used to predict daily-incidence of 2019-nCoV infection MESHD in China, Hubei Province and Wuhan City afterward. Results: We observed 50,995 (37001 on or before Feb. 8) incident cases in China from January 16 to February 15, 2020. The daily-incidence has peaked in China, Hubei Providence and Wuhan City, but with different downward slopes. If no major changes occur, our model shows that the daily-incidence of 2019-nCoV will drop to single-digit by February 25 for China and Hubei Province, but by March 8 HGNC for Wuhan city. However, predicted 75% confidence intervals of daily-incidence in all 3 regions of interest had an upward trend. The predicted trends overall match the prospectively-collected data, confirming usefulness of these models. Conclusions: This study shows the daily-incidence of 2019-nCoV in China, Hubei Province and Wuhan City has reached the peak and was decreasing. However, there is a possibility of upward trend.

    A descriptive study of the impact of diseases control and prevention on the epidemics dynamics and clinical features of SARS-CoV-2 outbreak in Shanghai, lessons learned for metropolis epidemics prevention

    Authors: Hongzhou Lu; Jingwen Ai; Yinzhong Shen; Yang Li; Tao Li; Xian Zhou; Haocheng Zhang; Qiran Zhang; Yun Ling; Sheng Wang; Hongping Qu; Yuan Gao; Yingchuan Li; Kanglong Yu; Duming Zhu; Hecheng Zhu; Rui Tian; Mei Zeng; Qiang Li; Yuanlin Song; Xiangyang Li; Jinfu Xu; Jie Xu; Enqiang Mao; Bijie Hu; Xin Li; Lei Zhu; Wenhong Zhang

    doi:10.1101/2020.02.19.20025031 Date: 2020-02-23 Source: medRxiv

    Objective: To describe and evaluate the impact of diseases control and prevention on epidemics dynamics and clinical features of SARS-CoV-2 outbreak in Shanghai. Design: A retrospective descriptive study Setting: China Participants: Epidemiology information was collected from publicly accessible database. 265 patients admitted to Shanghai Public Health Center with confirmed COVID-19 MESHD were enrolled for clinical features analysis. Main outcome measure: Prevention and control measures taken by Shanghai government, epidemiological, demographic, clinical, laboratory and radiology data were collected. Weibull distribution, Chi-square test, Fisher's exact test, t test or Mann-Whitney U test were used in statistical analysis. Results: COVID-19 MESHD transmission rate within Shanghai had reduced over 99% than previous speculated, and the exponential growth has been stopped so far. Epidemic was characterized by the first stage mainly composed of imported cases and the second stage where >50% of cases were local. The incubation period was 6.4 (95% CI 5.3 to 7.6) days and the mean onset-admission interval was 5.5 days (95% CI, 5.1 to 5.9). Median time for COVID-19 MESHD progressed to severe diseases MESHD were 8.5 days (IQR: 4.8-11.0 days). By February 11th, proportion of patients being mild, moderate, severe and critically ill were 1.9%(5/265), 89.8%(238/265), 3.8%(10/265), 4.5%(12/265), respectively; 47 people in our cohort were discharged, and 1 patient died. Conclusion: Strict controlling of the transmission rate at the early stage of an epidemic in metropolis can quickly prohibit the spread of the diseases. Controlling local clusters is the key to prevent outbreaks from imported cases. Most COVID-19 MESHD severe cases progressed within 14 days of disease onset. Multiple systemic laboratory abnormalities had been observed before significant respiratory dysfunction MESHD. Keyword: COVID-19 MESHD, SARS-CoV-2, epidemics dynamics, diseases control, clinical features

    The cross-sectional study of hospitalized coronavirus disease 2019 MESHD patients in Xiangyang, Hubei province

    Authors: Jinwei Ai; Junwen Chen; Yong Wang; Xiaoyun Liu; Wufeng Fan; Gaojing Qu; Meiling Zhang; Shengduo Polo Pei; Bowen Tang; Shuai Yuan; Yang Li; Lisha Wang; Guoxin Huang; Bin Pei

    doi:10.1101/2020.02.19.20025023 Date: 2020-02-23 Source: medRxiv

    Summary Objective To describe the epidemiological and clinical characteristics of the Coronavirus Disease 2019 MESHD ( COVID-19 MESHD) hospitalized patients and to offer suggestions to the urgent needs of COVID-19 MESHD prevention, diagnosis and treatment. Methods We included 102 confirmed COVID-19 MESHD cases hospitalized in Xiangyang No.1 peoples hospital, Hubei, China until Feb 9th, 2020. Demographic data, laboratory findings and chest computed tomographic (CT) images were obtained and analyzed. Findings All cases were confirmed by real-time RT-PCR, including 52 males and 50 females with a mean age of 50.38 years (SD 16.86). Incubation time ranged from one to twenty days with a mean period of 8.09 days (SD 4.99). Fever MESHD (86[84.3%] of 102 patients), cough (58[57%]), fatigue MESHD (28[27%]), shortness of breath MESHD (24[23%]), diarrhea MESHD (15[15%]), expectoration (13[12%]), inappetence (11[10%]) were common clinical manifestations. We observed a decreased blood leukocyte count and lymphopenia MESHD in 21 (20.6%) and 56 (54.9%) patients, respectively. There were 66 (68%) of 97 patients with elevated C-reactive protein HGNC levels and 49 (57.6%) of 85 with increased erythrocytes sedimentation rate. Higher levels of procalcitonin and ferritin were observed in 19 (25.3%) of 75 and 12 (92.3%) of 13 patients, respectively. Eight patients were admitted to intensive care unit (ICU), six developed respiratory failure MESHD, three had multiple organ failure MESHD and three died. The cumulative positivity rate over three rounds of real-time RT-PCR was 96%. One-hundred patients were found with typical radiological abnormalities in two rounds of chest CT scans, indicating a 98% consistency with real-time RT-PCR results. Interpretation Most COVID-19 MESHD patients in Xiangyang were secondary cases without sex difference, and the rate of severe cases and death MESHD was low. Middle-to-old-age individuals were more susceptible to the virus infection MESHD and the subsequent development of severe/fatal consequences. The average incubation period was longer among our patients. We recommend prolonging the quarantine period to three weeks. Three times real-time RT-PCR plus two times CT scans is a practical clinical diagnosis strategy at present and should be used to increase the accuracy of diagnosis, thereby controlling the source of infection more effectively. Key Words SARS-CoV-2; COVID-19 MESHD; epidemiological and clinical features; diagnosis

    The serial interval of COVID-19 MESHD from publicly reported confirmed cases

    Authors: Zhanwei Du; Xiaoke Xu; Ye Wu; Lin Wang; Benjamin J Cowling; Lauren Ancel Meyers

    doi:10.1101/2020.02.19.20025452 Date: 2020-02-23 Source: medRxiv

    As a novel coronavirus ( COVID-19 MESHD) continues to emerge throughout China and threaten the globe, its transmission characteristics remain uncertain. Here, we analyze the serial intervals-the time period between the onset of symptoms in an index (infector) case and the onset of symptoms in a secondary (infectee) case-of 468 infector-infectee pairs with confirmed COVID-19 MESHD cases reported by health departments in 18 Chinese provinces between January 21, 2020, and February 8, 2020. The reported serial intervals range from -11 days to 20 days, with a mean of 3.96 days (95% confidence interval: 3.53-4.39), a standard deviation of 4.75 days (95% confidence interval: 4.46-5.07), and 12.6% of reports indicating pre-symptomatic transmission.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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