Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (1623)

ProteinN (452)

NSP5 (380)

ComplexRdRp (216)

ProteinE (121)


SARS-CoV-2 Proteins
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    Epitope-based peptide vaccines predicted against novel coronavirus disease caused by SARS-CoV-2

    Authors: Lin Li; Ting Sun; YuFei He; Wendong Li; Yubo Fan; Jing Zhang

    doi:10.1101/2020.02.25.965434 Date: 2020-02-27 Source: bioRxiv

    The outbreak of the 2019 novel coronavirus (SARS-CoV-2) has infected thousands of people with a large number of deaths across 26 countries. The sudden appearance of the virus leads to the limited existing therapies for SARS-CoV-2. Therefore, vaccines and antiviral medicines are in desperate need. This study took immune-informatics approaches to identify B- and T-cell epitopes for surface glycoprotein (S PROTEIN) of SARS-CoV-2, followed by estimating their antigenicity and interactions with the human leukocyte antigen (HLA) alleles. We identified four B cell epitopes, two MHC class-I and nine MHC class-II binding T-cell epitopes, which showed highly antigenic features. Allergenicity, toxicity MESHD and physiochemical properties analysis confirmed the specificity and selectivity of epitopes. The stability and safety of epitopes were confirmed by digestion analysis. No mutations were observed in all the selected B- and T-cell epitopes across all isolates from different locations worldwide. Epitopes were thus identified and some of them can be potential candidates for vaccine development.

    Detection of 2019 novel coronavirus (2019-nCoV) in patients with influenza-like illness (ILI)

    Authors: Wen-Hua Kong; Yao Li; Ming-Wei Peng; De-Guang Kong; Xiao-Bing Yang; Leyi Wang; Man-Qing Liu

    doi:10.21203/rs.2.25199/v1 Date: 2020-02-27 Source: ResearchSquare

    2019 novel coronavirus (2019-nCoV) is firstly found in Wuhan and has caused over 14,000 infections all over the world. We retrospectively investigated the presence of 2019-nCoV among influenza-like illness patients in Wuhan. Nine cases in January 2020 were 2019-nCoV positive, suggesting the virus has established community transmission in Wuhan, the origin and center of this epidemic.Authors Wen-Hua Kong, Yao Li, and Ming-Wei Peng contributed equally to this work.

    Estimation of country-level basic reproductive ratios for novel Coronavirus ( COVID-19 MESHD) using synthetic contact matrices

    Authors: Joe Hilton; Matt J Keeling

    doi:10.1101/2020.02.26.20028167 Date: 2020-02-27 Source: medRxiv

    The outbreak of novel coronavirus ( COVID-19 MESHD) has the potential for global spread, infecting large numbers in all countries. In this case, estimating the country-specific basic reproductive ratio is a vital first step in public-health planning. The basic reproductive ratio (R0) is determined by both the nature of pathogen and the network of contacts through which the disease can spread - with this network determined by socio-demographics including age-structure and household composition. Here we focus on the age-structured transmission within the population, using data from China to inform age-dependent susceptibility and synthetic age-mixing matrices to inform the contact network. This allows us to determine the country-specific basic reproductive ratio as a multiplicative scaling of the value from China. We predict that R0 will be highest across Eastern Europe and Japan, and lowest across Africa, Central America and South-Western Asia. This pattern is largely driven by the ratio of children to older adults in each country and the observed propensity of clinical cases in the elderly.

    Comorbidity and its impact on 1,590 patients with COVID-19 MESHD in China: A Nationwide Analysis

    Authors: Wei-jie Guan; Wen-hua Liang; Yi Zhao; Heng-rui Liang; Zi-sheng Chen; Yi-min Li; Xiao-qing Liu; Ru-chong Chen; Chun-li Tang; Tao Wang; Chun-quan Ou; Li Li; Ping-yan Chen; Ling Sang; Wei Wang; Jian-fu Li; Cai-chen Li; Li-min Ou; Bo Cheng; Shan Xiong; Zheng-yi Ni; Yu Hu; Jie Xiang; Lei Liu; Hong Shan; Chun-liang Lei; Yi-xiang Peng; Li Wei; Yong Liu; Ya-hua Hu; Peng Peng; Jian-ming Wang; Ji-yang Liu; Zhong Chen; Gang Li; Zhi-jian Zheng; Shao-qin Qiu; Jie Luo; Chang-jiang Ye; Shao-yong Zhu; Lin-ling Cheng; Feng Ye; Shi-yue Li; Jin-ping Zheng; Nuo-fu Zhang; Nan-shan Zhong; Jian-xing He

    doi:10.1101/2020.02.25.20027664 Date: 2020-02-27 Source: medRxiv

    Objective: To evaluate the spectrum of comorbidities and its impact on the clinical outcome in patients with coronavirus disease 2019 MESHD ( COVID-19 MESHD). Design: Retrospective case studies Setting: 575 hospitals in 31 province/autonomous regions/provincial municipalities across China Participants: 1,590 laboratory-confirmed hospitalized patients. Data were collected from November 21st, 2019 to January 31st, 2020. Main outcomes and measures: Epidemiological and clinical variables (in particular, comorbidities) were extracted from medical charts. The disease severity was categorized based on the American Thoracic Society guidelines for community-acquired pneumonia MESHD. The primary endpoint was the composite endpoints, which consisted of the admission to intensive care unit (ICU), or invasive ventilation, or death MESHD. The risk of reaching to the composite endpoints was compared among patients with COVID-19 MESHD according to the presence and number of comorbidities. Results: Of the 1,590 cases, the mean age was 48.9 years. 686 patients (42.7%) were females. 647 (40.7%) patients were managed inside Hubei province, and 1,334 (83.9%) patients had a contact history of Wuhan city. Severe cases accounted for 16.0% of the study population. 131 (8.2%) patients reached to the composite endpoints. 399 (25.1%) reported having at least one comorbidity. 269 (16.9%), 59 (3.7%), 30 (1.9%), 130 (8.2%), 28 (1.8%), 24 (1.5%), 21 (1.3%), 18 (1.1%) and 3 (0.2%) patients reported having hypertension MESHD, cardiovascular diseases MESHD, cerebrovascular diseases MESHD, diabetes MESHD, hepatitis B infections MESHD, chronic obstructive pulmonary disease MESHD, chronic kidney diseases MESHD, malignancy and immunodeficiency MESHD, respectively. 130 (8.2%) patients reported having two or more comorbidities. Patients with two or more comorbidities had significantly escalated risks of reaching to the composite endpoint compared with those who had a single comorbidity, and even more so as compared with those without (all P<0.05). After adjusting for age and smoking status, patients with COPD MESHD (HR 2.681, 95%CI 1.424-5.048), diabetes MESHD (HR 1.59, 95%CI 1.03-2.45), hypertension MESHD (HR 1.58, 95%CI 1.07-2.32) and malignancy MESHD (HR 3.50, 95%CI 1.60-7.64) were more likely to reach to the composite endpoints than those without. As compared with patients without comorbidity, the HR (95%CI) was 1.79 (95%CI 1.16-2.77) among patients with at least one comorbidity and 2.59 (95%CI 1.61-4.17) among patients with two or more comorbidities. Conclusion: Comorbidities are present in around one fourth of patients with COVID-19 MESHD in China, and predispose to poorer clinical outcomes.

    Simulating the Spread of Epidemics in China on the Multi-layer Transportation Network: Beyond the Coronavirus in Wuhan

    Authors: Tianyi Li

    id:2002.12280v1 Date: 2020-02-27 Source: arXiv

    Based on the SEIR model and the modeling of urban transportation networks, a general-purpose simulator for the spread of epidemics in Chinese cities is built. The Chinese public transportation system between over 340 prefectural-level cities is modeled as a multi-layer bi-partite network, with layers representing different means of transportation (airlines, railways, sail routes and buses), and nodes divided into two categories (central cities, peripheral cities). At each city, an open-system SEIR model tracks the local spread of the disease, with population in- and out-flow exchanging with the overlying transportation network. The model accounts for (1) different transmissivities of the epidemic on different transportation media, (2) the transit of inbound flow at cities, (3) cross-infection MESHD on public transportation vehicles due to path overlap, and the realistic considerations that (4) the infected population are not entering public transportation and (5) the recovered population are not subject to repeated infections. The model could be used to simulate the city-level spread in China (and potentially other countries) of an arbitrary epidemic, characterized by its basic reproduction number, incubation period, infection period and zoonotic force, originated from any Chinese prefectural-level city(s), during the period before effective government interventions are implemented. Flowmaps are input into the system to trigger inter-city dynamics, assuming different flow strength, determined from empirical observation, within/between the bi-partite divisions of nodes. The model is used to simulate the 2019 Coronavirus epidemic in Wuhan; it shows that the framework is robust and reliable, and simulated results match public city-level datasets to an extraordinary extent.

    Correlation Analysis Between Disease Severity and Inflammation-related Parameters in Patients with COVID-19 MESHD Pneumonia

    Authors: Jing Gong; Hui Dong; Song Qing Xia; Yi Zhao Huang; Dingkun Wang; Yan Zhao; Wenhua Liu; Shenghao Tu; Mingmin Zhang; Qi Wang; Fuer Lu

    doi:10.1101/2020.02.25.20025643 Date: 2020-02-27 Source: medRxiv

    Aim: The new coronavirus pneumonia MESHD ( COVID-19 MESHD) outbreaking at the end of 2019 is highly contagious. Crude mortality rate reached 49% in critical patients. Inflammation matters MESHD on disease progression. This study analyzed blood inflammation MESHD indicators among mild, severe and critical patients, helping to identify severe or critical patients early. Methods: In this cross-sectional study, 100 patients were included and divided to mild, severe or critical groups. Correlation of peripheral blood inflammation MESHD-related indicators with disease criticality was analyzed. Cut-off values for critically ill MESHD patients were speculated through the ROC curve. ResultsSignificantly, disease severity were associated with age (R=-0.564, P<0.001), interleukin-2 receptor ( IL2R HGNC) (R=-0.534, P<0.001), interleukin-6 HGNC ( IL-6 HGNC) (R=-0.535, P<0.001), interleukin-8 HGNC ( IL-8 HGNC) (R=-0.308, P<0.001), interleukin-10 HGNC ( IL-10 HGNC) (R=-0.422, P<0.001), tumor MESHD tumor HGNC necrosis MESHD factor ( TNF HGNC) (R=-0.322, P<0.001), C-reactive protein HGNC ( CRP HGNC) (R=-0.604, P<0.001), ferroprotein (R=-0.508, P<0.001), procalcitonin (R=-0.650, P<0.001), white cell counts (WBC) (R=-0.54, P<0.001), lymphocyte counts (LC) (R=-0.56, P<0.001), neutrophil count (NC) (R=-0.585, P<0.001) and eosinophil counts (EC) (R=-0.299, P=0.01). ConclusionWith following parameters such as age >67.5 years, IL2R HGNC >793.5U/mL, CRP HGNC >30.7ng/mL, ferroprotein >2252g/L, WBC>9.5*10^9/L or NC >7.305*10^9/L, the progress of COVID-19 MESHD to critical stage should be closely observed and possibly prevented. Inflammation is closely related to severity of COVID-19 MESHD, and IL-6 HGNC, TNF HGNC and IL-8 HGNC might be promising therapeutic targets.

    An Effective CTL Peptide Vaccine for Ebola Zaire Based on Survivors' CD8+ Targeting of a Particular Nucleocapsid Protein PROTEIN Epitope with Potential Implications for COVID-19 MESHD Vaccine Design

    Authors: Charles V Herst; Scott Burkholz; John Sidney; Alessandro Sette; Paul E Harris; Shane Massey; Trevor Brasel; Edecio Cunha-Neto; Daniela S Rosa; William Chong Hang Chao; Richard Thomas Carback III; Tom Hodge; Lu Wang; Serban Ciotlos; Peter Lloyd; Reid Martin Rubsamen

    doi:10.1101/2020.02.25.963546 Date: 2020-02-27 Source: bioRxiv

    The 2013-2016 West Africa EBOV epidemic was the biggest EBOV outbreak to date. An analysis of virus-specific CD8+ T-cell immunity in 30 survivors showed that 26 of those individuals had a CD8+ response to at least one EBOV protein. The dominant response (25/26 subjects) was specific to the EBOV nucleocapsid protein PROTEIN (NP). It has been suggested that epitopes on the EBOV NP could form an important part of an effective T-cell vaccine for Ebola Zaire. We show that a 9-amino-acid peptide NP44-52 (YQVNNLEEI) located in a conserved region of EBOV NP provides protection against morbidity and mortality after mouse adapted EBOV challenge. A single vaccination in a C57BL/6 mouse using an adjuvanted microsphere peptide vaccine formulation containing NP44-52 is enough to confer immunity in mice. Our work suggests that a peptide vaccine based on CD8+ T-cell immunity in EBOV survivors is conceptually sound and feasible. Nucleocapsid proteins PROTEIN within SARS-CoV-2 contain multiple class I epitopes with predicted HLA restrictions consistent with broad population coverage. A similar approach to a CTL vaccine design may be possible for that virus.

    Community responses during the early phase of the COVID-19 MESHD epidemic in Hong Kong: risk perception, information exposure and preventive measures

    Authors: Kin On Kwok; Kin Kit Li; Ho Hin Chan; Yuan Yuan Yi; Arthur Tang; Wan In Wei; Yeung Shan Wong

    doi:10.1101/2020.02.26.20028217 Date: 2020-02-27 Source: medRxiv

    Background: Community responses are important for outbreak management during the early phase when non-pharmaceutical interventions are the major preventive options. Therefore, this study aims to examine the psychological and behavioral responses of the community during the early phase of the COVID-19 MESHD epidemic in Hong Kong. Method: A cross-sectional online survey was launched within 36 hours after confirmed COVID-19 MESHD cases were first reported. Councilors of all 452 district council constituency areas were approached for survey dissemination. Respondent demographics, anxiety MESHD level, risk perception, sources to retrieve COVID-19 MESHD information, actual adoption and perceived efficacy of precautionary measures were collected. Result: Analysis from 1715 complete responses indicated high perceived susceptibility (89%) and high perceived severity (97%). Most respondents were worried about COVID-19 MESHD (97%), and had their daily routines disrupted (slightly/greatly: 98%). The anxiety MESHD level, measured by the Hospital Anxiety and Depression MESHD Scale, was borderline abnormal (9.01). Nearly all respondents were alert to the disease progression (99.5%). The most trusted information sources were doctors (84%), followed by broadcast (57%) and newspaper (54%), but they were not common information sources (doctor: 5%; broadcast: 34%; newspaper: 40%). Only 16% respondents found official websites reliable. Enhanced personal hygiene practices and travel avoidance to China were frequently adopted (>77%) and considered effective (>90%). The adoption of social-distancing measures was lower (39%-88%), and their drivers for greater adoption include: being female (adjusted odds ratio [aOR]:1.27), living in the New Territories (aOR:1.32-1.55), perceived as having good understanding of COVID-19 MESHD (aOR:1.84) and being more anxious (aOR:1.07). Discussion: Risk perception towards COVID-19 MESHD in the community was high. Most respondents are alert to the disease progression, and adopt self-protective measures. This study contributes by examining the psycho-behavioral responses of hosts, in addition to the largely studied mechanistic aspects, during the early phase of the current COVID-19 MESHD epidemic. The timely psychological and behavioral assessment of the community is useful to inform subsequent interventions and risk communication strategies as the epidemic progresses.

    Clinical Characteristics of Coronavirus Disease 2019 MESHD ( COVID-19 MESHD) in Patients out of Wuhan from China

    Authors: Hua Zhang; Feng Du; Xiao-jun Cao; Xia-long Feng; He-ping Zhang; Zheng-xia Wu; Bao-Feng Wang; Hong-juan Zhang; Rui Liu; Jian-jun Yang; Bo Ning; Kai Chen; ZHENPENG HUANG

    doi:10.21203/ Date: 2020-02-27 Source: ResearchSquare

    Background: A large-scale global outbreak of coronavirus disease-19 MESHD ( COVID-19 MESHD) out of Wuhan, from China, occurred in January 2020. Objective: To examine the clinical characteristics of COVID-19 MESHDin infected patients out of Wuhan, from China. Patients and Methods: Thirteen patients were confirmed to be infected with novel coronavirus-2019 (2019-nCoV) between January 27andFebruary 8, 2020, in Baoji city, Shanxi, northwestern China. Epidemiological and clinical information, and computed to morphology imaging data from all COVID-19 MESHD patients were collected; cases were divided into two groups according to the severity of infection (mild or severe). Results: Nine (9/13) COVID-19 MESHDpatientsexhibitedmild disease severity, and defined as second-generation, human-to-human transmission cases. Most patients (11/13) had a history of travel to or from Wuhan. There were no differences in sex and age between the mild and severe cases (all P>0.05). A moderate degree of fever (11/13), cough (13/13), and fatigue (8/13) were common symptoms; however, there was no statistical difference between mild and severe cases in this regard (all P>0.05). Oxyhemoglobin saturation and oxygenation index decreased, and C-reactive protein HGNC ( CRP HGNC) and serum amyloid A (SAA) levels were elevated in all patients with COVID-19 MESHDinfection, with statistically significant differences between those with severe disease and mild infection (all P<0.05).Twelve of 13 COVID-19 MESHDpatients exhibited changes in chest CT imaging features, and time course changes were different between mild and severe cases (all P<0.05).Conclusion: Most cases of COVID-19 MESHDinfection were second-generation human-to-human transmissions from Wuhan and were mild in severity. The clinical characteristics of COVID-19 MESHDvaried.Oxyhemoglobin saturation, oxygenation index, CRP HGNC and SAA levels, and CT features were reliable parameters to evaluate the severity of COVID-19 MESHD infection. However, a few patients with mild COVID-19 MESHDdiseaselackedtypicalcharacteristics such as fever and changes in CT imaging features.

    Perceptions of the Adult US Population regarding the Novel Coronavirus Outbreak

    Authors: SarahAnn M McFadden; Amyn A Malik; Obianuju G Aguolu; Kathryn S Willebrand; Saad B Omer

    doi:10.1101/2020.02.26.20028308 Date: 2020-02-27 Source: medRxiv

    Background: COVID-19 MESHD outbreak is spreading globally. Although the risk of infection in the US is currently low, it is important to understand the public perception of risk and trust in sources of information to better inform public health messaging. In this study, we surveyed the adult US population to understand their risk perceptions about the COVID-19 MESHD outbreak. Methods and Findings: We used an online platform to survey 718 adults in the US in early February 2020 using a questionnaire that we developed. Our sample was fairly similar to the general adult US population in terms of age, gender, race, ethnicity and education. We found that 69% of the respondents wanted the scientific/public health leadership (either the CDC Director or NIH Director) to lead the US response to COVID-19 MESHD outbreak as compared to 14% who wanted the political leadership (either the president or the Congress) to lead the response. Risk perception was low (median score of 5 out of 10) with the respondents trusting health professionals and health officials for information on COVID-19 MESHD. Majority of the respondents were in favor of strict infection prevention policies to control the outbreak. Conclusion: Given our results, the public health/scientific leadership should be at the forefront of the COVID-19 MESHD response to promote trust.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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