Corpus overview


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MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (1599)

ProteinN (450)

NSP5 (321)

ComplexRdRp (189)

ProteinE (105)


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SARS-CoV-2 Proteins
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    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.

    Increasing Host Cellular Receptor--Angiotensin-Converting Enzyme 2 ( ACE2 HGNC) Expression by Coronavirus may Facilitate 2019-nCoV Infection MESHD

    Authors: Pei-Hui Wang

    doi:10.1101/2020.02.24.963348 Date: 2020-02-27 Source: bioRxiv

    The ongoing outbreak of a new coronavirus (2019-nCoV) causes an epidemic of acute respiratory syndrome MESHD in humans. 2019-nCoV rapidly spread to national regions and multiple other countries, thus, pose a serious threat to public health. Recent studies show that spike (S) proteins PROTEIN of 2019-nCoV and SARS-CoV MESHD may use the same host cell receptor called angiotensin-converting enzyme 2 ( ACE2 HGNC) for entering into host cells. The affinity between ACE2 HGNC and 2019-nCoV S is much higher than ACE2 HGNC binding to SARS-CoV S protein MESHD S protein PROTEIN, explaining that why 2019-nCoV seems to be more readily transmitted from the human to human. Here, we reported that ACE2 HGNC can be significantly upregulated after infection of various viruses including SARS-CoV MESHD and MERS-CoV. Basing on findings here, we propose that coronavirus infection MESHD can positively induce its cellular entry receptor to accelerate their replication and spread, thus drugs targeting ACE2 HGNC expression may be prepared for the future emerging infectious diseases MESHD caused by this cluster of viruses.

    An R package and a website with real-time data on the COVID-19 MESHD coronavirus outbreak

    Authors: Tianzhi Wu; Xijin Ge; Guangchuang Yu; Erqiang Hu

    doi:10.1101/2020.02.25.20027433 Date: 2020-02-27 Source: medRxiv

    To provide convenient access to epidemiological data on the coronavirus outbreak, we developed an R package, nCov2019 (https://github.com/GuangchuangYu/nCov2019). Besides detailed real-time statistics, it offers access to three data sources with detailed daily statistics from December 1, 2019, for 43 countries and more than 500 Chinese cities. We also developed a web app (http://www.bcloud.org/e/) with interactive plots and simple time-series forecasts. These analytics tools could be useful in informing the public and studying how this and similar viruses spread in populous countries.

    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/rs.3.rs-15311/v1 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. 

    The landscape of lung bronchoalveolar immune cells in COVID-19 MESHD revealed by single-cell RNA sequencing

    Authors: Minfeng Liao; Yang Liu; Jin Yuan; Yanling Wen; Gang Xu; Juanjuan Zhao; Lin Chen; Jinxiu Li; Xin Wang; Fuxiang Wang; Lei Liu; Shuye Zhang; Zheng Zhang

    doi:10.1101/2020.02.23.20026690 Date: 2020-02-26 Source: medRxiv

    The novel coronavirus SARS-CoV-2, etiological agent of recently named Coronavirus infected disease MESHD ( COVID-19 MESHD) by WHO, has caused more than 2, 000 deaths worldwide since its emergency in Wuhan City, Hubei province, China, in December, 2019. The symptoms of COVID-19 MESHD varied from modest, mild to acute respiratory distress syndrome MESHD ( ARDS MESHD), and the latter of which is generally associated with deregulated immune cytokine production; however, we currently know little as to the interplay between the extent of clinical symptoms and the compositions of lung immune microenvironment. Here, we comprehensively characterized the lung immune microenvironment with the bronchoalveolar lavage fluid (BALF) from 3 severe and 3 mild COVID-19 MESHD patients and 8 previously reported healthy lung controls through single-cell RNA sequence (scRNA-seq) combined with TCR-seq. Our data shows that monocyte-derived FCN1 HGNC+ macrophages, whereas notFABP4+ alveolar MESHD macrophages that represent a predominant macrophage subset in BALF from patients with mild diseases, overwhelm in the severely damaged lungs from patients with ARDS MESHD. These cells are highly inflammatory and enormous chemokine producers implicated in cytokine storm. Furthermore, the formation of tissue resident, highly expanded clonal CD8+ T cells in the lung microenvironment of mild symptom patients suggests a robust adaptive immune response connected to a better control of COVID-19 MESHD. This study first reported the cellular atlas of lung bronchoalveolar MESHD immune microenvironment in COVID-19 MESHD patients at the single-cell resolution, and unveiled the potential immune mechanisms underlying disease progression and protection in COVID-19 MESHD.

    The infection evidence of SARS-COV-2 in ocular surface: a single-center cross-sectional study

    Authors: Xufang Sun; Xian Zhang; Xuhui Chen; Liwen Chen; Chaohua Deng; Xiaojing Zou; Weiyong Liu; Huimin Yu

    doi:10.1101/2020.02.26.20027938 Date: 2020-02-26 Source: medRxiv

    Purpose: The aim of this study was to identify whether SARS-COV-2 infected MESHD in ocular surface. Methods: Cross-sectional study of patients presenting for who received a COVID-19 MESHD diagnosis, from December 30, 2019 to February 7, 2020, at Tongji hospital, Tongji medical college, Huazhong University of Science and Technology. Demographics, temperature was recorded, blood routine test (Rt), chest Computed Tomography (CT) were took intermittently, and SARS-COV-2 real-time reverse-transcriptase-polymerase-chain-reaction (RT-PCR) assay were arranged for the nasopharyngeal and conjunctival swab samples. Results: A total of 102 patients (48 Male [50%] and 54 Female [50%]) with clinical symptoms, Rt, and chest Computed Tomography (CT) abnormalities were identified with a clinical diagnosis of COVID-19 MESHD. Patients had a mean [SD] gestational age of 57.63 [14.90] years. Of a total of 102 patients identified, 72 patients (36 men [50%] and 36 women [50%]; mean [SD] age, 58.68 [14.81] years) confirmed by laboratory diagnosis with SARS-COV-2 RT-PCR assay. Only two patients (2.78%) with conjunctivitis MESHD was identified from 72 patients with a laboratory confirmed COVID-19 MESHD. However, SARS-COV-2 RNA fragments was found in ocular discharges by SARS-COV-2 RT-PCR only in one patient with conjunctivitis MESHD. Conclusions: Although we suspect the incidence of SARS-COV-2 infection MESHD through the ocular surface is extremely low, the nosocomial infection of SARS-CoV-2 MESHD through the eyes after occupational exposure is a potential route. The inefficient diagnostic method and the sampling time lag may contribute to the lower positive rate of conjunctival swab samples of SARS-COV-2. Therefore, to lower the SARS-COV-2 nosocomial infection MESHD, the protective goggles should be wore in all the health care workers.

    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.

    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: Preprints.org

    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.

    Deep learning-based model for detecting 2019 novel coronavirus pneumonia on high-resolution computed tomography: a prospective study in 27 patients

    Authors: Jun Chen; Lianlian Wu; Jun Zhang; Liang Zhang; Dexin Gong; Yilin Zhao; Shan Hu; Yonggui Wang; Xiao Hu; Biqing Zheng; Kuo Zhang; Huiling Wu; Zehua Dong; Youming Xu; Yijie Zhu; Xi Chen; Lilei Yu; Honggang Yu

    doi:10.1101/2020.02.25.20021568 Date: 2020-02-26 Source: medRxiv

    Background: Computed tomography (CT) is the preferred imaging method for diagnosing 2019 novel coronavirus ( COVID19 MESHD) pneumonia MESHD. Our research aimed to construct a system based on deep learning for detecting COVID-19 MESHD pneumonia MESHD on high resolution CT, relieve working pressure of radiologists and contribute to the control of the epidemic. Methods: For model development and validation, 46,096 anonymous images from 106 admitted patients, including 51 patients of laboratory confirmed COVID-19 MESHD pneumonia MESHD and 55 control patients of other diseases in Renmin Hospital of Wuhan University (Wuhan, Hubei province, China) were retrospectively collected and processed. Twenty-seven consecutive patients undergoing CT scans in Feb, 5, 2020 in Renmin Hospital of Wuhan University were prospectively collected to evaluate and compare the efficiency of radiologists against 2019-CoV pneumonia MESHD with that of the model. Findings: The model achieved a per-patient sensitivity of 100%, specificity of 93.55%, accuracy of 95.24%, PPV of 84.62%, and NPV of 100%; a per-image sensitivity of 94.34%, specificity of 99.16%, accuracy of 98.85%, PPV of 88.37%, and NPV of 99.61% in retrospective dataset. For 27 prospective patients, the model achieved a comparable performance to that of expert radiologist. With the assistance of the model, the reading time of radiologists was greatly decreased by 65%. Conclusion: The deep learning model showed a comparable performance with expert radiologist, and greatly improve the efficiency of radiologists in clinical practice. It holds great potential to relieve the pressure of frontline radiologists, improve early diagnosis, isolation and treatment, and thus contribute to the control of the epidemic.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins


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