Corpus overview


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MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinN (575)

ProteinS (199)

ComplexRdRp (33)

ProteinE (33)

ORF1ab (28)


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SARS-CoV-2 Proteins
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    Insufficient Sensitivity of RNA Dependent RNA Polymerase PROTEIN Gene of SARS-CoV-2 Viral Genome as Confirmatory Test using Korean COVID-19 MESHD Cases

    Authors: Soyoun Kim; Dong-Min Kim; Baeckseung Lee

    id:10.20944/preprints202002.0424.v1 Date: 2020-02-28 Source: Preprints.org

    Since mid-December of 2019, coronavirus disease 2019 MESHD ( COVID-19 MESHD) has been spreading from Wuhan, China. As of February 21, total 75,773 confirmed cases worldwide have spread to more than two dozen countries. Transmission of COVID-19 MESHD can occur early in the course of infection since SARS-CoV-2 viral loads in asymptomatic patients are similar to that in the symptomatic patients. Therefore, more sensitive diagnostic methods are needed to detect early phase of the infection to prevent secondary or tertiary spreads. Here, we compare the RT-PCR confirmatory test results using two different SARS-CoV-2 viral RNAs from two Korean COVID-19 MESHD confirmed cases.RT-PCR method targeting the RdRP PROTEIN gene, which was recommended by WHO guideline, was less sensitive than targeting N genes PROTEIN (as per CDC guideline). Because many countries follow the WHO guideline, our findings may contribute to the early diagnosis of COVID-19 MESHD.

    Can Search Query Forecast successfully in China’s novel coronavirus(2019-nCov)pneumonia?

    Authors: Li Xiaoxuan; Wu Qi; Lv Benfu

    doi:10.21203/rs.3.rs-15566/v1 Date: 2020-02-27 Source: ResearchSquare

    Background: Recently the 2019-nCov pneumonia MESHD outbreak in China then the world. Search Query performs well in forecasting the epidemics. It is still a suspense whether search query can forecast the drift and the inflexion in 2019-nCov pneumonia MESHD. Based on the Baidu Search Index, we propose three prediction models: composite Index, composite Index with filtering (Fourier Transform) and suspected NCP PROTEIN(Novel Coronavirus Pneumonia) cases. With the trained models, we predict the new confirmed cases of 2019-nCov of forecast-period from Feb. 3rd to 9th. Attempting to identify the next peak period, we further estimate 10 day out-of-sample of the new confirmed cases from Feb. 10th to 19th.Results: We select 16 search queries related to NCP PROTEIN and calculate the correlation coefficient. The maximum correlation coefficient of search queries is above 0.8. The composite Index performs 10 days ahead of the new confirmed cases. With the In-sample prediction, the result demonstrates that the predictive model of composite index with filtering performs the best with MAPE 24.98% and RMSE 192.71. By contract, the predictive model of the suspected NCP PROTEIN cases is calculated with the prediction error of MAPE 8.82% and RMSE 368.51(almost twice the best model). With the Out-of-sample prediction, we monitor that there might be a peak value in Feb. 16th to 17th in the next ten days.Conclusion: With noise filtering, the predictive model can forecast the new confirmed NCP PROTEIN cases more accurately. However, the filtering eliminates the violent fluctuations of the series and cannot capture the rising and declining details of the predicted values. On contrast, the prediction accuracy based on search composite index is sensitive to prediction of peak and valley although its prediction error is larger. These two predictive models can be combined: monitoring the further volatility trend with filtering model while identifying the inflexion with composite model.

    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.

    Comparative analysis of primer-probe sets for the laboratory confirmation of SARS-CoV-2

    Authors: Yu Jin Jung; Gun-Soo Park; Jun Hye Moon; Keunbon Ku; Seung-Hwa Beak; Seil Kim; Edmond Changkyun Park; Daeui Park; Jong-Hwan Lee; Cheol Woo Byeon; Joong Jin Lee; Jin-soo Maeng; Seong Jun Kim; Seung Il Kim; Bum-Tae Kim; Min Jun Lee; Hong Gi Kim

    doi:10.1101/2020.02.25.964775 Date: 2020-02-27 Source: bioRxiv

    Coronavirus disease 2019 MESHD ( COVID-19 MESHD) is newly emerging human infectious diseases MESHD, which is caused by Severe Acute Respiratory Syndrome Coronavirus 2 MESHD (SARS-CoV-2, also previously known as 2019-nCoV). Within two months of the outbreak, more than 80,000 cases of COVID-19 MESHD have been confirmed worldwide. Since the human to human transmission occurred easily and the human infection is rapidly increasing, the sensitive and early diagnosis is essential to prevent the global outbreak. Recently, World Health Organization (WHO) announced various primer and probe sets for SARS-CoV-2 previously developed in China, Germany, Hong Kong, Japan, Thailand, and USA. In this study, we compared the ability to detect SARS-CoV-2 RNA among the seven primer-probe sets for N gene PROTEIN and the three primer-probe sets for Orf1 PROTEIN gene. The result of the comparative analysis represented that the 2019-nCoV_N2, N3 of USA and the ORF1ab PROTEIN of China are the most sensitive primer-probe sets for N and Orf1 PROTEIN genes, respectively. Therefore, the appropriate combination from ORF1ab PROTEIN (China), 2019-nCoV_N2, N3 (USA), and NIID_2019-nCOV_N (Japan) sets should be selected for the sensitive and reliable laboratory confirmation of SARS-CoV-2.

    A simple magnetic nanoparticles-based viral RNA extraction method for efficient detection of SARS-CoV-2

    Authors: Zhen Zhao; Haodong Cui; Wenxing Song; Xiaoling Ru; Wenhua Zhou; Xuefeng Yu

    doi:10.1101/2020.02.22.961268 Date: 2020-02-27 Source: bioRxiv

    1The ongoing outbreak of the novel coronavirus disease 2019 MESHD ( COVID-19 MESHD) originating from Wuhan, China, draws worldwide concerns due to its long incubation period and strong infectivity. Although RT-PCR-based molecular diagnosis techniques are being widely applied for clinical diagnosis currently, timely and accurate diagnosis are still limited due to labour intensive and time-consuming operations of these techniques. To address the issue, herein we report the synthesis of poly (amino ester) with carboxyl groups (PC)-coated magnetic nanoparticles (pcMNPs), and the development of pcMNPs-based viral RNA extraction method for the sensitive detection of COVID-19 MESHD causing virus, the SARS-CoV-2. This method combines the lysis and binding steps into one step, and the pcMNPs-RNA complexes can be directly introduced into subsequent RT-PCR reactions. The simplified process can purify viral RNA from multiple samples within 20 min using a simple manual method or an automated high-throughput approach. By identifying two different regions (ORFlab and N gene PROTEIN) of viral RNA, a 10-copy sensitivity and a strong linear correlation between 10 and 105 copies of SARS-CoV-2 pseudovirus particles are achieved. Benefitting from the simplicity and excellent performances, this new extraction method can dramatically reduce the turn-around time and operational requirements in current molecular diagnosis of COVID-19 MESHD, in particular for the early clinical diagnosis.

    Generation of antibodies against COVID-19 MESHD virus for development of diagnostic tools

    Authors: Maohua Li; Ronghua Jin; Ya Peng; Cuiyan Wang; Wenlin Ren; Fudong Lv; Sitao Gong; Feng Fang; Qianyun Wang; Jianli Li; Tong Shen; Hunter Sun; Lei Zhou; Yali Cui; Hao Song; Le Sun

    doi:10.1101/2020.02.20.20025999 Date: 2020-02-25 Source: medRxiv

    The COVID-19 MESHD China coronavirus started in Dec 2019 was challenged by the lack of accurate serological diagnostic tool for this deadly disease to quickly identify and isolate the infected MESHD patients. The generation of COVID-19 MESHD-specific antibodies is essential for such tasks. Here we report that polyclonal and monoclonal antibodies were generated by immunizing animals with synthetic peptides corresponding to different areas of Nucleoprotein (N PROTEIN) of COVID-19 MESHD. The specificities of the COVID-19 MESHD antibodies were assessed by Western Blot analysis against NPs from COVID-19 MESHD, MERS and SARS. Antibodies were used for immunohistochemistry staining of the tissue sections from COVID-19 MESHD infected patient, as a potential diagnostic tool. A Sandwich ELISA kit was quickly assembled for quantitation of the virus/NP of COVID-19 MESHD concentrations in the vaccine preparations. Development of POCT is also aggressively undergoing.

    Early Prediction of Disease Progression in 2019 Novel Coronavirus Pneumonia Patients Outside Wuhan with CT and Clinical Characteristics

    Authors: Zhichao Feng; Qizhi Yu; Shanhu Yao; Lei Luo; Junhong Duan; Zhimin Yan; Min Yang; Hongpei Tan; Mengtian Ma; Ting Li; Dali Yi; Ze Mi; Huafei Zhao; Yi Jiang; Zhenhu He; Huiling Li; Wei Nie; Yin Liu; Jing Zhao; Muqing Luo; Xuanhui Liu; Pengfei Rong; Wei Wang

    doi:10.1101/2020.02.19.20025296 Date: 2020-02-23 Source: medRxiv

    Objective: To determine the predictive value of CT and clinical characteristics for short-term disease progression in patients with 2019 novel coronavirus pneumonia MESHD ( NCP PROTEIN). Materials and Methods: 224 patients with confirmed 2019 novel coronavirus ( COVID-19 MESHD) infection outside Wuhan who had chest CT examinations were retrospectively screened. Clinical data were obtained from electronic medical records. CT images were reviewed and scored for lesion distribution, lobe and segment involvement, ground-glass opacities, consolidation, and interstitial thickening. All included patients with moderate NCP PROTEIN were observed for at least 14 days from admission to determine whether they exacerbated to severe NCP PROTEIN (progressive group) or not (stable group). CT and clinical characteristics between the two groups were compared, and multivariate logistic regression and sensitivity analyses were performed to identify the risk factors for developing severe NCP PROTEIN. Results: A total of 141 patients with moderate NCP PROTEIN were included, of which 15 (10.6%) patients developed severe NCP PROTEIN during hospitalization and assigned to the progressive group. Multivariate logistic regression analysis showed that higher neutrophil-to-lymphocyte ratio (NLR) (odds ratio [OR] and 95% confidence interval [CI], 1.26 [1.04-1.53]; P = 0.018) and CT severity score (OR and 95% CI, 1.25 [1.08-1.46]; P = 0.004) on admission were independent predictors for progression to severe NCP PROTEIN, and sensitivity analysis confirmed the consistent results in nonimported patients but not in imported patients. However, no significant difference in lung involvement was found on CT between imported and nonimported patients (all P > 0.05). Patients who were admitted more than 4 days from symptom onset tended to have more severe lung involvement. Spearman correlation analysis showed the close association between CT severity score and inflammatory indexes (r = 0.17~0.47, all P < 0.05). Conclusion: CT severity score was associated with inflammatory levels and higher NLR and CT severity score on admission were independent risk factors for short-term progression in patients with NCP PROTEIN outside Wuhan. Furthermore, early admission and surveillance by CT should be recommended to improve clinical outcomes.

    A Note on NCP PROTEIN Diagnosis Number Prediction Model

    Authors:

    doi:10.1101/2020.02.19.20025262 Date: 2020-02-23 Source: medRxiv

    Importance: To predict the diagnosed COVID-19 MESHD patients and the trend of the epidemic in China. It may give the public some scientific information to ease the fear of the epidemic. Objective: In December 2019, pneumonia infected MESHD with the novel coronavirus burst in Wuhan, China. We aimed to use a mathematical model to predict number of diagnosed patients in future to ease anxiety MESHD on the emergent situation. Design: According to all diagnosis number from WHO website and combining with the transmission mode of infectious diseases MESHD, the mathematical model was fitted to predict future trend of outbreak. Setting: Our model was based on the epidemic situation in China, which could provide referential significance for disease prediction in other countries, and provide clues for prevention and intervention of relevant health authorities. Participants: In this retrospective, all diagnosis number from Jan 21 to Feb 10, 2020 reported from China was included and downloaded from WHO website. Main Outcome(s) and Measure(s): We develop a simple but accurate formula to predict the next day diagnosis number:N_i/N_( i-1 HGNC) =[(N_( i-1 HGNC)/N_(i-2) )]^where Ni is the total diagnosed patient till the ith day, and was estimated as 0.904 at Feb 10. Results: Based on this model, it is predicted that the rate of disease infection will decrease exponentially. The total number of infected people MESHD is limited; thus, the disease will have limited impact. However, new diagnosis will last to March. Conclusions and Relevance: Through the establishment of our model, we can better predict the trend of the epidemic in China.

    Correlation between the migration scale index and the number of new confirmed Novel Coronavirus Pneumonia cases in China

    Authors: Huijie Chen; Ye Chen; Baijun Sun; Ping Wang; Lihai Wen; Zhiyong Lian; Ying Lu; Ying Qi; Shuo Zhao; Linlin Zhang; Xiaodan Yi; Fengyu Liu

    doi:10.21203/rs.2.24409/v1 Date: 2020-02-22 Source: ResearchSquare

    Background: In late December, 2019, patients of atypical pneumonia MESHD due to an unidentified microbial agent were reported in Wuhan, Hubei Province, China. Subsequently, a novel coronavirus was identified as the causative pathogen which was named 2019 novel coronavirus (2019-nCoV). As of Feb 12, 2020, more than 44,000 cases of 2019-nCoV infection MESHD have been confirmed in China and continue to expand. Provinces, municipalities and autonomous regions of China have launched first-level response to major public health emergencies one after another from Jan 23.2020, which means restricting movement of people among provinces, municipalities and autonomous regions. The aim of this study was to explore the correlation between the migration scale index and the number of confirmed Novel Coronavirus Pneumonia ( NCP PROTEIN) cases and to depict the effect of restricting population movement. Methods: Excel 2010 was used to demonstrate the temporal distribution at the day level and SPSS 23.0 was used to analyze the correlation between the migration scale index and the number of confirmed NCP PROTEIN cases. Results: Since January 23, 2020, Wuhan migration scale index has dropped significantly and since January 26, 2020, Hubei province migration scale index has dropped significantly. New confirmed NCP PROTEIN cases per day in China except Wuhan gradually increased since January 24, 2020, and showed a downward trend from February 6, 2020. New confirmed NCP PROTEIN cases per day in China except Hubei province gradually increased since January 24, 2020, and maintained at a high level from January 24, 2020 to February 4, 2020, then showed a downward trend. Wuhan emigration scale index from January 9 to January 22, January 10 to January 23 and January 11 to January 24 was correlated with the number of new confirmed NCP PROTEIN cases per day in China except Wuhan from January 22 to February 4. Hubei province emigration scale index from January 10 to January 23 and January 11 to January 24 was correlated with the number of new confirmed NCP PROTEIN cases per day in China except Hubei province from January 22 to February 4.Conclusions: People who left Wuhan from January 9 to January 22 may lead to the outbreak in China except Wuhan and people who left Hubei province from January 10 to January 24 may lead to the outbreak in China except Hubei province. “Wuhan lockdown” and Hubei province launching first-level response to major public health emergencies may have had a good effect the control NCP PROTEIN epidemic. Because there were still new confirmed NCP PROTEIN cases in China except Wuhan and in China except Hubei province and this may indicate that the occurrence of second-generation cases.

    Evidence for gastrointestinal infection of SARS-CoV-2

    Authors: Fei Xiao; Meiwen Tang; Xiaobin Zheng; Chunna Li; Jianzhong He; Zhongsi Hong; Siwen Huang; Zhenyi Zhang; Xianqi Lin; Zhaoxiong Fang; Renxu Lai; Shoudeng Chen; Jing Liu; Jin Huang; Jinyu Xia; Zhonghe Li; Guanmin Jiang; Ye Liu; Xiaofeng Li; Hong Shan

    doi:10.1101/2020.02.17.20023721 Date: 2020-02-20 Source: medRxiv

    The new coronavirus (SARS-CoV-2) outbreak originating from Wuhan, China, poses a threat to global health. While it's evident that the virus invades respiratory tract and transmits from human to human through airway, other viral tropisms and transmission routes remain unknown. We tested viral RNA in stool from 73 SARS-CoV-2-infected MESHD hospitalized patients using rRT-PCR. 53.42% of the patients tested positive in stool. 23.29% of the patients remained positive in feces even after the viral RNA decreased to undetectable level in respiratory tract. The viral RNA was also detected in gastrointestinal tissues. Furthermore, gastric, duodenal and rectal epithelia showed positive immunofluorescent staining of viral host receptor ACE2 HGNC and viral nucleocapsid protein PROTEIN in a case of SARS-CoV-2 infection MESHD. Our results provide evidence for gastrointestinal infection of SARS-CoV-2 MESHD, highlighting its potential fecal-oral transmission route.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins


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