preVIEW: COVID-19

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Overview

MeSH Disease

COVID-19 (21310)

Severe Acute Respiratory Syndrome (2409)

Coronavirus Infections (2080)

Death (1868)

Pneumonia (1258)


HGNC Genes

angiotensin I converting enzyme 2 (1148)

C-reactive protein (466)

interleukin 6 (412)

transmembrane serine protease 2 (212)

tumor necrosis factor (120)


SARS-CoV-2 proteins

ProteinS (1763)

ProteinN (481)

NSP5 (390)

ComplexRdRp (223)

ProteinE (128)


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    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.

    The experience of high flow nasal cannula in hospitalized patients with 2019 novel coronavirus–infected pneumonia in Chongqing, China

    Authors: Ke Wang; Wei Zhao; Ji Li; Weiwei Shu; Jun Duan

    doi:10.21203/rs.2.24633/v1 Date: 2020-02-25 Source: ResearchSquare

    Background The outbreak of a novel coronavirus (2019-nCoV)– infected pneumonia MESHD (NCIP) is currently ongoing in China. Most of the critically ill patients received high flow nasal cannula (HFNC). However, the experience of HFNC in this population is lacking. Methods We retrospectively collected the NCIP patients who received HFNC in two hospital of Chongqing, China from January 1st to February 18th, 2020. The clinical characteristics were collected. Patients who required upgrading to noninvasive ventilation (NIV) were defined as HFNC failure MESHD. Results We enrolled 17 patients in this study. Of them, 7 patients (41%) experienced HFNC failure MESHD (6 required upgrading to NIV, and one to NIV and further to intubation). The HFNC failure rate was 0% (0/6), 57% (4/7) and 75% (3/4) (p =0.03 between 3 groups) in patients with PaO2/FiO2 >200, 150-200, and <150 mmHg, respectively. In the successful patients, the respiratory rate, heart rate and PaO2/FiO2 significantly improved from initiation to termination of HFNC (27±3 vs. 21±2 breaths/min, p <0.01; 86±15 vs. 76±12 beats/min, p =0.03; and 213±49 vs. 299±125 mmHg, p =0.04, respectively). However, in the unsuccessful patients, the respiratory rate and PaO2/FiO2 significantly deteriorated (22±3 vs. 25±3 breaths/min, p =0.04; and 160±27 vs. 105±24 mmHg, p =0.01, respectively). When they upgraded to NIV, the PaO2/FiO2 improved after 1-2 h of NIV (105±24 vs. 202±111 mmHg, p =0.04). In the total cohort, only PaO2/FiO2 at baseline was lower in unsuccessful patients than that in successful ones (213±49 vs. 160±27 mmHg, p =0.02). Conclusions This study firstly provides the experience of how to use HFNC in patients with NCIP. Patients with lower PaO2/FiO2 were more likely to experience HFNC failure MESHD. Among the failure MESHD patients, most of them can avoid intubation when they were ungraded to NIV.

    Higher severity and mortality in male patients with COVID-19 MESHD independent of age and susceptibility

    Authors: Jian-Min Jin; Peng Bai; Wei He; Fei Wu; Xiao-Fang Liu; De-Min Han; Shi Liu; Jin-Kui Yang

    doi:10.1101/2020.02.23.20026864 Date: 2020-02-25 Source: medRxiv

    Importance: The recent outbreak of Novel Coronavirus ( SARS-CoV-2) Disease MESHD ( COVID-19 MESHD) has put the world on alert, that is reminiscent of the SARS outbreak seventeen years ago. Objective: We aim to compare the severity and mortality between male and female patients with both COVID-19 MESHD and SARS, to explore the most useful prognostic factors for individualized assessment. Design, Setting, and Participants: We extracted the data from a case series of 43 hospitalized patients we treated, a public data set of the first 37 cases died of COVID-19 MESHD in Wuhan city and 1019 survived patients from six cities in China. We also analyzed the data of 524 patients with SARS, including 139 deaths MESHD, from Beijing city in early 2003. Main Outcomes and Measures: Severity and mortality. Results: Older age and high number of comorbidities were associated with higher severity and mortality in patients with both COVID-19 MESHD and SARS. The percentages of older age ([≥]65 years) were much higher in the deceased group than in the survived group in patients with both COVID-19 MESHD (83.8 vs. 13.2, P<0.001) and SARS (37.4 vs. 4.9, P<0.001). In the case series, men tend to be more serious than women (P=0.035), although age was comparable between men and women. In the public data set, age was also comparable between men and women in the deceased group or the survived group in patients with COVID-19 MESHD. Meanwhile, gender distribution was exactly symmetrical in the 1019 survivors of COVID-19 MESHD. However, the percentage of male were higher in the deceased group than in the survived group (70.3 vs. 50.0, P=0.015). The gender role in mortality was also observed in SARS patients. Survival analysis showed that men (hazard ratio [95% CI] 1.47 [1.05-2.06, P= 0.025) had a significantly higher mortality rate than women in patients with SARS. Conclusions and Relevance: Older age and male gender are risk factors for worse outcome in patients with COVID. While men and women have the same susceptibility to both SARS-CoV-2 and SARS-CoV MESHD, men may be more prone to have higher severity and mortality independent of age and susceptibility.

    Epidemiologic and Clinical Characteristics of 91 Hospitalized Patients with COVID-19 MESHD in Zhejiang, China: A retrospective, multi-centre case series

    Authors: Guo-Qing Qian; Nai-Bin Yang; Feng Ding; Ada Hoi Yan Ma; Zong-Yi Wang; Yue-Fei Shen; Chun-Wei Shi; Xiang Lian; Jin-Guo Chu; Lei Chen; Zhi-Yu Wang; Da-Wei Ren; Guo-Xiang Li; Xue-Qin Chen; Hua-Jiang Shen; Xiao-Min Chen

    doi:10.1101/2020.02.23.20026856 Date: 2020-02-25 Source: medRxiv

    Background Recent studies have focused initial clinical and Epidemiologic characteristics on the COVID-19 MESHD, mainly revealing situation in Wuhan, Hubei. Aim To reveal more data on the epidemiologic and clinical characteristics of COVID-19 MESHD patients outside of Wuhan, in Zhejiang, China. Design Retrospective case series. Methods 88 cases of laboratory-confirmed and 3 cases of clinical-confirmed COVID-19 MESHD were admitted to five hospitals in Zhejiang province, China. Data were collected from 20 January 2020 to 11 February 2020. Results Of all 91 patients, 88 (96.70%) were laboratory-confirmed COVID-19 MESHD with throat swab samples that tested positive for SARS-Cov-2 while 3 (3.30%) were clinical-diagnosed COVID-19 MESHD cases. The median age of the patients was 50 (36.5-57) years, and female accounted for 59.34%. In this sample 40 (43.96%) patients had contracted the diseases from local cases, 31 (34.07%) patients had been to Wuhan/Hubei, 8 (8.79%) cases had contacted with people from Wuhan, 11 (12.09%) cases were confirmed aircraft transmission. In particular within the city of Ningbo, 60.52% cases can be traced back to an event held in a temple. The most common symptoms were fever MESHD (71.43%), cough (60.44%) and fatigue MESHD (43.96%). The median of incubation period was 6 (IQR, 3-8) days and the median time from first visit to a doctor to confirmed diagnosis was 1 (1-2) days. According to the Chest computed tomography scans, 67.03% cases had bilateral pneumonia MESHD. Conclusions Social activity cluster, family cluster and travel by airplane were how COVID-19 MESHD patients get transmitted and could be rapidly diagnosed COVID-19 MESHD in Zhejiang.

    Temperature significant change COVID-19 MESHD Transmission in 429 cities

    Authors: Mao Wang; Aili Jiang; Lijuan Gong; Lina Luo; Wenbin Guo; Chuyi Li; Jing Zheng; Chaoyong Li; Bixing Yang; Jietong Zeng; Youping Chen; Ke Zheng; Hongyan Li

    doi:10.1101/2020.02.22.20025791 Date: 2020-02-25 Source: medRxiv

    Background There is no evidence supporting that temperature changes COVID-19 MESHD transmission. Methods We collected the cumulative number of confirmed cases of all cities and regions affected by COVID-19 MESHD in the world from January 20 to February 4, 2020, and calculated the daily means of the average, minimum and maximum temperatures in January. Then, restricted cubic spline function and generalized linear mixture model were used to analyze the relationships. Results There were in total 24,232 confirmed cases in China and 26 overseas countries. In total, 16,480 cases (68.01%) were from Hubei Province. The lgN rose as the average temperature went up to a peak of 8.72 and then slowly declined. The apexes of the minimum temperature and the maximum temperature were 6.70 and 12.42 respectively. The curves shared similar shapes. Under the circumstance of lower temperature, every 1 increase in average, minimum and maximum temperatures led to an increase of the cumulative number of cases by 0.83, 0.82 and 0.83 respectively. In the single-factor model of the higher-temperature group, every 1 increase in the minimum temperature led to a decrease of the cumulative number of cases by 0.86. Conclusion The study found that, to certain extent, temperature could significant change COVID-19 MESHD transmission, and there might be a best temperature for the viral transmission, which may partly explain why it first broke out in Wuhan. It is suggested that countries and regions with a lower temperature in the world adopt the strictest control measures to prevent future reversal.

    2019 Novel Coronavirus can be detected in urine, blood, anal swabs and oropharyngeal swabs samples

    Authors: Liang Peng; Jing Liu; Wenxiong Xu; Qiumin Luo; Keji Deng; Bingliang Lin; Zhiliang Gao

    doi:10.1101/2020.02.21.20026179 Date: 2020-02-25 Source: medRxiv

    We tested samples collected from nine patients diagnosed with coronavirus disease 2019 MESHD ( COVID-19 MESHD). The virus was found in urine, blood, anal swabs and oropharyngeal swabs. It is the first time for SARS-CoV-2 found in urine, though no urinary irritation was found.

    In vitro virucidal activity of Echinaforce®, an Echinacea purpurea preparation, against coronaviruses, including common cold coronavirus 229E and SARS-CoV-2

    Authors: Johanna Signer; Hulda R. Jonsdottir; Werner C. Albrich; Marc Strasser; Roland Züst; Sarah Ryter; Rahel Ackermann-Gäumann; Nicole Lenz; Denise Siegrist; Andreas Suter; Roland Schoop; Olivier B. Engler

    doi:10.21203/rs.2.24724/v3 Date: 2020-02-25 Source: ResearchSquare

    Background: Coronaviruses (CoVs) were long thought to only cause mild respiratory and gastrointestinal symptoms MESHD in humans but outbreaks of Middle Eastern Respiratory Syndrome (MERS)-CoV, Severe Acute Respiratory Syndrome MESHD (SARS)-CoV, and the recently identified SARS-CoV-2 have cemented their zoonotic potential and their capacity to cause serious morbidity and mortality, with case fatality rates ranging from 4 to 35%. Currently, no specific prophylaxis or treatment is available for CoV infections MESHD.Therefore we investigated the virucidal and antiviral potential of Echinacea purpurea (Echinaforce®) against human coronavirus (HCoV) 229E, highly pathogenic MERS- and SARS-CoVs MESHD, as well as the newly identified SARS-CoV-2, in vitro.Methods: To evaluate the antiviral potential of the extract we pre-treated virus particles and cells and evaluated remaining infectivity by limited dilution. Furthermore, we exposed cells to the extract after infection to further evaluate its potential as a prophylaxis and treatment against coronaviruses. We also determined the protective effect of Echinaforce® in re-constituted nasal epithelium.Results: In the current study, we found that HCoV-229E was irreversibly inactivated when exposed to Echinaforce® at 3.2mg/ml IC50. Pre-treatment of cell lines, however, did not inhibit infection with HCoV-229E and post-infection treatment had only a marginal effect on virus propagation at 50 mg/ml. However, we did observe a protective effect in an organotypic respiratory cell culture system by exposing pre-treated respiratory epithelium to droplets of HCoV-229E, imitating a natural infection. The observed virucidal activity of Echinaforce® was not restricted to common cold coronaviruses, as both SARS-CoV-1 and MERS-CoVs were inactivated at comparable concentrations. Finally, the causative agent of COVID-19 MESHD, SARS-CoV-2 was also inactivated upon treatment with 50ug/ml Echinaforce®.Conclusions: These results show that Echinaforce® is virucidal against HCoV-229E, upon direct contact and in an organotypic cell culture model. Furthermore, MERS-CoV MESHD and both SARS-CoV-1 and SARS-CoV-2 MESHD were inactivated at similar concentrations of the extract. Therefore we hypothesize that Echinacea purpurea preparations, such as Echinaforce®, could be effective as prophylactic treatment for all CoVs due to their structural similarities. 

    Clinical Implications of 37 Childhood Cases with SARS-COV-2 Infection MESHD in Shenzhen, China

    Authors: Yanrong Wang; Yingxia Liu; Yang Yang; Xianfeng Wang; Lei Liu

    doi:10.21203/rs.2.24730/v3 Date: 2020-02-25 Source: ResearchSquare

    Background SARS-CoV-2 was first identified in December 2019 in samples obtained from a 61 years old man who died of acute respiratory failure MESHD in the city of Wuhan, China with a subsequent outbreak in China. Till now, there were rare reports about childhood patients with SARS-CoV-2 infection MESHD.Methods We report 37 children diagnosed with SARS-CoV-2 infection MESHD admitted in the Third People’s hospital of Shenzhen from December 11, 2019 to February 11, 2020. Results There were 9 mild cases, 20 ordinary cases and 1 severe case and 7 cases with asymptomatic infection. The age ranged from 7 months to 17 years old and the median age was 7 years old. The median length of hospital stay is about 14 days. The time from illness onset to diagnosis ranged from 0.5 to 10 days (median time: 2 days). The common clinical features were fever MESHD (29.7%, 11/37) and cough (32.4%, 12/37). No death occurred among our patients. 86.5% (32/37) children were infected with SARS-CoV-2 after their family members (parents or grandparents). 1 child was identified with SARS-CoV-2 infection MESHD after 3 times testing. The majority (78.4%) of cases occurred in those children who travelled to Hubei Province. Conclusions The majority of childhood cases with SARS-CoV-2 infection MESHD was mild or ordinary COVID-19 MESHD and had travelled to Hubei Province. Family cluster transmission of SARS-CoV-2 was suspected in 86.5% of patients. Timely continuous SARS-CoV-2 pathogen testing is recommended. 

    The Reconstruction and Prediction Algorithm of the Fractional TDD for the Local Outbreak of COVID-19 MESHD

    Authors: Yu Chen; Jin Cheng; Xiaoying Jiang; Xiang Xu

    id:2002.10302v1 Date: 2020-02-24 Source: arXiv

    From late December, 2019, the novel Corona-Virus began to spread in the mainland of China. For predicting the trend of the Corona Virus spread, several time delay dynamic systems (TDD) are proposed. In this paper, we establish a novel fractional time delay dynamic system (FTDD) to describe the local outbreak of COVID-19 MESHD. The fractional derivative is introduced to account for the sub-diffusion process of the confirmed and cured peoples growth. Based on the public health data by the government, we propose a stable reconstruction algorithm of the coefficients. The reconstructed coefficients are used to predict the trend of the Corona-Virus. The numerical results are in good agreement with the public data.

    Cryo-EM structures of HKU2 and SADS-CoV spike glycoproteins PROTEIN and insights into coronavirus evolution

    Authors: Jinfang Yu; Shuyuan Qiao; Runyu Guo; Xinquan Wang

    doi:10.1101/2020.02.23.961912 Date: 2020-02-24 Source: bioRxiv

    A new porcine coronavirus SADS-CoV MESHD was recently identified from suckling piglets with severe diarrhea MESHD in southern China and its genome sequence is most identical (~95% identity) to that of bat -coronavirus HKU2. It again indicates bats are the natural reservoir of many coronaviruses that have great potential for cross-species transmission to animals and humans by recombination and/or mutation. Here we report the cryo-EM structures of HKU2 and SADS-CoV spike MESHD spike glycoprotein PROTEIN trimers at 2.38 [A] and 2.83 [A] resolution, respectively. HKU2 and SADS-CoV spikes MESHD exhibit very high structural similarity, with subtle differences mainly distributed in the NTD and CTD of the S1 subunit responsible for cell attachment and receptor binding. We systematically analyzed and compared the NTD, CTD, SD1 and SD2 domains of the S1 subunit and the S2 subunit of HKU2 spike with those of -, {beta}-, {gamma}-, and {delta}-coronavirus spikes. The results show that the NTD MESHD and CTD of HKU2/SADS-CoV are probably the most ancestral in the evolution of spike. Although the S2 subunit mediating membrane fusion is highly conserved, the connecting region after fusion peptide in HKU2/SADS-CoV S2 subunit also adopts a conformation distinct from other coronaviruses. These results structurally demonstrate a close evolutionary relationship between HKU2 /SADS-CoV and {beta}-coronavirus spikes and provide new insights into the evolution and cross-species transmission of coronaviruses.

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SARS-CoV-2 Proteins

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