Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (1608)

ProteinN (451)

NSP5 (379)

ComplexRdRp (215)

ProteinE (121)


SARS-CoV-2 Proteins
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    Transmission Dynamics of SARS-CoV-2 in a Mid-size City of China

    Authors: Zhao Hongjun; Xiaoxiao Lu; Tiegang Li; Boqi Rao; Dedong Wang; Di Wu; Fuman Qiu; Zhicong Yang; Jiachun Lu

    doi:10.21203/rs.2.23945/v3 Date: 2020-02-18 Source: ResearchSquare

    Background: An outbreak of pneumonia MESHD associated with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan city and then to other city. It is very urgent to delineate the epidemiological and clinical characteristics of these affected patients. Methods: To investigate the epidemiological characteristics of the COVID-19 MESHD, we describe a case series of 459 patients with confirmed COVID-19 MESHD in WZ of China from January 27 to February 12, 2020.Results: The median age of all patients was 48.0 years, and 46.8% were females. 37.5% of patients had a history of residence in Wuhan. Fever MESHD (72.1%) and cough (43.6%) were the most frequent symptoms. In addition, three kinds of unconventional cases were observed, in which included 4.4% confirmed virus carrier who were asymptomatic, 7.8% confirmed patients who had no link to Wuhan city but contact with individuals from Wuhan without any symptoms at the time of contact, and 10.7% confirmed patients who had no link to Wuhan city nor a history of intimate contact with patients or individuals from Wuhan without any symptoms, respectively.Conclusion: Our findings presented the possibility of asymptomatic carriers affected with SARS-CoV-2, and this phenomenon suggested that chances of uncontrollable transmission in the larger population might be higher than formerly estimated, and transmission by these three kinds of unconventional patients in WZ may be one of the characteristics of infection in other Chinese cities outside the Wuhan epidemic area.

    Simulating and Forecasting the Cumulative Confirmed Cases of SARS-CoV-2 in China by Boltzmann Function-based Regression Analyses

    Authors: Xinmiao Fu; Qi Ying; Tieyong Zeng; Tao Long; Yan Wang

    doi:10.1101/2020.02.16.20023564 Date: 2020-02-18 Source: medRxiv

    An ongoing outbreak of atypical pneumonia MESHD caused by the 2019 novel coronavirus (SARS-CoV-2) is hitting Wuhan City and has spread to other provinces/cities of China and overseas. It very urgent to forecast the future course of the outbreak. Here, we provide an estimate of the potential total number of confirmed cases in mainland China by applying Boltzmann-function based regression analyses. We found that the cumulative number of confirmed cases from Jan 21 to Feb 14, 2020 for mainland China, Hubei Province, Wuhan City and other provinces were all well fitted with the Boltzmann function (R2 being close to 0.999). The potential total number of confirmed cases in the above geographic regions were estimated at 95% confidence interval (CI) as 79589 (71576, 93855), 64817 (58223, 77895), 46562 (40812, 57678) and 13956 (12748, 16092), respectively. Notably, our results suggest that the number of daily new confirmed cases of SARS-CoV-2 in mainland China (including Hubei Province) will become minimal between Feb 28 and Mar 10, 2020, with 95% CI. In addition, we found that the data of cumulative confirmed cases of 2003 SARS-CoV MESHD in China and Worldwide were also well fitted to the Boltzmann function. To our knowledge this is the first study revealing that the Boltzmann function is suitable to simulate epidemics. The estimated potential total number of confirmed cases and key dates for the SARS-CoV-2 outbreak may provide certain guidance for governments, organizations and citizens to optimize preparedness and response efforts.

    Structural modeling of 2019-novel coronavirus (nCoV) spike protein PROTEIN reveals a proteolytically-sensitive activation loop as a distinguishing feature compared to SARS-CoV and related SARS-like coronaviruses

    Authors: Javier A. Jaimes; Nicole M Andre; Jean K Millet; Gary R. Whittaker

    doi:10.1101/2020.02.10.942185 Date: 2020-02-18 Source: bioRxiv

    The 2019 novel coronavirus (2019-nCoV) is currently causing a widespread outbreak centered on Hubei province, China and is a major public health concern. Taxonomically 2019-nCoV is closely related to SARS-CoV MESHD and SARS-related bat coronaviruses, and it appears to share a common receptor with SARS-CoV MESHD (ACE-2). Here, we perform structural modeling of the 2019-nCoV spike glycoprotein PROTEIN. Our data provide support for the similar receptor utilization between 2019-nCoV and SARS-CoV MESHD, despite a relatively low amino acid similarity in the receptor binding module. Compared to SARS-CoV MESHD, we identify an extended structural loop containing basic amino acids at the interface of the receptor binding (S1) and fusion (S2) domains, which we predict to be proteolytically-sensitive. We suggest this loop confers fusion activation and entry properties more in line with MERS-CoV MESHD and other coronaviruses, and that the presence of this structural loop in 2019-nCoV may affect virus stability and transmission.

    Evaluating new evidence in the early dynamics of the novel coronavirus COVID-19 MESHD outbreak in Wuhan, China with real time domestic traffic and potential asymptomatic transmissions

    Authors: Can Zhou

    doi:10.1101/2020.02.15.20023440 Date: 2020-02-18 Source: medRxiv

    The novel coronavirus ( COVID-19 MESHD), first detected in Wuhan, China in December 2019, has spread to 28 countries/regions with over 43,000 confirmed cases. Much about this outbreak is still unknown. At this early stage of the epidemic, it is important to investigate alternative sources of information to understand its dynamics and spread. With updated real time domestic traffic, this study aims to integrate recent evidence of international evacuees extracted from Wuhan between Jan. 29 and Feb. 2, 2020 to infer the dynamics of the COVD-19 outbreak in Wuhan. In addition, a modified SEIR model was used to evaluate the empirical support for the presence of asymptomatic transmissions. Based on the data examined, this study found little evidence for the presence of asymptomatic transmissions. However, it is still too early to rule out its presence conclusively due to sample size and other limitations. The updated basic reproductive number was found to be 2.12 on average with a 95% credible interval of [2.04, 2.18]. It is smaller than previous estimates probably because the new estimate factors in the social and non-pharmaceutical mitigation implemented in Wuhan through the evacuee dataset. Detailed predictions of infected individuals exported both domestically and internationally were produced. The estimated case confirmation rate has been low but has increased steadily to 23.37% on average. The findings of this study depend on the validity of the underlying assumptions, and continuing work is needed, especially in monitoring the current infection status of Wuhan residents.

    Structure of dimeric full-length human ACE2 HGNC in complex with B0AT HGNC1

    Authors: Qiang Zhou; Renhong Yan; Yuanyuan Zhang; Yaning Li; Lu Xia

    doi:10.1101/2020.02.17.951848 Date: 2020-02-18 Source: bioRxiv

    Angiotensin-converting enzyme 2 ( ACE2 HGNC) is the surface receptor for SARS coronavirus ( SARS-CoV MESHD), directly interacting with the spike glycoprotein PROTEIN ( S protein PROTEIN). ACE2 HGNC is also suggested to be the receptor for the new coronavirus (2019-nCoV), which is causing a serious epidemic in China manifested with severe respiratory syndrome MESHD. B0AT1 HGNC ( SLC6A19 HGNC) is a neutral amino acid transporter whose surface expression in intestinal cells requires ACE2 HGNC. Here we present the 2.9 [A] resolution cryo-EM structure of full-length human ACE2 HGNC in complex with B0AT1 HGNC. The complex, assembled as a dimer of ACE2 HGNC- B0AT1 HGNC heterodimers, exhibits open and closed conformations due to the shifts of the peptidase domains (PDs) of ACE2 HGNC. A newly resolved Collectrin-like domain (CLD) on ACE2 HGNC mediates homo-dimerization. Structural modelling suggests that the ACE2 HGNC- B0AT1 HGNC complex can bind two S proteins PROTEIN simultaneously, providing important clues to the molecular basis for coronavirus recognition and infection MESHD.

    Can Search Query Forecast successfully in China's 2019-nCov pneumonia?

    Authors: Li Xiaoxuan; Wu Qi; Lv Benfu

    doi:10.1101/2020.02.12.20022400 Date: 2020-02-18 Source: medRxiv

    Recently the novel coronavirus (2019-nCov) pneumonia MESHD outbreak in China then the world, and the Number of infections and death MESHD continues to increases. Search Query performs well in forecasting the epidemics. It is still a question whether search engine data 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 and suspected NCP PROTEIN(Novel Coronavirus Pneumonia). The result demonstrates that the predictive model of composite index with filtering performs the best while the model of suspected NCP PROTEIN has the highest forecast error. We further predict the out-of-the-set NCP PROTEIN confirmed cases and monitor that the next peak of new diagnoses will occur on February 16th and 17th.

    Two-week global trends on 2019-nCoV fatality and virulence rates: a cross-sectional study

    Authors: Jorge Arroz

    doi:10.21203/rs.2.23981/v1 Date: 2020-02-18 Source: ResearchSquare

    BackgroundThe recent Public Health Emergency of International Concern, caused by a novel coronavirus (2019-nCoV) is fast spreading, and contribution for the increase of knowledge about this outbreak is desired. The aim of this study is to analyse the global trend of 2019-nCoV fatality and virulence rates from 24 January to 06 February 2020.MethodsA cross-sectional study was carried out. Data from 2019-nCoV, Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) and Middle East Respiratory Syndrome coronavirus MESHD (MERS CoV) were obtained from World Health Organization. Only confirmed cases and deaths directly attributed to these viruses were considered. For 2019-nCoV, severe illness was also considered. Two endpoints of interest were analysed: trends in fatality rate (death among confirmed cases x 100) and virulence rate (severe illness MESHD among confirmed cases x 100).ResultsThe 2019-nCoV fatality and virulence rate decreased 1.0 and 7.3 percent points during the analysed time-frame, respectively. The SARS-CoV and MERS-CoV fatality MESHD rate are five and 17 times higher than the current 2019-nCoV fatality rate. The current cumulative 2019-nCoV confirmed cases exceeded 3.5 and 11.3 times the SARS-CoV MESHD and MERS-CoV confirmed cases, respectivelly.ConclusionsA reduction in fatality and virulence rate associated with the novel coronavirus was observed in the analyzed time-frame. The novel coronavirus is spreading at higher rates than SARS-CoV MESHD and MERS-CoV, although with comparative lower fatality rates. Continuous surveillance using additional indicators such as virulence rate (in addition to the fatality rate) may contribute to broaden and deepen the knowledge about the novel coronavirus.

    Assessing the impact of reduced travel on exportation dynamics of novel coronavirus infection ( COVID-19 MESHD)

    Authors: Asami Anzai; Tetsuro Kobayashi; Natalie M. Linton; Ryo Kinoshita; Katsuma Hayashi; Ayako Suzuki; Yichi Yang; Sungmok Jung; Takeshi Miyama; Andrei R. Akhmetzhanov; Hiroshi Nishiura

    doi:10.1101/2020.02.14.20022897 Date: 2020-02-17 Source: medRxiv

    The impact of the drastic reduction in travel volume within mainland China in January and February 2020 was quantified with respect to reports of novel coronavirus ( COVID-19 MESHD) infections outside China. Data on confirmed cases diagnosed outside China were analyzed using statistical models to estimate the impact of travel reduction on three epidemiological outcome measures: (i) the number of exported cases, (ii) the probability of a major epidemic, and (iii) the time delay to a major epidemic. From 28 January to 7 February 2020, we estimated that 226 exported cases (95% confidence interval: 86, 449) were prevented, corresponding to a 70.4% reduction in incidence compared to the counterfactual scenario. The reduced probability of a major epidemic ranged from 7% to 20% in Japan, which resulted in a median time delay to a major epidemic of two days. Depending on the scenario, the estimated delay may be less than one day. As the delay is small, the decision to control travel volume through restrictions on freedom of movement should be balanced between the resulting estimated epidemiological impact and predicted economic fallout.

    Impact of seasonal forcing on a potential SARS-CoV-2 pandemic

    Authors: Richard A Neher; Robert Dyrdak; Valentin Druelle; Emma B Hodcroft; Jan Albert

    doi:10.1101/2020.02.13.20022806 Date: 2020-02-17 Source: medRxiv

    A novel coronavirus (SARS-CoV-2) first detected in Wuhan, China, has spread rapidly since December 2019, causing more than 80,000 confirmed infections and 2,700 fatalities (as of Feb 27, 2020). Imported cases and transmission clusters of various sizes have been reported globally suggesting a pandemic is likely. Here, we explore how seasonal variation in transmissibility could modulate a SARS-CoV-2 pandemic. Data from routine diagnostics show a strong and consistent seasonal variation of the four endemic coronaviruses (229E, HKU1, NL63, OC43) and we parameterize our model for SARS-CoV-2 using these data. The model allows for many subpopulations of different size with variable parameters. Simulations of different scenarios show that plausible parameters result in a small peak in early 2020 in temperate regions of the Northern Hemisphere and a larger peak in winter 2020/2021. Variation in transmission and migration rates can result in substantial variation in prevalence between regions. While the uncertainty in parameters is large, the scenarios we explore show that transient reductions in the incidence rate might be due to a combination of seasonal variation and infection control efforts but do not necessarily mean the epidemic is contained. Seasonal forcing on SARS-CoV-2 should thus be taken into account in the further monitoring of the global transmission. The likely aggregated effect of seasonal variation, infection control measures and transmission rate variation is a prolonged pandemic wave with lower prevalence at any given time, thereby providing a window of opportunity for better preparation of health care systems.

    Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like Protease ( 3CLpro PROTEIN) Structure: Virtual Screening Reveals Velpatasvir, Ledipasvir, and Other Drug Repurposing Candidates

    Authors: Yu Wai Chen; Chin-Pang Yiu; Kwok-Yin Wong

    doi:10.26434/chemrxiv.11831103.v2 Date: 2020-02-17 Source: ChemRxiv

    We prepared the three-dimensional model of the 2019-nCoV 3C-like protease ( 3CLpro PROTEIN) using the crystal structure of the highly-similar (96% identity) ortholog from the SARS-CoV MESHD. All residues involved in the catalysis, substrate binding and dimerisation are 100% conserved. Comparison of the polyprotein PP1AB sequences showed 86% identity. The 3C-like cleavage sites on the coronaviral polyproteins are highly conserved. Based on the near-identical substrate specificities and high sequence identities, we are in the opinion that some of the previous progress of specific inhibitors development for the SARS-CoV MESHD enzyme can be conferred on its 2019-nCoV counterpart. With the 3CLpro PROTEIN molecular model, we performed virtual screening for purchasable drugs and proposed 16 candidates for consideration. Among these, the antivirals ledipasvir or velpatasvir are particularly attractive as therapeutics to combat the 2019-nCoV with minimal side effects, commonly fatigue MESHD and headache MESHD. The drugs Epclusa (velpatasvir / sofosbuvir) and Harvoni (ledipasvir / sofosbuvir) could be very effective owing to their dual inhibitory actions on two viral enzymes.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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