Moussab/ORKG-training-evaluation-set huggingface dataset:
Research field: Virology
Title: Report 3: transmissibility of 2019- nCoV
Abstract: Self-sustaining human-to-human transmission of the novel coronavirus (2019-nCov) is the only plausible explanation of the scale of the outbreak in Wuhan. We estimate that, on average, each case infected 2.6 (uncertainty range: 1.5-3.5) other people up to 18 January 2020, based on an analysis combining our past estimates of the size of the outbreak in Wuhan with computational modelling of potential epidemic trajectories. This implies that control measures need to block well over 60% of transmission to be effective in controlling the outbreak. It is likely, based on the experience of SARS and MERS-CoV, that the number of secondary cases caused by a case of 2019-nCoV is highly variable – with many cases causing no secondary infections, and a few causing many. Whether transmission is continuing at the same rate currently depends on the effectiveness of current control measures implemented in China and the extent to which the populations of affected areas have adopted risk-reducing behaviours. In the absence of antiviral drugs or vaccines, control relies upon the prompt detection and isolation of symptomatic cases. It is unclear at the current time whether this outbreak can be contained within China; uncertainties include the severity spectrum of the disease caused by this virus and whether cases with relatively mild symptoms are able to transmit the virus efficiently. Identification and testing of potential cases need to be as extensive as is permitted by healthcare and diagnostic testing capacity – including the identification, testing and isolation of suspected cases with only mild to moderate disease (e.g. influenza-like illness), when logistically feasible.
Extracted statement — 95% Confidence interval: 1.5-3.5
Research field: Virology
Title: Preliminary estimation of the basic reproduction number of novel coronavirus (2019-nCoV) in China, from 2019 to 2020: A data-driven analysis in the early phase of the outbreak
Abstract: Abstract Backgrounds An ongoing outbreak of a novel coronavirus (2019-nCoV) pneumonia hit a major city of China, Wuhan, December 2019 and subsequently reached other provinces/regions of China and countries. We present estimates of the basic reproduction number, R 0 , of 2019-nCoV in the early phase of the outbreak. Methods Accounting for the impact of the variations in disease reporting rate, we modelled the epidemic curve of 2019-nCoV cases time series, in mainland China from January 10 to January 24, 2020, through the exponential growth. With the estimated intrinsic growth rate ( γ ), we estimated R 0 by using the serial intervals (SI) of two other well-known coronavirus diseases, MERS and SARS, as approximations for the true unknown SI. Findings The early outbreak data largely follows the exponential growth. We estimated that the mean R 0 ranges from 2.24 (95%CI: 1.96-2.55) to 3.58 (95%CI: 2.89-4.39) associated with 8-fold to 2-fold increase in the reporting rate. We demonstrated that changes in reporting rate substantially affect estimates of R 0 . Conclusion The mean estimate of R 0 for the 2019-nCoV ranges from 2.24 to 3.58, and significantly larger than 1. Our findings indicate the potential of 2019-nCoV to cause outbreaks.
Extracted statement — 95% Confidence interval: 1.96-2.55
Research field: Virology
Title: Novel coronavirus 2019-nCoV: early estimation of epidemiological parameters and epidemic predictions
Abstract: Since first identified, the epidemic scale of the recently emerged novel coronavirus (2019-nCoV) in Wuhan, China, has increased rapidly, with cases arising across China and other countries and regions. using a transmission model, we estimate a basic reproductive number of 3.11 (95%CI, 2.39-4.13); 58-76% of transmissions must be prevented to stop increasing; Wuhan case ascertainment of 5.0% (3.6-7.4); 21022 (11090-33490) total infections in Wuhan 1 to 22 January.
Extracted statement — 95% Confidence interval: 2.39-4.13
Research field: Virology
Title: Preliminary estimation of the basic reproduction number of novel coronavirus (2019-nCoV) in China, from 2019 to 2020: A data-driven analysis in the early phase of the outbreak
Abstract: Abstract Backgrounds An ongoing outbreak of a novel coronavirus (2019-nCoV) pneumonia hit a major city of China, Wuhan, December 2019 and subsequently reached other provinces/regions of China and countries. We present estimates of the basic reproduction number, R 0 , of 2019-nCoV in the early phase of the outbreak. Methods Accounting for the impact of the variations in disease reporting rate, we modelled the epidemic curve of 2019-nCoV cases time series, in mainland China from January 10 to January 24, 2020, through the exponential growth. With the estimated intrinsic growth rate ( γ ), we estimated R 0 by using the serial intervals (SI) of two other well-known coronavirus diseases, MERS and SARS, as approximations for the true unknown SI. Findings The early outbreak data largely follows the exponential growth. We estimated that the mean R 0 ranges from 2.24 (95%CI: 1.96-2.55) to 3.58 (95%CI: 2.89-4.39) associated with 8-fold to 2-fold increase in the reporting rate. We demonstrated that changes in reporting rate substantially affect estimates of R 0 . Conclusion The mean estimate of R 0 for the 2019-nCoV ranges from 2.24 to 3.58, and significantly larger than 1. Our findings indicate the potential of 2019-nCoV to cause outbreaks.
Extracted statement — 95% Confidence interval: 2.89-4.39
Research field: Virology
Title: Estimation of the epidemic properties of the 2019 novel coronavirus: A mathematical modeling study
Abstract: Background The 2019 novel Coronavirus (COVID-19) emerged in Wuhan, China in December 2019 and has been spreading rapidly in China. Decisions about its pandemic threat and the appropriate level of public health response depend heavily on estimates of its basic reproduction number and assessments of interventions conducted in the early stages of the epidemic. Methods We conducted a mathematical modeling study using five independent methods to assess the basic reproduction number (R0) of COVID-19, using data on confirmed cases obtained from the China National Health Commission for the period 10th January to 8th February. We analyzed the data for the period before the closure of Wuhan city (10th January to 23rd January) and the post-closure period (23rd January to 8th February) and for the whole period, to assess both the epidemic risk of the virus and the effectiveness of the closure of Wuhan city on spread of COVID-19. Findings Before the closure of Wuhan city the basic reproduction number of COVID-19 was 4.38 (95% CI: 3.63-5.13), dropping to 3.41 (95% CI: 3.16-3.65) after the closure of Wuhan city. Over the entire epidemic period COVID-19 had a basic reproduction number of 3.39 (95% CI: 3.09-3.70), indicating it has a very high transmissibility. Interpretation COVID-19 is a highly transmissible virus with a very high risk of epidemic outbreak once it emerges in metropolitan areas. The closure of Wuhan city was effective in reducing the severity of the epidemic, but even after closure of the city and the subsequent expansion of that closure to other parts of Hubei the virus remained extremely infectious. Emergency planners in other cities should consider this high infectiousness when considering responses to this virus.
Extracted statement — 95% Confidence interval: 3.09-3.70
Research field: Virology
Title: Estimation of the epidemic properties of the 2019 novel coronavirus: A mathematical modeling study
Abstract: Background The 2019 novel Coronavirus (COVID-19) emerged in Wuhan, China in December 2019 and has been spreading rapidly in China. Decisions about its pandemic threat and the appropriate level of public health response depend heavily on estimates of its basic reproduction number and assessments of interventions conducted in the early stages of the epidemic. Methods We conducted a mathematical modeling study using five independent methods to assess the basic reproduction number (R0) of COVID-19, using data on confirmed cases obtained from the China National Health Commission for the period 10th January to 8th February. We analyzed the data for the period before the closure of Wuhan city (10th January to 23rd January) and the post-closure period (23rd January to 8th February) and for the whole period, to assess both the epidemic risk of the virus and the effectiveness of the closure of Wuhan city on spread of COVID-19. Findings Before the closure of Wuhan city the basic reproduction number of COVID-19 was 4.38 (95% CI: 3.63-5.13), dropping to 3.41 (95% CI: 3.16-3.65) after the closure of Wuhan city. Over the entire epidemic period COVID-19 had a basic reproduction number of 3.39 (95% CI: 3.09-3.70), indicating it has a very high transmissibility. Interpretation COVID-19 is a highly transmissible virus with a very high risk of epidemic outbreak once it emerges in metropolitan areas. The closure of Wuhan city was effective in reducing the severity of the epidemic, but even after closure of the city and the subsequent expansion of that closure to other parts of Hubei the virus remained extremely infectious. Emergency planners in other cities should consider this high infectiousness when considering responses to this virus.
Extracted statement — 95% Confidence interval: 3.16-3.65
Research field: Virology
Title: Risk estimation and prediction by modeling the transmission of the novel coronavirus (COVID-19) in mainland China excluding Hubei province
Abstract: Background: In December 2019, an outbreak of coronavirus disease (COVID-19)was identified in Wuhan, China and, later on, detected in other parts of China. Our aim is to evaluate the effectiveness of the evolution of interventions and self-protection measures, estimate the risk of partial lifting control measures and predict the epidemic trend of the virus in mainland China excluding Hubei province based on the published data and a novel mathematical model. Methods: A novel COVID-19 transmission dynamic model incorporating the intervention measures implemented in China is proposed. We parameterize the model by using the Markov Chain Monte Carlo (MCMC) method and estimate the control reproduction number Rc, as well as the effective daily reproduction ratio Re(t), of the disease transmission in mainland China excluding Hubei province. Results: The estimation outcomes indicate that the control reproduction number is 3.36 (95% CI 3.20-3.64) and Re(t) has dropped below 1 since January 31st, 2020, which implies that the containment strategies implemented by the Chinese government in mainland China excluding Hubei province are indeed effective and magnificently suppressed COVID-19 transmission. Moreover, our results show that relieving personal protection too early may lead to the spread of disease for a longer time and more people would be infected, and may even cause epidemic or outbreak again. By calculating the effective reproduction ratio, we proved that the contact rate should be kept at least less than 30% of the normal level by April, 2020. Conclusions: To ensure the epidemic ending rapidly, it is necessary to maintain the current integrated restrict interventions and self-protection measures, including travel restriction, quarantine of entry, contact tracing followed by quarantine and isolation and reduction of contact, like wearing masks, etc. People should be fully aware of the real-time epidemic situation and keep sufficient personal protection until April. If all the above conditions are met, the outbreak is expected to be ended by April in mainland China apart from Hubei province.
Extracted statement — 95% Confidence interval: 3.20-3.64
Research field: Virology
Title: Estimation of the epidemic properties of the 2019 novel coronavirus: A mathematical modeling study
Abstract: Background The 2019 novel Coronavirus (COVID-19) emerged in Wuhan, China in December 2019 and has been spreading rapidly in China. Decisions about its pandemic threat and the appropriate level of public health response depend heavily on estimates of its basic reproduction number and assessments of interventions conducted in the early stages of the epidemic. Methods We conducted a mathematical modeling study using five independent methods to assess the basic reproduction number (R0) of COVID-19, using data on confirmed cases obtained from the China National Health Commission for the period 10th January to 8th February. We analyzed the data for the period before the closure of Wuhan city (10th January to 23rd January) and the post-closure period (23rd January to 8th February) and for the whole period, to assess both the epidemic risk of the virus and the effectiveness of the closure of Wuhan city on spread of COVID-19. Findings Before the closure of Wuhan city the basic reproduction number of COVID-19 was 4.38 (95% CI: 3.63-5.13), dropping to 3.41 (95% CI: 3.16-3.65) after the closure of Wuhan city. Over the entire epidemic period COVID-19 had a basic reproduction number of 3.39 (95% CI: 3.09-3.70), indicating it has a very high transmissibility. Interpretation COVID-19 is a highly transmissible virus with a very high risk of epidemic outbreak once it emerges in metropolitan areas. The closure of Wuhan city was effective in reducing the severity of the epidemic, but even after closure of the city and the subsequent expansion of that closure to other parts of Hubei the virus remained extremely infectious. Emergency planners in other cities should consider this high infectiousness when considering responses to this virus.
Extracted statement — 95% Confidence interval: 3.63-5.13
Research field: Virology
Title: Estimation of the Transmission Risk of 2019-nCov and Its Implication for Public Health Interventions
Abstract: English Abstract: Background: Since the emergence of the first pneumonia cases in Wuhan, China, the novel coronavirus (2019-nCov) infection has been quickly spreading out to other provinces and neighbouring countries. Estimation of the basic reproduction number by means of mathematical modelling can be helpful for determining the potential and severity of an outbreak, and providing critical information for identifying the type of disease interventions and intensity. Methods: A deterministic compartmental model was devised based on the clinical progression of the disease, epidemiological status of the individuals, and the intervention measures. Findings: The estimation results based on likelihood and model analysis reveal that the control reproduction number may be as high as 6.47 (95% CI 5.71-7.23). Sensitivity analyses reveal that interventions, such as intensive contact tracing followed by quarantine and isolation, can effectively reduce the control reproduction number and transmission risk, with the effect of travel restriction of Wuhan on 2019-nCov infection in Beijing being almost equivalent to increasing quarantine by 100-thousand baseline value. Interpretation: It is essential to assess how the expensive, resource-intensive measures implemented by the Chinese authorities can contribute to the prevention and control of the 2019-nCov infection, and how long should be maintained. Under the most restrictive measures, the outbreak is expected to peak within two weeks (since January 23rd 2020) with significant low peak value. With travel restriction (no imported exposed individuals to Beijing), the number of infected individuals in 7 days will decrease by 91.14% in Beijing, compared with the scenario of no travel restriction. Mandarin Abstract: 背景：自从中国武汉出现第一例肺炎病例以来，新型冠状病毒（2019-nCov）感染已迅速传播到其他省份和周边国家。通过数学模型估计基本再生数，有助于确定疫情爆发的可能性和严重性，并为确定疾病干预类型和强度提供关键信息。 方法：根据疾病的临床进展，个体的流行病学状况和干预措施，设计确定性的仓室模型。 结果：基于似然函数和模型分析的估计结果表明，控制再生数可能高达6.47（95％CI 5.71-7.23）。敏感性分析显示，密集接触追踪和隔离等干预措施可以有效减少控制再生数和传播风险，武汉封城措施对北京2019-nCov感染的影响几乎等同于增加隔离措施10万的基线值。 解释：必须评估中国当局实施的昂贵，资源密集型措施如何有助于预防和控制2019-nCov感染，以及应维持多长时间。在最严格的措施下，预计疫情将在两周内（自2020年1月23日起）达到峰值，峰值较低。与没有出行限制的情况相比，有了出行限制（即没有输入的潜伏类个体进入北京），北京的7天感染者数量将减少91.14％。
Extracted statement — 95% Confidence interval: 5.71-7.23
Research field: Virology
Title: Alphacoronavirus in a Daubenton’s Myotis Bat (Myotis daubentonii) in Sweden.
Abstract: The ongoing COVID-19 pandemic has stimulated a search for reservoirs and species potentially involved in back and forth transmission. Studies have postulated bats as one of the key reservoirs of coronaviruses (CoVs), and different CoVs have been detected in bats. So far, CoVs have not been found in bats in Sweden and we therefore tested whether they carry CoVs. In summer 2020, we sampled a total of 77 adult bats comprising 74 Myotis daubentonii, 2 Pipistrellus pygmaeus, and 1 M. mystacinus bats in southern Sweden. Blood, saliva and feces were sampled, processed and subjected to a virus next-generation sequencing target enrichment protocol. An Alphacoronavirus was detected and sequenced from feces of a M. daubentonii adult female bat. Phylogenetic analysis of the almost complete virus genome revealed a close relationship with Finnish and Danish strains. This was the first finding of a CoV in bats in Sweden, and bats may play a role in the transmission cycle of CoVs in Sweden. Focused and targeted surveillance of CoVs in bats is warranted, with consideration of potential conflicts between public health and nature conservation required as many bat species in Europe are threatened and protected.
Extracted statement — Has Virus: COVID-19
Research field: Virology
Title: In vitro screening of a FDA approved chemical library reveals potential inhibitors of SARS-CoV-2 replication
Abstract: A novel coronavirus, named SARS-CoV-2, emerged in 2019 from Hubei region in China and rapidly spread worldwide. As no approved therapeutics exists to treat Covid-19, the disease associated to SARS-Cov-2, there is an urgent need to propose molecules that could quickly enter into clinics. Repurposing of approved drugs is a strategy that can bypass the time consuming stages of drug development. In this study, we screened the Prestwick Chemical Library® composed of 1,520 approved drugs in an infected cell-based assay. 90 compounds were identified. The robustness of the screen was assessed by the identification of drugs, such as Chloroquine derivatives and protease inhibitors, already in clinical trials. The hits were sorted according to their chemical composition and their known therapeutic effect, then EC50 and CC50 were determined for a subset of compounds. Several drugs, such as Azithromycine, Opipramol, Quinidine or Omeprazol present antiviral potency with 2<EC50<20µM. By providing new information on molecules inhibiting SARS-CoV-2 replication in vitro, this study could contribute to the short-term repurposing of drugs against Covid-19.
Extracted statement — has endpoint: EC50
Research field: Virology
Title: Broad anti-coronaviral activity of FDA approved drugs against SARS-CoV-2 in vitro and SARS-CoV in vivo
Abstract: Abstract SARS-CoV-2 emerged in China at the end of 2019 and has rapidly become a pandemic with roughly 2.7 million recorded COVID-19 cases and greater than 189,000 recorded deaths by April 23rd, 2020 (<jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://www.WHO.org">www.WHO.org</jats:ext-link>). There are no FDA approved antivirals or vaccines for any coronavirus, including SARS-CoV-2. Current treatments for COVID-19 are limited to supportive therapies and off-label use of FDA approved drugs. Rapid development and human testing of potential antivirals is greatly needed. A quick way to test compounds with potential antiviral activity is through drug repurposing. Numerous drugs are already approved for human use and subsequently there is a good understanding of their safety profiles and potential side effects, making them easier to fast-track to clinical studies in COVID-19 patients. Here, we present data on the antiviral activity of 20 FDA approved drugs against SARS-CoV-2 that also inhibit SARS-CoV and MERS-CoV. We found that 17 of these inhibit SARS-CoV-2 at a range of IC50 values at non-cytotoxic concentrations. We directly follow up with seven of these to demonstrate all are capable of inhibiting infectious SARS-CoV-2 production. Moreover, we have evaluated two of these, chloroquine and chlorpromazine, in vivo using a mouse-adapted SARS-CoV model and found both drugs protect mice from clinical disease.
Extracted statement — has endpoint: IC50
Research field: Animal Sciences
Title: Pharmacokinetics of levetiracetam after oral and intravenous administration of a single dose to clinically normal cats
Abstract: OBJECTIVE To determine whether therapeutic concentrations of levetiracetam can be achieved in cats and to establish reasonable i.v. and oral dosing intervals that would not be associated with adverse effects in cats. ANIMALS 10 healthy purpose-bred cats. PROCEDURES In a randomized crossover study, levetiracetam (20 mg/kg) was administered orally and i.v. to each cat. Blood samples were collected 0, 10, 20, and 40 minutes and 1, 1.5, 2, 3, 4, 6, 9, 12, and 24 hours after administration. Plasma levetiracetam concentrations were determined via high-performance liquid chromatography. RESULTS Mean ± SD peak concentration was 25.54 ± 7.97 μg/mL. The mean y-intercept for i.v. administration was 37.52 ± 6.79 μg/mL. Half-life (harmonic mean ± pseudo-SD) was 2.95 ± 0.95 hours and 2.86 ± 0.65 hours for oral and i.v. administration, respectively. Mean volume of distribution at steady state was 0.52 ± 0.09 L/kg, and mean clearance was 2.0 ± 0.60 mL/kg/min. Mean oral bioavailability was 102 ± 39%. Plasma drug concentrations were maintained in the therapeutic range reported for humans (5 to 45 μg/mL) for at least 9 hours after administration in 7 of 10 cats. Only mild, transient hypersalivation was evident in some cats after oral administration. CONCLUSIONS AND CLINICAL RELEVANCE Levetiracetam (20 mg/kg) administered orally or i.v. to cats every 8 hours should achieve and maintain concentrations within the therapeutic range for humans. Levetiracetam administration has favorable pharmacokinetics for clinical use, was apparently tolerated well, and may be a reasonable alternative antiepileptic drug in cats.
Extracted statement — Disease definitions (characterization): clear
Research field: Animal Sciences
Title: Use of continuous electroencephalography for diagnosis and monitoring of treatment of nonconvulsive status epilepticus in a cat
Abstract: CASE DESCRIPTION A 10-year-old domestic shorthair cat was evaluated because of presumed seizures. CLINICAL FINDINGS The cat had intermittent mydriasis, hyperthermia, and facial twitching. Findings of MRI and CSF sample analysis were unremarkable, and results of infectious disease testing were negative. Treatment was initiated with phenobarbital, zonisamide, and levetiracetam; however, the presumed seizure activity continued. Results of analysis of continuous electroencephalographic recording indicated the cat had nonconvulsive status epilepticus. TREATMENT AND OUTCOME The cat was treated with phenobarbital IV (6 mg/kg [2.7 mg/lb] q 30 min during a 9-hour period; total dose, 108 mg/kg [49.1 mg/lb]); treatment was stopped when a burst-suppression electroencephalographic pattern was detected. During this high-dose phenobarbital treatment period, an endotracheal tube was placed and the cat was monitored and received fluids, hetastarch, and dopamine IV. Continuous mechanical ventilation was not required. After treatment, the cat developed unclassified cardiomyopathy, azotemia, anemia, and pneumonia. These problems resolved during a 9-month period. CLINICAL RELEVANCE Findings for the cat of this report indicated electroencephalographic evidence of nonconvulsive status epilepticus. Administration of a high total dose of phenobarbital and monitoring of treatment by use of electroencephalography were successful for resolution of the problem, and treatment sequelae resolved.
Extracted statement — Pre-treatment SF (seizures/ month or year): continuous