Corpus overview


MeSH Disease

Human Phenotype


    displaying 821 - 830 records in total 940
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    The Population Attributable Fraction (PAF) of cases due to gatherings and groups with relevance to COVID-19 mitigation strategies

    Authors: Ellen Brooks-Pollock; Jonathan M Read; Thomas House; Graham Medley; Matt J Keeling; Leon Danon

    doi:10.1101/2020.03.20.20039537 Date: 2020-03-23 Source: medRxiv

    Background Many countries have banned groups and gatherings as part of their response to the pandemic caused by the coronavirus, SARS-CoV-2. Although there are outbreak reports involving mass gatherings, the contribution to overall transmission TRANS is unknown. Methods We used data from a survey of social contact behaviour that specifically asked about contact with groups to estimate the Population Attributable Fraction (PAF) due to groups as the relative change in the Basic Reproduction Number TRANS when groups are prevented. Findings We estimate that PAF due to groups of 50+ people is 2.2% (95%CI 1.1%, 3.6%); the PAF due to groups of 20+ people is 6.4% (5.0%, 8.0%); the PAF due to groups of 10+ is 11.3% (9.9%, 13.0%) Interpretation Large groups of individuals have a small epidemiological impact; small and medium sized groups between 10 and 50 people have a larger impact on an epidemic.

    COVID-19 attack rate TRANS increases with city size

    Authors: Andrew J. Stier; Marc G. Berman; Luis M. A. Bettencourt

    id:2003.10376v2 Date: 2020-03-23 Source: arXiv

    The current outbreak of novel coronavirus disease MESHD 2019 (COVID-19) poses an unprecedented global health and economic threat to interconnected human societies. Until a vaccine is developed, strategies for controlling the outbreak rely on aggressive social distancing. These measures largely disconnect the social network fabric of human societies, especially in urban areas. Here, we estimate the growth rates and reproductive numbers TRANS of COVID-19 in US cities from March 14th through March 19th to reveal a power-law scaling relationship to city population size. This means that COVID-19 is spreading faster on average in larger cities with the additional implication that, in an uncontrolled outbreak, larger fractions of the population are expected to become infected MESHD in more populous urban areas. We discuss the implications of these observations for controlling the COVID-19 outbreak, emphasizing the need to implement more aggressive distancing policies in larger cities while also preserving socioeconomic activity.

    The local stability of a modified multi-strain SIR model for emerging viral strains

    Authors: Miguel Fudolig; Reka Howard

    doi:10.1101/2020.03.19.20039198 Date: 2020-03-23 Source: medRxiv

    We study a novel multi-strain SIR epidemic model with selective immunity by vaccination. A newer strain is made to emerge in the population when a preexisting strain has reached equilibrium. We assume that this newer strain does not exhibit cross-immunity with the original strain, hence those who are vaccinated and recovered from the original strain become susceptible to the newer strain. Recent events involving the COVID-19 virus demonstrates that it is possible for a viral strain to emerge from a population at a time when the influenza virus, a well-known virus with a vaccine readily available for some of its strains, is active in a population. We solved for four different equilibrium points and investigated the conditions for existence and local stability. The reproduction number TRANS was also determined for the epidemiological model and found to be consistent with the local stability condition for the disease-free equilibrium.

    Estimation of Basic Reproduction Number TRANS of the COVID-19 Epidemic in Denmark using a Two-Step Model

    Authors: Jan Brink Valentin

    id:2003.09775v2 Date: 2020-03-22 Source: arXiv

    Objective: To conduct an early estimation of the Basic Reproduction Number TRANS (BRN) induced by government interference, and to project resulting day to day number of in-patients, ICU-patients and cumulative number of deaths MESHD in a Danish setting. Method: We used the Kermack and McKendrick model with varying basic reproduction number TRANS to estimate number infected MESHD and age TRANS stratified percentages to estimate number of in-patients, ICU-patients and cumulative number of deaths. Changes in basic reproduction number TRANS was estimated based on current in-patient numbers. Results: The basic reproductive number TRANS in the time period of February 27th to March 18th was found to be 2.65, however, this number was reduced to 1.99 after March 18th. Keywords: COVID-19, basic reproduction number TRANS, Danish population

    A SIDARTHE Model of COVID-19 Epidemic in Italy

    Authors: Giulia Giordano; Franco Blanchini; Raffaele Bruno; Patrizio Colaneri; Alessandro Di Filippo; Angela Di Matteo; Marta Colaneri; the COVID19 IRCCS San Matteo Pavia Task Force

    id:2003.09861v1 Date: 2020-03-22 Source: arXiv

    In late December 2019, a novel strand of Coronavirus (SARS-CoV-2) causing a severe, potentially fatal respiratory syndrome MESHD (COVID-19) was identified in Wuhan, Hubei Province, China and is causing outbreaks in multiple world countries, soon becoming a pandemic. Italy has now become the most hit country outside of Asia: on March 16, 2020, the Italian Civil Protection documented a total of 27980 confirmed cases TRANS and 2158 deaths of people tested positive for SARS-CoV-2. In the context of an emerging infectious disease outbreak, it is of paramount importance to predict the trend of the epidemic in order to plan an effective control strategy and to determine its impact. This paper proposes a new epidemic model that discriminates between infected individuals depending on whether they have been diagnosed and on the severity of their symptoms. The distinction between diagnosed and non-diagnosed is important because non-diagnosed individuals are more likely to spread the infection MESHD than diagnosed ones, since the latter are typically isolated, and can explain misperceptions of the case fatality rate and of the seriousness of the epidemic phenomenon. Being able to predict the amount of patients that will develop life-threatening symptoms is important since the disease frequently requires hospitalisation (and even Intensive Care Unit admission) and challenges the healthcare system capacity. We show how the basic reproduction number TRANS can be redefined in the new framework, thus capturing the potential for epidemic containment. Simulation results are compared with real data on the COVID-19 epidemic in Italy, to show the validity of the model and compare different possible predicted scenarios depending on the adopted countermeasures.

    Maximum entropy method for estimating the reproduction number TRANS: An investigation for COVID-19 in China

    Authors: Yong Tao

    doi:10.1101/2020.03.14.20035659 Date: 2020-03-20 Source: medRxiv

    The key parameter that characterizes the transmissibility TRANS of a disease is the reproduction number TRANS R. If it exceeds 1, the number of incident cases will inevitably grow over time, and a large epidemic is possible. To prevent the expansion of an epidemic, R must be reduced to a level below 1. To estimate the reproduction number TRANS, the probability distribution function of the generation interval of an infectious disease MESHD is required to be available; however, this distribution is often unknown. In this letter, given the incomplete information for the generation interval, we propose a maximum entropy method to estimate the reproduction number TRANS. Based on this method, given the mean value and variance of the generation interval, we first determine its probability distribution function and in turn estimate the real-time values of reproduction number TRANS of COVID-19 in China. By applying these estimated reproduction numbers TRANS into the susceptible-infectious-removed epidemic model, we simulate the evolutionary track of the epidemic in China, which is well in accordance with that of the real incident cases. The simulation results predict that China's epidemic will gradually tend to disappear by May 2020 if the quarantine measures can continue to be executed.

    The early phase of the COVID-19 outbreak in Lombardy, Italy

    Authors: D Cereda; M Tirani; F Rovida; V Demicheli; M Ajelli; P Poletti; F Trentini; G Guzzetta; V Marziano; A Barone; M Magoni; S Deandrea; G Diurno; M Lombardo; M Faccini; A Pan; R Bruno; E Pariani; G Grasselli; A Piatti; M Gramegna; F Baldanti; A Melegaro; S Merler

    id:2003.09320v1 Date: 2020-03-20 Source: arXiv

    In the night of February 20, 2020, the first case of novel coronavirus disease MESHD (COVID-19) was confirmed in the Lombardy Region, Italy. In the week that followed, Lombardy experienced a very rapid increase in the number of cases. We analyzed the first 5,830 laboratory- confirmed cases TRANS to provide the first epidemiological characterization of a COVID-19 outbreak in a Western Country. Epidemiological data were collected through standardized interviews of confirmed cases TRANS and their close contacts TRANS. We collected demographic backgrounds, dates of symptom onset TRANS, clinical features, respiratory tract specimen results, hospitalization, contact tracing TRANS. We provide estimates of the reproduction number TRANS and serial interval TRANS. The epidemic in Italy started much earlier than February 20, 2020. At the time of detection of the first COVID-19 case, the epidemic had already spread in most municipalities of Southern-Lombardy. The median age TRANS for of cases is 69 years (range, 1 month to 101 years). 47% of positive subjects were hospitalized. Among these, 18% required intensive care. The mean serial interval TRANS is estimated to be 6.6 days (95% CI, 0.7 to 19). We estimate the basic reproduction number TRANS at 3.1 (95% CI, 2.9 to 3.2). We estimated a decreasing trend in the net reproduction number TRANS starting around February 20, 2020. We did not observe significantly different viral loads in nasal swabs between symptomatic and asymptomatic TRANS. The transmission TRANS potential of COVID-19 is very high and the number of critical cases may become largely unsustainable for the healthcare system in a very short-time horizon. We observed a slight decrease of the reproduction number TRANS, possibly connected with an increased population awareness and early effect of interventions. Aggressive containment strategies are required to control COVID-19 spread and catastrophic outcomes for the healthcare system.

    Tracing TRANS DAY-ZERO and Forecasting the Fade out of the COVID-19 Outbreak in Lombardy, Italy: A Compartmental Modelling and Numerical Optimization Approach.

    Authors: Lucia Russo; Cleo Anastassopoulou; Athanassios Tsakris; Gennaro Nicola Bifulco; Emilio Fortunato Campana; Gerardo Toraldo; Constantinos Siettos

    doi:10.1101/2020.03.17.20037689 Date: 2020-03-20 Source: medRxiv

    Italy became the second epicenter of the novel coronavirus disease MESHD 2019 (COVID-19) pandemic after China, surpassing by far China's death MESHD toll. The disease swept through Lombardy, which remained in lockdown for about two months, starting from the 8th of March. As of that day, the isolation measures taken in Lombardy were extended to the entire country. Here, assuming that effectively there was one case ``zero" that introduced the virus to the region, we provide estimates for: (a) the DAY-ZERO of the outbreak in Lombardy, Italy; (b) the actual number of asymptomatic TRANS infected MESHD cases in the total population until March 8; (c) the basic reproduction number TRANS Ro based on the estimation of the actual number of infected cases. To demonstrate the efficiency of the model and approach, we also provide a tentative forecast two months ahead of time, i.e. until May 4, the date on which relaxation of the measures commenced, on the basis of the COVID-19 Community Mobility Reports released by Google on March 29. Methods. To deal with the uncertainty in the number of actual asymptomatic TRANS infected cases in the total population, we address a modified compartmental Susceptible/ Exposed/ Infectious Asymptomatic TRANS/ Infected Symptomatic/ Recovered/ Dead (SEIIRD) model with two compartments of infectious persons: one modelling the cases in the population that are asymptomatic TRANS or experience very mild symptoms and another modelling the infected cases with mild to severe symptoms. The parameters of the model corresponding to the recovery period, the time from the onset of symptoms TRANS to death MESHD and the time from exposure to the time that an individual starts to be infectious, have been set as reported from clinical studies on COVID-19. For the estimation of the DAY-ZERO of the outbreak in Lombardy, as well as of the "effective" per-day transmission TRANS rate for which no clinical data are available, we have used the proposed SEIIRD simulator to fit the numbers of new daily cases from February 21 to the 8th of March. This was accomplished by solving a mixed-integer optimization problem. Based on the computed parameters, we also provide an estimation of the basic reproduction number TRANS $ R_0 TRANS$. To examine the efficiency of the model and approach, we ran the simulator to forecast the epidemic two months ahead of time, i.e. from March 8 to May 4. For this purpose, we considered the reduction in mobility in Lombardy as released on March 29 by Google COVID-19 Community Mobility Reports, and the effects of social distancing and of the draconian measures taken by the government on March 20 and March 21, 2020. Results. Based on the proposed methodological procedure, we estimated that the expected DAY-ZERO was January 14 (min-max rage: January 5 to January 23, interquartile range: January 11 to January 18). The actual cumulative number of asymptomatic TRANS infected MESHD cases in the total population in Lombardy on March 8 was of the order of 15 times the confirmed cumulative number of infected cases, while the expected value of the basic reproduction number TRANS Ro was found to be 4.53 (min-max range: 4.40- 4.65). The model approximated adequately two months ahead of time the evolution of reported cases until May 4, the day on which the phase I of the relaxation of measures was implemented over all of Italy.

    Pandemic dynamics of COVID-19 using epidemic stage, instantaneous reproductive number TRANS and pathogen genome identity (GENI) score: modeling molecular epidemiology

    Authors: DJ Darwin R Bandoy; Bart C Weimer

    doi:10.1101/2020.03.17.20037481 Date: 2020-03-20 Source: medRxiv

    Background: Global spread of COVID-19 created an unprecedented infectious disease MESHD crisis that progressed to a pandemic with >180,000 cases in >100 countries. Reproductive number (R TRANS) is an outbreak metric estimating the transmission TRANS of a pathogen. Initial R values TRANS were published based on the early outbreak in China with limited number of cases with whole genome sequencing. Initial comparisons failed to show a direct relationship viral genomic diversity and epidemic severity was not established for SARS-Cov-2. Methods: Each country's COVID-19 outbreak status was classified according to epicurve stage (index, takeoff, exponential, decline). Instantaneous R estimates (Wallinga and Teunis method) with a short and standard serial interval TRANS examined asymptomatic TRANS spread. Whole genome sequences were used to quantify the pathogen genome identity score that were used to estimate transmission TRANS time and epicurve stage. Transmission TRANS time was estimated based on evolutionary rate of 2 mutations/month. Findings: The country-specific R revealed variable infection dynamics between and within outbreak stages. Outside China, R estimates revealed propagating epidemics poised to move into the takeoff and exponential stages. Population density and local temperatures had variable relationship to the outbreaks. GENI scores differentiated countries in index stage with cryptic transmission TRANS. Integration of incidence data with genome variation directly increases in cases with increased genome variation. Interpretation: R was dynamic for each country and during the outbreak stage. Integrating the outbreak dynamic, dynamic R, and genome variation found a direct association between cases and genome variation. Synergistically, GENI provides an evidence-based transmission TRANS metric that can be determined by sequencing the virus from each case. We calculated an instantaneous country-specific R at different stages of outbreaks and formulated a novel metric for infection MESHD dynamics using viral genome sequences to capture gaps in untraceable transmission TRANS. Integrating epidemiology with genome sequencing allows evidence-based dynamic disease outbreak tracking with predictive evidence.

    Extended SIR prediction of the epidemics trend of COVID-19 in Italy and compared with Hunan, China

    Authors: Wangping Jia; Ke Han; Yang Song; Wenzhe Cao; Shengshu Wang; Shanshan Yang; Jianwei Wang; Fuyin Kou; Penggang Tai; Jing Li; Miao Liu; Yao He

    doi:10.1101/2020.03.18.20038570 Date: 2020-03-20 Source: medRxiv

    Background: Coronavirus Disease MESHD 2019 (COVID19) is currently a global public health threat. Outside of China, Italy is one of the most suffering countries with the COVID19 epidemic. It is important to predict the epidemics trend of COVID19 epidemic in Italy to help develop public health strategies. Methods: We used time series data of COVID 19 from Jan 22,2020 to Mar 16,2020. An infectious disease MESHD dynamic extended susceptible infected removed (eSIR) model, which covers the effects of different intervention measures in dissimilar periods, was applied to estimate the epidemic trend in Italy. The basic reproductive number TRANS was estimated using Markov Chain Monte Carlo methods and presented using the resulting posterior mean and 95% credible interval (CI). Hunan, with similar total number of populations in Italy, was used as a comparative item. Results: In the eSIR model, we estimated that the basic reproductive number TRANS for COVID 19 was respectively 4.10 (95% CI: 2.15 to 6.77) in Italy and 3.15(95% CI: 1.71 to 5.21) in Hunan. There would be totally 30 086 infected cases (95%CI:7920-81 869) under the current country blockade and the endpoint would be Apr 25 (95%CI: Mar 30 to Aug 07) in Italy. If the country blockade is imposed 5 day later, the total number of infected MESHD cases would expand the infection scale 1.50 times. Conclusion: Italy's current strict measures can efficaciously prevent the further spread of COVID19 and should be maintained. Necessary strict public health measures be implemented as soon as possible in other European countries with a high number of COVID19 cases. The most effective strategy needs to be confirmed in further studies.

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MeSH Disease
Human Phenotype

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