Corpus overview


Overview

MeSH Disease

Human Phenotype

Transmission

Seroprevalence
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    Modeling latent infection MESHD transmissions TRANS through biosocial stochastic dynamics

    Authors: Bosiljka Tadic; Roderick Melnik

    doi:10.1101/2020.07.30.20164491 Date: 2020-08-01 Source: medRxiv

    The events of the recent SARS-CoV-02 epidemics have shown the importance of social factors, especially given the large number of asymptomatic TRANS cases that effectively spread the virus, which can cause a medical emergency MESHD to very susceptible individuals. Besides, the SARS-CoV-02 virus survives for several hours on different surfaces, where a new host can contract it with a delay. These passive modes of infection MESHD transmission TRANS remain an unexplored area for traditional mean-field epidemic models. Here, we design an agent-based model for simulations of infection MESHD transmission TRANS in an open system driven by the dynamics of social activity; the model takes into account the personal characteristics of individuals, as well as the survival time of the virus and its potential mutations. A growing bipartite graph embodies this biosocial process, consisting of active carriers TRANS (host) nodes that produce viral nodes during their infectious period TRANS. With its directed edges passing through viral nodes between two successive hosts, this graph contains complete information about the routes leading to each infected individual. We determine temporal fluctuations of the number of exposed and the number of infected individuals, the number of active carriers TRANS and active viruses at hourly resolution. The simulated processes underpin the latent infection MESHD transmissions TRANS, contributing significantly to the spread of the virus within a large time window. More precisely, being brought by social dynamics and exposed to the currently existing infection MESHD, an individual passes through the infectious state until eventually spontaneously recovers or otherwise is moves to a controlled hospital environment. Our results reveal complex feedback mechanisms that shape the dependence of the infection MESHD curve on the intensity of social dynamics and other sociobiological factors. In particular, the results show how the lockdown effectively reduces the spread of infection MESHD and how it increases again after the lockdown is removed. Furthermore, a reduced level of social activity but prolonged exposure of susceptible individuals have adverse effects. On the other hand, virus mutations that can gradually reduce the transmission TRANS rate by hopping to each new host along the infection MESHD path can significantly reduce the extent of the infection MESHD, but can not stop the spreading without additional social strategies. Our stochastic processes, based on graphs at the interface of biology and social dynamics, provide a new mathematical framework for simulations of various epidemic control strategies with high temporal resolution and virus traceability.

    Mechanistic modelling of coronavirus infections MESHD and the impact of confined neighbourhoods on a short time scale

    Authors: Danish A Ahmed; Ali R Ansari; Mudassar Imran; Kamaludin Dingle; Naveed Ahmed; Michael A Bonsall

    doi:10.1101/2020.07.28.20163634 Date: 2020-07-30 Source: medRxiv

    Background: To mitigate the spread of the COVID-19 coronavirus, some countries have adopted more stringent non-pharmaceutical interventions in contrast to those widely used (for e.g. the state of Kuwait). In addition to standard practices such as enforcing curfews, social distancing, and closure of non-essential service industries, other non-conventional policies such as the total confinement of highly populated areas has also been implemented. Methods: In this paper, we model the movement of a host population using a mechanistic approach based on random walks, which are either diffusive or super-diffusive. Infections MESHD are realised through a contact process, whereby a susceptible host may be infected if in close spatial proximity of the infectious host. Our focus is only on the short-time scale prior to the infectious period TRANS, so that no further transmission TRANS is assumed. Results: We find that the level of infection MESHD depends heavily on the population dynamics, and increases in the case of slow population diffusion, but remains stable for a high or super-diffusive population. Also, we find that the confinement of homogeneous or overcrowded sub-populations has minimal impact in the short term. Conclusions: Our results indicate that on a short time scale, confinement restrictions or complete lock down of whole residential areas may not be effective. Finally, we discuss the possible implications of our findings for total confinement in the context of the current situation in Kuwait.

    The basic reproduction number TRANS of SARS-CoV-2: a scoping review of available evidence

    Authors: Ann Barber; John M Griffin; Miriam Casey; Aine Collins; Elizabeth A Lane; Quirine Ten Bosch; Mart De Jong; David Mc Evoy; Andrew W Byrne; Conor G McAloon; Francis Butler; Kevin Hunt; Simon J More

    doi:10.1101/2020.07.28.20163535 Date: 2020-07-30 Source: medRxiv

    Background: The transmissibility TRANS of SARS-CoV-2 determines both the ability of the virus to invade a population and the strength of intervention that would be required to contain or eliminate the spread of infection MESHD. The basic reproduction number TRANS, R0 TRANS, provides a quantitative measure of the transmission TRANS potential of a pathogen. Objective: Conduct a scoping review of the available literature providing estimates of R0 TRANS for SARS-CoV-2, provide an overview of the drivers of variation in R0 TRANS estimates and the considerations taken in the calculation of the parameter. Design: Scoping review of available literature between the 01 December 2019 and 07 May 2020. Data sources: Both peer-reviewed and pre-print articles were searched for on PubMed, Google Scholar, MedRxiv and BioRxiv. Selection criteria: Studies were selected for review if (i) the estimation of R0 TRANS represented either the initial stages of the outbreak or the initial stages of the outbreak prior to the onset of widespread population restriction (lockdown), (ii) the exact dates of the study period were provided and (iii) the study provided primary estimates of R0 TRANS. Results: A total of 20 R0 TRANS estimates were extracted from 15 studies. There was substantial variation in the estimates reported. Estimates derived from mathematical models fell HP within a wider range of 1.94-6.94 than statistical models which fell HP between the range of 2.2 to 4.4. Several studies made assumptions about the length of the infectious period TRANS which ranged from 5.8-20 days and the serial interval TRANS which ranged from 4.41-14 days. For a given set of parameters a longer duration of infectiousness or a longer serial interval TRANS equates to a higher R0 TRANS. Several studies took measures to minimise bias in early case reporting, to account for the potential occurrence of super-spreading events, and to account for early sub-exponential epidemic growth. Conclusions: The variation in reported estimates of R0 TRANS reflects the complex nature of the parameter itself, including the context (i.e. social/spatial structure), the methodology used to estimate the parameter, and model assumptions. R0 TRANS is a fundamental parameter in the study of infectious disease MESHD dynamics however it provides limited practical applicability outside of the context in which it was estimated, and should be calculated and interpreted with this in mind.

    Mechanistic Modelling of Coronavirus Infections MESHD and the Impact of Confined Neighbourhoods on a Short Time Scale

    Authors: Danish Ali Ahmed; Ali Ansari; Mudassar Imran; Kamal Dingle; Naveed Ahmed; Michael Bonsall

    doi:10.21203/rs.3.rs-48823/v1 Date: 2020-07-25 Source: ResearchSquare

    Background: To mitigate the spread of the COVID-19 coronavirus, some countries have adopted more stringent non-pharmaceutical interventions in contrast to those widely used (for e.g. the state of Kuwait). In addition to standard practices such as enforcing curfews, social distancing, and closure of non-essential service industries, other non-conventional policies such as the total confinement of highly populated areas has also been implemented. Methods: In this paper, we model the movement of a host population using a mechanistic approach based on random walks, which are either diffusive or super-diffusive. Infections MESHD are realised through a contact process, whereby a susceptible host may be infected if in close spatial proximity of the infectious host. Our focus is only on the short-time scale prior to the infectious period TRANS, so that no further transmission TRANS is assumed. Results: We find that the level of infection MESHD depends heavily on the population dynamics, and increases in the case of slow population diffusion, but remains stable for a high or super-diffusive population. Also, we find that the confinement of homogeneous or overcrowded sub-populations has minimal impact in the short term. Conclusions: Our results indicate that on a short time scale, confinement restrictions or complete lock down of whole residential areas may not be effective. Finally, we discuss the possible implications of our findings for total confinement in the context of the current situation in Kuwait.

    The collective wisdom in the COVID-19 research: comparison and synthesis of epidemiological parameter estimates in preprints and peer-reviewed articles

    Authors: Yuejiao Wang; Zhidong Cao; Dajun Zeng; Qingpeng Zhang; Tianyi Luo

    doi:10.1101/2020.07.22.20160291 Date: 2020-07-24 Source: medRxiv

    Background Research papers related to COVID-19 have exploded. We aimed to explore the academic value of preprints through comparing with peer-reviewed publications, and synthesize the parameter estimates of the two kinds of literature. Method We collected papers regarding the estimation of four key epidemiological parameters of the COVID-19 in China: the basic reproduction number TRANS ( R0 TRANS), incubation period TRANS, infectious period TRANS, and case-fatality-rate (CFR). PubMed, Google Scholar, medRxiv, bioRxiv, arRxiv, and SSRN were searched by 20 March, 2020. Distributions of parameters and timeliness of preprints and peer-reviewed papers were compared. Further, four parameters were synthesized by bootstrap, and their validity was verified by susceptible-exposed-infectious-recovered-dead-cumulative (SEIRDC) model based on the context of China. Findings 106 papers were included for analysis. The distributions of four parameters in two literature groups were close, despite that the timeliness of preprints was better. Four parameter estimates changed over time. Synthesized estimates of R0 TRANS (3.18, 95% CI 2.85-3.53), incubation period TRANS (5.44 days, 95% CI 4.98-5.99), infectious period TRANS (6.25 days, 95% CI 5.09-7.51), and CFR (4.51%, 95% CI 3.41%-6.29%) were obtained from the whole parameters space, all with p<0.05. Their validity was evaluated by simulated cumulative cases of SEIRDC model, which matched well with the onset cases in China. Interpretation Preprints could reflect the changes of epidemic situation sensitively, and their academic value shouldn't be neglected. Synthesized results of literatures could reduce the uncertainty and be used for epidemic decision making. Funding The National Natural Science Foundation of China and Beijing Municipal Natural Science Foundation.

    Mechanistic Modelling of Coronavirus Infections MESHD and the Impact of Confined Neighbourhoods on a Short Time Scale

    Authors: Danish Ahmed; Ali Ansari; Mudassar Imran; Kamaludin Dingle; Naveed Ahmed; Michael Bonsall

    id:10.20944/preprints202007.0577.v1 Date: 2020-07-24 Source: preprints.org

    To mitigate the spread of the COVID-19 coronavirus, some countries have enforced more stringent non-pharmaceutical interventions in contrast to those widely adopted (for e.g. the state of Kuwait). In addition to standard practices such as enforcing curfews, social distancing, and closure of non-essential service industries, other non-conventional policies such as the total confinement of highly populated areas has also been implemented. In this paper, we model the movement of a host population using a mechanistic approach based on random walks, which are either diffusive or super-diffusive. Infections MESHD are realised through a contact process, whereby a susceptible host may be infected if in close spatial proximity of the infectious host. Our focus is only on the short-time scale prior to the infectious period TRANS, so that no further transmission TRANS is assumed. We find that the level of infection MESHD depends heavily on the population dynamics, and increases in the case of slow population diffusion, but remains stable for a high or super-diffusive population. Also, we find that the confinement of homogeneous or overcrowded sub-populations has minimal impact in the short term. Finally, we discuss the possible implications of our findings for total confinement in the context of the current situation in Kuwait.

    Reopening universities during the COVID-19 pandemic: A testing strategy to minimize active cases and delay outbreaks

    Authors: Lior Rennert; Corey Andrew Kalbaugh; Lu Shi; Christopher McMahan

    doi:10.1101/2020.07.06.20147272 Date: 2020-07-07 Source: medRxiv

    Background: University campuses present an ideal environment for viral spread and are therefore at extreme risk of serving as a hotbed for a COVID-19 outbreak. While active surveillance throughout the semester such as widespread testing, contact tracing TRANS, and case isolation, may assist in detecting and preventing early outbreaks, these strategies will not be sufficient should a larger outbreak occur. It is therefore necessary to limit the initial number of active cases at the start of the semester. We examine the impact of pre-semester NAT testing on disease MESHD disease spread TRANS spread in a university setting. Methods: We implement simple dynamic transmission TRANS models of SARS-CoV-2 infection MESHD to explore the effects of pre-semester testing strategies on the number of active infections MESHD and occupied isolation beds throughout the semester. We assume an infectious period TRANS of 3 days and vary R0 TRANS to represent the effectiveness of disease MESHD mitigation strategies throughout the semester. We assume the prevalence SERO of active cases at the beginning of the semester is 5%. The sensitivity SERO of the NAT test is set at 90%. Results: If no pre-semester screening is mandated, the peak number of active infections MESHD occurs in under 10 days and the size of the peak is substantial, ranging from 5,000 active infections MESHD when effective mitigation strategies ( R0 TRANS = 1.25) are implemented to over 15,000 active infections MESHD for less effective strategies ( R0 TRANS = 3). When one NAT test is mandated within one week of campus arrival, effective ( R0 TRANS = 1.25) and less effective ( R0 TRANS = 3) mitigation strategies delay the onset of the peak to 40 days and 17 days, respectively, and result in peak size ranging from 1,000 to over 15,000 active infections MESHD. When two NAT tests are mandated, effective ( R0 TRANS = 1.25) and less effective ( R0 TRANS = 3) mitigation strategies delay the onset of the peak through the end of fall HP semester and 20 days, respectively, and result in peak size ranging from less than 1,000 to over 15,000 active infections MESHD. If maximum occupancy of isolation beds is set to 2% of the student population, then isolation beds would only be available for a range of 1 in 2 confirmed cases TRANS ( R0 TRANS = 1.25) to 1 in 40 confirmed cases TRANS ( R0 TRANS = 3) before maximum occupancy is reached. Conclusion: Even with highly effective mitigation strategies throughout the semester, inadequate pre-semester testing will lead to early and large surges of the disease MESHD and result in universities quickly reaching their isolation bed capacity. We therefore recommend NAT testing within one week of campus return. While this strategy is sufficient for delaying the timing of the outbreak, pre-semester testing would need to be implemented in conjunction with effective mitigation strategies to reduce the outbreak size.

    Characteristics and outcomes of coronavirus disease MESHD 2019 (COVID-19) patients with cancer: A single-center retrospective observational study in Tokyo, Japan

    Authors: Shohei Nakamura; Yusuke Kanemasa; Yuya Atsuta; Sho Fujiwara; Masaru Tanaka; Kazuaki Fukushima; Taiichiro Kobayashi; Tatsu Shimoyama; Yasushi Omuro; Noritaka Sekiya; Akifumi Imamura

    doi:10.21203/rs.3.rs-39157/v1 Date: 2020-06-30 Source: ResearchSquare

    BackgroundAlthough severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) has caused an international outbreak of coronavirus disease MESHD 2019 (COVID-19), data on the clinical characteristics of COVID-19 patients with cancer are limited. This study aimed to evaluate the clinical characteristics and outcomes including mortality and viral shedding period in COVID-19 patients with cancer in Japan.MethodsWe retrospectively analyzed 32 patients with a history of cancer who were referred to our hospital between January 31, 2020 and May 25, 2020. We evaluated the association between clinical outcomes and potential prognostic factors using univariate analyses.ResultsThe median age TRANS was 74.5 (range, 24–90) years and 22 patients (69%) were men. A total of 11 patients (34%) died. Our analyses demonstrated that the mortality was significantly associated with lymphocyte count, albumin, lactate dehydrogenase, serum SERO ferritin, and C-reactive protein on admission. The median period between illness TRANS onset and the first effective negative SARS-CoV-2 PCR result was 22 days (interquartile range, 18–25) in survivors. Of four patients with hematological malignancy who developed COVID-19 within the rest period of chemotherapy, three died and the other patient, who received bendamustine plus rituximab therapy, had the longest duration of viral shedding (56 days).ConclusionOur study suggested that the risk factors for mortality previously reported in general COVID-19 patients, including lymphocytopenia, were also effective in cancer patients. Patients who received cytotoxic chemotherapy recently or were treated with chemotherapy, which can lead to lymphocyte reduction, had poor prognosis and prolonged periods of viral shedding.

    Estimating the state of the Covid-19 epidemic in France using a non-Markovian model

    Authors: Raphael Forien; Guodong Pang; Etienne Pardoux

    doi:10.1101/2020.06.27.20141671 Date: 2020-06-29 Source: medRxiv

    In this paper, we use a deterministic non-Markovian epidemic model to estimate the state of the Covid-19 epidemic in France. This model allows us to consider realistic distributions for the exposed and infectious periods TRANS in a SEIR model, contrary to standard ODE models which only consider exponentially distributed exposed and infectious periods TRANS. We present theoretical results linking the (unobserved) parameters of the model to various quantities which are more easily measured during the early stages of an epidemic. We also stress the main quantitative differences between the non-Markovian and the Markovian (ODE) model. We then apply these results to estimate the state of the Covid-19 epidemic in France by analyzing three regions: the Paris region, the northeast regions and the rest of the country, based on current knowledge on the infection MESHD fatality ratio and the exposed and infectious periods TRANS distributions for Covid-19. Our analysis is based on the hospital data published daily by Sante Publique France (daily hospital admissions, intensive care unit admissions and hospital deaths MESHD).

    Modelling Excess Mortality in Covid-19-like Epidemics

    Authors: Zdzislaw Burda

    id:2006.15583v1 Date: 2020-06-28 Source: arXiv

    We discuss a stochastic model to assess cumulative excess deaths MESHD during Covid-19-like epidemics for various non-pharmaceutic interventions. The model simulates three interrelated stochastic processes: epidemic spreading, availability of respiratory ventilators and changes in death MESHD statistics. Epidemic may spread either locally or globally. The local mode simulates virus transmission TRANS through contacts in the vicinity of the place of residence while the global mode simulates virus transmission TRANS through social mixing in public places, sport arenas, airports, etc, where many people meet, who live in remote geographic locations. Epidemic is modelled as a discrete time stochastic process on random geometric networks. In the simulations we assume that the basic reproduction number TRANS is $R_0=2.5$ and the infectious period TRANS lasts ca. ten days. We also assume that the virus leads to severe acute respiratory syndrome MESHD in about one percent of cases, which in turn almost surely lead to respiratory default and death MESHD, unless the patient receives an appropriate medical treatment supported by respiratory ventilation. For other parameters, like mortality rate or the number of respiratory ventilators per million of inhabitants, we take values typical for developed countries. We simulate populations of $10^5-10^6$ people. We compare different strategies: do-nothing, social distancing, reduction of social mixing and lockdown, assuming that there is no vaccine and no efficient medicine. The results of the simulations show that strategies that slow down the spread of epidemic too much are inefficient in reducing the cumulative excess of deaths MESHD. A hybrid strategy in which lockdown is in place for some time and is then completely released is inefficient as well.

The ZB MED preprint Viewer preVIEW includes all COVID-19 related preprints from medRxiv and bioRxiv, from ChemRxiv, from ResearchSquare, from arXiv and from Preprints.org and is updated on a daily basis (7am CET/CEST).

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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