Corpus overview


Overview

MeSH Disease

Human Phenotype

Falls (2)

Pneumonia (1)

Fever (1)


Transmission

Seroprevalence
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    The impact of digital contact tracing TRANS on the SARS-CoV-2 pandemic - a comprehensive modelling study

    Authors: Tina R Pollmann; Julia Pollmann; Christoph Wiesinger; Christian Haack; Lolian Shtembari; Andrea Turcati; Birgit Neumair; Stephan Meighen-Berger; Giovanni Zattera; Matthias Neumair; Uljana Apel; Augustine Okolie; Johannes Mueller; Stefan Schoenert; Elisa Resconi; Monica I Lupei; Christopher J Tignanelli

    doi:10.1101/2020.09.13.20192682 Date: 2020-09-14 Source: medRxiv

    Contact tracing TRANS is one of several strategies employed in many countries to curb the spread of SARS-CoV-2. Digital contact tracing TRANS (DCT) uses tools such as cell-phone applications to improve tracing TRANS speed and reach. We model the impact of DCT on the spread of the virus for a large epidemiological parameter space consistent with current literature on SARS-CoV-2. We also model DCT in combination with random testing (RT) and social distancing (SD). Modelling is done with two independently developed individual-based (stochastic) models that use the Monte Carlo technique, benchmarked against each other and against two types of deterministic models. For current best estimates of the number of asymptomatic TRANS SARS-CoV-2 carriers TRANS (approximately 40\%), their contagiousness (similar to that of symptomatic carriers TRANS), the reproductive number TRANS before interventions ( R0 TRANS at least 3) we find that DCT must be combined with other interventions such as SD and/or RT to push the reproductive number TRANS below one. At least 60\% of the population would have to use the DCT system for its effect to become significant. On its own, DCT cannot bring the reproductive number TRANS below 1 unless nearly the entire population uses the DCT system and follows quarantining and testing protocols strictly. For lower uptake of the DCT system, DCT still reduces the number of people that become infected. When DCT is deployed in a population with an ongoing outbreak where O(0.1\%) of the population have already been infected, the gains of the DCT intervention come at the cost of requiring up to 15% of the population to be quarantined (in response to being traced TRANS) on average each day for the duration of the epidemic, even when there is sufficient testing capability to test every traced TRANS person.

    Long, thin transmission chains TRANS of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2 MESHD) may go undetected for several weeks at low to moderate reproductive numbers TRANS: Implications for containment and elimination strategy

    Authors: Gerry F Killeen; Deanna C Clemmer; Justin B Cox; Yetunde I Kayode; Victoria Zoccoli-Rodriguez; Harry E Taylor; Timothy P Endy; Joel R Wilmore; Gary Winslow; Sarah Tschudin-Sutter; Simon Fuchs; Julia Anna Bielicki; Hans Pargger; Martin Siegemund; Christian H. Nickel; Roland Bingisser; Michael Osthoff; Stefano Bassetti; Rita Schneider-Sliwa; Manuel Battegay; Hans H. Hirsch; Adrian Egli

    doi:10.1101/2020.09.04.20187948 Date: 2020-09-05 Source: medRxiv

    Especially at low to moderate reproductive numbers TRANS, the generally mild, non-specific symptomology of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) allows long MESHD, thin transmission chains TRANS to go undetected by passive surveillance over several weeks. This phenomenon has important implications: (1) Surveillance becomes less sensitive and reliable as an indicator of freedom from infection at the low reproductive numbers TRANS required to achieve elimination end points, passive surveillance systems may need to document an absence of new cases for at least a month to establish certainty of elimination. (2) Reproductive numbers TRANS should be kept as low as possible throughout such follow up periods without confirmed cases TRANS, to ensure such long, thin, undetected transmission chains TRANS all collapse before restrictions are eased and reproduction numbers TRANS are allowed to rebound. (3) While contact tracing TRANS systems may be highly effective when applied to large clusters in foci of elevated transmission TRANS where wide, rapidly expanding transmission chains TRANS are detected within two viral generations, large fractions of community transmission TRANS occurring through thinner, more extended transmission chains TRANS at lower reproductive numbers TRANS are often be too long to trace TRANS retrospectively and will be underrepresented in surveillance data. (4) Wherever surveillance systems are weak and/or younger age groups TRANS with lower rates of overt symptoms dominate transmission TRANS, containment effectiveness of contact tracing TRANS and isolation may be more severely limited, even at the higher reproduction numbers TRANS associated with larger outbreaks. While, contact tracing TRANS and isolation will remain vital for at least partially containing larger outbreaks, containment and elimination of SARS-CoV-2 will have to rely primarily upon the more burdensome and presumptive population-wide prevention measures that have proven so effective thus far against community transmission TRANS. Furthermore, these will have to be sustained at a much more stringent level and for longer periods after the last detected case than was necessary for SARS-CoV-1.

    Transmission TRANS dynamics of COVID-19 in household and community settings in the United Kingdom

    Authors: Jamie Lopez Bernal; Nikolaos Panagiotopoulos; Chloe Byers; Tatiana Garcia Vilaplana; Nicola L Boddington; XuSheng Zhang; Andre Charlett; Suzanne Elgohari; Laura Coughlan; Rosie Whillock; Sophie Logan; Hikaru Bolt; Mary Sinnathamby; Louise Letley; Pauline MacDonald; Roberto Vivancos; Obaghe Edeghere; Charlotte Anderson; Karthik Paranthaman; Simon Cottrell; Jim McMenamin; Maria Zambon; Gavin Dabrera; Mary Ramsay; Vanessa Saliba

    doi:10.1101/2020.08.19.20177188 Date: 2020-08-22 Source: medRxiv

    Background: Households appear to be the highest risk setting for transmission TRANS of COVID-19. Large household transmission TRANS studies were reported in the early stages of the pandemic in Asia with secondary attack rates TRANS ranging from 5-30% but few large scale household transmission TRANS studies have been conducted outside of Asia. Methods: A prospective case ascertained study design based on the World Health Organization FFX protocol was undertaken in the UK following the detection of the first case in late January 2020. Household contacts TRANS of cases were followed using enhanced surveillance forms to establish whether they developed symptoms of COVID-19, became confirmed cases TRANS and their outcomes. Household secondary attack rates TRANS and serial intervals TRANS were estimated. Individual and household basic reproduction numbers TRANS were also estimated. The incubation period TRANS was estimated using known point source exposures that resulted in secondary cases TRANS. Results: A total of 233 households with two or more people were included with a total of 472 contacts. The overall household SAR TRANS was 37% (95% CI 31-43%) with a mean serial interval TRANS of 4.67 days, an R0 TRANS of 1.85 and a household reproduction number TRANS of 2.33. We find lower secondary attack rates TRANS in larger households. SARs were highest when the primary case TRANS was a child TRANS. We estimate a mean incubation period TRANS of around 4.5 days. Conclusions: High rates of household transmission TRANS of COVID-19 were found in the UK emphasising the need for preventative measures in this setting. Careful monitoring of schools reopening is needed to monitor transmission TRANS from children TRANS.

    Epidemiological Characteristics of COVID-19 under Government-mandated Control Measures in Inner Mongolia, China

    Authors: Sha Du; Haiwen Lu; Yuenan Su; Shufeng Bi; Jing Wu; Wenrui Wang; Xinhui Yu; Min Yang; Huiqiu Zheng; Xuemei Wang

    doi:10.21203/rs.3.rs-57472/v1 Date: 2020-08-11 Source: ResearchSquare

    BackgroundThere were 75 local confirmed cases TRANS during the COVID-19 epidemic followed by an outbreak of Wuhan in Inner Mongolia. The aims of our study were to provide reference to control measures of COVID-19 and scientific information for supporting government decision-making for serious infectious disease MESHD, in remote regions with relatively insufficient medical resources like Inner Mongolia.MethodsThe data published by Internet were summarized in order to describe the epidemiological and clinical characteristics of patients with COVID-19. The basic reproductive number (R TRANS 0 ), incubation period TRANS, time from illness onset to confirmed and the duration of hospitalization were analyzed. The composition of imported and local secondary cases TRANS and the mild/common and severe/critical cases among different ages TRANS, genders TRANS and major clinical symptoms were compared.ResultsIn 2020, from January 23 to February 19 (less than 1 month), 75 local cases of COVID-19 were confirmed in Inner Mongolia. Among them, the median age TRANS was 45 years old (34.0, 57.0), and 61.1% were male TRANS and 33 were imported (44.0%). 29 (38.7%) were detected through close contact TRANS tracking, more than 80.0% were mild/common cases. The fatality rate was 1.3% and the basic reproductive number (R TRANS 0 ) was estimated to be 2.3. The median incubation period TRANS was 8.5 days (6.0~12.0) and the maximum incubation period TRANS reached 28 days. There was a statistically difference in the incubation period TRANS between imported and local secondary cases TRANS ( P <0.001). The duration of hospitalization of patients with incubation period TRANS <8.5 days was higher than that of patients with incubation period TRANS ≥8.5 days (30.0 vs. 24.0 days).ConclusionIn Inner Mongolia, an early and mandatory control strategy by government associated with the rapidly reduced incidence of COVID-19, by which the epidemic growth was controlled completely. And the fatality rate of COVID-19 was relatively low.

    COVID-19 pandemic in Djibouti: epidemiology and the response strategy followed to contain the virus during the first two months, 17 March to 16 May 2020

    Authors: Mohamed Elhakim; Saleh Banoita Tourab; Ahmed Zouiten

    doi:10.1101/2020.08.03.20167692 Date: 2020-08-04 Source: medRxiv

    Background: First cases of COVID-19 were reported from Wuhan, China, in December 2019, and it progressed rapidly. On 30 January, WHO declared the new disease as a PHEIC, then as a Pandemic on 11 March. By mid-March, the virus spread widely; Djibouti was not spared and was hit by the pandemic with the first case detected on 17 March. Djibouti worked with WHO and other partners to develop a preparedness and response plan, and implemented a series of intervention measures. MoH together with its civilian and military partners, closely followed WHO recommended strategy based on four pillars: testing, isolating, early case management, and contact tracing TRANS. From 17 March to 16 May, Djibouti performed the highest per capita tests in Africa and isolated, treated and traced the contacts TRANS of each positive case, which allowed for a rapid control of the epidemic. Methods: COVID-19 data included in this study was collected through MoH Djibouti during the period from 17 March to 16 May 2020. Results: A total of 1,401 confirmed cases TRANS of COVID-19 were included in the study with 4 related deaths (CFR: 0.3%) and an attack rate TRANS of 0.15%. Males TRANS represented (68.4%) of the cases, with the age group TRANS 31-45 years old (34.2%) as the most affected. Djibouti conducted 17,532 tests, and was considered as a champion for COVID-19 testing in Africa with 18.2 tests per 1000 habitant. All positive cases were isolated, treated and had their contacts traced TRANS, which led to early and proactive diagnosis of cases and in turn yielded up to 95-98% asymptomatic TRANS cases. Recoveries reached 69% of the infected cases with R0 TRANS (0.91). The virus was detected in 4 regions in the country, with the highest percentage in the capital (83%). Conclusion: Djibouti responded to COVID-19 pandemic following an efficient and effective strategy, using a strong collaboration between civilian and military health assets that increased the response capacities of the country. Partnership, coordination, solidarity, proactivity and commitment were the pillars to confront COVID-19 pandemic.

    Estimating the time-varying reproduction number TRANS of COVID-19 with a state-space method

    Authors: Shinsuke Koyama; Taiki Horie; Shigeru Shinomoto

    doi:10.1101/2020.07.09.20150219 Date: 2020-07-11 Source: medRxiv

    After slowing down the spread of the novel coronavirus COVID-19, many countries have started to relax their severe confinement measures in the face of critical damage to socioeconomic structures. At this point, it is desirable to monitor the degree to which political measures or social affairs have exerted influence on the spread of disease TRANS; however, tracing TRANS back individual transmission TRANS of infections whose incubation periods TRANS are long and highly variable seems to be difficult. Nevertheless, it may be possible to estimate the changes that may have occurred in the past, if we can suitably fit a proper model to daily event-occurrences. We have devised a state-space method for fitting the Hawkes process to a given dataset of daily confirmed cases TRANS. This method detects changes occurring in the spread of the contagion in each country. Furthermore, this method can assess the impact of social events in terms of the temporally varying reproduction number TRANS representing the average number of cases directly caused by a single infected case. This information might serve as a reference for the behavioral guidelines that should be adopted according to the varying risk of infection TRANS risk of infection TRANS infection MESHD.

    An Agent Based Modeling of COVID-19: Validation, Analysis, and Recommendations

    Authors: Md. Salman Shamil; Farhanaz Farheen; Nabil Ibtehaz; Irtesam Mahmud Khan; M. Sohel Rahman

    doi:10.1101/2020.07.05.20146977 Date: 2020-07-08 Source: medRxiv

    The Coronavirus disease 2019 (COVID-19) has resulted in an ongoing pandemic worldwide. Countries have adopted Non-pharmaceutical Interventions (NPI) to slow down the spread. This study proposes an Agent Based Model that simulates the spread of COVID-19 among the inhabitants of a city. The Agent Based Model can be accommodated for any location by integrating parameters specific to the city. The simulation gives the number of daily confirmed cases TRANS. Considering each person as an agent susceptible to COVID-19, the model causes infected individuals to transmit the disease via various actions performed every hour. The model is validated by comparing the simulation to the real data of Ford county, Kansas, USA. Different interventions including contact tracing TRANS are applied on a scaled down version of New York city, USA and the parameters that lead to a controlled epidemic are determined. Our experiments suggest that contact tracing TRANS via smartphones with more than 60% of the population owning a smartphone combined with a city-wide lock-down results in the effective reproduction number TRANS (Rt) to fall HP below 1 within three weeks of intervention. In the case of 75% or more smartphone users, new infections are eliminated and the spread is contained within three months of intervention. Contact tracing TRANS accompanied with early lock-down can suppress the epidemic growth of COVID-19 completely with sufficient smartphone owners. In places where it is difficult to ensure a high percentage of smartphone ownership, tracing TRANS only emergency service providers during a lock-down can go a long way to contain the spread. No particular funding was available for this project.

    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 spread TRANS 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 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 occurs in under 10 days and the size of the peak is substantial, ranging from 5,000 active infections when effective mitigation strategies ( R0 TRANS = 1.25) are implemented to over 15,000 active infections 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. 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. 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 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.

    The reproduction number TRANS R for COVID-19 in England: Why hasn't ''lockdown'' been more effective?

    Authors: Alastair Grant

    doi:10.1101/2020.07.02.20144840 Date: 2020-07-05 Source: medRxiv

    The reproduction number TRANS R, the average number of people that a single individual with a contagious disease infects MESHD, is central to understanding the dynamics of the COVID-19 epidemic. Values greater than one correspond to increasing rates of infection MESHD, and values less than one indicate that control measures are being effective. Here, we summarise how changes in the behaviour of individuals alter the value of R TRANS. We also use matrix models that correctly recreate distributions of times that individuals spend incubating the disease and being infective to demonstrate the accuracy of a simple approximation to estimate R directly from time series of case numbers, hospital admissions or deaths. The largest uncertainty is that the generation time of the infection is not precisely known, but this challenge also affects most of the more complex methods of calculating R. We use this approximation to examine changes in R in response to the introduction of lockdown restrictions in England. This suggests that there was a substantial reduction in R before large scale compulsory restrictions on economic and social activity were imposed on 23rd March 2020. From mid-April to mid-June decline of the epidemic at national and regional level has been relatively slow, despite these restrictions ( R values TRANS clustered around 0.81). However, these estimates of R are consistent with the relatively high average numbers of close contacts TRANS reported by confirmed cases TRANS combined with directly measured attack rates TRANS via close interactions. This implies that a significant portion of transmission TRANS is occurring in workplaces; overcrowded housing or through close contacts TRANS that are not currently lawful, routes on which nationwide lockdown will have limited impact.

    Contact Tracing TRANS Evaluation for COVID-19 Transmission TRANS during the Reopening Phase in a Rural College Town

    Authors: Sifat afroj Moon; Caterina Scoglio

    doi:10.1101/2020.06.24.20139204 Date: 2020-06-26 Source: medRxiv

    Contact tracing TRANS can play a vital role in controlling human-to-human transmission TRANS of a highly contagious disease such as COVID-19. To investigate the benefits and costs of contact tracing TRANS, we develop an individual- based contact TRANS-network model and a susceptible-exposed-infected-confirmed (SEIC) epidemic model for the stochastic simulations of COVID-19 transmission TRANS. We estimate the unknown parameters (reproductive ratio R0 TRANS and confirmed rate {delta}2) by using observed confirmed case TRANS data. After a two month-lockdown, states in the USA have started the reopening process. We provide simulations for four different reopening situations: under "stay-at-home" order or no reopening, 25% reopening, 50% reopening, and 75% reopening. We model contact tracing TRANS in a two-layer network by modifying the basic SEIC epidemic model. The two-layer network is composed by the contact network in the first layer and the tracing TRANS network in the second layer. Since the full contact list of an infected individual patient can be hard to obtain, then we consider different fractions of contacts from 60% to 5%. The goal of this paper is to assess the effectiveness of contact tracing TRANS to control the COVID-19 spreading in the reopening process. In terms of benefits, simulation results show that increasing the fraction of traced contacts TRANS decreases the size of the epidemic. For example, tracing TRANS 20% of the contacts is enough for all four reopening scenarios to reduce the epidemic size by half. Considering the act of quarantining susceptible households as the contact TRANS tracing TRANS cost, we have observed an interesting phenomenon. When we increase the fraction of traced contacts TRANS from 5% to 20%, the number of quarantined susceptible people increases because each individual confirmed case TRANS is mentioning more contacts. However, when we increase the fraction of traced contacts TRANS from 20% to 60%, the number of quarantined susceptible people decreases because the increment of the mentioned contacts is balanced by a reduced number of confirmed cases TRANS. The main contribution of this research lies in the investigation of the effectiveness of contact tracing TRANS for the containment of COVID-19 spreading during the initial phase of the reopening process of the USA.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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