Corpus overview


Overview

MeSH Disease

Human Phenotype

Transmission

Seroprevalence
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    A comprehensive analysis of R0 TRANS with different lockdown phase during covid-19 in India

    Authors: Mayank Chhabra; Tushant Agrawal

    doi:10.1101/2020.07.10.20150631 Date: 2020-07-11

    Background: World Health organization declared Covid-19 as an outbreak, hence preventive measure like lockdown should be taken to control the spread of infection MESHD. This study offers an exhaustive analysis of the reproductive number TRANS ( R0 TRANS) in India with major intervention for COVID-19 outbreaks and analysed the lockdown effects on the Covid-19. Methodology: Covid-19 data extracted from Ministry of Health and Family Welfare, Government of India. Then, a novel method implemented in the incidence and Optimum function in desolve package to the data of cumulative daily new confirmed cases TRANS for robustly estimating the reproduction number TRANS in the R software. Result: Analysis has been seen that the lockdown was really quite as effective, India has already shown a major steady decline. The growth rate has fluctuated about 20 percent with trend line projections in various lockdown. A comparative analysis gives an idea of decline in value of R0 TRANS from 1.73 to 1.08. Annotation plot showing the predicted R0 TRANS values based on previous lockdown in month of June and July. Conclusion: Without lockdown, the growth might not have been contained in India and may have gone into the exponential zone. We show that, the lockdown in India was fairly successful. The effect partial lifting of the lockdown (unlock) is also seen in the results, in terms of increment in R0 TRANS values. Hence this study provides a platform for policy makers and government authorities for implementing the strategies to prevent the spread of infection MESHD.

    What can the ideal gas say about global pandemics? Reinterpreting the basic reproduction number TRANS

    Authors: Bradley M Dickson

    doi:10.1101/2020.07.09.20150128 Date: 2020-07-11

    Through analysis of the ideal gas, we construct a random walk that on average matches the standard susceptible-infective-removed (SIR) model. We show that the most widely referenced parameter, the ' basic reproduction number TRANS' ( R0 TRANS), is fundamentally connected to the relative odds of increasing or decreasing the infectives population. As a consequence, for R0 TRANS > 1 the probability that no outbreak occurs is 1/ R0 TRANS. In stark contrast to a deterministic SIR, when R0 TRANS = 1.5 the random walk has a 67% chance of avoiding outbreak. Thus, an alternative, probabilistic, interpretation of R0 TRANS arises, which provides a novel estimate of the critical population density {gamma}/r without fitting SIR models. We demonstrate that SARS-CoV2 in the United States is consistent with our model and attempt an estimate of {gamma}/r. In doing so, we uncover a significant source of bias in public data reporting. Data are aggregated on political boundaries, which bear no concern for dispersion of population density. We show that this introduces bias in fits and parameter estimates, a concern for understanding fundamental virus parameters and for policy making. Anonymized data at the resolution required for contact tracing TRANS would afford access to {gamma}/r without fitting. The random walk SIR developed here highlights the intuition that any epidemic is stochastic and recovers all the key parameter values noted by Kermack and McKendrick in 1927.

    Transmission TRANS dynamics and control measures of COVID-19 outbreak in China: a modelling study

    Authors: XuSheng Zhang; Emilia Vynnycky; Andre Charlett; Daniela de Angelis; Zhengji Chen; Wei Liu

    doi:10.1101/2020.07.09.20150086 Date: 2020-07-11

    COVID-19 is reported to have been effectively brought under control in China at its initial start place. To understand the COVID-19 outbreak in China and provide potential lessons for other parts of the world, in this study we combine a mathematical modelling with multiple datasets to estimate its transmissibility TRANS and severity and how it was affected by the unprecedented control measures. Our analyses show that before 29th January 2020, the ascertainment rate is 6.9%(95%CI: 3.5 - 14.6%); then it increased to 41.5%(95%CI: 30.6 - 65.1%). The basic reproduction number TRANS ( R0 TRANS) was 2.23(95%CI: 1.86 - 3.22) before 8th February 2020; then it dropped to 0.04(95%CI: 0.01 - 0.10). This estimation also indicates that the effect on transmissibility TRANS of control measures taken since 23rd January 2020 emerged about two weeks late. The confirmed case TRANS fatality rate is estimated at 4.41%(95%CI: 3.65 - 5.30%). This shows that SARS-CoV-2 virus is highly transmissible but less severe than SARS-CoV-1 and MERS-CoV. We found that at the early stage, the majority of R0 TRANS comes from the undetected infected people. This implies that the successful control in China was achieved through decreasing the contact rates among people in general populations and increasing the rate of detection and quarantine of the infected cases.

    Undocumented infectives in the Covid-19 pandemic

    Authors: Maurizio Melis; Roberto Littera

    doi:10.1101/2020.07.09.20149682 Date: 2020-07-11

    Background. A crucial role in epidemics is played by the number of undetected infective individuals who continue to circulate and spread the disease TRANS disease MESHD. Epidemiological investigations and mathematical models have revealed that the rapid diffusion of Covid-19 can mostly be attributed to the large percentage of undocumented infective individuals who escape testing. Methods. The dynamics of an infection MESHD can be described by the SIR model, which divides the population into susceptible (S), infective (I) and removed (R) subjects. In particular, we exploited the Kermack and McKendrick epidemic model which can be applied when the population is much larger than the fraction of infected subjects. Results. We proved that the fraction of undocumented infectives, in comparison to the total number of infected subjects, is given by 1-1/ R0 TRANS , where R0 TRANS is the basic reproduction number TRANS. Its mean value R0=2.10 (2.09-2.11) in three Italian regions for the Covid-19 epidemic yielded a percentage of undetected infectives of 52.4% (52.2% - 52.6%) compared to the total number of infectives. Conclusions. Our results, straightforwardly obtained from the SIR model, highlight the role played by undetected carriers TRANS in the transmission TRANS and spread of the SARS-CoV-2 infection MESHD. Such evidence strongly recommends careful monitoring of the infective population and ongoing adjustment of preventive measures for disease MESHD control until a vaccine becomes available.

    A minimal model for household effects in epidemics

    Authors: Greg Huber; Mason Kamb; Kyle Kawagoe; Lucy Li; Boris Veytsman; David Yllanes; Dan Zigmond

    doi:10.1101/2020.07.09.20150227 Date: 2020-07-11

    Shelter-in-place and other confinement strategies implemented in the current COVID-19 pandemic have created stratified patterns of contacts between people: close contacts TRANS within households and more distant contacts between the households TRANS. The epidemic transmission TRANS dynamics is significantly modified as a consequence. We introduce a minimal model that incorporates these household effects in the framework of mean-field theory and numerical simulations. We show that the reproduction number TRANS R0 TRANS depends on the household size in a surprising way: linearly for relatively small households, and as a square root of size for larger households. We discuss the implications of the findings for the lockdown, test, tracing TRANS, and isolation policies.

    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

    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 disease MESHD; however, tracing TRANS back individual transmission TRANS of infections MESHD 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.

    Societal heterogeneity contributes to complex dynamic patterns of the COVID-19 pandemics: insights from a novel Stochastic Heterogeneous Epidemic Model (SHEM)

    Authors: Alexander V Maltsev; Michael Stern

    doi:10.1101/2020.07.10.20150813 Date: 2020-07-11

    After months of COVID-19 quarantine, businesses are reopening their doors and people are reentering society. Within the current COVID-19 data, after a slow-down of infection MESHD, a new peak in active cases is already forming. Here we developed a new Stochastic Heterogeneous Epidemic Model (SHEM) to investigate genesis of complex pandemic patterns with the focus on the role of heterogenous societal structure. Using this model with R0 TRANS of COVID-19, we simulated viral infection MESHD in different scenarios where isolated, communities surround the main cluster of the population. Depending on the parameters of heterogeneity and isolation period, our simulations generated a multimodal growth periods with multiple peaks, an extended plateau, a prolonged tail, or a delayed second wave of infection MESHD. We show that timing and magnitude of infection MESHD for previously unaffected isolated clusters of people, such as suburban neighborhoods, are critical aspects of these patterns. Our model can be applied to communities at any given scale of population described as a fractal-like structure, i.e. from the entire human population, to a country, down to a province or city levels with relevant societal heterogeneity structure. The current COVID-19 pandemic development worldwide and in the US follows a bimodal rise pattern, qualitatively similar to that in our simulations. We interpret our data to indicate that the secondary peak in the pattern is contributed by the states and counties in the US with late infection MESHD surges that are analogous to isolated suburbs in our model. Furthermore, the on-going early reopening, i.e. premature partial reopening in our model, is further accelerating the peak rise. This peak now reaches new heights, forcing many states in the US to reverse their policies and reestablish their quarantine measures. Our results support these timely and effective measures: we show that longer quarantine periods can reduce the number of deaths MESHD and transform the current trend into a substantially delayed (>1 year) second wave. If this scenario becomes a reality, it is important (i) to develop the vaccine and/or effective treatment before the second wave; (ii) to warn people living in suburbs that it is these isolated areas that may hold a false sense of security, but they should continue to take extra care for their public health.

    Community prevalence SERO of SARS-CoV-2 virus in England during May 2020: REACT study

    Authors: Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Benjamin Jeffrey; Caroline E. Walters; Christina J Atchison; Peter J. Diggle; Deborah Ashby; Christl A. Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Graham Taylor; Ara Darzi; Paul Elliott

    doi:10.1101/2020.07.10.20150524 Date: 2020-07-11

    Background England has experienced one of the highest rates of confirmed COVID-19 mortality in the world. SARS-CoV-2 virus has circulated in hospitals, care homes and the community since January 2020. Our current epidemiological knowledge is largely informed by clinical cases with far less understanding of community transmission TRANS. Methods The REal-time Assessment of Community Transmission TRANS (REACT) study is a nationally representative prevalence SERO survey of SARS-CoV-2 virus swab-positivity in the community in England. We recruited participants regardless of symptom status. Results We found 159 positives from 120,610 swabs giving an average prevalence SERO of 0.13% (95% CI: 0.11%,0.15%) from 1st May to 1st June 2020. We showed decreasing prevalence SERO with a halving time of 8.6 (6.2, 13.6) days, implying an overall reproduction number TRANS R of 0.57 (0.45, 0.72). Adults TRANS aged TRANS 18 to 24 yrs had the highest swab-positivity rates, while those >64 yrs had the lowest. Of the 126 participants who tested positive with known symptom status in the week prior to their swab, 39 reported symptoms while 87 did not, giving an estimate that 69% (61%,76%) of people were symptom-free for the 7 days prior testing positive in our community sample. Symptoms strongly associated with swab-positivity were: nausea MESHD nausea and/or vomiting HP and/or vomiting MESHD, diarrhoea, blocked nose, loss of smell, loss of taste, headache MESHD headache HP, chills MESHD chills HP and severe fatigue MESHD fatigue HP. Recent contact with a known COVID-19 case was associated with odds of 24 (16, 38) for swab-positivity. Compared with non-key workers, odds of swab-positivity were 7.7 (2.4, 25) among care home (long-term care facilities) workers and 5.2 (2.9, 9.3) among health care workers. However, some of the excess risk associated with key worker status was explained by recent contact with COVID-19 cases. We found no strong evidence for geographical variability in positive swab results. Conclusion Our results provide a reliable baseline against which the impact of subsequent relaxation of lockdown can be assessed to inform future public health efforts to control transmission TRANS.

    Estimating the Effect of Social Distancing Interventions on COVID-19 in the United States

    Authors: Andrew M. Olney; Jesse Smith; Saunak Sen; Fridtjof Thomas; H. Juliette T. Unwin

    doi:10.1101/2020.07.10.20151001 Date: 2020-07-11

    Since its global emergence in 2020, severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) has caused multiple epidemics in the United States. Because medical treatments for the virus are still emerging and a vaccine is not yet available, state and local governments have sought to limit its spread by enacting various social distancing interventions such as school closures and lockdown, but the effectiveness of these interventions is unknown. We applied an established, semi-mechanistic Bayesian hierarchical model of these interventions on SARS-CoV-2 spread in Europe to the United States. We estimated the effect of interventions across all states, contrasted the estimated reproduction number TRANS, Rt , for each state before and after lockdown, and contrasted predicted future fatalities with actual fatalities as a check on the model's validity. Overall, school closures and lockdown are the only interventions modeled that have a reliable impact on Rt , and lockdown appears to have played a key role in reducing Rt below 1.0. We conclude that reversal of lockdown, without implementation of additional, equally effective interventions, will enable continued, sustained transmission TRANS of SARS-CoV-2 in the United States.

    Repeat SARS-CoV-2 Testing Models for Residential College Populations

    Authors: Joseph T. Chang; Forrest W. Crawford; Edward H. Kaplan

    doi:10.1101/2020.07.09.20149351 Date: 2020-07-10

    Residential colleges are considering re-opening under uncertain futures regarding the COVID-19 pandemic. We consider repeat SARS-CoV-2 testing models for the purpose of containing outbreaks in the residential campus community. The goal of repeat testing is to rapidly SERO detect and isolate new infections MESHD as they occur to block transmission TRANS that would otherwise occur on campus and, of arguably greater importance, off. The models allow for the evolution of test sensitivity SERO with time from infection MESHD, scheduled on-campus resident screening at a given frequency, imported infections MESHD from off campus throughout the school year, and a lag from testing until student isolation due to laboratory turnaround and student relocation delay. For early- (late-) transmission TRANS of SARS-CoV-2 by age TRANS of infection MESHD, we find that weekly screening cannot reliably contain outbreaks with reproductive numbers TRANS above 1.4 (1.6) if more than one imported exposure per 10,000 students occurs daily. Screening every three days can contain outbreaks providing the reproductive number TRANS remains below 1.75 (2.3) if transmission TRANS happens earlier (later) with time from infection MESHD, but at the cost of greatly increased false positive rates requiring more isolation quarters for students testing positive. Testing frequently while minimizing the delay from testing until isolation for those found positive are the most controllable levers for preventing large residential college outbreaks.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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