Corpus overview


Overview

MeSH Disease

Human Phenotype

Pneumonia (465)

Fever (273)

Cough (217)

Hypertension (192)

Respiratory distress (119)


Transmission

Seroprevalence
    displaying 21 - 30 records in total 6385
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    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.

    Dynamics of RT-qPCR SARS-CoV-2 Detection Rates Prior to and After Symptom Onset TRANS

    Authors: Scott Sherrill-Mix

    doi:10.1101/2020.07.09.20149245 Date: 2020-07-11

    Effective RT-qPCR testing for SARS-CoV-2 is essential for treatment, surveillance and control of the COVID-19 pandemic. A recent meta-analysis suggested that testing prior to the onset of symptoms TRANS is likely to miss the majority of infected individuals. These findings cast severe doubts on the effectiveness of mass screening efforts intended to detect SARS-CoV-2 prior to the onset of symptoms TRANS and decrease community transmissions TRANS from pre-/ asymptomatic TRANS individuals. However, alternative analyses and additional data described herein refine these estimates and suggest that many SARS-CoV-2 infections MESHD could potentially be detected prior to symptom onset TRANS.

    Association of Cancer with Risk and Mortality of COVID-19: Results from the UK Biobank

    Authors: Zhuqing Shi; W. Kyle Resurreccion; Chi-Hsiung Wang; Jun Wei; Rong Na; S. Lilly Zheng; Liana K. Billings; Brian T. Helfand; Janardan Khandekar; Jianfeng Xu

    doi:10.1101/2020.07.10.20151076 Date: 2020-07-11

    Although cancer has been associated with COVID-19 risk and mortality in hospital-based studies, few population-based studies have been reported. Utilizing data from the UK Biobank (UKB), a population-based prospective cohort, we formally tested the association of over 44 different types of cancer with COVID-19 infection MESHD and mortality among 7,661 subjects who were tested by June 17, 2020. Compared to non-cancer subjects, cancer subjects (N=1,521) had significantly lower overall risk for COVID-19 infection MESHD [odds ratio (OR) and 95% confidence interval (CI): 0.79 (0.68-0.92), P=2.60E-03]. However, a trend of higher risk for COVID-19 mortality was found among 256 COVID-19 positive cancer patients, especially for hematologic cancers such as non-Hodgkin lymphoma MESHD non-Hodgkin lymphoma HP [3.82 (1.17-12.01), P=0.02]. In cancer patients, while few demographic, lifestyle, genetic and comorbidity factors predicted risk for COVID-19 infection MESHD, older age TRANS, male TRANS sex, heart disease MESHD and hypertension MESHD hypertension HP significantly predicted COVID-19 mortality. The lower risk for COVID-19 infection MESHD is likely due to extra caution in COVID-19 prevention and more testing among cancer patients, an encouraging finding that demonstrates the feasibility of intervention. These results, if confirmed in future releases of UKB data and other independent populations, may provide guidance for COVID-19 prevention and treatment among cancer patients.

    In-house modification and improvement of the CDC real-time PCR diagnostic assay for SARS-CoV-2 detection.

    Authors: Srirupa Das; Candice Dowell-Martino; Lisa Arrigo; Paul N. Fiedler; Sandra Lobo

    doi:10.1101/2020.07.10.20150771 Date: 2020-07-11

    The world is currently facing an unprecedented pandemic caused by the novel coronavirus SARS-CoV-2 (COVID-19) which was first reported in late 2019 by China to the World Health Organization (WHO). The containment strategy for COVID-19, which has non-specific flu-like symptoms and where upwards of 80% of the affected has either mild or no symptoms, is critically centered upon diagnostic testing, tracking and isolation. Thus, the development of specific and sensitive diagnostic tests for COVID-19 is key towards the first successful step of disease MESHD management. Public health organizations like the WHO and the US-based Centers for Disease MESHD Control and Prevention (CDC) have developed real-time PCR (RT-PCR) based diagnostic tests to aid in the detection of acute infection MESHD. In this study we sought to modify the CDC RT-PCR diagnostic assay protocol to increase its sensitivity SERO and to make the assay directly portable to health care providers in a community-based hospital setting. A number of modifications to the original protocol were tested. Increasing the RT-PCR annealing temperature by 7{degrees}C to 62{degrees}C was associated with the most significant improvement in sensitivity SERO, wherein the cycle-threshold (Ct) value for the N2 assay was reduced by ~3 units, in effect both reducing the overall number of inconclusive results and yielding N1/N2 assays to have similar Ct values. The limit of detection of the modified assay was also improved (0.86 RNA copies/l for both nCoV 2019_N1/N2 assays) compared to the CDC RT-PCR diagnostic assay (1 and 3.16 RNA copies/l for nCoV 2019_N1 and N2 assay, respectively). Using this modification, there was no significant effect on SARS-CoV-2 detection rate when viral RNA extraction was performed either manually or through an automated extraction method. We believe this modified protocol allows for more sensitive detection of the virus which in turn will be useful for pandemic management.

    Antibody SERO dynamics to SARS-CoV-2 in Asymptomatic TRANS and Mild COVID-19 patients

    Authors: Qing Lei; Yang Li; Hongyan Hou; Feng Wang; Yandi Zhang; Danyun Lai; Banga Ndzouboukou Jo-Lewis; Zhaowei Xu; Bo Zhang; Hong Chen; Zhuqing Ouyang; Junbiao Xue; Xiaosong Lin; Yunxiao Zheng; Zhongjie Yao; Xuening Wang; Caizheng Yu; Jeremy Jiang; Hainan Zhang; Huan Qi; Shujuan Guo; Shenghai Huang; Ziyong Sun; Sheng-ce Tao; Xionglin Fan

    doi:10.1101/2020.07.09.20149633 Date: 2020-07-11

    Humoral immunity in asymptomatic infections MESHD asymptomatic TRANS with SARS-CoV-2 has not been well established. 63 healthy contacts, 63 asymptomatic TRANS individuals, and 51 mild patients were enrolled in this study and screened using nucleic acid testing (NAT) and commercial kits of serum SERO IgM and IgG antibodies SERO against recombinant nucleoprotein (N) and spike (S) proteins of SARS-CoV-2. Asymptomatic TRANS and mild patients were classified into at least four types based on NAT and serological tests SERO, especially 81% and 25.4% negative NAT but positive IgM/IgG responses, respectively. Antibody SERO dynamics were further demonstrated by IgM and IgG profile responses to SARS-CoV-2 proteome. IgM antibody SERO responses against S1 were elicited in asymptomatic TRANS individuals as early to the seventh day after exposure and peaked on days from 17d to 25d, which might be used as early diagnostic biomarkers. Moreover, asymptomatic TRANS individuals evoked weaker S1 specific IgM and neutralizing antibody SERO responses than mild patients. Most importantly, S1 specific IgM/IgG responses and the titers of neutralizing antibody SERO in asymptomatic TRANS individuals gradually vanished in two months. Our findings might have important implications for serological survey, public health and immunization strategy.

    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.

    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.

    Saliva offers a sensitive, specific and non-invasive alternative to upper respiratory swabs for SARS-CoV-2 diagnosis.

    Authors: Rachel Louise Byrne; Grant A Kay; Konstantina Kontogianni; Lottie Brown; Andrea M Collins; Luis E Cuevas; Daniela Ferreira; Alice J Fraser; Gala Garrod; Helen Hill; Stefanie Menzies; Elena Mitsi; Sophie I Owen; Christopher T Williams; Angela Hyder-Wright; Emily R Adams; Ana I Cubas-Atienzar

    doi:10.1101/2020.07.09.20149534 Date: 2020-07-11

    RT-qPCR utilising upper respiratory swabs are the diagnostic gold standard for SARS-CoV-2 despite reported low sensitivity SERO and limited scale up due to global shortages. Saliva is a non-invasive, equipment independent alternative to swabs. We collected 145 paired saliva and nasal/throat (NT) swabs at diagnosis (day 0) and repeated on day 2 and day 7 dependent on inpatient care and day 28 for study follow up. Laboratory cultured virus was used to determine the analytical sensitivity SERO of spiked saliva and swabs containing amies preservation media. Self-collected saliva samples were found to be consistent, and in some cases superior when compared to healthcare worker collected NT swabs from COVID-19 suspected participants. We report for the first time the analytical limit of detection of 10-2 and 100 pfu/ml for saliva and swabs respectively. Saliva is a easily self-collected, highly sensitive specimen for the detection of SARS-CoV-2.

    Diagnostic value of skin manifestation MESHD of SARS-CoV-2 infection MESHD

    Authors: Veronique Bataille; Alessia Visconti; Niccolo' Rossi; Benjamin Murray; Abigail Bournot; Jonathan Wolf; Sebastien Ourselin; Claire Steves; Timothy Spector; Mario Falchi

    doi:10.1101/2020.07.10.20150656 Date: 2020-07-11

    SARS-CoV-2 causes multiple immune-related reactions at various stages of the disease MESHD. The wide variety of skin presentations has delayed linking these to the virus. Previous studies had attempted to look at the prevalence SERO and timing of SARS-COV-2 rashes but were based on mostly hospitalized severe cases and had little follow up. Using data collected on a subset of 336,847 eligible UK users of the COVID Symptom Study app, we observed that 8.8% of the swab positive cases (total: 2,021 subjects) reported either a body rash or an acral rash, compared to 5.4% of those with a negative swab test (total: 25,136). Together, these two skin presentations showed an odds ratio (OR) of 1.67 (95% confidence interval [CI]: 1.41-1.96) for being swab positive. Skin rashes HP were also predictive in the larger untested group of symptomatic app users (N=54,652), as 8.2% of those who had reported at least one classical COVID-19 symptom, i.e., fever MESHD fever HP, persistent cough MESHD cough HP, and/or anosmia HP, also reported a rash. Data from an independent online survey of 11,546 respondents with a rash showed that in 17% of swab positive cases, the rash was the initial presentation. Furthermore, in 21%, the rash was the only clinical sign. Skin rashes HP cluster with other COVID-19 symptoms, are predictive of a positive swab test and occur in a significant number of cases, either alone or before other classical symptoms. Recognising rashes is important in identifying new and earlier COVID-19 cases.

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Annotations

All
MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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