Corpus overview


Overview

MeSH Disease

Human Phenotype

Pneumonia (156)

Fever (106)

Cough (106)

Falls (51)

Fatigue (26)


Transmission

Seroprevalence
    displaying 41 - 50 records in total 2531
    records per page




    Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility TRANS and pathogenicity

    Authors: Erik M Volz; Verity Hill; John T McCrone; Anna Price; David Jorgensen; Aine O'Toole; Joel Alexander Southgate; Robert Johnson; Ben Jackson; Fabricia F. Nascimento; Sara M. Rey; Samuel M. Nicholls; Rachel M. Colquhoun; Ana da Silva Filipe; Nicole Pacchiarini; Matthew Bull; Lily Geidelberg; Igor Siveroni; Ian G. Goodfellow; Nicholas James Loman; Oliver Pybus; David L Robertson; Emma C Thomson; Andrew Rambaut; Thomas R Connor; - The COVID-19 Genomics UK Consortium

    doi:10.1101/2020.07.31.20166082 Date: 2020-08-04 Source: medRxiv

    In February 2020 a substitution at the interface between SARS-CoV-2 Spike protein subunits, Spike D614G, was observed in public databases. The Spike 614G variant subsequently increased in frequency in many locations throughout the world. Global patterns of dispersal of Spike 614G are suggestive of a selective advantage of this variant, however the origin of Spike 614G is associated with early colonization events in Europe and subsequent radiations to the rest of the world. Increasing frequency of 614G may therefore be due to a random founder effect. We investigate the hypothesis for positive selection of Spike 614G at the level of an individual country, the United Kingdom, using more than 25,000 whole genome SARS-CoV-2 sequences collected by COVID-19 Genomics UK Consortium. Using phylogenetic analysis, we identify Spike 614G and 614D clades with unique origins in the UK and from these we extrapolate and compare growth rates of co-circulating transmission TRANS clusters. We find that Spike 614G clusters are introduced in the UK later on average than 614D clusters and grow to larger size after adjusting for time of introduction. Phylodynamic analysis does not show a significant increase in growth rates for clusters with the 614G variant, but population genetic modelling indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We also investigate the potential influence of Spike 614D versus G on virulence by matching a subset of records to clinical data on patient outcomes. We do not find any indication that patients infected with the Spike 614G variant have higher COVID-19 mortality, but younger patients have slightly increased odds of 614G carriage. Despite the availability of a very large data set, well represented by both Spike 614 variants, not all approaches showed a conclusive signal of higher transmission TRANS rate for 614G, but significant differences in growth, size, and composition of these lineages indicate a need for continued study.

    Extended lifetime of respiratory droplets in a turbulent vapour puff and its implications on airborne disease MESHD transmission TRANS

    Authors: Kai Leong Chong; Chong Shen Ng; Naoki Hori; Rui Yang; Roberto Verzicco; Detlef Lohse

    id:2008.01841v1 Date: 2020-08-04 Source: arXiv

    To mitigate the COVID-19 pandemic, it is key to slow down the spreading of the life-threatening coronavirus (SARS-CoV-2). This spreading mainly occurs through virus-laden droplets expelled at speaking, coughing MESHD coughing HP, sneezing MESHD sneezing HP, or even breathing. To reduce infections MESHD through such respiratory droplets, authorities all over the world have introduced the so-called "2-meter distance rule" or "6-foot rule". However, there is increasing empirical evidence, e.g. through the analysis of super-spreading events, that airborne transmission TRANS of the coronavirus over much larger distances plays a major role with tremendous implications for the risk assessment of coronavirus transmission TRANS. Here we employ direct numerical simulations of a typical respiratory aerosol in a turbulent jet of the respiratory event within a Lagrangian-Eulerian approach with 5000 droplets, coupled to the ambient velocity, temperature, and humidity fields to allow for exchange of mass and heat and to realistically account for the droplet evaporation under different ambient conditions. We found that for an ambient relative humidity RH of 50% the lifetime of the smallest droplets of our study with initial diameter of 10 um gets extended by a factor of more than 30 as compared to what is suggested by the classical picture of Wells, due to collective effects during droplet evaporation and the role of the respiratory humidity, while the larger droplets basically behave ballistically. With increasing ambient RH the extension of the lifetimes of the small droplets further increases and goes up to 150 times for 90% RH, implying more than two meters advection range of the respiratory droplets within one second. Smaller droplets live even longer and travel TRANS further. Our results may explain why COVID-19 superspreading events can occur for large ambient RH such as in cooled-down meat-processing plants or in pubs with poor ventilation.

    Analytical Model of COVID-19 for lifting non-pharmaceutical interventions

    Authors: Garry Jacyna; James R. Thompson; Matt Koehler; David M. Slater

    doi:10.1101/2020.07.31.20166025 Date: 2020-08-04 Source: medRxiv

    In the present work, we outline a set of coarse-grain analytical models that can be used by decision-makers to bound the potential impact of the COVID-19 pandemic on specific communities with known or estimated social contact structure and to assess the effects of various non-pharmaceutical interventions on slowing the progression of disease MESHD disease spread TRANS. This work provides a multi-dimensional view of the problem by examining steady-state and dynamic disease MESHD disease spread TRANS spread using a network-based approach. In addition, Bayesian-based estimation procedures are used to provide a realistic assessment of the severity of outbreaks based on estimates of the average and instantaneous basic reproduction number TRANS R0 TRANS.

    Viable SARS-CoV-2 in the air of a hospital room with COVID-19 patients

    Authors: John A Lednicky; Michael Lauzardo; Z. Hugh Fan; Antarpreet S Jutla; Trevor B Tilly; Mayank Gangwar; Moiz Usmani; Sripriya N Shankar; Karim Mohamed; Arantza Eiguren-Fernandez; Caroline J Stephenson; Md. Mahbubul Alam; Maha A Elbadry; Julia C Loeb; Kuttichantran Subramaniam; Thomas B Waltzek; Kartikeya Cherabuddi; John Glenn Morris Jr.; Chang-Yu Wu

    doi:10.1101/2020.08.03.20167395 Date: 2020-08-04 Source: medRxiv

    Background - There currently is substantial controversy about the role played by SARS-CoV-2 in aerosols in disease MESHD transmission TRANS, due in part to detections of viral RNA but failures to isolate viable virus from clinically generated aerosols. Methods - Air samples were collected in the room of two COVID-19 patients, one of whom had an active respiratory infection MESHD with a nasopharyngeal (NP) swab positive for SARS-CoV-2 by RT-qPCR. By using VIVAS air samplers that operate on a gentle water-vapor condensation principle, material was collected from room air and subjected to RT-qPCR and virus culture. The genomes of the SARS-CoV-2 collected from the air and of virus isolated in cell culture from air sampling and from a NP swab from a newly admitted patient in the room were sequenced. Findings - Viable virus was isolated from air samples collected 2 to 4.8m away from the patients. The genome sequence of the SARS-CoV-2 strain isolated from the material collected by the air samplers was identical to that isolated from the NP swab from the patient with an active infection MESHD. Estimates of viable viral concentrations ranged from 6 to 74 TCID50 units/L of air. Interpretation - Patients with respiratory manifestations of COVID-19 produce aerosols in the absence of aerosol-generating procedures that contain viable SARS-CoV-2, and these aerosols may serve as a source of transmission TRANS of the virus.

    Land Use Change and Coronavirus Emergence Risk

    Authors: Maria Cristina Rulli; Paolo D'Odorico; Nikolas Galli; David Hayman

    doi:10.1101/2020.07.31.20166090 Date: 2020-08-04 Source: medRxiv

    Coronavirus disease MESHD 2019 (COVID-19) and severe acute respiratory syndrome MESHD (SARS) causing coronaviruses are mostly discovered in Asian horseshoe bats. It is still unclear how ongoing land use changes may facilitate SARS-related coronavirus transmission TRANS to humans. Here we use a multivariate hotspot analysis of high-resolution land-use data to show that regions of China populated by horseshoe bats are hotspots of forest fragmentation, livestock and human density. We also identify areas susceptible to new hotspot emergence in response to moderate expansion of urbanization, livestock production, or forest disturbance, thereby highlighting regions vulnerable to SARS-CoV spillover under future land-use change. In China population growth and increasing meat consumption associated with urbanization and economic development have expanded the footprint of agriculture, leading to human encroachment in wildlife habitat and increased livestock density in areas adjacent to fragmented forests. The reduced distance between horseshoe-bats and humans elevates the risk for SARS-related coronavirus transmission TRANS to humans.

    Face masks prevent transmission TRANS of respiratory diseases MESHD: a meta-analysis of randomized controlled trials

    Authors: Hanna M Ollila; Markku Partinen; Jukka Koskela; Riikka Savolainen; Anna Rotkirch; Liisa T Laine

    doi:10.1101/2020.07.31.20166116 Date: 2020-08-04 Source: medRxiv

    Background: Coronavirus Disease MESHD 2019 (COVID-19) is caused by Severe Acute Respiratory Syndrome MESHD Coronavirus 2 (SARS-CoV-2) and spreads through droplet-mediated transmission TRANS on contaminated surfaces and in air. Mounting scientific evidence from observational studies suggests that face masks for the general public may reduce the spread of infections MESHD. However, results from randomized control trials (RCT) have been presented as inconclusive, and concerns related to the safety and efficacy of non-surgical face masks in non-clinical settings remain. This controversy calls for a meta-analysis which considers non-compliance in RCTs, the time-lag in benefits of universal masking, and possible adverse effects. Methods: We performed a meta-analysis of RCTs of non-surgical face masks in preventing viral respiratory infections MESHD in non-hospital and non-household settings at cumulative and maximum follow-up as primary endpoints. The search for RCTs yielded five studies published before May 29th, 2020. We pooled estimates from the studies and performed random-effects meta-analysis and mixed-effects meta-regression across studies, accounting for covariates in compliance vs. non-compliance in treatment. Results: Face masks decreased infections across MESHD all studies at maximum follow-up (p=0.0318$, RR=0.608 [0.387 - 0.956]), and particularly in studies without non-compliance bias. We found significant between-study heterogeneity in studies with bias (I^2=71.2%, p=0.0077). We also used adjusted meta-regression to account for heterogeneity. The results support a significant protective effect of masking (p=0.0006, beta=0.0214, SE= 0.0062). No severe adverse effects were detected. Interpretation: The meta-analysis of existing randomized control studies found support for the efficacy of face masks among the general public. Our results show that face masks protect populations from infections MESHD and do not pose a significant risk to users. Recommendations and clear communication concerning the benefits of face masks should be provided to limit the number of COVID-19 and other respiratory infections MESHD.

    Containing the Spread of Infectious Disease MESHD on College Campuses

    Authors: Mirai Shah; Gabrielle Ferra; Susan Fitzgerald; Paul Barreira; Pardis Sabeti; Andres Colubri

    doi:10.1101/2020.07.31.20166348 Date: 2020-08-04 Source: medRxiv

    College campuses in the United States are highly vulnerable to infectious diseases MESHD outbreaks, and there is a mounting need to develop strategies that best mitigate their size and duration, particularly as colleges consider reopening their campuses in the midst of the COVID-19 pandemic. Towards addressing this need, we applied a stochastic transmission TRANS model to quantify the impact of university-level responses to past outbreaks on their campuses and used it to determine which control interventions are most effective. The model aims to simultaneously overcome three crucial issues: stochastic variation in small populations, missing or unobserved case data, and changes in disease MESHD transmission TRANS rates post-intervention. We tested the model and assessed various interventions using data from the 2014 and 2016 mumps MESHD outbreaks at Ohio State University and Harvard University, respectively. Our results suggest that universities should design more aggressive diagnostic procedures and stricter isolation policies to decrease infectious disease MESHD incidence on campus. Our model can be applied to data from other outbreaks in college campuses and similar small-population settings.

    Implication of backward contact tracing TRANS in the presence of overdispersed transmission TRANS in COVID-19 outbreak

    Authors: Akira Endo; - Centre for the Mathematical Modelling of Infectious Diseases (CMMID) COVID-19 Working Group; Quentin J Leclerc; Gwenan M Knight; Graham F Medley; Katherine E Atkins; Sebastian Funk; Adam J Kucharski

    doi:10.1101/2020.08.01.20166595 Date: 2020-08-04 Source: medRxiv

    Unlike forward contact tracing TRANS, backward contact tracing TRANS identifies the source of newly detected cases. This approach is particularly valuable when there is high individual-level variation in the number of secondary transmissions TRANS. By using a simple branching process model, we explored the potential of combining backward contact tracing TRANS with more conventional forward contact tracing TRANS for control of COVID-19.

    A Study on Survival Scenario of COVID-19 patients in India: An Application of Survival Analysis on patient demographics

    Authors: Sampurna Kundu; Kirti; Debarghya Mandal

    doi:10.1101/2020.08.01.20162115 Date: 2020-08-04 Source: medRxiv

    The study of transmission TRANS dynamics of COVID-19, have depicted the rate, patterns and predictions of the pandemic cases. In order to combat the disease MESHD transmission TRANS in India, the Government had declared lockdown on the 25th of March. Even after a strict lockdown nationwide, the cases are increasing and have crossed 4.5 lakh positive cases. A positive point to be noted amongst all that the recovered cases are slowly exceeding the active cases. The survival of the patients, taking death MESHD as the event that varies over age groups TRANS and gender TRANS wise is noteworthy. This study aims in carrying out a survival analysis to establish the variability in survivorship among age groups TRANS and sex, at different levels, that is, national, state and district level. The open database of COVID-19 tracker (covid19india.org) of India has been utilized to fulfill the objectives of the study. The study period has been taken from the beginning of the first case which was on 30th Jan 2020 till 30th June. Due to the amount of under-reporting of data and dropping missing columns a total of 26,815 sample patients were considered. The entry point of each patient is different and event of interest is death MESHD in the study. Kaplan Meier survival estimation, Cox proportional hazard model and multilevel survival model has been used to perform survival analysis. Kaplan Meier survival function, shows that the probability of survival has been declining during the study period of five months. A significant variability has been observed in the age groups TRANS, as evident from all the survival estimates, with increasing age TRANS the risk of dying from COVID-19 increases. When Western and Central India show ever decreasing survival rate in the framed time period then Eastern , North Eastern and Southern India shows a slightly better picture in terms of survival. Maharashtra, Gujarat, Delhi, Rajasthan and West bengal showed alrmingly poor survival as well. This study has depicted a grave scenario of gradation of ever decreasing survival rates in various regions and shows the variability by age TRANS and gender TRANS.

    Trends of Interventional Radiology procedures during the Covid-19 pandemic: The first 27 weeks in the eye of the storm

    Authors: Guo Yuan How; Uei Pua

    doi:10.21203/rs.3.rs-53608/v1 Date: 2020-08-04 Source: ResearchSquare

    ObjectivesWhile the Novel Coronavirus (COVID-19) pandemic looks to persist, institutions promote delaying procedures. Understanding trends and demands of interventional radiology (IR) procedures in the infected and COVID-free populations are needed in long-term planning. We detail IR procedure trends in the first 27 weeks of the pandemic and compare with the pre-pandemic era. MethodsIn this IRB approved retrospective electronic case review, all IR patients in our institution from 1 January to 9 July 2020, the same period in 2019 pre-pandemic and the Severe Acute Respiratory Syndrome MESHD (SARS-CoV) outbreak were included. IR procedures were classified using Interventional Radiology – Procedure Acuity Scale (IR-PAS) and category of IR procedures. Along with descriptive frequencies, the Mann-Whitney U test and Chi-square test of independence were performed.ResultsDuring the pandemic, 3655 IR procedures were performed compared to 3851 procedures pre-pandemic. No statistically significant difference in weekly IR caseloads across IR-PAS tiers between both periods (p = .088) and category of procedure (p = .054) were noted. General intervention procedures remained the largest proportion and musculoskeletal procedures the minority, in both periods. More general intervention radiology and oncology procedures were performed during the Covid-19 pandemic compared to the SARS-CoV outbreak. Thirty-four (0.93%) IR procedures were performed on 30 COVID-19 patients. There was no IR procedure-related COVID-19 cross- transmission TRANS. ConclusionsDemand for IR procedures among COVID-free patients remains high, and IR procedures involving COVID-19 represents a fraction of the IR caseload. A sustainable model in providing timely IR services to COVID-free patients needs to be considered.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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