Corpus overview


Overview

MeSH Disease

Human Phenotype

Pneumonia (1024)

Fever (631)

Cough (507)

Hypertension (349)

Anxiety (277)


Transmission

age categories (2567)

Transmission (2371)

gender (1183)

fomite (1083)

contact tracing (854)


Seroprevalence
    displaying 61 - 70 records in total 12533
    records per page




    Sustained Cellular Immune Dysregulation HP in Individuals Recovering from SARS-CoV-2 Infection MESHD

    Authors: Jacob K Files; Sushma Boppana; Mildred D Perez; Sanghita Sarkar; Kelsey E Lowman; Kai Qin; Sarah Sterrett; Eric Carlin; Anju Bansal; Steffanie Sabbaj; Dustin M Long; Olaf Kutsch; James Kobie; Paul A Goepfert; Nathan Erdmann

    doi:10.1101/2020.07.30.20165175 Date: 2020-08-01 Source: medRxiv

    SARS-CoV-2 causes a wide spectrum of clinical manifestations and significant mortality. Studies investigating underlying immune characteristics are needed to understand disease MESHD pathogenesis and inform vaccine design. In this study, we examined immune cell subsets in hospitalized and non-hospitalized individuals. In hospitalized patients, many adaptive and innate immune cells were decreased in frequency compared to healthy and convalescent individuals, with the exception of B lymphocytes which increased. Our findings show increased frequencies of T-cell activation markers (CD69, Ox40, HLA-DR and CD154) in hospitalized patients, with other T-cell activation/exhaustion markers (CD25, PD-L1 and TIGIT) remaining elevated in hospitalized and non-hospitalized individuals. B cells had a similar pattern of activation/exhaustion, with increased frequency of CD69 and CD95 during hospitalization, followed by an increase in PD1 frequencies in non-hospitalized individuals. Interestingly, many of these changes were found to increase over time in non-hospitalized longitudinal samples, suggesting a prolonged period of immune dysregulation HP following SARS-CoV-2 infection MESHD. Changes in T-cell activation/exhaustion in non-hospitalized patients were found to positively correlate with age TRANS. Severely infected individuals had increased expression of activation and exhaustion markers. These data suggest a prolonged period of immune dysregulation HP following SARS-CoV-2 infection MESHD highlighting the need for additional studies investigating immune dysregulation HP in convalescent individuals.

    Hybrid capture-based sequencing enables unbiased recovery of SAR TRANS-CoV-2 genomes from fecal samples and characterization of the dynamics of intra-host variants

    Authors: Mingkun Li; Yi Xu; Lu Kang; Zijie Shen; Xufang Li; Weili Wu; Wentai Ma; Chunxiao Fang; Fengxia Yang; Xuan Jiang; Sitang Gong; Li Zhang

    doi:10.1101/2020.07.30.230102 Date: 2020-08-01 Source: bioRxiv

    Background: In response to the current COVID-19 pandemic, it is crucial to understand the origin, transmission TRANS, and evolution of SARS-CoV-2, which relies on close surveillance of genomic diversity in clinical samples. Although the mutation at the population level had been extensively investigated, how the mutations evolve at the individual level is largely unknown, partly due to the difficulty of obtaining unbiased genome coverage of SARS-CoV-2 directly from clinical samples. Methods: Eighteen time series fecal samples were collected from nine COVID-19 patients during the convalescent phase. The nucleic acids of SARS-CoV-2 were enriched by the hybrid capture method with different rounds of hybridization. Results: By examining the sequencing depth, genome coverage, and allele frequency change, we demonstrated the impeccable performance SERO of the hybrid capture method in samples with Ct value < 34, as well as significant improvement comparing to direct metatranscriptomic sequencing in samples with lower viral loads. We identified 229 intra-host variants at 182 sites in 18 fecal samples. Among them, nineteen variants presented frequency changes > 0.3 within 1-5 days, reflecting highly dynamic intra-host viral populations. Meanwhile, we also found that the same mutation showed different frequency changes in different individuals, indicating a strong random drift. Moreover, the evolving of the viral genome demonstrated that the virus was still viable in the gastrointestinal tract during the convalescent period. Conclusions: The hybrid capture method enables reliable analyses of inter- and intra-host variants of SARS-CoV-2 genome, which changed dramatically in the gastrointestinal tract; its clinical relevance warrants further investigation.

    Forecasting COVID-19: Using SEIR-D quantitative modelling for healthcare demand and capacity

    Authors: Eduard Campillo-Funollet; James Van Yperen; Phil Allman; Michael Bell; Warren Beresford; Jacqueline Clay; Graham Evans; Matthew Dorey; Kate Gilchrist; Pannu Gurprit; Ryan Walkley; Mark Watson; Anotida Madzvamuse

    doi:10.1101/2020.07.29.20164566 Date: 2020-08-01 Source: medRxiv

    Rapid evidence-based decision-making and public policy based on quantitative modelling and forecasting by local and regional National Health Service (NHS-UK) managers and planners in response to the deadly severe acute respiratory syndrome MESHD coronavirus 2 (SARS-Cov-2), a virus causing COVID-19, has largely been missing. In this pilot study, we present a data-driven epidemiological modelling framework that allows to integrate quantitative modelling, validation and forecasting based on current available local and regional datasets to investigate and mitigate the impact of COVID-19 on local NHS hospitals in terms of healthcare demand and capacity as well as allowing for a systematic evaluation of the predictive accuracy of the modelling framework for long-term forecasting. We present an epidemiological model tailored and designed to meet the needs of the local health authorities, formulated to be fitted naturally to datasets which incorporate regional and local demographics. The model yields quantitative information on the healthcare demand and capacity required to manage and mitigate the COVID pandemic at the regional level. Furthermore, the model is rigorously validated using partial historical datasets, which is then used to demonstrate the forecasting power of the model and also to quantify the risk associated with the decision taken by healthcare managers and planners. Model parameters are fully justified, these are derived purely based on the time series data available at the regional level, with minimal assumptions. Using these inferred parameters, the model is able to make predictions under which secondary waves and re- infection MESHD scenarios could occur. Hence, our modelling approach addresses one of the major criticisms associated with the lack of transparency and precision of current COVID-19 models. Our approach offers a robust quantitative modelling framework where the probability of the model giving a wrong or correct prediction can be quantified.

    A prospective study to identify rates of SARS-CoV-2 virus in the peritoneum and lower genital tract of patients having surgery

    Authors: Dominique Jones; David Faluyi; Sarah Hamilton; Nicholas Stylianides; Kenneth Ma; Sarah Duff; Nicholas Machin; Richard Edmondson

    doi:10.1101/2020.07.30.20165043 Date: 2020-08-01 Source: medRxiv

    Introduction The risks to surgeons of carrying out aerosol generating procedures during the COVID pandemic are unknown. To start to define these risks, in a systematic manner, we investigated the presence of SARS-CoV-2 virus in the abdominal fluid and lower genital tract of patients undergoing surgery. Methods We carried out a prospective cross sectional observational study of 113 patients undergoing abdominal surgery or instrumentation of the lower genital tract. We took COVID swabs from the peritoneal cavity and from the vagina from all eligible patients. Results were stratified by pre operative COVID status. Results In patients who were presumed COVID negative at the time of surgery SARS-CoV-2 virus RNA was detected in 0/102 peritoneal samples and 0/98 vaginal samples. Peritoneal and vaginal swabs were also negative in one patient who had a positive nasopharyngeal swab immediately prior to surgery. Conclusions The presence of SARS-CoV-2 RNA in the abdominal fluid or lower genital tract of presumed negative patients is nil or extremely low. These data will inform surgeons of the risks of restarting laparoscopic surgery at a time when COVID19 is endemic in the population.

    Quantification of the association between predisposing health conditions, demographic, and behavioural factors with hospitalisation, intensive care unit admission, and death MESHD from COVID-19: a systematic review and meta-analysis

    Authors: Nathalie Veronica Fernandez Villalobos; Joerdis Jennifer Ott; Carolina Judith Klett-Tammen; Annabelle Bockey; Patrizio Vanella; Gerard Krause; Berit Lange

    doi:10.1101/2020.07.30.20165050 Date: 2020-08-01 Source: medRxiv

    Background Comprehensive evidence synthesis on the associations between comorbidities and behavioural factors with hospitalisation, Intensive Care Unit (ICU) admission, and death MESHD due to COVID-19 is lacking leading to inconsistent national and international recommendations on who should be targeted for non-pharmaceutical interventions and vaccination strategies. Methods We performed a systematic review and meta-analysis on studies and publicly available data to quantify the association between predisposing health conditions, demographics, and behavioural factors with hospitalisation, ICU admission, and death MESHD from COVID-19. We provided ranges of reported and calculated effect estimates and pooled relative risks derived from a meta-analysis and meta-regression. Results 75 studies were included into qualitative and 74 into quantitative synthesis, with study populations ranging from 19 - 44,672 COVID-19 cases. The risk of dying from COVID-19 was significantly associated with cerebrovascular [pooled RR 2.7 (95% CI 1.7-4.1)] and cardiovascular [RR 3.2 (CI 2.3-4.5)] diseases MESHD, hypertension MESHD hypertension HP [RR 2.6 (CI 2.0-3.4)], and renal disease MESHD [RR 2.5 (CI 1.8-3.4)]. Health care workers had lower risk for death MESHD and severe outcomes of disease MESHD (RR 0.1 (CI 0.1-0.3). Our meta-regression showed a decrease of the effect of some comorbidities on severity of disease MESHD with higher median age TRANS of study populations. Associations between comorbidities and hospitalisation and ICU admission were less strong than for death MESHD. Conclusions We obtained robust estimates on the magnitude of risk for COVID-19 hospitalisation, ICU admission, and death MESHD associated with comorbidities, demographic, and behavioural risk factors. We identified and confirmed population groups that are vulnerable and that require targeted prevention approaches.

    Engineered ACE2 receptor traps potently neutralize SARS-CoV-2

    Authors: Anum Glasgow; Jeff Edward Glasgow; Daniel Limonta; Paige Solomon; Irene Lui; Yang Zhang; Matthew A Nix; Nicholas J Rettko; Shion A Lim; Shoshana Zha; Rachel Yamin; Kevin Kao; Oren S Rosenberg; Jeffrey V Ravetch; Arun P Wiita; Kevin K Leung; Xin X Zhou; Tom C Hobman; Tanja K Kortemme; James A. Wells

    doi:10.1101/2020.07.31.231746 Date: 2020-08-01 Source: bioRxiv

    An essential mechanism for SARS-CoV-1 and -2 infection MESHD begins with the viral spike protein binding to the human receptor protein angiotensin-converting enzyme II (ACE2). Here we describe a stepwise engineering approach to generate a set of affinity optimized, enzymatically inactivated ACE2 variants that potently block SARS-CoV-2 infection MESHD of cells. These optimized receptor traps tightly bind the receptor binding domain (RBD) of the viral spike protein and prevent entry into host cells. We first computationally designed the ACE2-RBD interface using a two-stage flexible protein backbone design process that improved affinity for the RBD by up to 12-fold. These designed receptor variants were affinity matured an additional 14-fold by random mutagenesis and selection using yeast surface display. The highest affinity variant contained seven amino acid changes and bound to the RBD 170-fold more tightly than wild-type ACE2. With the addition of the natural ACE2 collectrin domain and fusion to a human Fc domain for increased stabilization and avidity, the most optimal ACE2 receptor traps neutralized SARS-CoV-2 pseudotyped lentivirus and authentic SARS-CoV-2 virus with half-maximal inhibitory concentrations (IC50) in the tens of ng/ml range. Engineered ACE2 receptor traps offer a promising route to fighting infections MESHD by SARS-CoV-2 and other ACE2-utilizing coronaviruses, with the key advantage that viral resistance would also likely impair viral entry. Moreover, such traps can be pre- designed for viruses with known entry receptors for faster therapeutic response without the need for neutralizing antibodies SERO isolated or generated from convalescent patients.

    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.

    Comparative experimental evidence on compliance with social distancing during the COVID-19 pandemic

    Authors: Michael Becher; Daniel Stegmueller; Sylvain Brouard; Eric Kerrouche

    doi:10.1101/2020.07.29.20164806 Date: 2020-08-01 Source: medRxiv

    Social distancing is a central public health measure in the fight against the COVID-19 pandemic, but individuals' compliance cannot be taken for granted. We use a survey experiment to examine the prevalence SERO of non-compliance with social distancing in nine countries and test pre-registered hypotheses about individual-level characteristics associated with less social distancing. Leveraging a list experiment to control for social desirability bias, we find large cross-national variation in adherence to social distancing guidelines. Compliance varies systematically with COVID-19 fatalities and the strictness of lockdown measures. We also find substantial heterogeneity in the role of individual-level predictors. While there is an ideological gap in social distancing in the US and New Zealand, this is not the case in European countries. Taken together, our results suggest caution when trying to model pandemic health policies on other countries' experiences. Behavioral interventions targeted towards specific demographics that work in one context might fail in another.

    Rapid real-time tracking of non-pharmaceutical interventions and their association SARS-CoV-2 positivity: The COVID-19 Pandemic Pulse Study

    Authors: Steven J. Clipman; Amy P. Wesolowski; Dustin G. Gibson; Smisha Agarwal; Anastasia S. Lambrou; Gregory D. Kirk; Alain B. Labrique; Shruti H. Mehta; Sunil S. Solomon

    doi:10.1101/2020.07.29.20164665 Date: 2020-08-01 Source: medRxiv

    Background: Current mitigation strategies for severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) rely on population-wide adoption of non-pharmaceutical interventions (NPIs). Collecting demographically and geographically resolved data on NPIs and their association with SARS-CoV-2 infection MESHD history can provide critical information related to reopening geographies. Methods: We sampled 1,030 individuals in Maryland from June 17 - June 28, 2020 to capture socio-demographically and geographically resolved information about NPI adoption, access to SARS-CoV-2 testing, and examine associations with self-reported SARS-CoV-2 positivity. Results: Median age TRANS of the sample was 43 years and 45% were men; Whites and Blacks/African Americans represented 60% and 23%, respectively. Overall, 96% of the sample reported traveling TRANS outside their home for non-employment related services: most commonly cited reasons were essential services (92%) and visiting friends TRANS/family (66%). Use of public transport was reported by 18% of respondents. 68% reported always social distancing indoors and 53% always wearing masks indoors; indoor social distancing was significantly less common among younger vs. older individuals, and race/ethnicity and income were significantly associated with mask use (p<0.05 for all). 55 participants (5.3%) self-reported ever testing positive for SARS-CoV-2 with strong dose-response relationships between movement frequency and SARS-CoV-2 positivity that were significantly attenuated by social distancing. In multivariable analysis, history of SARS-CoV-2 infection MESHD was negatively associated with the practice of social distancing (adjusted Odd Ratio [aOR]: 0.10; 95% Confidence Interval: 0.03 - 0.33); the only travel TRANS associated with higher likelihood of SARS-CoV-2 infection MESHD was use of public transport (aOR for 7 or more times vs. never: 4.29) and visiting a place of worship (aOR for 3 or more times vs. never: 16.0) after adjusting for social distancing. Conclusions: Using a rapid cost-efficient approach, we highlight the role of movement and social distancing on SARS-CoV-2 transmission risk TRANS. Continued monitoring of NPI uptake, access to testing, and the subsequent impact on SARS-CoV-2 transmission TRANS will be critical for pandemic control and decisions about reopening geographies.

    COVID-19 case-fatality rate and demographic and socioeconomic influencers: a worldwide spatial regression analysis based on country-level data

    Authors: Yang Cao; Ayako Hiyoshi; Scott Montgomery

    doi:10.1101/2020.07.31.20165811 Date: 2020-07-31 Source: medRxiv

    We used the COVID-19 dataset obtained from the Our World in Data website and investigated the associations between COVID-19 CFR and nine country-level indices of 209 countries/territories using the Matern correlation regression model. Spatial dependence among the data was controlled using the latitude and longitude of the centroid of the countries/territories. Stratified analyses were conducted by economic level and COVID-19 testing policy. The average of country/territory-specific COVID-19 CFR is about 2-3% worldwide, which is higher than previously reported at 0.7-1.3%. Statistically significant associations were observed between COVID-19 CFR and population size and proportion of female TRANS smokers. The open testing policies are associated with decreased CFR. Strictness of anti-COVID-19 measures was not statistically significantly associated with CFR overall, but the higher stringency index was associated with higher CFR in higher income countries with active testing policies. The statistically significant association between population size and COVID-19 CRF suggests the healthcare strain and lower treatment efficiency in countries with large populations. The observed association between smoking in females TRANS and COVID-19 CFR might be due to that the proportion of female TRANS smokers reflected broadly income level of a country. When testing is warranted and healthcare resources are sufficient, strict quarantine and/or lockdown measures might result in excess deaths MESHD in underprivileged populations.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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